======================================================================

Originator: Chris Fischer 
Date: 1-30-2020
Tag: cime5.6.32
Answer Changes: None
Tests: Prealpha tests on izumi
Dependencies:

Brief Summary:
    - Update intel and cprnc on izumi

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
7a0b1a48f Merge pull request #3382 from ESMCI/fischer/izumi


Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_machines.xml


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 1-28-2020
Tag: cime5.6.31
Answer Changes: None
Tests: scripts_regression_tests, f19_g17.I1850Clm50BgcCropCmip6waccm, T62_g16.GIAF
Dependencies:

Brief Summary:

User interface changes: 
    - Fixes domain filename in input_data_list.

PR summary: git log --oneline --first-parent [previous_tag]..master 
    - c55bcd226 Merge pull request #3378 from ESMCI/fischer/domainfile

Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/nmlgen.py


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 1-24-2020
Tag: cime5.6.30
Answer Changes: None
Tests: scripts_regression_tests, hand testing of downloads
Dependencies:

Brief Summary:
    - Add timeouts for ftp and wget logins.
    - Fix chmod command in safe_copy

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
291fc8e41 Merge pull request #3367 from jedwards4b/server_timeouts
3688f02bb Merge pull request #3364 from billsacks/fix_safe_copy

Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/Servers/ftp.py
M       scripts/lib/CIME/Servers/wget.py
M       scripts/lib/CIME/case/check_input_data.py
M       scripts/lib/CIME/utils.py

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 1-22-2020
Tag: cime5.6.29
Answer Changes: None
Tests: examine namelist for GIAF_JRA..., scripts_regression_tests
Dependencies:

Brief Summary:
    - Stampede2 module updates.
    - Restore 2.1.1 behavior for JRA compsets.
    - Allow writing T-forcing cplhist files even when running with SGLC.
    - Updates for the cesm2 ensemble run on aleph.
    - Convert user requested walltime to match walltime_format.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
7489690af Merge pull request #3362 from ESMCI/fischer/stampede2
be1255262 Merge pull request #3361 from klindsay28/cesm2_omip_take2
123742d6e Merge pull request #3356 from billsacks/t_forcing_cplhist_with_sglc
77e30d80d Merge pull request #3355 from jedwards4b/aleph_updates
22afa61fe Merge pull request #3342 from ESMCI/fischer/walltime_format

Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_grids.xml
M       config/cesm/machines/config_batch.xml
M       config/cesm/machines/config_machines.xml
M       config/cesm/machines/config_workflow.xml
M       config/cesm/machines/cylc_suite.rc.template
M       scripts/lib/CIME/XML/env_batch.py
M       src/components/data_comps/datm/cime_config/config_component.xml
M       src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M       src/components/data_comps/drof/cime_config/config_component.xml
M       src/components/data_comps/drof/cime_config/namelist_definition_drof.xml
M       src/drivers/mct/main/cime_comp_mod.F90
M       src/drivers/mct/main/prep_glc_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer
Date: 12-12-2019 
Tag: cime5.6.28
Answer Changes: None
Tests: 
Dependencies:

Brief Summary:
    - Update CIME_OUTPUT_ROOT for aleph.
    - Update exp_types.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
fd98044f7 Merge branch 'maint-5.6' of https://github.com/ESMCI/cime into maint-5.6
cfcce68b9 update scratch directory

Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_machines.xml
M       scripts/Tools/archive_metadata

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 12-2-2019
Tag: cime5.6.27
Answer Changes: Only RCE
Tests: QPRCEMIP 
Dependencies:

Brief Summary:
    - Change sst_aquap11 to sst_aquap_constant.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
b92cea675 Merge pull request #3316 from cacraigucar/maint-5.6


Modified files: git diff --name-status [previous_tag]
M       src/drivers/mct/cime_config/namelist_definition_drv.xml


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 11-25-2019
Tag: cime5.6.26
Answer Changes: None
Tests: CLM PFunit testing on izumi, scripts_regression_tests
       SMS_Ld5.f09_g16.B1850G.cheyenne_intel.allactive-cism-test_coupling
Dependencies:

Brief Summary:
    - Add path for PFUNIT on izumi and add path for batch commands to $PATH.
    - Initialize albdif and albdir

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
0f0531e18 Merge pull request #3302 from ekluzek/izumipgi
21476986b Merge pull request #3295 from jedwards4b/seq_flux_vars_init


Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_compilers.xml
M       config/cesm/machines/config_machines.xml
M       src/drivers/mct/main/seq_flux_mct.F90

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 10-25-2019
Tag: cime5.6.25
Answer Changes: None
Tests: SMS_Ld1_D.f19_g17.I1850Clm50BgcCropCmip6.cheyenne_gnu.clm-default
Dependencies:

Brief Summary:
    - Cherry-picked AQPCONST changes.
    - Fix mpi_bcast in seq_flux_mct.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
03cb90660 Merge pull request #3266 from ESMCI/aqp_cherrypick
f75914619 Merge pull request #3261 from jedwards4b/seq_flux_mct_fix

Modified files: git diff --name-status [previous_tag]
M       src/components/data_comps/docn/cime_config/buildnml
M       src/components/data_comps/docn/cime_config/config_component.xml
M       src/components/data_comps/docn/cime_config/namelist_definition_docn.xml
M       src/components/data_comps/docn/docn_comp_mod.F90
M       src/components/data_comps/docn/docn_shr_mod.F90
M       src/drivers/mct/main/seq_flux_mct.F90
M       src/share/util/shr_scam_mod.F90


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 9-30-2019
Tag: cime5.6.24
Answer Changes: None
Tests: aux_cam tests, cime_developer tests, scripts_regression_tests 
       tested workflow by hand
Dependencies:

Brief Summary:
    - Add namelist for minimum wind speed for atmOcn fluxes.
    - Address objection to using case in workflow.
    - Fix case of workflow job prior to case.run or case.test.
    - Fix bug in SCAM.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
cf62e3524 Merge pull request #3251 from cacraigucar/atmOcn_wind
98d8115ac Merge pull request #3246 from jedwards4b/workflow_casetoworkflow_id
829138e73 Merge pull request #3242 from jedwards4b/workflow_before_run_fix
7b1b3208c Merge pull request #3238 from cacraigucar/maint-5.6


Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_workflow.xml
M       config/e3sm/machines/config_workflow.xml
M       config/xml_schemas/config_workflow.xsd
M       scripts/Tools/preview_run
M       scripts/create_newcase
M       scripts/lib/CIME/XML/env_batch.py
M       scripts/lib/CIME/XML/workflow.py
M       scripts/lib/CIME/case/case.py
M       scripts/lib/CIME/case/case_submit.py
M       src/drivers/mct/cime_config/namelist_definition_drv.xml
M       src/drivers/mct/main/seq_flux_mct.F90
M       src/share/util/shr_flux_mod.F90
M       src/share/util/shr_scam_mod.F90



======================================================================

======================================================================

Originator: Chris Fischer 
Date: 9-11-2019
Tag: cime5.6.23
Answer Changes: climate changing for C & G compsets.
Tests: cime_developers, aux_cam, scripts_regression_tests
Dependencies:

Brief Summary:
    - Change rce_sst to fixed_sst to better reflect its purpose.
    - Fix wallclocks in testlists.
    - Archive metadata add support for lens experiment type.
    - Changes to support Radiative Convective Equilibrium.
    - Add support for CMIP6 OMIP, update JRA forcing files.
    - Make the streams file legitiment xml files.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
e7e14698a Merge pull request #3236 from cacraigucar/fixed_sst
189ac85c6 Merge pull request #3234 from ESMCI/fischer/wallclocks
751d24c99 Merge pull request #3228 from bertinia/maint-5.6_archive_metadata
3a3fa6fab Merge pull request #3231 from cacraigucar/rce_release
3418675b0 Merge pull request #3223 from klindsay28/cesm2_omip
38117f02d Merge pull request #3217 from jedwards4b/maint-5.6_user_streamfix

Modified files: git diff --name-status [previous_tag]
M	config/cesm/config_archive.xml
M	config/cesm/config_grids.xml
M	scripts/Tools/archive_metadata
A	scripts/lib/CIME/XML/stream.py
M	scripts/lib/CIME/case/case_setup.py
M	scripts/lib/CIME/nmlgen.py
M	src/components/data_comps/datm/cime_config/buildnml
M	src/components/data_comps/datm/cime_config/config_component.xml
M	src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M	src/components/data_comps/datm/datm_comp_mod.F90
M	src/components/data_comps/dice/cime_config/buildnml
M	src/components/data_comps/dlnd/cime_config/buildnml
M	src/components/data_comps/docn/cime_config/buildnml
M	src/components/data_comps/docn/cime_config/config_component.xml
M	src/components/data_comps/docn/cime_config/namelist_definition_docn.xml
M	src/components/data_comps/docn/docn_comp_mod.F90
M	src/components/data_comps/docn/docn_shr_mod.F90
M	src/components/data_comps/drof/cime_config/buildnml
M	src/components/data_comps/drof/cime_config/namelist_definition_drof.xml
M	src/components/data_comps/dwav/cime_config/buildnml
M	src/drivers/mct/cime_config/buildnml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/cime_config/testdefs/testlist_drv.xml
M	src/drivers/mct/main/cime_comp_mod.F90
M	src/drivers/mct/main/seq_flux_mct.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90
M	src/share/streams/shr_tInterp_mod.F90
M	src/share/util/shr_orb_mod.F90


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 8-26-2019
Tag: cime5.6.22
Answer Changes: None
Tests: scripts_regression_tests 
Dependencies:

Brief Summary:
    - Fix nag on izumi.
    - Update for cori modules.
    - Update regex to match changing cheyenne login name.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
b37b70c3b Merge pull request #3207 from ESMCI/fischer/nag
8d2fa1ec6 Merge pull request #3212 from ESMCI/fischer/cori_updates
7f8173207 Merge pull request #3214 from ESMCI/fischer/cheyenne_hostname


Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_compilers.xml
M       config/cesm/machines/config_machines.xml
M       scripts/Tools/Makefile


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 8-14-2019
Tag: cime5.6.21
Answer Changes: None
Tests: 
Dependencies:

Brief Summary:
    - Update config_machines to update pgi software stack on cheyenne
    - If filename is abspath use for filepath.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
80ae90470 Merge pull request #3202 from ESMCI/fischer/cheyenne_pgi
1c3da2440 Merge pull request #3200 from jedwards4b/aquap_fix

Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_machines.xml
M       scripts/lib/CIME/nmlgen.py


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 7-23-2019
Tag: cime5.6.20
Answer Changes: None
Tests: scripts_regression_tests 
Dependencies:

Brief Summary:
    - Fix mkDepends issue with shr_assert_mod.
    - Server 0 file length fix.
    - Avoid undefined variable error.
    - More workflow updates.
    - Adds a --ensemble option to create_clone.
    - Workflow development.
    - Fix error in job_id
    - Put correct wallclock format for cheyenne.
    - Changes to continue workflow development.
    - Aleph port.
    - Add nemo.
    - presaero file for SSP1-2.6
    - Add workflow xml.
    - Avoid divide by 0 when timing file is bad.

User interface changes: 
    - Add --ensemble to generate_cylc_workflow generating an ensemble driver 
      for cylc workflow, this driver is generated in the first ensemble member 
      and controls all members from a single cylc suite.
    - Adds --ensemble to create_clone, to use this option the original case 
      must end in one or more integers, so for example if the case is named 
      case.001 and --ensemble 4 is used you will get case.002, case.003, case.004 
      created.
    - Adds support for external workflow engine cylc.
    - New file for SSP1-2.6.
    - Adds a --workflow-case option to create_newcase.


PR summary: git log --oneline --first-parent [previous_tag]..master 
35e24bb50 Merge pull request #3179 from jedwards4b/mkDepends_fix
3e0b00a6d Merge pull request #3176 from jedwards4b/Server0filelengthfix
5f5408d4e avoid undefined variable error
c5bd8567c Merge pull request #3173 from jedwards4b/jedwards/more_workflow
12ca87021 Merge pull request #3169 from jedwards4b/ensemble_clone
a2a48c423 Merge pull request #3168 from jedwards4b/jedwards/workflow_development
802bf0dd1 fix error in job_id
ba17f31f0 Merge pull request #3164 from jedwards4b/maint-5.6_cheyenne_wallclock_fix
35b78be10 Merge pull request #3160 from jedwards4b/workflow_changes
09c0a969e Merge pull request #3159 from jedwards4b/aleph_port
735053ce7 Merge pull request #3153 from ESMCI/peano/nemo
2e842025c Merge pull request #3152 from ekluzek/presaerossp2126
fc70da142 Merge pull request #3125 from jedwards4b/add_workflow_xml
958190cf2 Merge pull request #3138 from jedwards4b/timing_0_fix


Modified files: git diff --name-status [previous_tag]
M	config/cesm/config_files.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
A	config/cesm/machines/config_workflow.xml
A	config/cesm/machines/cylc_suite.rc.template
M	config/config_headers.xml
M	config/e3sm/config_files.xml
M	config/e3sm/machines/config_batch.xml
A	config/e3sm/machines/config_workflow.xml
M	config/xml_schemas/config_batch.xsd
M	config/xml_schemas/config_compilers_v2.xsd
A	config/xml_schemas/config_workflow.xsd
M	scripts/Tools/Makefile
A	scripts/Tools/generate_cylc_workflow.py
M	scripts/Tools/mkDepends
M	scripts/Tools/preview_run
M	scripts/create_clone
M	scripts/create_newcase
M	scripts/lib/CIME/Servers/ftp.py
M	scripts/lib/CIME/XML/batch.py
M	scripts/lib/CIME/XML/env_base.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_specific.py
A	scripts/lib/CIME/XML/env_workflow.py
M	scripts/lib/CIME/XML/generic_xml.py
A	scripts/lib/CIME/XML/workflow.py
M	scripts/lib/CIME/aprun.py
M	scripts/lib/CIME/case/case.py
M	scripts/lib/CIME/case/case_clone.py
M	scripts/lib/CIME/case/case_run.py
M	scripts/lib/CIME/case/case_setup.py
M	scripts/lib/CIME/case/case_st_archive.py
M	scripts/lib/CIME/case/case_submit.py
M	scripts/lib/CIME/case/check_input_data.py
M	scripts/lib/CIME/get_timing.py
M	scripts/tests/scripts_regression_tests.py
M	src/build_scripts/buildlib.csm_share
M	src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/share/timing/Makefile
M	src/share/util/shr_file_mod.F90


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 6-6-2019
Tag: cime5.6.19
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:

Brief Summary:
    - Remove changes to case_run, fix a module issue on cori-knl.
    - Fix was not py2 compatible, this one is.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
1adcdeb Merge pull request #3136 from jedwards4b/cori_and_case_run
40615b7 Merge pull request #3134 from jedwards4b/encodefixagain


Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_machines.xml
M       scripts/lib/CIME/case/case_run.py


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 6-5-2019
Tag: cime5.6.18
Answer Changes: Round Off for centos7-linux and cori
Tests: scripts_regression_tests on cori and cheyenne
Dependencies:

Brief Summary:
   - Update modules for centos7-linux, fix py3 error in case_run.py.
   - Update modules on cori-haswell and cori-knl.
   - Add test_release as a test category consulted to determine if a compset -- grid combination is supported.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
6704570 Merge pull request #3133 from jedwards4b/centos7-update
d40e715 Merge pull request #3132 from jedwards4b/cori_update
d86457d Merge pull request #3128 from gold2718/add_test_release


Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_machines.xml
M       scripts/lib/CIME/case/case.py
M       scripts/lib/CIME/case/case_run.py


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 5-29-2019
Tag: cime5.6.17
Answer Changes: None
Tests:  Manually ran archive_metadata
        By hand
Dependencies:

Brief Summary:
    - Update archive_metadata strip to lstrip.
    - Correct error messages from wget interface.
    - Fix README

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
bacf1db Merge pull request #3122 from bertinia/maint-5.6_archive_metadata
c050233 Merge pull request #3119 from jedwards4b/wget_message_fix
bd7e7fd fix README

Modified files: git diff --name-status [previous_tag]
M       ChangeLog
M       scripts/Tools/archive_metadata
M       scripts/lib/CIME/Servers/wget.py
M       tools/statistical_ensemble_test/README


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 5-15-2019
Tag: cime5.6.16
Answer Changes: climate-changing -- new datasets
Tests:  Ran all 8 ISSP's 
	SMS_D_Ln9.f19_f19_mg16.FX2000.pleiades-has_intel (Overall: PASS) 
	SMS_D_Ln9.f19_f19_mg16.FX2000.pleiades-san_intel (Overall: PASS) 
	SMS_Ld1.f19_f19_mg16.FX2000.pleiades-bro_intel (Overall: PASS) 
	SMS_Ld1.f19_f19_mg16.FX2000.pleiades-has_intel (Overall: PASS) 
	SMS_Ld1.f19_f19_mg16.FX2000.pleiades-ivy_intel (Overall: PASS) 
	SMS_Ld1.f19_f19_mg16.FX2000.pleiades-san_intel (Overall: PASS) 
Dependencies:

Brief Summary:
    - Add CO2 time-series for CMIP6 future scenarios and three prescribed 
      aerosol CMIP6 future scenarios.
    - Bring changes to datm Present Day compsets from master to maint-5.6.
    - pdate intel compiler version and ESMF lib for pleiades.
    - Fix archive dir for stampede.

User interface changes: 
    - Changes default settings for some compsets.

PR summary: git log --oneline --first-parent [previous_tag]..master 
59960d9 Merge pull request #3112 from ekluzek/addSSPCO2npresaero
f43ef89 Merge pull request #3110 from ekluzek/datmsettings4PDcompsets
1e703d8 Merge pull request #3108 from fvitt/pleiades
29536e1 fix archive dir for stampede

Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_compilers.xml
M       config/cesm/machines/config_machines.xml
M       doc/source/users_guide/compsets.rst
M       src/components/data_comps/datm/cime_config/config_component.xml
M       src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M       src/drivers/mct/cime_config/config_component_cesm.xml
M       src/drivers/mct/cime_config/config_compsets.xml


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 4-26-2019
Tag: cime5.6.15
Answer Changes: None
Tests: scripts_regression_tests.py, by hand, SMS_P45.f19_g16.X 
       manually test archive_metadata
Dependencies:

Brief Summary:
    - Improve reporting of invalid settings in REFCASE when GET_REFCASE=TRUE.
    - Remove ESMF modules on edison.
    - Fix issue with setting 2 io tasks.
    - maint-5.6 archive_metadata update.


User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
a1c0e9d Merge pull request #3095 from jedwards4b/get_refcase_errors
4abc89e Merge pull request #3080 from ESMCI/fischer/edison
bfd3e22 Merge pull request #3078 from jedwards4b/shr_pio_bug_fix
93bd063 Merge pull request #3076 from bertinia/maint-5.6_archive_metadata


Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_machines.xml
M       scripts/Tools/archive_metadata
M       scripts/lib/CIME/case/check_input_data.py
M       src/share/util/shr_pio_mod.F90


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 4-08-2019
Tag: cime5.6.14
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:

Brief Summary:
    - Update modules for cori.
    - Update A compsets to avoid needing a 6GB inputdata file for testing.
    - Minor bug fixes for xml interface.
    - Update modules for cheyenne pgi.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
ff65ad0 Merge pull request #3070 from ESMCI/fischer/cori_module_update
4f5b655 Merge pull request #3069 from ESMCI/fischer/3053
e3fbee4 Merge pull request #3057 from jedwards4b/maint-5.6-xml_fixes
398df65 Merge pull request #3049 from ESMCI/fischer/cheyenne_mpt_pgi


Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_machines.xml
M       scripts/lib/CIME/XML/entry_id.py
M       scripts/lib/CIME/XML/generic_xml.py
M       src/components/data_comps/datm/cime_config/config_component.xml

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 3-13-2019
Tag: cime5.6.13
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:

Brief Summary:
    - Only download chksum file(s) if requested.
    - mpiexec_mpt argument fix on cheyenne

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
170db73 Merge pull request #3038 from jedwards4b/chksum_fixes_maint-5.6
cc6fe0f for mpt/2.19 -p must preceed -np in mpiexec_mpt arguments


Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_machines.xml
M       scripts/lib/CIME/Servers/ftp.py
M       scripts/lib/CIME/Servers/gftp.py
M       scripts/lib/CIME/Servers/svn.py
M       scripts/lib/CIME/Servers/wget.py
M       scripts/lib/CIME/case/check_input_data.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 3-7-219
Tag: cime5.6.12
Answer Changes: None
Tests: scripts_regression_tests, code_checker
Dependencies:

Brief Summary:
    - Fix issue with chksum option, update cheyenne.
    - Add checksum support for inputdata.
    - PIO performance optimization merge.
    - Move the logic to check and update batch options.
    - Update Ensemble Consistency Test README.
    - Update to archive_metadata stand-alone functionality.
    - Consolidate inputdata for stamepede2 and lonestar5.
    - Port to tacc system lonestar5.
    - Initial port to izumi.
    - Allow specifying directives to use for an unknown queue.
    - Update bluewaters machine interface.
    - Minor update to archive_metadata.
    - Change the default RUN_REFDIR from ccsm4_init to cesm2_init.
    - cd to correct directory after running create_clone.
    - List mpi-serial's include directory before any system-level includes.
    - Fix nag & pgi CAM COSP build.
    - Do not allow trailing / in filename.
    - Update the version of ESMF used by the mapping tools on cheyenne.
    - Update fv1.9x2.5,gx1v7 grids.
    - _PNETCDF needs to be defined in csm_share build.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
dc2fef7 fix issue with chksum option, update cheyenne
38b96b6 Merge pull request #3018 from jedwards4b/checksum_inputdata
852fa8d Merge pull request #3023 from jedwards4b/pio1_merge
1c0bf27 Merge pull request #3019 from jedwards4b/batch_and_resubmit
a6e3349 Merge pull request #3012 from ESMCI/fischer/ECT_doc
e7f2e6f Merge pull request #3004 from bertinia/maint-5.6_archive_metadata
497dd69 Merge pull request #3005 from jedwards4b/lonestar5-port
6faac40 Merge pull request #3002 from jedwards4b/lonestar5-port
277c28c Merge pull request #2999 from jedwards4b/izumi_port_5.6
766d923 Merge pull request #2995 from billsacks/unknown_queue_maint56
25f45ac Merge pull request #2996 from ESMCI/jedwards/bluewaters_update
9416ba8 Merge pull request #2977 from bertinia/maint-5.6_archive_metadata
bc71697 Merge pull request #2973 from jedwards4b/default_run_refdir
5a1afac Merge pull request #2961 from billsacks/create_clone_doc
8f97ec9 Merge pull request #2960 from billsacks/fix_unit_test_mpi_serial
5e2af84 Merge pull request #2951 from ESMCI/fischer/cosp_fix
27d9f2f Merge pull request #2938 from jedwards4b/catch_illegal_name
d699d16 Merge pull request #2940 from mnlevy1981/mlevy/update_esmf_in_mapping-maint5.6
4f54ec6 Merge pull request #2943 from ESMCI/fischer/f19_gx1v7
7d9ed6c Merge pull request #2925 from jedwards4b/fix64bit_data_issue


Modified files: git diff --name-status [previous_tag]
M	CMakeLists.txt
M	config/cesm/config_grids.xml
M	config/cesm/config_inputdata.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/xml_schemas/config_batch.xsd
M	doc/source/misc_tools/ect.rst
M	doc/source/users_guide/cloning-a-case.rst
M	scripts/Tools/Makefile
M	scripts/Tools/archive_metadata
M	scripts/Tools/check_input_data
M	scripts/lib/CIME/Servers/ftp.py
M	scripts/lib/CIME/Servers/wget.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/inputdata.py
M	scripts/lib/CIME/case/case_submit.py
M	scripts/lib/CIME/case/check_input_data.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/utils.py
M	src/drivers/mct/cime_config/config_component.xml
M	src/externals/pio1/pio/pio_types.F90
M	src/externals/pio1/pio/piodarray.F90.in
M	src/externals/pio1/pio/pionfput_mod.F90.in
M	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/create_ESMF_map.sh

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 11-29-2018
Tag: cime_cesm2_1_rel_06
Answer Changes: None
Tests: scripts_regression_tests 
Dependencies:

Brief Summary:
    - Fix new pylint errors.
    - Update addmetadata for POP-ECT tests.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
5a86646 Merge pull request #2921 from jedwards4b/fixpylint3errors
98821ff Merge pull request #2919 from ESMCI/fischer/addmetadata

Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/BuildTools/macrowriterbase.py
M       scripts/lib/CIME/SystemTests/erio.py
M       scripts/lib/CIME/SystemTests/ers.py
M       scripts/lib/CIME/SystemTests/ers2.py
M       scripts/lib/CIME/SystemTests/homme.py
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M       scripts/lib/CIME/case/case_run.py
M       scripts/lib/CIME/case/case_setup.py
M       scripts/lib/CIME/case/case_st_archive.py
M       scripts/lib/CIME/provenance.py
M       scripts/lib/e3sm_cime_mgmt.py
M       src/build_scripts/buildlib.gptl
M       src/build_scripts/buildlib.pio
M       tools/statistical_ensemble_test/addmetadata.sh

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 11-17-2018
Tag: cime_cesm2_1_rel_05
Answer Changes: None
Tests:  ./create_test cime_developer on cheyenne
Dependencies:

Brief Summary:
    - Do not include time of day in cpl auxiliary hist file names.

User interface changes: 
    - Changes names of cpl auxiliary history files.

PR summary: git log --oneline --first-parent [previous_tag]..master 
b3fc9d6 Merge pull request #2914 from billsacks/auxhist_no_time

Modified files: git diff --name-status [previous_tag]
M       src/drivers/mct/main/seq_hist_mod.F90

======================================================================
======================================================================

Originator: Chris Fischer 
Date: 11-13-2018
Tag: cime_cesm2_1_rel_04
Answer Changes: None
Tests: 
Dependencies:

Brief Summary:
    - Fix 2010 period for datm GSWP3v1.
    - Update pyCECT to v3.0.8

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
2e72d20 Merge pull request #2908 from ekluzek/fix2010datm
5f4a911 Merge pull request #2905 from ESMCI/fischer/pyCECT_v3.0.8

Modified files: git diff --name-status [previous_tag]
M       src/components/data_comps/datm/cime_config/config_component.xml
M       tools/statistical_ensemble_test/pyCECT/README_pyCECT.rst
M       tools/statistical_ensemble_test/pyCECT/README_pyEnsSum.rst
M       tools/statistical_ensemble_test/pyCECT/README_pyEnsSumPop.rst
M       tools/statistical_ensemble_test/pyCECT/pyCECT.py
M       tools/statistical_ensemble_test/pyCECT/pyEnsLib.py
M       tools/statistical_ensemble_test/pyCECT/pyEnsSum.py
M       tools/statistical_ensemble_test/pyCECT/pyEnsSumPop.py
D       tools/statistical_ensemble_test/pyCECT/pyEnsSumPop_test.sh
M       tools/statistical_ensemble_test/pyCECT/test_pop_CECT.sh
D       tools/statistical_ensemble_test/pyCECT/test_pop_ensemble.sh
A       tools/statistical_ensemble_test/pyCECT/test_pyEnsSumPop.sh

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 11-5-2018
Tag: cime_cesm2_1_rel_03
Answer Changes: None
Tests: code_checker, stand-alone tests, scripts_regression_tests
Dependencies:

Brief Summary:
    - Add Total Time parsing for timeseries and xconform to archive_metadata
    - Fine tuning for CMIP6 cases in archive_metadata.
    - CESM-CECT update.
    - Python3 compatibility update for archive_metadata.
    - Remove reference to deleted testmods directories.
    - Compute tasks_per_node via floor division.
    - Response to review comments of pr 2844 and remove user-grid option.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
c515c37 Merge pull request #2900 from bertinia/maint-5.6_archive_metadata
47f3970 Merge pull request #2884 from bertinia/maint-5.6_archive_metadata
3ad6a6e Merge pull request #2866 from jedwards4b/set_update
a2b6885 Merge pull request #2865 from bertinia/maint-5.6_archive_metadata
b56664c Merge pull request #2862 from billsacks/doc_testmods
ad361d2 Merge pull request #2860 from jedwards4b/py3fix
7e82e9b Merge pull request #2853 from jedwards4b/cleanuppr


Modified files: git diff --name-status [previous_tag]
M       doc/source/users_guide/testing.rst
M       scripts/Tools/archive_metadata
M       scripts/create_newcase
M       scripts/fortran_unit_testing/run_tests.py
M       scripts/lib/CIME/XML/env_mach_pes.py
M       tools/statistical_ensemble_test/README
M       tools/statistical_ensemble_test/ensemble.py
D       tools/statistical_ensemble_test/ensemble.sh
M       tools/statistical_ensemble_test/single_run.py
D       tools/statistical_ensemble_test/single_run.sh

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 10-12-2018
Tag: cime_cesm2_1_rel_02
Answer Changes: None
Tests: Z_FullSystemTest, scripts_regression_tests, hand tests
Dependencies:

Brief Summary:
    - Add a default value of idmap_ignore for certain mapping files.
    - Improve clean function.
    - Add ability for testfile to contain comments.
    - Clean and alphabetize (by MACH name) the config/cesm/machines/*.xml files. 
    - Improve case clone functionality.
    - Improve error message for issues in user_nl_* namelist files.
    - Write cpl.hr2x files at ENDOFRUN when forecast is < 24 hours.
    - Backporting PR #2833(Propagate logging settings to submitted jobs) to maint-5.6 branch.
    - Remove overzelous debug code.
    - Change default for flux_convergence for all but 1 degree case.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
fd439ba Merge pull request #2845 from jedwards4b/improve_idmap_test
be6c214 Merge pull request #2844 from jedwards4b/run_tests_clean
c2cab2f Merge pull request #2838 from jedwards4b/testfile_comments
d68fa9c Merge pull request #2849 from jedwards4b/cleanup_xml
cb81444 Merge pull request #2843 from jedwards4b/clone_modified_Tools
f3f5f69 Merge pull request #2840 from jedwards4b/user_nl_error_msg
61132ee Merge pull request #2832 from kdraeder/hr2x_at_endofrun
d3457ec Merge pull request #2842 from jedwards4b/propagate_logging
ad9c0f5 Merge pull request #2839 from jedwards4b/remove_debug_code
6a7d374 Merge pull request #2837 from jedwards4b/tuning1.9


Modified files: git diff --name-status [previous_tag]
M       .travis.yml
M       config/cesm/machines/config_batch.xml
M       config/cesm/machines/config_compilers.xml
M       config/cesm/machines/config_machines.xml
M       scripts/Tools/archive_metadata
M       scripts/create_newcase
M       scripts/create_test
M       scripts/fortran_unit_testing/run_tests.py
M       scripts/lib/CIME/XML/batch.py
M       scripts/lib/CIME/XML/compilers.py
M       scripts/lib/CIME/XML/env_batch.py
M       scripts/lib/CIME/XML/generic_xml.py
M       scripts/lib/CIME/XML/machines.py
M       scripts/lib/CIME/XML/namelist_definition.py
M       scripts/lib/CIME/case/case.py
M       scripts/lib/CIME/case/case_clone.py
M       scripts/lib/CIME/nmlgen.py
M       scripts/tests/scripts_regression_tests.py
M       src/CMake/FindpFUnit.cmake
M       src/drivers/mct/cime_config/buildnml
M       src/drivers/mct/cime_config/config_component.xml
M       src/drivers/mct/cime_config/namelist_definition_drv.xml
M       src/drivers/mct/main/cime_comp_mod.F90
M       src/share/streams/shr_stream_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 10-8-2018
Tag: cime_cesm2_1_rel_01
Answer Changes: None
Tests: scripts_regression_test
Dependencies:

Brief Summary:
    - Update presaero and CO2 datasets for datm7 to new CMIP6 version.
    - Better format for seq_flds_YYY_{fluxes,states} log messages.
    - Attach the instance number to 'cpl' in cpl history file names.
    - Fix inputdata issue for multi_instance cases.


User interface changes: 
    - Added clim_2010 option for DATM_PRESAERO
      Added 20tr.latbnd option for DATM_CO2_TSERIES
      GSWP3v1 and CRUNCEPv7 forcing sets appropriate years for compsets starting with 2010

PR summary: git log --oneline --first-parent [previous_tag]..master 
88d9297 Merge pull request #2828 from ekluzek/newpresaero
6568ded Merge pull request #2824 from kdraeder/kdr_seq_flds_log_msgs
fcf60c8 Merge pull request #2782 from kdraeder/kdr_fix_cpl_hist_names
6511798 Merge pull request #2823 from jedwards4b/multi_inst_check_input

Modified files: git diff --name-status [previous_tag]
M       scripts/Tools/archive_metadata
M       scripts/create_newcase
M       scripts/lib/CIME/case/case.py
M       scripts/lib/CIME/nmlgen.py
M       src/components/data_comps/datm/cime_config/buildnml
M       src/components/data_comps/datm/cime_config/config_component.xml
M       src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M       src/components/data_comps/desp/cime_config/buildnml
M       src/components/data_comps/dice/cime_config/buildnml
M       src/components/data_comps/dlnd/cime_config/buildnml
M       src/components/data_comps/docn/cime_config/buildnml
M       src/components/data_comps/drof/cime_config/buildnml
M       src/components/data_comps/dwav/cime_config/buildnml
M       src/drivers/mct/main/cime_comp_mod.F90
M       src/drivers/mct/main/seq_hist_mod.F90
M       src/drivers/mct/shr/seq_flds_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 10-2-2018
Tag: cime_cesm2_0_rel_06
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:

Brief Summary:
    - Archive_metadata updates for CMIP6 experiments.
    - OS is not generic env var.
    - New machines at ETH and CSCS.
    - Update ESMF library on cheyenne.
    - Fix documentation for histaux_r2x namelist variable.
    - Dont allow zero ntasks nthrds.
    - Add lapack and blas libraries to pgi compile on cheyenne.
    - Updates for compatibility with XML to html tools.
    - Remove additional rad->deg conversion to radians when creating ocean
      domain files.
    - ESMF logging fix.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
12e1c4d41 (HEAD -> maint-5.6, origin/maint-5.6) Merge pull request #2815 from bertinia/maint-5.6_archive_metadata
767511a79 OS is not generic env var
bec49f0c2 Merge pull request #2807 from beyerle/euler_daint
9e74b8ab3 Merge pull request #2806 from ESMCI/fischer/ESMF_710r
0f20ab46e Merge pull request #2774 from billsacks/fix_histaux_r2x_docs
1c10e58e8 Merge pull request #2768 from jedwards4b/dont_allow_zero_ntasks_nthrds
6a1069ce3 Merge pull request #2753 from jedwards4b/pgi_lapack
5a0a56721 Merge pull request #2742 from bertinia/maint-5.6-component-return-values
cbf8f2216 Merge pull request #2736 from jtruesdal/domainfix
2e34a0305 Merge pull request #2733 from gold2718/esmf_log_fix


Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_grids.xml
M       config/cesm/machines/config_batch.xml
M       config/cesm/machines/config_compilers.xml
M       config/cesm/machines/config_machines.xml
M       scripts/Tools/archive_metadata
M       scripts/lib/CIME/XML/component.py
M       scripts/lib/CIME/XML/compsets.py
M       scripts/lib/CIME/XML/env_mach_pes.py
M       scripts/lib/CIME/XML/machines.py
M       scripts/lib/CIME/utils.py
M       src/components/data_comps/docn/cime_config/config_component.xml
M       src/drivers/mct/cime_config/config_component.xml
M       src/drivers/mct/cime_config/namelist_definition_drv.xml
M       src/drivers/mct/main/cime_comp_mod.F90
M       src/drivers/mct/main/cime_driver.F90
M       src/drivers/mct/shr/seq_comm_mct.F90
M       src/drivers/mct/shr/seq_infodata_mod.F90
M       src/share/esmf_wrf_timemgr/ESMF_Stubs.F90
M       tools/mapping/gen_domain_files/src/gen_domain.F90

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 7-24-2018
Tag: cime_cesm2_0_rel_05
Answer Changes: None
Tests: scripts_regression_tests.py 
Dependencies:

Brief Summary:
    - Theta enviroment updates.
    - Fix wget option for directories.
    - Remove trailing whitespace.
    - Correct mpich for intel, clean up cprnc on hobart.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
59ef62860 (HEAD -> maint-5.6, origin/maint-5.6) Merge pull request #2727 from jedwards4b/more_theta_config
d44d58a82 Merge pull request #2700 from jedwards4b/wget_fix
41842b411 remove trailing whitespace
1af4f4569 Merge pull request #2718 from jedwards4b/hobart_machine_cleanup

Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_machines.xml
M       scripts/lib/CIME/Servers/wget.py
M       scripts/lib/CIME/utils.py

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 7-13-2018
Tag: cime5.6.10
Answer Changes: None
Tests: hand test
       code_checker on create_newcase; manually checked create_newcase --help
       ERS_Ln9.f19_g17.X.hobart_intel , ERS_Ln9.f19_g17.X.hobart_gnu,
       ERS_Ln9.f19_g17.X.hobart_nag
Dependencies:

Brief Summary:
   - Add scripts/Tools/archive_metadata to CIME for use in CESM cases only. 
   - Change DIN_LOC_ROOT_CLMFORC for new glade setup on cheyenne.
   - Make docs more consistent.
   - cprnc compiler updates for hobart.

User interface changes: 
    - archive_metadata --help stand_alone script.

PR summary: git log --oneline --first-parent [previous_tag]..master 
9f4377c Merge pull request #2715 from bertinia/maint-5.6_archive_metadata
ef2f2e4 Merge pull request #2714 from ekluzek/newgladedinlocclmfrc
154b475 Merge pull request #2693 from billsacks/make_docs_more_consistent
631869c Merge pull request #2709 from ESMCI/fischer/hobart_cprnc


Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_machines.xml
M       doc/source/users_guide/create-a-case.rst
A       scripts/Tools/archive_metadata
M       scripts/create_newcase
M       scripts/lib/CIME/case/case.py
M       scripts/lib/CIME/utils.py

======================================================================

======================================================================

Originator: Chris Fiscehr 
Date: 7-5-2018
Tag: cime5.6.9
Answer Changes: None
Tests: prealpha on edison, cori-haswell, cori-knl
       scripts_regression_tests, ect-uf on bluewaters
Dependencies:

Brief Summary:
    - Maint-5.6 nersc update.
    - Maint-5.6 hobart update.
    - Fix issue with rebuilding csm_share.
    - Bluewaters update.
    - Edit and cleanup parts of CCS users guide.
    - Change -v to --env for theta.
    - Fix unittest.
    - Tryagain with tput code.
    - ww3 data staging fix.
    - Fix refcase logiv.
    - Add and clarify pieces that describe adding a test to the prebeta testing.
    - Archive test refinement.

User interface changes: 
    -  --test becomes --test-all and --test-case is added

PR summary: git log --oneline --first-parent [previous_tag]..master 
3ee8b07 Merge pull request #2697 from jedwards4b/maint-5.6-nersc-update
b76c449 Merge pull request #2701 from jedwards4b/maint-5.6-hobart-update
34677a4 Merge pull request #2684 from jedwards4b/improve_shared_build_performance
57c8924 Merge pull request #2675 from jedwards4b/bluewaters_update
3a5281d Merge pull request #2662 from ESMCI/rljacob/doc/ug1-read
f8cc2a7 Merge pull request #2666 from jedwards4b/theta_fix
2e9973f fix unittest
49f59b6 tryagain with tput code
0819198 Merge branch 'ww3_data_staging' into maint-5.6
7478f2f Merge branch 'fix_refcase_logic' into maint-5.6
cd64838 Merge pull request #2647 from ESMCI/fischer/augment_testing_doc
3016427 Merge pull request #2656 from jedwards4b/archive_test_refinement

Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_batch.xml
M       config/cesm/machines/config_compilers.xml
M       config/cesm/machines/config_machines.xml
M       config/cesm/machines/template.st_archive
M       config/e3sm/machines/template.st_archive
M       config/xml_schemas/config_machines.xsd
M       config/xml_schemas/testlist.xsd
M       doc/source/users_guide/building-a-case.rst
M       doc/source/users_guide/cime-change-namelist.rst
A       doc/source/users_guide/cime-dir.rst
M       doc/source/users_guide/compsets.rst
M       doc/source/users_guide/create-a-case.rst
M       doc/source/users_guide/index.rst
M       doc/source/users_guide/introduction-and-overview.rst
M       doc/source/users_guide/pes-threads.rst
M       doc/source/users_guide/running-a-case.rst
M       doc/source/users_guide/setting-up-a-case.rst
M       doc/source/users_guide/testing.rst
M       scripts/Tools/Makefile
M       scripts/Tools/preview_run
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/XML/env_batch.py
M       scripts/lib/CIME/case/case.py
M       scripts/lib/CIME/case/case_st_archive.py
M       scripts/lib/CIME/case/case_submit.py
M       scripts/lib/CIME/case/check_input_data.py
M       scripts/lib/CIME/test_scheduler.py
M       scripts/lib/CIME/test_status.py
M       scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
M       scripts/tests/scripts_regression_tests.py
M       src/build_scripts/buildlib.csm_share

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 6-5-2018
Tag: cime_cesm2_0_rel_04
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:

Brief Summary:
    - Remove a "this is a test" line.
    - Module updates for theta and edison
    - Update PyCECT tool to v3.0.7
    - Improvements to addmetadata script.
    - More doc updates.
    - Check options in config sections main and create_test and make sure each is supported. 
    - Remove entries duplicated in components.
    - Add half degree grid.
    - Allow space after string in namelist.
    - Fix issues with mpi-serial build.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
1da3a1d Merge pull request #2638 from billsacks/fix_doc
e2fd6fa Merge pull request #2637 from ESMCI/fischer/machines_update
db6080f Merge pull request #2634 from ESMCI/fischer/pyCECT
87648e4 Merge pull request #2632 from ESMCI/fischer/addmetadata
84ffa89 Merge pull request #2628 from ESMCI/mvertens/more_doc_updates
827272e Merge pull request #2626 from jedwards4b/config_sanity
3fd63b6 Merge pull request #2625 from jedwards4b/config_archive_update
d3073e9 Merge pull request #2624 from jedwards4b/new_half_degree
0e6c7a7 allow space after string in namelists
30d0879 Merge pull request #2623 from jedwards4b/mpi_serial_bugfix


Modified files: git diff --name-status [previous_tag]
M	config/cesm/config_archive.xml
M	config/cesm/config_files.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_machines.xml
M	doc/source/users_guide/create-a-case.rst
M	doc/source/users_guide/pes-threads.rst
M	doc/source/users_guide/timers.rst
M	doc/source/users_guide/workflows.rst
M	scripts/create_newcase
M	scripts/create_test
M	scripts/lib/CIME/XML/machines.py
M	scripts/lib/CIME/compare_namelists.py
M	scripts/lib/CIME/utils.py
M	scripts/tests/scripts_regression_tests.py
M	src/externals/pio1/pio/box_rearrange.F90.in
M	src/externals/pio1/pio/pio_support.F90
M	src/externals/pio1/pio/piolib_mod.F90
M	tools/statistical_ensemble_test/addmetadata.sh
A	tools/statistical_ensemble_test/pyCECT/.gitignore
A	tools/statistical_ensemble_test/pyCECT/EET.py
M	tools/statistical_ensemble_test/pyCECT/LICENSE.txt
M	tools/statistical_ensemble_test/pyCECT/README_pyCECT.rst
M	tools/statistical_ensemble_test/pyCECT/README_pyEnsSum.rst
M	tools/statistical_ensemble_test/pyCECT/ens_excluded_varlist.json
A	tools/statistical_ensemble_test/pyCECT/ens_sub.pbs
M	tools/statistical_ensemble_test/pyCECT/ens_sub.sh
A	tools/statistical_ensemble_test/pyCECT/exclude_empty.json
A	tools/statistical_ensemble_test/pyCECT/included_varlist.json
M	tools/statistical_ensemble_test/pyCECT/pyCECT.py
M	tools/statistical_ensemble_test/pyCECT/pyEnsLib.py
M	tools/statistical_ensemble_test/pyCECT/pyEnsSum.py
M	tools/statistical_ensemble_test/pyCECT/pyEnsSumPop.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 5-22-2018
Tag: cime_cesm2_0_rel_03
Answer Changes: None
Tests: scripts_regression_tests, build tests on Cori.
Dependencies:

Brief Summary: Third release candidate.
    - Update environment modules for Cori.
    - Change PRE.f09_f09.ADESP_TEST.hobart_nag test to f19_f19.
    - Tweaks to cism-specific documentation.
    - Update for Sphinx v1.7 and doc version 5.6.
    - More doc updates.
    - Maint 5.6 - documentation updates.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
ed9ced8 Merge pull request #2619 from ESMCI/fischer/nersc
c1dade4 Merge pull request #2618 from ESMCI/fischer/testfix
1f41bc6 Merge pull request #2617 from billsacks/update_cism_doc
08f12ea Merge pull request #2616 from bertinia/maint-5.6
72ed273 Merge pull request #2615 from ESMCI/mvertens/more_doc_updates
7049dab Merge pull request #2614 from bertinia/maint-5.6

Modified files: git diff --name-status [previous_tag]
M	.gitignore
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.case.run
M	config/cesm/machines/template.case.test
M	config/cesm/machines/template.st_archive
M	doc/Makefile
M	doc/README
D	doc/source/README
M	doc/source/conf.py
M	doc/source/users_guide/building-a-case.rst
A	doc/source/users_guide/cime-change-namelist.rst
M	doc/source/users_guide/cloning-a-case.rst
M	doc/source/users_guide/compsets.rst
M	doc/source/users_guide/create-a-case.rst
M	doc/source/users_guide/grids.rst
M	doc/source/users_guide/index.rst
M	doc/source/users_guide/introduction-and-overview.rst
M	doc/source/users_guide/machine.rst
M	doc/source/users_guide/pes-threads.rst
M	doc/source/users_guide/porting-cime.rst
M	doc/source/users_guide/running-a-case.rst
M	doc/source/users_guide/setting-up-a-case.rst
M	doc/source/users_guide/testing.rst
M	doc/source/users_guide/timers.rst
M	doc/source/users_guide/troubleshooting.rst
M	doc/source/users_guide/unit_testing.rst
D	doc/source/users_guide/use_cases/basics-a-basic-example.rst
D	doc/source/users_guide/use_cases/basics-setting-up-a-branch-or-hybrid-run.rst
D	doc/source/users_guide/use_cases/cesm-nml.rst
D	doc/source/users_guide/use_cases/datamod-nml.rst
D	doc/source/users_guide/use_cases/driver-nml.rst
D	doc/source/users_guide/use_cases/namelist-gen.rst
D	doc/source/users_guide/use_cases/use-cases.rst
A	doc/source/users_guide/workflows.rst
M	doc/tools_autodoc.cfg
M	doc/tools_autodoc.py
M	scripts/Tools/xmlquery
D	scripts/manage_pes
M	src/drivers/mct/cime_config/testdefs/testlist_drv.xml

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 5-17-2018
Tag: cime_cesm2_0_rel_02
Answer Changes: Round Off for Cheyenne gnu
Tests: scripts_regression_tests, prealpha gnu tests on cheyenne
Dependencies:

Brief Summary:
    - Update Cheyenne gnu compiler to 7.3.0

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
    Merge pull request #2611 from ESMCI/fischer/gnu7

Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_compilers.xml
M       config/cesm/machines/config_machines.xml

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 5-17-2018
Tag: cime_cesm2_0_rel_01
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:

Brief Summary:
    - Move cam section out of config archive.
    - Add commas to output using --value.
    - Fix multisubmit tests were not resubmitting.
    - A new script to add additional metadata for stat ensemble test.
    - Fix formatting issue.
    - Update iyear for 2000 runs.
    - Merge branch 'master' of github.com:ESMCI/cime
    - These grids are needed for cime standalone testing.
    - Updated the wrappers for the ESMF mapping tools to work on NCAR machines. 

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
950cda0 Merge pull request #2608 from jedwards4b/config_archive_dist
2e997e0 Merge pull request #2607 from jedwards4b/xmlquery_multivalue
f1d501f Merge pull request #2600 from jedwards4b/test_issues
5c256ec Merge pull request #2582 from jedwards4b/stattest_add_metadata
8ce38a4 fix formatting issue
6c53cfc Merge pull request #2594 from jedwards4b/orb_iyear_2000
c04da3c Merge branch 'master' of github.com:ESMCI/cime
166a40c these grids are needed for cime standalone testing
7cef855 Merge pull request #2589 from mnlevy1981/mlevy/mapping_on_geyser

Modified files: git diff --name-status [previous_tag]
M	config/cesm/config_archive.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.case.test
M	config/cesm/machines/template.st_archive
M	scripts/Tools/xmlquery
M	scripts/lib/CIME/SystemTests/pet.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/env_base.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/case/case_st_archive.py
M	scripts/lib/CIME/test_scheduler.py
M	src/components/data_comps/datm/datm_comp_mod.F90
M	src/components/data_comps/datm/mct/atm_comp_mct.F90
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	tools/mapping/check_maps/README
M	tools/mapping/check_maps/check_map.sh
M	tools/mapping/check_maps/src/ESMF_RegridWeightGenCheck.F90
M	tools/mapping/check_maps/src/Makefile
M	tools/mapping/gen_domain_files/src/.gitignore
M	tools/mapping/gen_domain_files/src/Makefile
A	tools/mapping/gen_mapping_files/.gitignore
M	tools/mapping/gen_mapping_files/README
M	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/.gitignore
M	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/README
M	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/create_ESMF_map.sh
D	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/regridbatch.yellowstone.sh
M	tools/mapping/gen_mapping_files/gen_cesm_maps.sh
M	tools/mapping/gen_mapping_files/runoff_to_ocn/.gitignore
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/Makefile
M	tools/mapping/map_field/.gitignore
M	tools/mapping/map_field/README
M	tools/mapping/map_field/src/Makefile
M	tools/statistical_ensemble_test/README
A	tools/statistical_ensemble_test/addmetadata.sh
A	tools/statistical_ensemble_test/ensemble.py
A	tools/statistical_ensemble_test/single_run.py


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 5-14-2018
Tag: cime5.6.7
Answer Changes: None
Tests: scripts_regression_tests, xmlquery --listall --file env_run.xml
Dependencies:

Brief Summary:
    - xmlquery fix.
    - Fixes an issue when selecting mpilib on cheyenne.
    - Fixed some print format bugs left over from the string rewrite of a year ago.
    - Documentation updates, including major updates to --help for scripts.
    - Need to append config files.
    - Get model_version working.
    - Adds T85_T85_mg17 grid.
    - Correct spelling of protocol.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
5a54b88 Merge pull request #2588 from jedwards4b/xmlquery_fix
0b07cb5 Merge pull request #2591 from jedwards4b/configure_mpilib
5f4c8e4 Merge pull request #2586 from gold2718/pelayout_fixes
6ebcd23 Merge pull request #2585 from ESMCI/mvertens/documentation_updates
940e29c need this to append config files
72a1cf6 Merge pull request #2579 from ekluzek/clm50r1/cime5.6.3
b86853d Merge pull request #2575 from jedwards4b/newgrid
fcebaad Merge pull request #2571 from jedwards4b/misspelling_protocol


Modified files: git diff --name-status [previous_tag]
M	config/cesm/config_grids.xml
M	config/cesm/config_inputdata.xml
M	config/e3sm/config_inputdata.xml
M	config/xml_schemas/config_inputdata.xsd
M	doc/source/conf.py
M	doc/source/users_guide/building-a-case.rst
M	doc/source/users_guide/cime-config.rst
M	doc/source/users_guide/cloning-a-case.rst
M	doc/source/users_guide/porting-cime.rst
M	doc/source/users_guide/running-a-case.rst
M	doc/source/users_guide/testing.rst
M	scripts/Tools/case.build
M	scripts/Tools/case.cmpgen_namelists
M	scripts/Tools/case.qstatus
M	scripts/Tools/case.setup
M	scripts/Tools/case.submit
M	scripts/Tools/check_case
M	scripts/Tools/check_input_data
M	scripts/Tools/pelayout
M	scripts/Tools/preview_namelists
M	scripts/Tools/preview_run
M	scripts/Tools/xmlchange
M	scripts/Tools/xmlquery
M	scripts/create_clone
M	scripts/create_newcase
M	scripts/create_test
M	scripts/lib/CIME/Servers/ftp.py
M	scripts/lib/CIME/Servers/gftp.py
M	scripts/lib/CIME/Servers/svn.py
M	scripts/lib/CIME/Servers/wget.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/XML/inputdata.py
M	scripts/lib/CIME/case/check_input_data.py
M	scripts/lib/CIME/utils.py
M	scripts/query_config
M	scripts/query_testlists
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	tools/configure

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 5-02-2018
Tag: cime5.6.3
Answer Changes: None
Tests: 
Dependencies:

Brief Summary:
    - Fix config write of logical.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
974839b fix config write of logical

Modified files: git diff --name-status [previous_tag]
M       scripts/Tools/case.submit


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 5-01-2018
Tag: cime5.6.2
Answer Changes: None
Tests: load_balancing_test.py
       hand tested create_newcase --case foo --compset QSC6 --res f19_f19_mg17 
Dependencies:

Brief Summary:
    - Refine distinction of E vs Q compset.
    - Update load balance tool.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
b2a19cd Merge pull request #2525 from jedwards4b/better_distinguish_compset_Q_from_E
28b8634 Merge pull request #2520 from ESMCI/sarich/update-loadbalancingtool

Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/case/case.py
M       tools/load_balancing_tool/load_balancing_submit.py
M       tools/load_balancing_tool/tests/load_balancing_test.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 5-01-2018
Tag: cime5.6.1
Answer Changes: None, PR #2195 has roundoff for code not currently used.
Tests: scripts_regression_tests, code_checker, by-hand
Dependencies:

Brief Summary:
    - Refine cheyenne retry method.
    - Save submit options for resubmit.
    - Need schema description for NODE_FAIL_REGEX.
    - Use nodefail code for cheyenne.
    - Make st_archive handle DART's restart history files.
    - Check input logic fix.
    - Only check for rundir if not a test.
    - Jgfouca/branch for acme split 2018-04-26.
    - Correct equations of the form **(1/3) to be **(1.0_R8/3.0_R8) to evaluate correctly.
    - Remove debug print statements.
    - Revert change to cheyenne mpt.
    - Remove manage_testlist.
    - Testreporter fix.
    - Match entire string for XML attribute selectors for env_mach_specific.
    - Fix undefined variable in some circumstances.
    - wait_for_tests needs to upload case2 logs if there are some
    - Another fix for testreporter.py.

User interface changes: 
    - manage_testlist was removed.
    - Changes to matching behavior in env_mach_specific.
    - New option to wait_for_tests.

PR summary: git log --oneline --first-parent [previous_tag]..master 
5af0e02 Merge pull request #2516 from jedwards4b/refine_retry
5e8a173 Merge pull request #2518 from jedwards4b/save_submit_options
1d7a27d need schema description for NODE_FAIL_REGEX
879249b Merge pull request #2509 from jedwards4b/cheyenne_nodefail
40cf173 Merge pull request #2491 from kdraeder/dart_rh_files
988eff2 Merge pull request #2501 from jedwards4b/check_input_logic_fix
7ee7a0d Merge pull request #2508 from jedwards4b/test_init_fix
fbe0814 Merge pull request #2505 from ESMCI/jgfouca/branch-for-acme-split-2018-04-26
8977e55 Merge pull request #2195 from jedwards4b/diurnal_atmocn_flux_bugfix
4e489b7 remove debug print statements
438e1f0 revert change to cheyenne mpt
2e0ba3b Merge pull request #2503 from ESMCI/fischer/rm_manage_testlist
cf19590 Merge pull request #2502 from ESMCI/fischer/testreporter_fix
1a7dac9 Merge pull request #2499 from ESMCI/jgfouca/match_entire_string
71be68f Fix undefined variable in some circumstances
6673d6a Merge pull request #2498 from ESMCI/jgfouca/wait_for_tests_case2
8360ddc Merge pull request #2494 from ESMCI/fischer/test_reporter


Modified files: git diff --name-status [previous_tag]
M	config/cesm/config_archive.xml
M	config/cesm/machines/config_machines.xml
M	config/e3sm/allactive/config_compsets.xml
M	config/e3sm/allactive/config_pesall.xml
M	config/e3sm/config_archive.xml
M	config/e3sm/config_files.xml
M	config/e3sm/config_grids.xml
M	config/e3sm/config_inputdata.xml
M	config/e3sm/machines/Depends.titan.pgi
M	config/e3sm/machines/config_batch.xml
M	config/e3sm/machines/config_compilers.xml
M	config/e3sm/machines/config_machines.xml
M	config/e3sm/testmods_dirs/allactive/v1cmip6/user_nl_cam
M	config/e3sm/tests.py
A	config/e3sm/usermods_dirs/README
D	config/e3sm/usermods_dirs/b1850/shell_commands
D	config/e3sm/usermods_dirs/b1850_cism/include_user_mods
D	config/e3sm/usermods_dirs/b1850_cism/user_nl_cism
M	config/xml_schemas/config_machines.xsd
M	doc/source/users_guide/testing.rst
M	scripts/Tools/case.submit
M	scripts/Tools/jenkins_generic_job
M	scripts/Tools/wait_for_tests
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/test_reporter.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case/case_run.py
M	scripts/lib/CIME/case/case_st_archive.py
M	scripts/lib/CIME/case/case_submit.py
M	scripts/lib/CIME/case/check_input_data.py
M	scripts/lib/CIME/wait_for_tests.py
M	scripts/lib/get_tests.py
D	scripts/manage_testlists
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_e3sm.xml
M	src/drivers/mct/main/cime_comp_mod.F90
M	src/share/util/shr_flux_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 4-19-2018
Tag: cime5.6.0
Answer Changes: None
Tests: scripts_regression_tests 
Dependencies:

Brief Summary:
    - Don't access data servers if no data is needed.
    - Add a test of the st_archive capability.
    - Improve help message for resubmitting to dash.
    - Simple compare improvement.
    - Force the NODEFAIL test to run on the cheyenne regular queue.
    - Download refcase from servers for hybrid.
    - Add a warning if an unsupported testlist.xml is encountered.
    - Replace TOTALPES with total_tasks.
    - Fix massive misuse of TOTALPES for mpi -np all across e3sm.
    - Fix test_scheduler's computation of procs needed for a test.
    - Transition CIME to using a custom util for copying files.
    - Minor fix to help msgs for options for e3sm mgmt tools.

User interface changes: 
    - case.st_archive now has a --test option.

PR summary: git log --oneline --first-parent [previous_tag]..master 
0cd58a7 Merge pull request #2489 from jedwards4b/nodatanoserver
aeb0f47 Merge pull request #2470 from jedwards4b/st_archive_test
f1c2759 Improve help message for resubmitting to dash
afc640c Merge pull request #2487 from jedwards4b/simple_compare_improvement
9410812 Merge pull request #2486 from jedwards4b/nodefail_fix
d3c73b7 Merge pull request #2481 from jedwards4b/cid_decesm
b0afec2 Merge pull request #2482 from jedwards4b/testlist_format
3874d08 replace TOTALPES with total_tasks
28265be Fix massive misuse of TOTALPES for mpi -np all across e3sm
9344b16 Merge pull request #2479 from ESMCI/jgfouca/fix_test_sched_procs_needed
f48c994 Merge pull request #2475 from ESMCI/jgfouca/safer_copy
adae0ae Minor fix to help msgs for options for e3sm mgmt tools

Modified files: git diff --name-status [previous_tag]
M	config/cesm/config_archive.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.st_archive
M	config/e3sm/config_archive.xml
M	config/e3sm/machines/config_machines.xml
M	config/e3sm/machines/template.st_archive
M	config/xml_schemas/config_archive.xsd
M	scripts/Tools/e3sm_cime_merge
M	scripts/Tools/e3sm_cime_split
M	scripts/lib/CIME/BuildTools/configure.py
M	scripts/lib/CIME/Servers/ftp.py
M	scripts/lib/CIME/Servers/gftp.py
M	scripts/lib/CIME/Servers/svn.py
M	scripts/lib/CIME/Servers/wget.py
M	scripts/lib/CIME/SystemTests/eri.py
M	scripts/lib/CIME/SystemTests/err.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/archive.py
A	scripts/lib/CIME/XML/archive_base.py
M	scripts/lib/CIME/XML/env_archive.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/XML/testlist.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case/case.py
M	scripts/lib/CIME/case/case_clone.py
M	scripts/lib/CIME/case/case_cmpgen_namelists.py
M	scripts/lib/CIME/case/case_run.py
M	scripts/lib/CIME/case/case_setup.py
M	scripts/lib/CIME/case/case_st_archive.py
M	scripts/lib/CIME/case/check_input_data.py
M	scripts/lib/CIME/case/preview_namelists.py
M	scripts/lib/CIME/get_timing.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/locked_files.py
M	scripts/lib/CIME/simple_compare.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/user_mod_support.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/CIME/wait_for_tests.py
M	scripts/lib/jenkins_generic_job.py
M	scripts/tests/scripts_regression_tests.py
M	src/drivers/mct/cime_config/config_archive.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 4-17-2018
Tag: cime5.4.0-alpha.30
Answer Changes: None
Tests: scripts_regression_tests, code checker 
Dependencies:

Brief Summary:
    - Change the CESM inputdata server precedence order to gridftp, svn, ftp, wget.
    - Fix totalpes to properly include threads.
    - Refactor BUILD_THREADED case value.

User interface changes: 
    - New FORCE_BUILD_THREADED.

PR summary: git log --oneline --first-parent [previous_tag]..master 
9af0120 Merge pull request #2477 from ESMCI/fischer/gftp_svn_ftp
d556876 Merge pull request #2465 from jedwards4b/fix_totalpes
ed78b14 Merge pull request #2466 from ESMCI/jgfouca/refactor_build_threaded

Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_inputdata.xml
M       config/cesm/machines/config_batch.xml
M       config/config_tests.xml
M       scripts/Tools/Makefile
M       scripts/create_test
M       scripts/fortran_unit_testing/run_tests.py
M       scripts/lib/CIME/case/case.py
M       scripts/lib/CIME/case/case_setup.py
M       scripts/lib/CIME/hist_utils.py
M       scripts/lib/CIME/test_utils.py
M       scripts/manage_pes
M       scripts/manage_testlists
M       scripts/tests/scripts_regression_tests.py
M       src/build_scripts/buildlib.gptl
M       src/build_scripts/buildlib.pio
M       src/drivers/mct/cime_config/config_component.xml

======================================================================

======================================================================
Originator: Chris Fischer 
Date: 4-13-2018
Tag: cime5.4.0-alpha.29
Answer Changes: None
Tests: scripts_regression_tests
       code_checker, testing by hand
Dependencies:

Brief Summary:
    - Fix variable initialization.
    - Add model doi url to seq_infodata and to cpl history global attributes.
    - Remove the LOGDIR variable and stop copying logs back to the case directory.
    - Fix env_mach_specific.sh file when module init is None.
    - Support renamed glimmer-cism directory; add README files to SourceMods directories.
    - Add f10_f10_mg37 grid.
    - Update casename restrictions.
    - Update statistical ensemble test for new verison of CESM.
    - Add PEM test to cime developer.
    - Add inputdata servers for grid ftp, ftp, and wget.
    - Use --no-logging in call to checkout_externals.
    - Add support for stampede2-skx and stampede2-knl at TACC.
    - split_test_py
    - Merge commit '20e3277dd143e4058ffa0ef610180c199cbb6ea1'
    - E3SM split.
    - PEA and PEM need to call case_setup for case2.
    - Revert small piece of #2299.
    - Fixes the potential leak reported by address sanitizer in PIO.
    - Reorganize Users Guide part 1 and 2 content.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
057e8a5 fix variable initialization
4913315 Merge pull request #2468 from ESMCI/mvertens/model_doi_url
37985f4 Merge pull request #2461 from jedwards4b/remove_logdir
f1f498f Merge pull request #2464 from ESMCI/jgfouca/never_source_none
b16ec34 Merge pull request #2462 from billsacks/rename_glimmer_cism_v2
0cead4e Merge pull request #2463 from ESMCI/fischer/f10_f10_mg37
08e05e2 Merge pull request #2460 from jedwards4b/update_casename_restrictions
578a7ab Merge pull request #2447 from allibco/master
356cec0 Merge pull request #2449 from ESMCI/jgfouca/add_pem_test_to_cimedev
a1d7814 Merge pull request #2439 from jedwards4b/addgridftp
0126382 Merge pull request #2444 from billsacks/manic_no_logging
dd58d01 Merge pull request #2440 from ESMCI/fischer/stampede2
9febe47 Merge branch 'jgfouca/split_test_py'
35a70fc Merge commit '20e3277dd143e4058ffa0ef610180c199cbb6ea1'
b06a755 Merge pull request #2433 from ESMCI/jgfouca/branch-for-acme-split-2018-04-09
f18bc36 Merge pull request #2437 from jedwards4b/fixpeaandpem
826c8ec Merge pull request #2434 from ESMCI/jgfouca/minor_seq_comm_mct_revert
35ce6f1 Merge pull request #2432 from ESMCI/mfdeakin-sandia/fix_pio_reported_leak
67088a3 Merge pull request #2407 from ESMCI/rljacob/docs/reorg-ug


Modified files: git diff --name-status [previous_tag]
M	config/cesm/config_grids.xml
M	config/cesm/config_inputdata.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/e3sm/allactive/config_compsets.xml
M	config/e3sm/allactive/config_pesall.xml
M	config/e3sm/config_archive.xml
M	config/e3sm/config_files.xml
A	config/e3sm/machines/Depends.summit.ibm
A	config/e3sm/machines/Depends.theta.intel
M	config/e3sm/machines/config_batch.xml
M	config/e3sm/machines/config_compilers.xml
M	config/e3sm/machines/config_machines.xml
D	config/e3sm/testmods_dirs/allactive/cam/cosplite/user_nl_cam
D	config/e3sm/testmods_dirs/allactive/cam/cosplite/xmlchange_cmnds
D	config/e3sm/testmods_dirs/allactive/cam/cosplite_nhtfrq5/user_nl_cam
D	config/e3sm/testmods_dirs/allactive/cam/cosplite_nhtfrq5/xmlchange_cmnds
D	config/e3sm/testmods_dirs/allactive/cam/outfrq9s/user_nl_cam
D	config/e3sm/testmods_dirs/allactive/cam/outfrq9s/user_nl_clm
D	config/e3sm/testmods_dirs/allactive/cam/outfrq9s/xmlchange_cmnds
D	config/e3sm/testmods_dirs/allactive/cam/rtm_null/xmlchange_cmnds
D	config/e3sm/testmods_dirs/allactive/clm/betr/xmlchange_cmnds
D	config/e3sm/testmods_dirs/allactive/clm/bgcexp/user_nl_clm
D	config/e3sm/testmods_dirs/allactive/clm/bgcexp/xmlchange_cmnds
D	config/e3sm/testmods_dirs/allactive/clm/bgcinterface/user_nl_clm
D	config/e3sm/testmods_dirs/allactive/clm/eca/user_nl_clm
D	config/e3sm/testmods_dirs/allactive/clm/fates/user_nl_clm
D	config/e3sm/testmods_dirs/allactive/clm/rd/user_nl_clm
D	config/e3sm/testmods_dirs/allactive/clm/vst/user_nl_clm
D	config/e3sm/testmods_dirs/allactive/drv/y100k
D	config/e3sm/testmods_dirs/allactive/force_netcdf_pio/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/v1cmip6/shell_commands
D	config/e3sm/testmods_dirs/allactive/v1cmip6/xmlchange_cmnds
A	config/e3sm/tests.py
M	config/xml_schemas/config_inputdata.xsd
M	doc/source/index.rst
D	doc/source/users_guide/adding-cases.rst
D	doc/source/users_guide/case-basics.rst
A	doc/source/users_guide/cime-config.rst
M	doc/source/users_guide/cime-internals.rst
A	doc/source/users_guide/compsets.rst
M	doc/source/users_guide/create-a-case.rst
D	doc/source/users_guide/creating-new-compsets.rst
D	doc/source/users_guide/customizing-a-case.rst
A	doc/source/users_guide/grids.rst
M	doc/source/users_guide/index.rst
A	doc/source/users_guide/machine.rst
D	doc/source/users_guide/optimizing-processor-layout.rst
A	doc/source/users_guide/pes-threads.rst
M	doc/source/users_guide/porting-cime.rst
M	doc/source/users_guide/running-a-case.rst
M	doc/source/users_guide/testing.rst
A	doc/source/users_guide/timers.rst
M	doc/source/users_guide/use_cases/basics-a-basic-example.rst
D	doc/source/users_guide/use_cases/basics-mpi-example.rst
A	doc/source/users_guide/use_cases/cesm-nml.rst
A	doc/source/users_guide/use_cases/datamod-nml.rst
A	doc/source/users_guide/use_cases/driver-nml.rst
A	doc/source/users_guide/use_cases/namelist-gen.rst
M	doc/source/users_guide/use_cases/use-cases.rst
M	scripts/Tools/Makefile
M	scripts/Tools/list_e3sm_tests
D	scripts/Tools/update_e3sm_tests
M	scripts/create_test
M	scripts/lib/CIME/Servers/__init__.py
M	scripts/lib/CIME/Servers/ftp.py
A	scripts/lib/CIME/Servers/gftp.py
M	scripts/lib/CIME/SystemTests/pea.py
M	scripts/lib/CIME/SystemTests/pem.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case/case.py
M	scripts/lib/CIME/case/case_clone.py
M	scripts/lib/CIME/case/case_run.py
M	scripts/lib/CIME/case/check_input_data.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/utils.py
A	scripts/lib/get_tests.py
D	scripts/lib/update_e3sm_tests.py
M	scripts/tests/scripts_regression_tests.py
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/drivers/mct/cime_config/config_component_e3sm.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/main/seq_hist_mod.F90
M	src/drivers/mct/main/seq_io_mod.F90
M	src/drivers/mct/shr/seq_comm_mct.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90
M	src/externals/pio1/pio/piodarray.F90.in
M	src/share/timing/ChangeLog
M	src/share/timing/gptl.h
M	src/share/timing/private.h
M	tools/statistical_ensemble_test/README
M	tools/statistical_ensemble_test/ensemble.sh
M	tools/statistical_ensemble_test/single_run.sh
======================================================================
======================================================================

Originator: Chris Fischer 
Date: 4-06-2018
Tag: cime5.4.0-alpha.28
Answer Changes: None
Tests: ERI.f09_g17.B1850.cheyenne_intel.allactive-defaultio 
       scripts_regression_tests.py
       code_checker
Dependencies:

Brief Summary:
    - py3 fix
    - Fix for ERI test.
    - More fixes for archiver and tests.
    - cime_bisect improvements.
    - ERS and ERI tests need skip_pnl=False.
    - More fixes related to cesm testing.
    - CESM test fixes.
    - Refactor crucial run_sub_or_cmd method.
    - Restore shell batch capability.

User interface changes: 
    - New custom script option.

PR summary: git log --oneline --first-parent [previous_tag]..master 
35fd3d1 py3 fix
6c6d3b5 Merge pull request #2429 from jedwards4b/eri_fix
83ef1ba Merge pull request #2426 from jedwards4b/archiver_and_test_fixes
58f020d Merge pull request #2425 from ESMCI/jgfouca/cime_bisect_improvements
3c3fdeb Merge pull request #2424 from jedwards4b/cesm_sta_fixes
603d5da Merge pull request #2423 from jedwards4b/cesm_sta_fixes
fc83e87 Merge pull request #2422 from jedwards4b/cesm_sta_fixes
7602f4b Merge pull request #2420 from ESMCI/jgfouca/refactor_run_sub_or_cmd
d9e3cdf Merge pull request #2419 from ESMCI/jgfouca/restore_shell_batch

Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_archive.xml
M       scripts/Tools/cime_bisect
M       scripts/Tools/mkSrcfiles
M       scripts/lib/CIME/SystemTests/eri.py
M       scripts/lib/CIME/SystemTests/erp.py
M       scripts/lib/CIME/SystemTests/ers.py
M       scripts/lib/CIME/SystemTests/irt.py
M       scripts/lib/CIME/SystemTests/nck.py
M       scripts/lib/CIME/SystemTests/seq.py
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M       scripts/lib/CIME/XML/env_batch.py
M       scripts/lib/CIME/build.py
M       scripts/lib/CIME/case/case_run.py
M       scripts/lib/CIME/case/case_setup.py
M       scripts/lib/CIME/case/case_st_archive.py
M       scripts/lib/CIME/test_scheduler.py
M       scripts/lib/CIME/utils.py
M       src/drivers/mct/cime_config/config_archive.xml
M       src/share/util/shr_scam_mod.F90


======================================================================


======================================================================

Originator: Chris Fischer
Date: 4-03-2018
Tag: cime5.4.0-alpha.27
Answer Changes: None
Tests: 
Dependencies:

Brief Summary:
    - Avoid encode error.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
018c8e9 avoid encode error


Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/test_scheduler.py

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 4-02-2018
Tag: cime5.4.0-alpha.26
Answer Changes: None
Tests: scripts_regression_tests
       high-res couple runs on Theta and Cori-KNL
       ./create_test cime_developer on hobart
       hand testing
       e3sm_developer
       code_checker
Dependencies:

Brief Summary:
    - Remove the run_e3sm testing scripts from the CIME repo.
    - Fix pylint
    - Update hobart queue limits.
    - Allow env vars to be unresolved.
    - Add mosart restart history to archive list.
    - Improve cprnc build.
    - External script handling.
    - Update MPI message tags in coupler-component exchanges.
    - Always downscale walltime for tests.
    - st_archive the DART restart history files.
    - Do not make unnecessary env_batch jobs or batch job scripts.
    - Add unofficial support for shell version of case.run batch script.
    - Remove test mod from cime_developer PET test.
    - Only set and check glcrun_avg_alarm if glc_prognostic is true.
    - Branch for acme split 2018-03-27.
    - Allow case_diff to work on cases that are not tests.
    - Locals method did not work in py3, using getattr instead works in both.
    - env_mach_specific was coded to always try to combine module operations. 
      Instead, it should only do that for "module" module systems.
    - Rearrange case subdirectory.
    - Remove text 'ccsm' and 'cesm' and replace appropriately.
    - Add comment.
    - Permit IOErrors as well as OSErrors when trying to copy crpnc log.
    - Update MCT to 2.10rc2.
    - Make case tools part of the Case object.
    - Cleanup acme -> e3sm references in rst documentation.
    - Add an A and X compset test to aux_cime_baselines.
    - Compare two case setup.
    - Remove old pointclm directory.
    - Update key concepts documentation.
    - Fix skip-pnl for tests.
    - Order e3sm test list by runtime.
    - Update to newer version of cprnc on hobart.
    - Support full matching restrictions for batch directives.
    - Ignore files beginning in test_.
    - More updates to e3sm cime mgmt.
    - Rename and reorg upper level contents. 
    - Move example of query_config to introduction.
    - Add switch to list of module actions that cannot be batched.
    - Improve create_test error message.
    - Allow custom batch directive prefixes.
    - Provide infrastructure to allow single column model to run with SE dycore.
    - Branch for acme split 2018-03-13. 
    - Add better output to cime mgmt tool.
    - Add stack size modifier to hobart.
    - Add ability to xmlquery derived attributes.
    - Modify regex for hobart to work on compute nodes.
    - Make sure to clean repo before doing cime updates.
    - st archive/encapsulate datetime.
    - lawrencium machine cesm entries.
    - Add a CONTRIBUTING file welcoming contributions and giving some brief guidance.
    - Documentation updates for user customization.
    - Fix XML errors in config_archive for E3SM.
    - Implement improvements to st_archive regular expressions.
    - Remove the run_e3sm testing scripts from the CIME repo.

User interface changes: 
    - env_archive.xml
    - .case.run.sh file generated for E3SM.
    - New selectors allowed for batch directives.
    - Source code files beginning in test_ will be ignored in build.
    - New prefix attribute available for batch directives.
    - xmlquery will now accept derived attributes.
    - Users may run on lawrencium lr3/lr2.
    - In env_archive.xml.

PR summary: git log --oneline --first-parent [previous_tag]..master 
de9dc73 Merge pull request #2418 from ESMCI/mfdeakin-sandia/rm_run_e3sm_testing
e9e89bc Fix pylint
150db63 Merge pull request #2362 from mnlevy1981/cesm/hobart_updates
bf467f3 Merge pull request #2412 from jedwards4b/allow_unresolved_envvars
6605d4d add mosart restart history to archive list
6652100 Merge pull request #2417 from jedwards4b/cprnc_build
ed4130b Merge pull request #2413 from jedwards4b/external_script_handling
020fd34 Merge pull request #2397 from ESMCI/azamat/update-msgtag-in-cpl-comp-exchanges
43bfaef Merge pull request #2410 from ESMCI/jgfouca/downscale_walltime_force_queue
8799abc Merge pull request #2415 from kdraeder/dart_rest_hist
7d9c9c5 Merge pull request #2405 from ESMCI/jgfouca/cleanup_envbatch_and_batch_scripts
74696ed Merge pull request #2386 from ESMCI/jgfouca/e3sm_bash_batch
5539ece Remove test mod from cime_developer PET test
39fd78e Merge pull request #2404 from billsacks/glcrun_avg_alarm
356fda0 Merge pull request #2406 from ESMCI/jgfouca/branch-for-acme-split-2018-03-27
19675f9 Merge pull request #2398 from ESMCI/jgfouca/fix_case_diff_newcase
07a6b94 Merge pull request #2400 from jedwards4b/py3_fix
04929cf Merge pull request #2396 from ESMCI/jgfouca/fix_soft_env_files
e425f67 Merge pull request #2389 from jedwards4b/rearrange_case
c1a43b2 Merge pull request #2392 from jedwards4b/deccsmize
1178fe3 Add coment
6ea8e9e Permit IOErrors as well as OSErrors when trying to copy crpnc log
ac82489 Merge pull request #2374 from ESMCI/rljacob/update-mct-2.10rc2
0ca70da Merge pull request #2382 from jedwards4b/compare_two_case_setup
bbf8938 Merge pull request #2384 from bertinia/master
81674ac Merge pull request #2383 from ESMCI/fischer/aux_cime
d8c4c98 Merge pull request #2378 from jedwards4b/compare_two_case_setup
191d9f2 Merge pull request #2380 from ESMCI/rljacob/remove-old-pointclm
aca08fb Merge pull request #2370 from ESMCI/rljacob/update-concepts
c3b080b Merge pull request #2373 from ESMCI/jgfouca/fix_skip_pnl_tests
8fc1332 Merge pull request #2372 from ESMCI/jgfouca/create_test_order_tests
02d9896 Merge pull request #2371 from ESMCI/fischer/cprnc
8f4dadd Merge pull request #2369 from ESMCI/jgfouca/support_full_matching_for_batch_directives
5dc8b87 Merge pull request #2366 from jedwards4b/mkSrcchange
18ca549 Merge pull request #2367 from ESMCI/jgfouca/more_updates_to_e3sm_cime_mgmt
e952232 Merge pull request #2365 from ESMCI/rljacob/update-contents
1f355e1 Merge pull request #2364 from ESMCI/rljacob/move-querydoc
8fce4aa Add switch to list of module actions that cannot be batched
72bfc32 Merge pull request #2352 from ESMCI/jgfouca/improve_create_test_err_msg
a61a911 Merge pull request #2359 from ESMCI/jgfouca/allow_custom_directive_prefix
5e97685 Merge pull request #2344 from ESMCI/bogensch/SCM_SESCM
ec55a15 Merge pull request #2357 from ESMCI/jgfouca/branch-for-acme-split-2018-03-13
3bdab2c Add better output to cime mgmt tool
336f6d4 Merge pull request #2356 from jedwards4b/hobart_regex_update
e078c25 Merge pull request #2355 from ESMCI/jgfouca/xmlquery_derived_attributes
156458f Merge pull request #2354 from jedwards4b/hobart_regex_update
8597596 Make sure to clean repo before doing cime updates
0fe7a9e Merge pull request #2347 from ESMCI/mfdeakin-sandia/st_archive/encapsulate_datetime
c0272bf Merge pull request #2350 from rgknox/rgknox-lawrencium-mach
28270b7 Merge pull request #2346 from ESMCI/rljacob/add-contributing
46f371a Merge pull request #2345 from ESMCI/mvertens/addition_to_docs
2b51643 Fix XML errors in config_archive for e3
df4f779 Implement improvements to st_archive regular expressions


Modified files: git diff --name-status [previous_tag]
M	.gitignore
A	CONTRIBUTING.md
M	ChangeLog
M	config/cesm/config_archive.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.case.run
M	config/cesm/machines/template.case.test
M	config/cesm/machines/template.st_archive
M	config/config_headers.xml
M	config/e3sm/allactive/config_compsets.xml
M	config/e3sm/allactive/config_pesall.xml
D	config/e3sm/allactive/usermods_dirs/b1850/shell_commands
D	config/e3sm/allactive/usermods_dirs/b1850_cism/include_user_mods
D	config/e3sm/allactive/usermods_dirs/b1850_cism/user_nl_cism
M	config/e3sm/config_archive.xml
M	config/e3sm/config_files.xml
M	config/e3sm/config_grids.xml
A	config/e3sm/machines/Depends.summit.pgiacc
M	config/e3sm/machines/config_batch.xml
M	config/e3sm/machines/config_compilers.xml
M	config/e3sm/machines/config_machines.xml
M	config/e3sm/machines/syslog.anvil
M	config/e3sm/machines/syslog.cetus
M	config/e3sm/machines/syslog.cori-haswell
M	config/e3sm/machines/syslog.cori-knl
M	config/e3sm/machines/syslog.edison
M	config/e3sm/machines/syslog.mira
M	config/e3sm/machines/syslog.theta
M	config/e3sm/machines/syslog.titan
M	config/e3sm/machines/template.case.run
A	config/e3sm/machines/template.case.run.sh
M	config/e3sm/machines/template.case.test
M	config/e3sm/machines/template.st_archive
A	config/e3sm/testmods_dirs/allactive/clm/bgcexp/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/clm/bgcexp/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/mach/pet/shell_commands
A	config/e3sm/testmods_dirs/allactive/v1cmip6/README
A	config/e3sm/testmods_dirs/allactive/v1cmip6/user_nl_cam
A	config/e3sm/testmods_dirs/allactive/v1cmip6/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/v1cmip6/xmlchange_cmnds
A	config/e3sm/usermods_dirs/b1850/shell_commands
A	config/e3sm/usermods_dirs/b1850_cism/include_user_mods
A	config/e3sm/usermods_dirs/b1850_cism/user_nl_cism
M	config/xml_schemas/config_batch.xsd
M	doc/source/build_cpl/index.rst
M	doc/source/conf.py
M	doc/source/data_models/data-ocean.rst
M	doc/source/data_models/index.rst
M	doc/source/driver_cpl/index.rst
M	doc/source/index.rst
A	doc/source/misc_tools/ect.rst
M	doc/source/misc_tools/index.rst
M	doc/source/users_guide/adding-cases.rst
M	doc/source/users_guide/building-a-case.rst
M	doc/source/users_guide/case-basics.rst
M	doc/source/users_guide/cime-internals.rst
A	doc/source/users_guide/creating-new-compsets.rst
M	doc/source/users_guide/index.rst
M	doc/source/users_guide/introduction-and-overview.rst
M	doc/source/users_guide/porting-cime.rst
M	doc/source/users_guide/testing.rst
M	doc/source/what_cime/index.rst
D	doc/source/xml_files/acme.rst
M	doc/source/xml_files/drivers.rst
A	doc/source/xml_files/e3sm.rst
M	doc/source/xml_files/index.rst
M	doc/tools_autodoc.cfg
M	scripts/Tools/case.cmpgen_namelists
M	scripts/Tools/case.setup
M	scripts/Tools/case.submit
M	scripts/Tools/case_diff
M	scripts/Tools/check_case
M	scripts/Tools/check_input_data
M	scripts/Tools/check_lockedfiles
M	scripts/Tools/e3sm_cime_merge
M	scripts/Tools/e3sm_cime_split
M	scripts/Tools/mkSrcfiles
D	scripts/Tools/pointclm/README
D	scripts/Tools/pointclm/makepointdata.py
D	scripts/Tools/pointclm/pointCLM.py
D	scripts/Tools/pointclm/post_process.py
D	scripts/Tools/pointclm/site_fullrun.py
M	scripts/Tools/preview_namelists
M	scripts/Tools/preview_run
M	scripts/Tools/xmlchange
M	scripts/Tools/xmlquery
M	scripts/create_test
M	scripts/fortran_unit_testing/run_tests.py
M	scripts/lib/CIME/SystemTests/dae.py
M	scripts/lib/CIME/SystemTests/eri.py
M	scripts/lib/CIME/SystemTests/erp.py
M	scripts/lib/CIME/SystemTests/err.py
M	scripts/lib/CIME/SystemTests/irt.py
M	scripts/lib/CIME/SystemTests/ldsta.py
M	scripts/lib/CIME/SystemTests/mcc.py
M	scripts/lib/CIME/SystemTests/nck.py
M	scripts/lib/CIME/SystemTests/ncr.py
M	scripts/lib/CIME/SystemTests/pea.py
M	scripts/lib/CIME/SystemTests/pem.py
M	scripts/lib/CIME/SystemTests/pet.py
M	scripts/lib/CIME/SystemTests/pre.py
M	scripts/lib/CIME/SystemTests/seq.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/XML/pes.py
M	scripts/lib/CIME/build.py
D	scripts/lib/CIME/case.py
A	scripts/lib/CIME/case/README
A	scripts/lib/CIME/case/__init__.py
A	scripts/lib/CIME/case/case.py
A	scripts/lib/CIME/case/case_clone.py
A	scripts/lib/CIME/case/case_cmpgen_namelists.py
A	scripts/lib/CIME/case/case_run.py
A	scripts/lib/CIME/case/case_setup.py
A	scripts/lib/CIME/case/case_st_archive.py
A	scripts/lib/CIME/case/case_submit.py
A	scripts/lib/CIME/case/case_test.py
A	scripts/lib/CIME/case/check_input_data.py
A	scripts/lib/CIME/case/check_lockedfiles.py
A	scripts/lib/CIME/case/preview_namelists.py
D	scripts/lib/CIME/case_clone.py
D	scripts/lib/CIME/case_cmpgen_namelists.py
D	scripts/lib/CIME/case_run.py
D	scripts/lib/CIME/case_setup.py
D	scripts/lib/CIME/case_st_archive.py
D	scripts/lib/CIME/case_submit.py
D	scripts/lib/CIME/case_test.py
D	scripts/lib/CIME/check_input_data.py
D	scripts/lib/CIME/check_lockedfiles.py
M	scripts/lib/CIME/compare_test_results.py
A	scripts/lib/CIME/date.py
M	scripts/lib/CIME/hist_utils.py
A	scripts/lib/CIME/locked_files.py
D	scripts/lib/CIME/preview_namelists.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/tests/case_fake.py
M	scripts/lib/CIME/user_mod_support.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/e3sm_cime_mgmt.py
M	scripts/lib/jenkins_generic_job.py
M	scripts/lib/update_e3sm_tests.py
D	scripts/tests/run_e3sm_ctest/CMakeLists.txt
D	scripts/tests/run_e3sm_ctest/CTestConfig.cmake
D	scripts/tests/run_e3sm_ctest/runE3smTest_template.sh
M	scripts/tests/scripts_regression_tests.py
M	src/components/data_comps/datm/cime_config/config_archive.xml
M	src/components/data_comps/dice/cime_config/config_archive.xml
M	src/components/data_comps/dlnd/cime_config/config_archive.xml
M	src/components/data_comps/docn/cime_config/config_archive.xml
M	src/components/data_comps/drof/cime_config/config_archive.xml
M	src/components/data_comps/dwav/cime_config/config_archive.xml
M	src/drivers/mct/cime_config/config_archive.xml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/drivers/mct/cime_config/config_component_e3sm.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/cime_config/testdefs/testlist_drv.xml
M	src/drivers/mct/main/cime_comp_mod.F90
M	src/drivers/mct/main/component_mod.F90
M	src/drivers/mct/shr/seq_comm_mct.F90
M	src/drivers/mct/shr/seq_timemgr_mod.F90
M	src/externals/mct/README
M	src/externals/mct/doc/mct_APIs.tex
M	src/externals/mct/mct/m_Rearranger.F90
M	src/share/streams/shr_dmodel_mod.F90
M	src/share/util/shr_flux_mod.F90
M	src/share/util/shr_scam_mod.F90
M	tools/cprnc/Makefile

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 3-06-2018
Tag: cime5.4.0-alpha.25
Answer Changes: Climate Changing for non-B 1850 compsets in CESM
Tests:  scripts_regression_tests.py
        hand test SMS_P1x4.f19_g16.X
        code checker
        edison build test for A,X, and B1850 compsets
Dependencies:

Brief Summary:
    - Add support for environment and module to depend on job.
    - Fix mistake in scripts-regression-tests help dump.
    - Env batch cleanup
    - Add queue attribute (small cheyenne jobs go to share queue).
    - For Travis-CI build: kick off build on master whenever it's pushed.
    - Reinstate ability to select queue by num tasks.
    - Give st_archive an extra 10 min just to be sure.
    - Refactor handling of small jobs.
    - Report lock file info as debug output.
    - Auto-regen batch files in case_submit.
    - Add travis_ci testing.
    - Supported attribute is string.
    - Cleanup xml.
    - Redo orb_year_defaults for cesm only.
        Expected to change answers for non-B 1850 compsets in CESM
    - Add supported flag to testlist.xml.
    - Big upgrade to scripts_regression_tests argument handling.
    - Update esmf module for edison.nersc.gov.
    - New allow_error field for module system.
    - Fix trivial pylint problem.
    - Add the comment from config_pes.xml to the env_mach_pes.xml file.
    - Refactor _get_datenames to count the correct number of cpl.r files.
    - Change subtree split method.
    - Jgfouca/branch for acme split 2018-02-22.
    - Fix uninitialized variable.
    - python2 needs an init file in Servers.
    - Catch more errors in the testlist schema, remove generic GSW DATM_MODE ignore scripts/cases.
    - Add support for ftp and wget.
    - Add support for provenance in cesm.
    - Swap command cannot be batched together.
    - Add xml support for inputdata server.
    - Fix bug when providing -p PROJECT flag to create_test.
    - Rename acme to e3sm everywhere.
    - Update components' communicator initialization.
    - Make get_components return None instead of fail.

User interface changes: 
    - (cesm only) create_test and query_testlist now have --supported-only flag
    - New allow_error attribute for module systems. 
    - check_input_data replace --svn-loc with --server and --protocol
    - Some Tools with "acme" in the name now say "e3sm".

PR summary: git log --oneline --first-parent [previous_tag]..master 
c9c5695 Merge pull request #2341 from jedwards4b/mpirun_depends_on_queue
7dff579 Fix mistake in scripts-regression-tests help dump
bfb23dd Merge pull request #2339 from jedwards4b/env_batch_cleanup
c19fd3f Merge pull request #2335 from jedwards4b/cheyenne_share_queue
8311f8e Merge pull request #2333 from billsacks/travis_build_master
a5ed418 Merge pull request #2327 from ESMCI/jgfouca/allow_queue_selection_by_task
8f6f199 Give st_archive an extra 10 min just to be sure
751c895 Merge pull request #2326 from ESMCI/jgfouca/refacor_small_jobs
d4fc951 Merge pull request #2325 from ESMCI/jgfouca/adjust_lock_output
a9607d7 Merge pull request #2320 from ESMCI/jgfouca/upgrade_batch_script_handling
e93296a Merge pull request #2324 from jedwards4b/travis_ci
41ef5a3 Merge pull request #2321 from jedwards4b/supported_flag_for_testlist
a714422 Merge pull request #2323 from jedwards4b/cleanup_xml
43c0308 Merge pull request #2290 from jedwards4b/orb_year_defaults
c5aa74b Merge pull request #2316 from jedwards4b/supported_flag_for_testlist
1ac42bb Merge pull request #2319 from ESMCI/jgfouca/script_regr_test_arg_upgrade
fdf7757 Merge pull request #2318 from ESMCI/fischer/edison
68e7b765 Merge pull request #2317 from ESMCI/jgfouca/allow_stderr_in_env_modules
ab6d933 Fix trivial pylint problem
93dde2b Merge pull request #2315 from jedwards4b/add_comment_pes_file
cae9f9a Merge pull request #2285 from kdraeder/multi_drv_kdr
7f8c26a Merge pull request #2314 from ESMCI/jgfouca/chg_subtree_split_method
92ccb83 Merge pull request #2312 from ESMCI/jgfouca/branch-for-acme-split-2018-02-22
c82664e fix uninitialized variable
8a86965 python2 needs an init file in Servers
5af94aa Merge pull request #2300 from ekluzek/testlistxsdgitig
69e35b2 Merge pull request #2311 from jedwards4b/ftpandwget
8baf2bb Merge pull request #2305 from jedwards4b/cesm_provenance
8ac3dd2 Merge pull request #2310 from ESMCI/jgfouca/fix_env_module_operation_batching
ec9483c Merge pull request #2309 from jedwards4b/inputdata
ba3c1fb Merge pull request #2306 from ESMCI/jgfouca/fix_bug_when_setting_proj
6405d72 Merge pull request #2296 from ESMCI/rljacob/acme2e3sm
219ee5a Merge pull request #2299 from ESMCI/azamat/update-seq_comm_setcomm-calls
6c3f484 Merge pull request #2298 from ESMCI/jgfouca/fix_query_config_again


Modified files: git diff --name-status [previous_tag]
M	.gitignore
A	.travis.yml
D	config/acme/allactive/config_compsets.xml
D	config/acme/allactive/config_pesall.xml
D	config/acme/allactive/testlist_allactive.xml
D	config/acme/allactive/usermods_dirs/b1850/shell_commands
D	config/acme/allactive/usermods_dirs/b1850_cism/include_user_mods
D	config/acme/allactive/usermods_dirs/b1850_cism/user_nl_cism
D	config/acme/config_archive.xml
D	config/acme/config_files.xml
D	config/acme/config_grids.xml
D	config/acme/machines/Depends.cetus
D	config/acme/machines/Depends.cray
D	config/acme/machines/Depends.gnu
D	config/acme/machines/Depends.intel
D	config/acme/machines/Depends.mira
D	config/acme/machines/Depends.nag
D	config/acme/machines/Depends.summitdev.ibm
D	config/acme/machines/Depends.summitdev.pgiacc
D	config/acme/machines/Depends.titan.cray
D	config/acme/machines/Depends.titan.intel
D	config/acme/machines/Depends.titan.pgi
D	config/acme/machines/Depends.titan.pgiacc
D	config/acme/machines/README
D	config/acme/machines/config_batch.xml
D	config/acme/machines/config_batch.xsd
D	config/acme/machines/config_compilers.xml
D	config/acme/machines/config_machines.xml
D	config/acme/machines/config_pio.xml
D	config/acme/machines/syslog.anvil
D	config/acme/machines/syslog.cetus
D	config/acme/machines/syslog.cori-haswell
D	config/acme/machines/syslog.cori-knl
D	config/acme/machines/syslog.edison
D	config/acme/machines/syslog.mira
D	config/acme/machines/syslog.noop
D	config/acme/machines/syslog.theta
D	config/acme/machines/syslog.titan
D	config/acme/machines/template.case.run
D	config/acme/machines/template.case.test
D	config/acme/machines/template.ocn_diagnostics
D	config/acme/machines/template.st_archive
D	config/acme/machines/template.timeseries
D	config/acme/machines/userdefined_laptop_template/README.md
D	config/acme/machines/userdefined_laptop_template/config_compilers.xml
D	config/acme/machines/userdefined_laptop_template/config_machines.xml
D	config/acme/machines/userdefined_laptop_template/config_pes.xml
D	config/acme/testmods_dirs/allactive/cam/cosplite/user_nl_cam
D	config/acme/testmods_dirs/allactive/cam/cosplite/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/cam/cosplite_nhtfrq5/user_nl_cam
D	config/acme/testmods_dirs/allactive/cam/cosplite_nhtfrq5/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/cam/outfrq9s/user_nl_cam
D	config/acme/testmods_dirs/allactive/cam/outfrq9s/user_nl_clm
D	config/acme/testmods_dirs/allactive/cam/outfrq9s/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/cam/rtm_null/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/clm/betr/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/clm/bgcinterface/user_nl_clm
D	config/acme/testmods_dirs/allactive/clm/eca/user_nl_clm
D	config/acme/testmods_dirs/allactive/clm/fates/user_nl_clm
D	config/acme/testmods_dirs/allactive/clm/rd/user_nl_clm
D	config/acme/testmods_dirs/allactive/clm/vst/user_nl_clm
D	config/acme/testmods_dirs/allactive/drv/y100k
D	config/acme/testmods_dirs/allactive/force_netcdf_pio/shell_commands
D	config/acme/testmods_dirs/allactive/force_netcdf_pio/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/mach_mods/shell_commands
M	config/cesm/config_files.xml
A	config/cesm/config_inputdata.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.case.run
A	config/e3sm/allactive/config_compsets.xml
A	config/e3sm/allactive/config_pesall.xml
A	config/e3sm/allactive/testlist_allactive.xml
A	config/e3sm/allactive/usermods_dirs/b1850/shell_commands
A	config/e3sm/allactive/usermods_dirs/b1850_cism/include_user_mods
A	config/e3sm/allactive/usermods_dirs/b1850_cism/user_nl_cism
A	config/e3sm/config_archive.xml
A	config/e3sm/config_files.xml
A	config/e3sm/config_grids.xml
A	config/e3sm/config_inputdata.xml
A	config/e3sm/machines/Depends.cetus
A	config/e3sm/machines/Depends.cray
A	config/e3sm/machines/Depends.gnu
A	config/e3sm/machines/Depends.intel
A	config/e3sm/machines/Depends.mira
A	config/e3sm/machines/Depends.nag
A	config/e3sm/machines/Depends.summitdev.ibm
A	config/e3sm/machines/Depends.summitdev.pgiacc
A	config/e3sm/machines/Depends.titan.cray
A	config/e3sm/machines/Depends.titan.intel
A	config/e3sm/machines/Depends.titan.pgi
A	config/e3sm/machines/Depends.titan.pgiacc
A	config/e3sm/machines/README
A	config/e3sm/machines/config_batch.xml
A	config/e3sm/machines/config_compilers.xml
A	config/e3sm/machines/config_machines.xml
A	config/e3sm/machines/config_pio.xml
A	config/e3sm/machines/syslog.anvil
A	config/e3sm/machines/syslog.cetus
A	config/e3sm/machines/syslog.cori-haswell
A	config/e3sm/machines/syslog.cori-knl
A	config/e3sm/machines/syslog.edison
A	config/e3sm/machines/syslog.mira
A	config/e3sm/machines/syslog.noop
A	config/e3sm/machines/syslog.theta
A	config/e3sm/machines/syslog.titan
A	config/e3sm/machines/template.case.run
A	config/e3sm/machines/template.case.test
A	config/e3sm/machines/template.ocn_diagnostics
A	config/e3sm/machines/template.st_archive
A	config/e3sm/machines/template.timeseries
A	config/e3sm/machines/userdefined_laptop_template/README.md
A	config/e3sm/machines/userdefined_laptop_template/config_compilers.xml
A	config/e3sm/machines/userdefined_laptop_template/config_machines.xml
A	config/e3sm/machines/userdefined_laptop_template/config_pes.xml
A	config/e3sm/testmods_dirs/allactive/cam/cosplite/user_nl_cam
A	config/e3sm/testmods_dirs/allactive/cam/cosplite/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/cam/cosplite_nhtfrq5/user_nl_cam
A	config/e3sm/testmods_dirs/allactive/cam/cosplite_nhtfrq5/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/cam/outfrq9s/user_nl_cam
A	config/e3sm/testmods_dirs/allactive/cam/outfrq9s/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/cam/outfrq9s/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/cam/rtm_null/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/clm/betr/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/clm/bgcinterface/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/clm/eca/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/clm/fates/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/clm/rd/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/clm/vst/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/drv/y100k
A	config/e3sm/testmods_dirs/allactive/force_netcdf_pio/shell_commands
A	config/e3sm/testmods_dirs/allactive/force_netcdf_pio/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/mach_mods/shell_commands
M	config/xml_schemas/config_batch.xsd
A	config/xml_schemas/config_inputdata.xsd
M	config/xml_schemas/config_machines.xsd
M	config/xml_schemas/env_batch.xsd
M	config/xml_schemas/env_mach_pes.xsd
M	config/xml_schemas/env_mach_specific.xsd
M	config/xml_schemas/testlist.xsd
D	scripts/Tools/acme_check_env
D	scripts/Tools/acme_cime_merge
D	scripts/Tools/acme_cime_split
M	scripts/Tools/check_input_data
M	scripts/Tools/code_checker
A	scripts/Tools/e3sm_check_env
A	scripts/Tools/e3sm_cime_merge
A	scripts/Tools/e3sm_cime_split
M	scripts/Tools/jenkins_generic_job
D	scripts/Tools/list_acme_tests
A	scripts/Tools/list_e3sm_tests
M	scripts/Tools/preview_run
D	scripts/Tools/update_acme_tests
A	scripts/Tools/update_e3sm_tests
M	scripts/Tools/wait_for_tests
M	scripts/create_test
M	scripts/lib/CIME/BuildTools/makemacroswriter.py
A	scripts/lib/CIME/Servers/__init__.py
A	scripts/lib/CIME/Servers/ftp.py
A	scripts/lib/CIME/Servers/generic_server.py
A	scripts/lib/CIME/Servers/svn.py
A	scripts/lib/CIME/Servers/wget.py
M	scripts/lib/CIME/SystemTests/homme.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_pes.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/files.py
M	scripts/lib/CIME/XML/generic_xml.py
A	scripts/lib/CIME/XML/inputdata.py
M	scripts/lib/CIME/XML/namelist_definition.py
M	scripts/lib/CIME/XML/pes.py
M	scripts/lib/CIME/XML/testlist.py
M	scripts/lib/CIME/aprun.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/case_submit.py
M	scripts/lib/CIME/check_input_data.py
M	scripts/lib/CIME/check_lockedfiles.py
M	scripts/lib/CIME/code_checker.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/CIME/wait_for_tests.py
D	scripts/lib/acme_cime_mgmt.py
A	scripts/lib/e3sm_cime_mgmt.py
M	scripts/lib/jenkins_generic_job.py
D	scripts/lib/update_acme_tests.py
A	scripts/lib/update_e3sm_tests.py
D	scripts/tests/run_acme_ctest/CMakeLists.txt
D	scripts/tests/run_acme_ctest/CTestConfig.cmake
D	scripts/tests/run_acme_ctest/runAcmeTest_template.sh
A	scripts/tests/run_e3sm_ctest/CMakeLists.txt
A	scripts/tests/run_e3sm_ctest/CTestConfig.cmake
A	scripts/tests/run_e3sm_ctest/runE3smTest_template.sh
M	scripts/tests/scripts_regression_tests.py
M	src/components/data_comps/datm/cime_config/config_component.xml
M	src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M	src/drivers/mct/cime_config/buildnml
M	src/drivers/mct/cime_config/config_component.xml
D	src/drivers/mct/cime_config/config_component_acme.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
A	src/drivers/mct/cime_config/config_component_e3sm.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/main/seq_diag_mct.F90
M	src/drivers/mct/shr/seq_comm_mct.F90
M	src/drivers/mct/shr/seq_flds_mod.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 4-06-2018
Tag: cime5.4.0-alpha.28
Answer Changes: None
Tests: ERI.f09_g17.B1850.cheyenne_intel.allactive-defaultio 
       scripts_regression_tests.py
       code_checker
Dependencies:

Brief Summary:
    - py3 fix
    - Fix for ERI test.
    - More fixes for archiver and tests.
    - cime_bisect improvements.
    - ERS and ERI tests need skip_pnl=False.
    - More fixes related to cesm testing.
    - CESM test fixes.
    - Refactor crucial run_sub_or_cmd method.
    - Restore shell batch capability.

User interface changes: 
    - New custom script option.

PR summary: git log --oneline --first-parent [previous_tag]..master 
35fd3d1 py3 fix
6c6d3b5 Merge pull request #2429 from jedwards4b/eri_fix
83ef1ba Merge pull request #2426 from jedwards4b/archiver_and_test_fixes
58f020d Merge pull request #2425 from ESMCI/jgfouca/cime_bisect_improvements
3c3fdeb Merge pull request #2424 from jedwards4b/cesm_sta_fixes
603d5da Merge pull request #2423 from jedwards4b/cesm_sta_fixes
fc83e87 Merge pull request #2422 from jedwards4b/cesm_sta_fixes
7602f4b Merge pull request #2420 from ESMCI/jgfouca/refactor_run_sub_or_cmd
d9e3cdf Merge pull request #2419 from ESMCI/jgfouca/restore_shell_batch

Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_archive.xml
M       scripts/Tools/cime_bisect
M       scripts/Tools/mkSrcfiles
M       scripts/lib/CIME/SystemTests/eri.py
M       scripts/lib/CIME/SystemTests/erp.py
M       scripts/lib/CIME/SystemTests/ers.py
M       scripts/lib/CIME/SystemTests/irt.py
M       scripts/lib/CIME/SystemTests/nck.py
M       scripts/lib/CIME/SystemTests/seq.py
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M       scripts/lib/CIME/XML/env_batch.py
M       scripts/lib/CIME/build.py
M       scripts/lib/CIME/case/case_run.py
M       scripts/lib/CIME/case/case_setup.py
M       scripts/lib/CIME/case/case_st_archive.py
M       scripts/lib/CIME/test_scheduler.py
M       scripts/lib/CIME/utils.py
M       src/drivers/mct/cime_config/config_archive.xml
M       src/share/util/shr_scam_mod.F90


======================================================================

======================================================================

Originator: Chris Fischer
Date: 4-03-2018
Tag: cime5.4.0-alpha.27
Answer Changes: None
Tests: 
Dependencies:

Brief Summary:
    - Avoid encode error.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
018c8e9 avoid encode error


Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/test_scheduler.py

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 4-02-2018
Tag: cime5.4.0-alpha.26
Answer Changes: None
Tests: scripts_regression_tests
       high-res couple runs on Theta and Cori-KNL
       ./create_test cime_developer on hobart
       hand testing
       e3sm_developer
       code_checker
Dependencies:

Brief Summary:
    - Remove the run_e3sm testing scripts from the CIME repo.
    - Fix pylint
    - Update hobart queue limits.
    - Allow env vars to be unresolved.
    - Add mosart restart history to archive list.
    - Improve cprnc build.
    - External script handling.
    - Update MPI message tags in coupler-component exchanges.
    - Always downscale walltime for tests.
    - st_archive the DART restart history files.
    - Do not make unnecessary env_batch jobs or batch job scripts.
    - Add unofficial support for shell version of case.run batch script.
    - Remove test mod from cime_developer PET test.
    - Only set and check glcrun_avg_alarm if glc_prognostic is true.
    - Branch for acme split 2018-03-27.
    - Allow case_diff to work on cases that are not tests.
    - Locals method did not work in py3, using getattr instead works in both.
    - env_mach_specific was coded to always try to combine module operations. 
      Instead, it should only do that for "module" module systems.
    - Rearrange case subdirectory.
    - Remove text 'ccsm' and 'cesm' and replace appropriately.
    - Add comment.
    - Permit IOErrors as well as OSErrors when trying to copy crpnc log.
    - Update MCT to 2.10rc2.
    - Make case tools part of the Case object.
    - Cleanup acme -> e3sm references in rst documentation.
    - Add an A and X compset test to aux_cime_baselines.
    - Compare two case setup.
    - Remove old pointclm directory.
    - Update key concepts documentation.
    - Fix skip-pnl for tests.
    - Order e3sm test list by runtime.
    - Update to newer version of cprnc on hobart.
    - Support full matching restrictions for batch directives.
    - Ignore files beginning in test_.
    - More updates to e3sm cime mgmt.
    - Rename and reorg upper level contents. 
    - Move example of query_config to introduction.
    - Add switch to list of module actions that cannot be batched.
    - Improve create_test error message.
    - Allow custom batch directive prefixes.
    - Provide infrastructure to allow single column model to run with SE dycore.
    - Branch for acme split 2018-03-13. 
    - Add better output to cime mgmt tool.
    - Add stack size modifier to hobart.
    - Add ability to xmlquery derived attributes.
    - Modify regex for hobart to work on compute nodes.
    - Make sure to clean repo before doing cime updates.
    - st archive/encapsulate datetime.
    - lawrencium machine cesm entries.
    - Add a CONTRIBUTING file welcoming contributions and giving some brief guidance.
    - Documentation updates for user customization.
    - Fix XML errors in config_archive for E3SM.
    - Implement improvements to st_archive regular expressions.
    - Remove the run_e3sm testing scripts from the CIME repo.

User interface changes: 
    - env_archive.xml
    - .case.run.sh file generated for E3SM.
    - New selectors allowed for batch directives.
    - Source code files beginning in test_ will be ignored in build.
    - New prefix attribute available for batch directives.
    - xmlquery will now accept derived attributes.
    - Users may run on lawrencium lr3/lr2.
    - In env_archive.xml.

PR summary: git log --oneline --first-parent [previous_tag]..master 
de9dc73 Merge pull request #2418 from ESMCI/mfdeakin-sandia/rm_run_e3sm_testing
e9e89bc Fix pylint
150db63 Merge pull request #2362 from mnlevy1981/cesm/hobart_updates
bf467f3 Merge pull request #2412 from jedwards4b/allow_unresolved_envvars
6605d4d add mosart restart history to archive list
6652100 Merge pull request #2417 from jedwards4b/cprnc_build
ed4130b Merge pull request #2413 from jedwards4b/external_script_handling
020fd34 Merge pull request #2397 from ESMCI/azamat/update-msgtag-in-cpl-comp-exchanges
43bfaef Merge pull request #2410 from ESMCI/jgfouca/downscale_walltime_force_queue
8799abc Merge pull request #2415 from kdraeder/dart_rest_hist
7d9c9c5 Merge pull request #2405 from ESMCI/jgfouca/cleanup_envbatch_and_batch_scripts
74696ed Merge pull request #2386 from ESMCI/jgfouca/e3sm_bash_batch
5539ece Remove test mod from cime_developer PET test
39fd78e Merge pull request #2404 from billsacks/glcrun_avg_alarm
356fda0 Merge pull request #2406 from ESMCI/jgfouca/branch-for-acme-split-2018-03-27
19675f9 Merge pull request #2398 from ESMCI/jgfouca/fix_case_diff_newcase
07a6b94 Merge pull request #2400 from jedwards4b/py3_fix
04929cf Merge pull request #2396 from ESMCI/jgfouca/fix_soft_env_files
e425f67 Merge pull request #2389 from jedwards4b/rearrange_case
c1a43b2 Merge pull request #2392 from jedwards4b/deccsmize
1178fe3 Add coment
6ea8e9e Permit IOErrors as well as OSErrors when trying to copy crpnc log
ac82489 Merge pull request #2374 from ESMCI/rljacob/update-mct-2.10rc2
0ca70da Merge pull request #2382 from jedwards4b/compare_two_case_setup
bbf8938 Merge pull request #2384 from bertinia/master
81674ac Merge pull request #2383 from ESMCI/fischer/aux_cime
d8c4c98 Merge pull request #2378 from jedwards4b/compare_two_case_setup
191d9f2 Merge pull request #2380 from ESMCI/rljacob/remove-old-pointclm
aca08fb Merge pull request #2370 from ESMCI/rljacob/update-concepts
c3b080b Merge pull request #2373 from ESMCI/jgfouca/fix_skip_pnl_tests
8fc1332 Merge pull request #2372 from ESMCI/jgfouca/create_test_order_tests
02d9896 Merge pull request #2371 from ESMCI/fischer/cprnc
8f4dadd Merge pull request #2369 from ESMCI/jgfouca/support_full_matching_for_batch_directives
5dc8b87 Merge pull request #2366 from jedwards4b/mkSrcchange
18ca549 Merge pull request #2367 from ESMCI/jgfouca/more_updates_to_e3sm_cime_mgmt
e952232 Merge pull request #2365 from ESMCI/rljacob/update-contents
1f355e1 Merge pull request #2364 from ESMCI/rljacob/move-querydoc
8fce4aa Add switch to list of module actions that cannot be batched
72bfc32 Merge pull request #2352 from ESMCI/jgfouca/improve_create_test_err_msg
a61a911 Merge pull request #2359 from ESMCI/jgfouca/allow_custom_directive_prefix
5e97685 Merge pull request #2344 from ESMCI/bogensch/SCM_SESCM
ec55a15 Merge pull request #2357 from ESMCI/jgfouca/branch-for-acme-split-2018-03-13
3bdab2c Add better output to cime mgmt tool
336f6d4 Merge pull request #2356 from jedwards4b/hobart_regex_update
e078c25 Merge pull request #2355 from ESMCI/jgfouca/xmlquery_derived_attributes
156458f Merge pull request #2354 from jedwards4b/hobart_regex_update
8597596 Make sure to clean repo before doing cime updates
0fe7a9e Merge pull request #2347 from ESMCI/mfdeakin-sandia/st_archive/encapsulate_datetime
c0272bf Merge pull request #2350 from rgknox/rgknox-lawrencium-mach
28270b7 Merge pull request #2346 from ESMCI/rljacob/add-contributing
46f371a Merge pull request #2345 from ESMCI/mvertens/addition_to_docs
2b51643 Fix XML errors in config_archive for e3
df4f779 Implement improvements to st_archive regular expressions


Modified files: git diff --name-status [previous_tag]
M	.gitignore
A	CONTRIBUTING.md
M	ChangeLog
M	config/cesm/config_archive.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.case.run
M	config/cesm/machines/template.case.test
M	config/cesm/machines/template.st_archive
M	config/config_headers.xml
M	config/e3sm/allactive/config_compsets.xml
M	config/e3sm/allactive/config_pesall.xml
D	config/e3sm/allactive/usermods_dirs/b1850/shell_commands
D	config/e3sm/allactive/usermods_dirs/b1850_cism/include_user_mods
D	config/e3sm/allactive/usermods_dirs/b1850_cism/user_nl_cism
M	config/e3sm/config_archive.xml
M	config/e3sm/config_files.xml
M	config/e3sm/config_grids.xml
A	config/e3sm/machines/Depends.summit.pgiacc
M	config/e3sm/machines/config_batch.xml
M	config/e3sm/machines/config_compilers.xml
M	config/e3sm/machines/config_machines.xml
M	config/e3sm/machines/syslog.anvil
M	config/e3sm/machines/syslog.cetus
M	config/e3sm/machines/syslog.cori-haswell
M	config/e3sm/machines/syslog.cori-knl
M	config/e3sm/machines/syslog.edison
M	config/e3sm/machines/syslog.mira
M	config/e3sm/machines/syslog.theta
M	config/e3sm/machines/syslog.titan
M	config/e3sm/machines/template.case.run
A	config/e3sm/machines/template.case.run.sh
M	config/e3sm/machines/template.case.test
M	config/e3sm/machines/template.st_archive
A	config/e3sm/testmods_dirs/allactive/clm/bgcexp/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/clm/bgcexp/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/mach/pet/shell_commands
A	config/e3sm/testmods_dirs/allactive/v1cmip6/README
A	config/e3sm/testmods_dirs/allactive/v1cmip6/user_nl_cam
A	config/e3sm/testmods_dirs/allactive/v1cmip6/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/v1cmip6/xmlchange_cmnds
A	config/e3sm/usermods_dirs/b1850/shell_commands
A	config/e3sm/usermods_dirs/b1850_cism/include_user_mods
A	config/e3sm/usermods_dirs/b1850_cism/user_nl_cism
M	config/xml_schemas/config_batch.xsd
M	doc/source/build_cpl/index.rst
M	doc/source/conf.py
M	doc/source/data_models/data-ocean.rst
M	doc/source/data_models/index.rst
M	doc/source/driver_cpl/index.rst
M	doc/source/index.rst
A	doc/source/misc_tools/ect.rst
M	doc/source/misc_tools/index.rst
M	doc/source/users_guide/adding-cases.rst
M	doc/source/users_guide/building-a-case.rst
M	doc/source/users_guide/case-basics.rst
M	doc/source/users_guide/cime-internals.rst
A	doc/source/users_guide/creating-new-compsets.rst
M	doc/source/users_guide/index.rst
M	doc/source/users_guide/introduction-and-overview.rst
M	doc/source/users_guide/porting-cime.rst
M	doc/source/users_guide/testing.rst
M	doc/source/what_cime/index.rst
D	doc/source/xml_files/acme.rst
M	doc/source/xml_files/drivers.rst
A	doc/source/xml_files/e3sm.rst
M	doc/source/xml_files/index.rst
M	doc/tools_autodoc.cfg
M	scripts/Tools/case.cmpgen_namelists
M	scripts/Tools/case.setup
M	scripts/Tools/case.submit
M	scripts/Tools/case_diff
M	scripts/Tools/check_case
M	scripts/Tools/check_input_data
M	scripts/Tools/check_lockedfiles
M	scripts/Tools/e3sm_cime_merge
M	scripts/Tools/e3sm_cime_split
M	scripts/Tools/mkSrcfiles
D	scripts/Tools/pointclm/README
D	scripts/Tools/pointclm/makepointdata.py
D	scripts/Tools/pointclm/pointCLM.py
D	scripts/Tools/pointclm/post_process.py
D	scripts/Tools/pointclm/site_fullrun.py
M	scripts/Tools/preview_namelists
M	scripts/Tools/preview_run
M	scripts/Tools/xmlchange
M	scripts/Tools/xmlquery
M	scripts/create_test
M	scripts/fortran_unit_testing/run_tests.py
M	scripts/lib/CIME/SystemTests/dae.py
M	scripts/lib/CIME/SystemTests/eri.py
M	scripts/lib/CIME/SystemTests/erp.py
M	scripts/lib/CIME/SystemTests/err.py
M	scripts/lib/CIME/SystemTests/irt.py
M	scripts/lib/CIME/SystemTests/ldsta.py
M	scripts/lib/CIME/SystemTests/mcc.py
M	scripts/lib/CIME/SystemTests/nck.py
M	scripts/lib/CIME/SystemTests/ncr.py
M	scripts/lib/CIME/SystemTests/pea.py
M	scripts/lib/CIME/SystemTests/pem.py
M	scripts/lib/CIME/SystemTests/pet.py
M	scripts/lib/CIME/SystemTests/pre.py
M	scripts/lib/CIME/SystemTests/seq.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/XML/pes.py
M	scripts/lib/CIME/build.py
D	scripts/lib/CIME/case.py
A	scripts/lib/CIME/case/README
A	scripts/lib/CIME/case/__init__.py
A	scripts/lib/CIME/case/case.py
A	scripts/lib/CIME/case/case_clone.py
A	scripts/lib/CIME/case/case_cmpgen_namelists.py
A	scripts/lib/CIME/case/case_run.py
A	scripts/lib/CIME/case/case_setup.py
A	scripts/lib/CIME/case/case_st_archive.py
A	scripts/lib/CIME/case/case_submit.py
A	scripts/lib/CIME/case/case_test.py
A	scripts/lib/CIME/case/check_input_data.py
A	scripts/lib/CIME/case/check_lockedfiles.py
A	scripts/lib/CIME/case/preview_namelists.py
D	scripts/lib/CIME/case_clone.py
D	scripts/lib/CIME/case_cmpgen_namelists.py
D	scripts/lib/CIME/case_run.py
D	scripts/lib/CIME/case_setup.py
D	scripts/lib/CIME/case_st_archive.py
D	scripts/lib/CIME/case_submit.py
D	scripts/lib/CIME/case_test.py
D	scripts/lib/CIME/check_input_data.py
D	scripts/lib/CIME/check_lockedfiles.py
M	scripts/lib/CIME/compare_test_results.py
A	scripts/lib/CIME/date.py
M	scripts/lib/CIME/hist_utils.py
A	scripts/lib/CIME/locked_files.py
D	scripts/lib/CIME/preview_namelists.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/tests/case_fake.py
M	scripts/lib/CIME/user_mod_support.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/e3sm_cime_mgmt.py
M	scripts/lib/jenkins_generic_job.py
M	scripts/lib/update_e3sm_tests.py
D	scripts/tests/run_e3sm_ctest/CMakeLists.txt
D	scripts/tests/run_e3sm_ctest/CTestConfig.cmake
D	scripts/tests/run_e3sm_ctest/runE3smTest_template.sh
M	scripts/tests/scripts_regression_tests.py
M	src/components/data_comps/datm/cime_config/config_archive.xml
M	src/components/data_comps/dice/cime_config/config_archive.xml
M	src/components/data_comps/dlnd/cime_config/config_archive.xml
M	src/components/data_comps/docn/cime_config/config_archive.xml
M	src/components/data_comps/drof/cime_config/config_archive.xml
M	src/components/data_comps/dwav/cime_config/config_archive.xml
M	src/drivers/mct/cime_config/config_archive.xml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/drivers/mct/cime_config/config_component_e3sm.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/cime_config/testdefs/testlist_drv.xml
M	src/drivers/mct/main/cime_comp_mod.F90
M	src/drivers/mct/main/component_mod.F90
M	src/drivers/mct/shr/seq_comm_mct.F90
M	src/drivers/mct/shr/seq_timemgr_mod.F90
M	src/externals/mct/README
M	src/externals/mct/doc/mct_APIs.tex
M	src/externals/mct/mct/m_Rearranger.F90
M	src/share/streams/shr_dmodel_mod.F90
M	src/share/util/shr_flux_mod.F90
M	src/share/util/shr_scam_mod.F90
M	tools/cprnc/Makefile

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 3-06-2018
Tag: cime5.4.0-alpha.25
Answer Changes: Climate Changing for non-B 1850 compsets in CESM
Tests:  scripts_regression_tests.py
        hand test SMS_P1x4.f19_g16.X
        code checker
        edison build test for A,X, and B1850 compsets
Dependencies:

Brief Summary:
    - Add support for environment and module to depend on job.
    - Fix mistake in scripts-regression-tests help dump.
    - Env batch cleanup
    - Add queue attribute (small cheyenne jobs go to share queue).
    - For Travis-CI build: kick off build on master whenever it's pushed.
    - Reinstate ability to select queue by num tasks.
    - Give st_archive an extra 10 min just to be sure.
    - Refactor handling of small jobs.
    - Report lock file info as debug output.
    - Auto-regen batch files in case_submit.
    - Add travis_ci testing.
    - Supported attribute is string.
    - Cleanup xml.
    - Redo orb_year_defaults for cesm only.
        Expected to change answers for non-B 1850 compsets in CESM
    - Add supported flag to testlist.xml.
    - Big upgrade to scripts_regression_tests argument handling.
    - Update esmf module for edison.nersc.gov.
    - New allow_error field for module system.
    - Fix trivial pylint problem.
    - Add the comment from config_pes.xml to the env_mach_pes.xml file.
    - Refactor _get_datenames to count the correct number of cpl.r files.
    - Change subtree split method.
    - Jgfouca/branch for acme split 2018-02-22.
    - Fix uninitialized variable.
    - python2 needs an init file in Servers.
    - Catch more errors in the testlist schema, remove generic GSW DATM_MODE ignore scripts/cases.
    - Add support for ftp and wget.
    - Add support for provenance in cesm.
    - Swap command cannot be batched together.
    - Add xml support for inputdata server.
    - Fix bug when providing -p PROJECT flag to create_test.
    - Rename acme to e3sm everywhere.
    - Update components' communicator initialization.
    - Make get_components return None instead of fail.

User interface changes: 
    - (cesm only) create_test and query_testlist now have --supported-only flag
    - New allow_error attribute for module systems. 
    - check_input_data replace --svn-loc with --server and --protocol
    - Some Tools with "acme" in the name now say "e3sm".

PR summary: git log --oneline --first-parent [previous_tag]..master 
c9c5695 Merge pull request #2341 from jedwards4b/mpirun_depends_on_queue
7dff579 Fix mistake in scripts-regression-tests help dump
bfb23dd Merge pull request #2339 from jedwards4b/env_batch_cleanup
c19fd3f Merge pull request #2335 from jedwards4b/cheyenne_share_queue
8311f8e Merge pull request #2333 from billsacks/travis_build_master
a5ed418 Merge pull request #2327 from ESMCI/jgfouca/allow_queue_selection_by_task
8f6f199 Give st_archive an extra 10 min just to be sure
751c895 Merge pull request #2326 from ESMCI/jgfouca/refacor_small_jobs
d4fc951 Merge pull request #2325 from ESMCI/jgfouca/adjust_lock_output
a9607d7 Merge pull request #2320 from ESMCI/jgfouca/upgrade_batch_script_handling
e93296a Merge pull request #2324 from jedwards4b/travis_ci
41ef5a3 Merge pull request #2321 from jedwards4b/supported_flag_for_testlist
a714422 Merge pull request #2323 from jedwards4b/cleanup_xml
43c0308 Merge pull request #2290 from jedwards4b/orb_year_defaults
c5aa74b Merge pull request #2316 from jedwards4b/supported_flag_for_testlist
1ac42bb Merge pull request #2319 from ESMCI/jgfouca/script_regr_test_arg_upgrade
fdf7757 Merge pull request #2318 from ESMCI/fischer/edison
68e7b765 Merge pull request #2317 from ESMCI/jgfouca/allow_stderr_in_env_modules
ab6d933 Fix trivial pylint problem
93dde2b Merge pull request #2315 from jedwards4b/add_comment_pes_file
cae9f9a Merge pull request #2285 from kdraeder/multi_drv_kdr
7f8c26a Merge pull request #2314 from ESMCI/jgfouca/chg_subtree_split_method
92ccb83 Merge pull request #2312 from ESMCI/jgfouca/branch-for-acme-split-2018-02-22
c82664e fix uninitialized variable
8a86965 python2 needs an init file in Servers
5af94aa Merge pull request #2300 from ekluzek/testlistxsdgitig
69e35b2 Merge pull request #2311 from jedwards4b/ftpandwget
8baf2bb Merge pull request #2305 from jedwards4b/cesm_provenance
8ac3dd2 Merge pull request #2310 from ESMCI/jgfouca/fix_env_module_operation_batching
ec9483c Merge pull request #2309 from jedwards4b/inputdata
ba3c1fb Merge pull request #2306 from ESMCI/jgfouca/fix_bug_when_setting_proj
6405d72 Merge pull request #2296 from ESMCI/rljacob/acme2e3sm
219ee5a Merge pull request #2299 from ESMCI/azamat/update-seq_comm_setcomm-calls
6c3f484 Merge pull request #2298 from ESMCI/jgfouca/fix_query_config_again


Modified files: git diff --name-status [previous_tag]
M	.gitignore
A	.travis.yml
D	config/acme/allactive/config_compsets.xml
D	config/acme/allactive/config_pesall.xml
D	config/acme/allactive/testlist_allactive.xml
D	config/acme/allactive/usermods_dirs/b1850/shell_commands
D	config/acme/allactive/usermods_dirs/b1850_cism/include_user_mods
D	config/acme/allactive/usermods_dirs/b1850_cism/user_nl_cism
D	config/acme/config_archive.xml
D	config/acme/config_files.xml
D	config/acme/config_grids.xml
D	config/acme/machines/Depends.cetus
D	config/acme/machines/Depends.cray
D	config/acme/machines/Depends.gnu
D	config/acme/machines/Depends.intel
D	config/acme/machines/Depends.mira
D	config/acme/machines/Depends.nag
D	config/acme/machines/Depends.summitdev.ibm
D	config/acme/machines/Depends.summitdev.pgiacc
D	config/acme/machines/Depends.titan.cray
D	config/acme/machines/Depends.titan.intel
D	config/acme/machines/Depends.titan.pgi
D	config/acme/machines/Depends.titan.pgiacc
D	config/acme/machines/README
D	config/acme/machines/config_batch.xml
D	config/acme/machines/config_batch.xsd
D	config/acme/machines/config_compilers.xml
D	config/acme/machines/config_machines.xml
D	config/acme/machines/config_pio.xml
D	config/acme/machines/syslog.anvil
D	config/acme/machines/syslog.cetus
D	config/acme/machines/syslog.cori-haswell
D	config/acme/machines/syslog.cori-knl
D	config/acme/machines/syslog.edison
D	config/acme/machines/syslog.mira
D	config/acme/machines/syslog.noop
D	config/acme/machines/syslog.theta
D	config/acme/machines/syslog.titan
D	config/acme/machines/template.case.run
D	config/acme/machines/template.case.test
D	config/acme/machines/template.ocn_diagnostics
D	config/acme/machines/template.st_archive
D	config/acme/machines/template.timeseries
D	config/acme/machines/userdefined_laptop_template/README.md
D	config/acme/machines/userdefined_laptop_template/config_compilers.xml
D	config/acme/machines/userdefined_laptop_template/config_machines.xml
D	config/acme/machines/userdefined_laptop_template/config_pes.xml
D	config/acme/testmods_dirs/allactive/cam/cosplite/user_nl_cam
D	config/acme/testmods_dirs/allactive/cam/cosplite/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/cam/cosplite_nhtfrq5/user_nl_cam
D	config/acme/testmods_dirs/allactive/cam/cosplite_nhtfrq5/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/cam/outfrq9s/user_nl_cam
D	config/acme/testmods_dirs/allactive/cam/outfrq9s/user_nl_clm
D	config/acme/testmods_dirs/allactive/cam/outfrq9s/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/cam/rtm_null/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/clm/betr/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/clm/bgcinterface/user_nl_clm
D	config/acme/testmods_dirs/allactive/clm/eca/user_nl_clm
D	config/acme/testmods_dirs/allactive/clm/fates/user_nl_clm
D	config/acme/testmods_dirs/allactive/clm/rd/user_nl_clm
D	config/acme/testmods_dirs/allactive/clm/vst/user_nl_clm
D	config/acme/testmods_dirs/allactive/drv/y100k
D	config/acme/testmods_dirs/allactive/force_netcdf_pio/shell_commands
D	config/acme/testmods_dirs/allactive/force_netcdf_pio/xmlchange_cmnds
D	config/acme/testmods_dirs/allactive/mach_mods/shell_commands
M	config/cesm/config_files.xml
A	config/cesm/config_inputdata.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.case.run
A	config/e3sm/allactive/config_compsets.xml
A	config/e3sm/allactive/config_pesall.xml
A	config/e3sm/allactive/testlist_allactive.xml
A	config/e3sm/allactive/usermods_dirs/b1850/shell_commands
A	config/e3sm/allactive/usermods_dirs/b1850_cism/include_user_mods
A	config/e3sm/allactive/usermods_dirs/b1850_cism/user_nl_cism
A	config/e3sm/config_archive.xml
A	config/e3sm/config_files.xml
A	config/e3sm/config_grids.xml
A	config/e3sm/config_inputdata.xml
A	config/e3sm/machines/Depends.cetus
A	config/e3sm/machines/Depends.cray
A	config/e3sm/machines/Depends.gnu
A	config/e3sm/machines/Depends.intel
A	config/e3sm/machines/Depends.mira
A	config/e3sm/machines/Depends.nag
A	config/e3sm/machines/Depends.summitdev.ibm
A	config/e3sm/machines/Depends.summitdev.pgiacc
A	config/e3sm/machines/Depends.titan.cray
A	config/e3sm/machines/Depends.titan.intel
A	config/e3sm/machines/Depends.titan.pgi
A	config/e3sm/machines/Depends.titan.pgiacc
A	config/e3sm/machines/README
A	config/e3sm/machines/config_batch.xml
A	config/e3sm/machines/config_compilers.xml
A	config/e3sm/machines/config_machines.xml
A	config/e3sm/machines/config_pio.xml
A	config/e3sm/machines/syslog.anvil
A	config/e3sm/machines/syslog.cetus
A	config/e3sm/machines/syslog.cori-haswell
A	config/e3sm/machines/syslog.cori-knl
A	config/e3sm/machines/syslog.edison
A	config/e3sm/machines/syslog.mira
A	config/e3sm/machines/syslog.noop
A	config/e3sm/machines/syslog.theta
A	config/e3sm/machines/syslog.titan
A	config/e3sm/machines/template.case.run
A	config/e3sm/machines/template.case.test
A	config/e3sm/machines/template.ocn_diagnostics
A	config/e3sm/machines/template.st_archive
A	config/e3sm/machines/template.timeseries
A	config/e3sm/machines/userdefined_laptop_template/README.md
A	config/e3sm/machines/userdefined_laptop_template/config_compilers.xml
A	config/e3sm/machines/userdefined_laptop_template/config_machines.xml
A	config/e3sm/machines/userdefined_laptop_template/config_pes.xml
A	config/e3sm/testmods_dirs/allactive/cam/cosplite/user_nl_cam
A	config/e3sm/testmods_dirs/allactive/cam/cosplite/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/cam/cosplite_nhtfrq5/user_nl_cam
A	config/e3sm/testmods_dirs/allactive/cam/cosplite_nhtfrq5/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/cam/outfrq9s/user_nl_cam
A	config/e3sm/testmods_dirs/allactive/cam/outfrq9s/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/cam/outfrq9s/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/cam/rtm_null/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/clm/betr/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/clm/bgcinterface/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/clm/eca/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/clm/fates/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/clm/rd/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/clm/vst/user_nl_clm
A	config/e3sm/testmods_dirs/allactive/drv/y100k
A	config/e3sm/testmods_dirs/allactive/force_netcdf_pio/shell_commands
A	config/e3sm/testmods_dirs/allactive/force_netcdf_pio/xmlchange_cmnds
A	config/e3sm/testmods_dirs/allactive/mach_mods/shell_commands
M	config/xml_schemas/config_batch.xsd
A	config/xml_schemas/config_inputdata.xsd
M	config/xml_schemas/config_machines.xsd
M	config/xml_schemas/env_batch.xsd
M	config/xml_schemas/env_mach_pes.xsd
M	config/xml_schemas/env_mach_specific.xsd
M	config/xml_schemas/testlist.xsd
D	scripts/Tools/acme_check_env
D	scripts/Tools/acme_cime_merge
D	scripts/Tools/acme_cime_split
M	scripts/Tools/check_input_data
M	scripts/Tools/code_checker
A	scripts/Tools/e3sm_check_env
A	scripts/Tools/e3sm_cime_merge
A	scripts/Tools/e3sm_cime_split
M	scripts/Tools/jenkins_generic_job
D	scripts/Tools/list_acme_tests
A	scripts/Tools/list_e3sm_tests
M	scripts/Tools/preview_run
D	scripts/Tools/update_acme_tests
A	scripts/Tools/update_e3sm_tests
M	scripts/Tools/wait_for_tests
M	scripts/create_test
M	scripts/lib/CIME/BuildTools/makemacroswriter.py
A	scripts/lib/CIME/Servers/__init__.py
A	scripts/lib/CIME/Servers/ftp.py
A	scripts/lib/CIME/Servers/generic_server.py
A	scripts/lib/CIME/Servers/svn.py
A	scripts/lib/CIME/Servers/wget.py
M	scripts/lib/CIME/SystemTests/homme.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_pes.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/files.py
M	scripts/lib/CIME/XML/generic_xml.py
A	scripts/lib/CIME/XML/inputdata.py
M	scripts/lib/CIME/XML/namelist_definition.py
M	scripts/lib/CIME/XML/pes.py
M	scripts/lib/CIME/XML/testlist.py
M	scripts/lib/CIME/aprun.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/case_submit.py
M	scripts/lib/CIME/check_input_data.py
M	scripts/lib/CIME/check_lockedfiles.py
M	scripts/lib/CIME/code_checker.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/CIME/wait_for_tests.py
D	scripts/lib/acme_cime_mgmt.py
A	scripts/lib/e3sm_cime_mgmt.py
M	scripts/lib/jenkins_generic_job.py
D	scripts/lib/update_acme_tests.py
A	scripts/lib/update_e3sm_tests.py
D	scripts/tests/run_acme_ctest/CMakeLists.txt
D	scripts/tests/run_acme_ctest/CTestConfig.cmake
D	scripts/tests/run_acme_ctest/runAcmeTest_template.sh
A	scripts/tests/run_e3sm_ctest/CMakeLists.txt
A	scripts/tests/run_e3sm_ctest/CTestConfig.cmake
A	scripts/tests/run_e3sm_ctest/runE3smTest_template.sh
M	scripts/tests/scripts_regression_tests.py
M	src/components/data_comps/datm/cime_config/config_component.xml
M	src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M	src/drivers/mct/cime_config/buildnml
M	src/drivers/mct/cime_config/config_component.xml
D	src/drivers/mct/cime_config/config_component_acme.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
A	src/drivers/mct/cime_config/config_component_e3sm.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/main/seq_diag_mct.F90
M	src/drivers/mct/shr/seq_comm_mct.F90
M	src/drivers/mct/shr/seq_flds_mod.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 2-13-2018
Tag: cime5.4.0-alpha.24
Answer Changes: None
Tests: scripts_regression_tests, code_checker
Dependencies:

Brief Summary:
    - Query_config parsing fix to find correct component.
    - Leverage env command options to assist parsing.
    - Add a test that compares a case created using the compset alias to
      one created using the longname for the same compset.
    - Disable caching withing the main test_scheduler process. 
    - Upgrade cime_bisect.
    - Another exception for read only in config files.
    - Add pstrid to pes.
    - Fix issues with read only xml.
    - Separate post-DA from pause/resume and add resume signal at init.
    - Restore case.st_archive.
    - Allow merge of xml files without extra child level.
    - Fix unused import.
    - Reinstate xml file caching, but only for read-only files.
    - Backout gnu changes.
    - Update modules and mod paths for cheyenne.
    - Jgfouca/branch for acme split 2018-01-30.
    - Fix bug in generic env load.
    - Improve python interface to environment modules.
    

User interface changes: 
    - cime_bisect changes.
    - New XML variables, PAUSE_ACTIVE_XXX.
    - module_lmod no longer a support module type.

PR summary: git log --oneline --first-parent [previous_tag]..master 
b4eae37 Merge pull request #2293 from jedwards4b/query_config_fix
c20690e Merge pull request #2292 from ESMCI/jgfouca/fix_soft_env_handling
efcd17f Merge pull request #2288 from jedwards4b/test_compset_vs_alias
51fbde3 Merge pull request #2287 from ESMCI/jgfouca/disable_caching_in_test_sched
0ea9941 Merge pull request #2286 from ESMCI/jgfouca/upgrade_cime_bisect
76a5b5e Merge pull request #2281 from jedwards4b/another_read_only_exception
877250b Merge pull request #2279 from jedwards4b/add_pstrid_to_pes
29b7ccf Merge pull request #2278 from jedwards4b/fix_query_config
b9a79dc Merge pull request #2267 from gold2718/da_support
9706e13 Merge pull request #2273 from ESMCI/jgfouca/restore_case_st_archive
7cfb8ac Merge pull request #2272 from jedwards4b/xmlmerge_fix
964fd19 Fix unused import
4441ff3 Merge pull request #2269 from ESMCI/jgfouca/reinstate_xml_file_caching
4e41375 Merge pull request #2271 from jedwards4b/cheyenne_updates
4ab197e Merge pull request #2270 from jedwards4b/cheyenne_updates
d3740b3 Jgfouca/branch for acme split 2018 01 30 (#2264)
939613e Merge pull request #2265 from ESMCI/jgfouca/fix_env_setup_bug
1e57bf0 Merge pull request #2260 from ESMCI/jgfouca/improve_env_module_interface


Modified files: git diff --name-status [previous_tag]
M	config/acme/allactive/config_compsets.xml
M	config/acme/allactive/config_pesall.xml
M	config/acme/machines/Depends.intel
D	config/acme/machines/Depends.intel18
M	config/acme/machines/config_batch.xml
M	config/acme/machines/config_compilers.xml
M	config/acme/machines/config_machines.xml
M	config/acme/machines/config_pio.xml
M	config/cesm/machines/config_machines.xml
M	config/config_tests.xml
D	scripts/Tools/case.st_archive
M	scripts/Tools/cime_bisect
M	scripts/data_assimilation/da_no_data_mod.sh
M	scripts/lib/CIME/SystemTests/dae.py
M	scripts/lib/CIME/SystemTests/err.py
M	scripts/lib/CIME/SystemTests/homme.py
M	scripts/lib/CIME/SystemTests/pre.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/XML/archive.py
M	scripts/lib/CIME/XML/entry_id.py
M	scripts/lib/CIME/XML/env_archive.py
M	scripts/lib/CIME/XML/env_base.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/files.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/XML/pes.py
M	scripts/lib/CIME/bless_test_results.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/check_lockedfiles.py
M	scripts/lib/CIME/compare_test_results.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/acme_cime_mgmt.py
M	scripts/query_config
M	scripts/tests/scripts_regression_tests.py
M	src/components/data_comps/desp/cime_config/namelist_definition_desp.xml
M	src/components/data_comps/dwav/cime_config/namelist_definition_dwav.xml
M	src/components/data_comps/dwav/dwav_comp_mod.F90
M	src/components/data_comps/dwav/mct/wav_comp_mct.F90
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_compsets.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/cime_config/testdefs/testlist_drv.xml
M	src/drivers/mct/main/cime_comp_mod.F90
M	src/drivers/mct/main/component_mod.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90
M	src/drivers/mct/shr/seq_timemgr_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 01-27-2018
Tag: cime5.4.0-alpha.23
Answer Changes: None
Tests: scripts_regression_tests.py on hobart 
Dependencies:

Brief Summary:
    - Fix compare of env_batch.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
7b88f00 Merge pull request #2261 from jedwards4b/check_locked_files2

Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/XML/env_batch.py


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 01-26-2018 
Tag: cime5.4.0-alpha.22
Answer Changes: None
Tests: scripts_regression_tests.py
Dependencies:

Brief Summary:
    - Remove debug print statement
    - Second fix for user compsets.
    - Rearrange code in case.py so that compset alias and 
      compset longname get the same result.
    - Minor fix to get acme provenance test working again.
    - Fix for LockedFiles.
    - Change PET to be a multisubmit job.
    - Minor fix to get query config test working on melvin.
    - Disable file caching for now.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
2a235e5 remove debug print statement
d6f6e08 Merge pull request #2257 from jedwards4b/user_compset_fix
fea933c Merge pull request #2253 from jedwards4b/user_compset_fix
169518c Minor fix to get acme provenance test working again
91451ed Merge pull request #2254 from jedwards4b/lockedfiles_fix
1878159 Merge pull request #2255 from ESMCI/jgfouca/change_pet_to_multisubmit
2dc1cf6 Minor fix to get query config test working on melvin
d3ab655 Merge pull request #2251 from jedwards4b/disable_file_caching

Modified files: git diff --name-status [previous_tag]
M       config/config_tests.xml
M       scripts/lib/CIME/SystemTests/pet.py
M       scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M       scripts/lib/CIME/XML/component.py
M       scripts/lib/CIME/XML/entry_id.py
M       scripts/lib/CIME/XML/env_batch.py
M       scripts/lib/CIME/XML/generic_xml.py
M       scripts/lib/CIME/case.py
M       scripts/lib/CIME/case_run.py
M       scripts/lib/CIME/case_setup.py
M       scripts/lib/CIME/utils.py
M       scripts/tests/scripts_regression_tests.py


======================================================================

======================================================================

Originator: Chris Fischer
Date: 01-24-2018
Tag: cime5.4.0-alpha.21
Answer Changes: None
Tests: scripts-regression-tests
Dependencies:

Brief Summary:
    - Turn off XML file caching in test scheduler.
    - Fix typo in cime_bisect.
    - Cache file reads to avoid re-parsing XML files.
    - Fix some minor log formatting issues.
    - Fixed a broken hyperlink in the data ocean model rst documentation.
    - Always want to see test-scheduler time taken.
    - Query config update.
    - Fix formatting of rst documentation for load balancing tool.
    - Implement walltime stash to support more-accurate walltimes.
    - Merge branch 'master' of github.com:ESMCI/cime.
    - Hot fix for acme xsd error.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
d2850d5 Merge pull request #2247 from ESMCI/jgfouca/turn_off_caching_in_testsched
29006c6 Fix typo in cime_bisect
263c909 Merge pull request #2243 from ESMCI/jgfouca/cache_file_reads
ace29c3 Merge pull request #2239 from jedwards4b/format_issues
367ca98 Merge pull request #2238 from bertinia/master
f52a005 Always want to see test-scheduler time taken
f272ecf Merge pull request #2236 from jedwards4b/query_config_update
39ac021 Merge pull request #2235 from ESMCI/sarich/fix-load-balance-docs
b978107 Merge pull request #2234 from ESMCI/jgfouca/walltime_optimization
52b22fa Merge branch 'master' of github.com:ESMCI/cime
b9e0c52 hot fix for acme xsd error


Modified files: git diff --name-status [previous_tag]
M       config/acme/config_files.xml
M       config/acme/machines/config_machines.xml
M       config/cesm/config_files.xml
M       doc/source/data_models/data-ocean.rst
M       doc/source/misc_tools/load-balancing-tool.rst
M       scripts/Tools/cime_bisect
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/XML/component.py
M       scripts/lib/CIME/XML/compsets.py
M       scripts/lib/CIME/XML/env_mach_specific.py
M       scripts/lib/CIME/XML/generic_xml.py
M       scripts/lib/CIME/XML/grids.py
M       scripts/lib/CIME/XML/machines.py
M       scripts/lib/CIME/check_lockedfiles.py
M       scripts/lib/CIME/provenance.py
M       scripts/lib/CIME/test_scheduler.py
M       scripts/query_config
M       scripts/tests/scripts_regression_tests.py
M       src/drivers/mct/cime_config/config_component_acme.xml
M       src/drivers/mct/shr/seq_infodata_mod.F90
M       src/drivers/mct/shr/seq_timemgr_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer 
Date: 01-16-2018
Tag: cime5.4.0-alpha.20
Answer Changes: None
Tests: 
Dependencies:

Brief Summary:
    - Revert src/share/util/changes in shr_spfn_mod.F90

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
b146127 revert changes in this file (failing pgi test)

Modified files: git diff --name-status [previous_tag]
M       src/share/util/shr_spfn_mod.F90


======================================================================

======================================================================

Originator: Chris Fischer 
Date: 01-16-2018
Tag: cime5.4.0-alpha.19
Answer Changes: None
Tests: code_checker, scripts_regression_tests
Dependencies:

Brief Summary:
    - CPL user mods.
    - Update slurm queueing for NERSC.
    - Change grid in testlist schema to NMTOKEN.
    - py3 pylint fix.
    - Add minimal pgi compiler support cheyenne, fix an output error.
    - Make doctest for get_current_branch more robust.
    - Remove stale help section comments.
    - Fix print statements that were corrupted by py3 changes.
    - Updates for laramie.
    - Fix K_TestCimeCase.test_cime_case_prereq for LSF machines.
    - Fix regression test K_TestCimeCase.test_cime_case_test_custom_project.

User interface changes: 

PR summary: git log --oneline --first-parent [previous_tag]..master 
16766d6 Merge pull request #2231 from jedwards4b/CPL_USER_MODS
0722686 Merge pull request #2233 from ESMCI/fischer/nersc_cori
45e4895 Merge pull request #2232 from ekluzek/testlistschema
40a02fa Merge pull request #2230 from ESMCI/jedwards/py3pylintfix
6b8f1a8 Merge pull request #2229 from jedwards4b/add_pgi
06d3317 Merge pull request #2220 from ESMCI/jgfouca/make_branch_doctest_more_robust
7f4951f Merge pull request #2219 from ESMCI/jgfouca/remove_stale_help
37122e8 Merge pull request #2226 from ESMCI/jgfouca/improve_preview_run
1920d8b Merge pull request #2225 from jedwards4b/laramie_updates
c3a1141 Merge pull request #2224 from ESMCI/jgfouca/fix_cime_case_test_for_lsf
b968e77 Merge pull request #2223 from ESMCI/jgfouca/fix_regr_test

Modified files: git diff --name-status [previous_tag]
M       config/acme/allactive/config_compsets.xml
M       config/cesm/machines/config_batch.xml
M       config/cesm/machines/config_machines.xml
M       config/xml_schemas/testlist.xsd
M       scripts/Tools/preview_run
M       scripts/lib/CIME/XML/env_base.py
M       scripts/lib/CIME/buildlib.py
M       scripts/lib/CIME/utils.py
M       scripts/tests/scripts_regression_tests.py
M       src/drivers/mct/cime_config/config_component.xml
M       src/drivers/mct/cime_config/config_component_acme.xml
M       src/drivers/mct/cime_config/config_component_cesm.xml
M       src/drivers/mct/cime_config/config_compsets.xml

======================================================================

======================================================================

Originator: Jim Edwards
Date: 01-10-2018
Tag: cime5.4.0-alpha.18
Answer Changes: Round Off, possibly Climate Changing
Tests:
Dependencies:

Brief Summary:

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
18358ce Merge pull request #2212 from ESMCI/jgfouca/branch-for-acme-split-2018-01-09
ddeb398 Merge pull request #2216 from jedwards4b/correct_bld_output
7f3c93b Merge pull request #2217 from jedwards4b/more_fortran_cleanup
f44bca3 Merge pull request #2213 from jedwards4b/more_fortran_cleanup
559d421 Merge pull request #2211 from jedwards4b/fixforxlf
d151642 Merge pull request #2179 from billsacks/fix_advdate
507b9dd Merge pull request #2158 from ESMCI/mvertens/dicemods
89015ca Merge pull request #2205 from ESMCI/jgfouca/remove_scans
3eb054d Merge pull request #2202 from jedwards4b/refactor_seq_diag_mod
cdb7b3f fix doctest for py3
5872dda Merge pull request #2208 from jedwards4b/py3fix
8e2319f Merge pull request #2206 from ESMCI/jgfouca/fix_desc_stride
e3cf1f3 Merge pull request #2198 from jedwards4b/more_atmocn_flux
cf9e427 Merge pull request #2204 from gold2718/lowresSEgrid
1bd046f Use https for cdash
bd9b5f1 Minor fixes for cdash interaction
a2ef582 Merge pull request #2201 from jedwards4b/fix_long_line
14176a0 Merge pull request #2192 from jedwards4b/reduce_fortran_warnings1
a44965e Merge pull request #2196 from ESMCI/jgfouca/remove_run_with_submit
ef10d62 Minor fix for ACME
7e28a21 Merge pull request #2148 from ESMCI/jgfouca/hide_xml_interface
05ba5c5 Merge pull request #2087 from ekluzek/addmachmodex
1ab0e78 Merge pull request #2193 from jedwards4b/always_set_baselineroot_in_tests
8a401cb Merge pull request #2189 from ESMCI/jgfouca/fix_melvin
d5e21de Merge pull request #2188 from ESMCI/jgfouca/fix_create_test_cesm_doc
7c607cb Merge pull request #2187 from ESMCI/jgfouca/max_task_fixes
ddb968b Merge pull request #2186 from ESMCI/jgfouca/improve_acme_cime_mgt
295e91c Merge pull request #2184 from jedwards4b/indent_consistantly

Modified files: git diff --name-status [previous_tag]

======================================================================

======================================================================

Originator: Chris Fischer
Date: 1-4-2018
Tag: cime5.4.0-alpha.17
Answer Changes: Round Off allactive
Tests: ERS_Ld7.f19_g17.B1850.hobart_pgi.allactive-defaultio
       scripts_regression_tests
Dependencies:

Brief Summary:
    - Add flux convergence criteria.
    - Pass CIMEROOT to CMake unit test builds.
    - scripts_regression_tests.py should use values in .cime/config if provided.
    - Testing/multiinst baselines.
    - Fix pylint error that I introduced in #2168.
    - Generalize some paths to support a standalone CISM checkout.
    - Revert to previous cheyenne gnu environment.
    - Y10k fix.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
1b4fa36 Merge pull request #2180 from jedwards4b/flux_convergence
6a07ef1 Merge pull request #2176 from billsacks/run_tests_pass_cimeroot
8932a90 Merge pull request #2173 from jedwards4b/srt_use_cimeconfig
5a9d270 Merge pull request #2170 from mnlevy1981/testing/multiinst_baselines
cade91d Merge pull request #2169 from billsacks/fix_pylint_error
9e6cee6 Merge pull request #2168 from billsacks/cism_standalone
d59c285 Merge pull request #2167 from billsacks/backout_cheyenne_gnu
abc6354 Merge pull request #2145 from jedwards4b/y10k_fix

Modified files: git diff --name-status [previous_tag]
M	config/cesm/machines/config_machines.xml
M	scripts/Tools/Makefile
M	scripts/fortran_unit_testing/run_tests.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/update_acme_tests.py
M	scripts/tests/scripts_regression_tests.py
M	src/components/data_comps/datm/datm_comp_mod.F90
M	src/components/data_comps/desp/desp_comp_mod.F90
M	src/components/data_comps/dice/dice_comp_mod.F90
M	src/components/data_comps/dlnd/dlnd_comp_mod.F90
M	src/components/data_comps/docn/docn_comp_mod.F90
M	src/components/data_comps/drof/drof_comp_mod.F90
M	src/components/data_comps/dwav/dwav_comp_mod.F90
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
A	src/drivers/mct/cime_config/testdefs/testmods_dirs/drv/y100k/README
A	src/drivers/mct/cime_config/testdefs/testmods_dirs/drv/y100k/shell_commands
M	src/drivers/mct/main/cime_comp_mod.F90
M	src/drivers/mct/main/seq_flux_mct.F90
M	src/drivers/mct/main/seq_hist_mod.F90
M	src/drivers/mct/main/seq_io_mod.F90
M	src/drivers/mct/main/seq_rest_mod.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90
M	src/drivers/mct/shr/seq_timemgr_mod.F90
M	src/drivers/mct/unit_test/CMakeLists.txt
M	src/share/test/unit/CMakeLists.txt
A	src/share/test/unit/shr_cal_test/CMakeLists.txt
A	src/share/test/unit/shr_cal_test/test_shr_cal.pf
M	src/share/util/CMakeLists.txt
M	src/share/util/shr_cal_mod.F90
M	src/share/util/shr_flux_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer
Date: 12-22-2017
Tag: cime5.4.0-alpha.16
Answer Changes: None
Tests: scripts_regression_tests.py
       aux_clm test suite
       scripts_regression_tests.py py2 and py3
Dependencies:

Brief Summary:
    - Fix pylint issue.
    - Allows available and default MPILIBS to be specified per compiler.
    - Find test dir must use case object to fully resolve vars.
    - Always use GLC_NEC=10 for CLM45/CLM5; remove tropicAtl grid in CESM.
    - Updates for nersc systems.
    - DATM and DROF jra55 mode, new grids tx0.1v3, TL319, JRA025.
    - Fix typo in template.
    - Remove unused doctests.
    - Add the batch jobid to the lid.
    - Fix typo of xcpl_comps dir in buildlib.csm_share.
    - Fix max tasks for homebrew.
    - Use the encoding flag to open in py3 to set utf-8.

User interface changes:
    - Remove dead --test options.

PR summary: git log --oneline --first-parent [previous_tag]..master
d1723aa fix pylint issue
d7d96b5 Merge pull request #2160 from jedwards4b/allowmultiplempilibs
2a53df8 Merge pull request #2156 from jedwards4b/findtestdir
e127d7e Merge pull request #2150 from billsacks/always_glcmec
39d7442 Merge pull request #2147 from jedwards4b/machine_updates
c3780a5 Merge pull request #2136 from ESMCI/altuntas/jra55
5ff8d82 fix typo in template
ff04547 Merge pull request #2144 from ESMCI/jgfouca/remove_unused_doctest
c072407 Merge pull request #2141 from jedwards4b/jobid_in_lid
46627b1 Merge pull request #2143 from ESMCI/agsalin/xcpl_dir_fix
60f3603 fix max tasks for homebrew
4729f6a Merge pull request #2139 from jedwards4b/utf8_encoding

Modified files: git diff --name-status [previous_tag]
M	config/acme/machines/template.case.run
M	config/acme/machines/template.case.test
M	config/acme/machines/template.st_archive
M	config/cesm/config_grids.xml
M	config/cesm/machines/Depends.intel
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.case.run
M	config/cesm/machines/template.case.test
M	config/cesm/machines/template.st_archive
M	config/xml_schemas/config_machines.xsd
M	doc/source/data_models/data-atm.rst
M	doc/source/data_models/data-river.rst
M	scripts/Tools/bless_test_results
M	scripts/Tools/case.build
M	scripts/Tools/case.cmpgen_namelists
M	scripts/Tools/case.qstatus
M	scripts/Tools/case.setup
M	scripts/Tools/case.submit
M	scripts/Tools/case_diff
M	scripts/Tools/check_case
M	scripts/Tools/check_input_data
M	scripts/Tools/check_lockedfiles
M	scripts/Tools/cime_bisect
M	scripts/Tools/code_checker
M	scripts/Tools/compare_namelists
M	scripts/Tools/compare_test_results
M	scripts/Tools/component_compare_baseline
M	scripts/Tools/component_compare_copy
M	scripts/Tools/component_compare_test
M	scripts/Tools/component_generate_baseline
M	scripts/Tools/cs.status
M	scripts/Tools/jenkins_generic_job
M	scripts/Tools/list_acme_tests
M	scripts/Tools/normalize_cases
M	scripts/Tools/pelayout
M	scripts/Tools/preview_namelists
M	scripts/Tools/preview_run
M	scripts/Tools/save_provenance
M	scripts/Tools/simple_compare
M	scripts/Tools/standard_script_setup.py
M	scripts/Tools/update_acme_tests
M	scripts/Tools/wait_for_tests
M	scripts/Tools/xmlchange
M	scripts/Tools/xmlquery
M	scripts/create_test
M	scripts/lib/CIME/XML/compilerblock.py
M	scripts/lib/CIME/XML/compilers.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/buildlib.py
M	scripts/lib/CIME/buildnml.py
M	scripts/lib/CIME/namelist.py
M	scripts/lib/CIME/utils.py
M	scripts/manage_pes
M	scripts/query_config
M	scripts/tests/scripts_regression_tests.py
M	src/build_scripts/buildlib.csm_share
M	src/build_scripts/buildlib.gptl
M	src/build_scripts/buildlib.mct
M	src/build_scripts/buildlib.mpi-serial
M	src/build_scripts/buildlib.pio
M	src/components/data_comps/datm/cime_config/config_component.xml
M	src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M	src/components/data_comps/datm/datm_comp_mod.F90
M	src/components/data_comps/datm/datm_shr_mod.F90
M	src/components/data_comps/drof/cime_config/config_component.xml
M	src/components/data_comps/drof/cime_config/namelist_definition_drof.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	tools/configure
M	tools/load_balancing_tool/load_balancing_submit.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 12-14-2017
Tag: cime5.4.0-alpha.15
Answer Changes: None
Tests: external pio2 test suite using pnetcdf/1.9.0 candidate as well as
       pnetcdf/1.8.1 and netcdf 4.4.1.1
       scrtips_regression_tests.py
Dependencies:

Brief Summary:
    - PIO2 update.
    - Replace fancy quotes with standard ones.
    - Add some debug info and correct PYTHON.
    - Allow python to be specified in environment.
    - Avoid continue run if resubmit_sets_continue_run is false.
    - PIO1 update.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
1fec3c1 Merge pull request #2125 from jedwards4b/pio2_update
851918d replace fancy quotes with standard ones
fdd3ddf add some debug info and correct PYTHON
994a250 Merge pull request #2138 from jedwards4b/python_path_fix
e189ba6 Merge pull request #2133 from jedwards4b/continue_run_check
261cb8a Merge pull request #2124 from jedwards4b/pio1_update

Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/case_run.py
M       scripts/tests/CMakeLists.txt
M       src/components/data_comps/docn/cime_config/config_component.xml
M       src/externals/pio1/pio/pio_types.F90
M       src/externals/pio2/configure.ac
M       src/externals/pio2/ctest/runcdash-nwscla-intel.sh
M       src/externals/pio2/doc/source/mach_walkthrough.txt
M       src/externals/pio2/src/clib/pio_darray.c
M       src/externals/pio2/src/clib/pio_getput_int.c
M       src/externals/pio2/src/clib/pio_msg.c
M       src/externals/pio2/src/clib/pio_nc4.c
M       src/externals/pio2/src/clib/pioc_support.c
M       src/externals/pio2/src/flib/pio_types.F90


======================================================================

======================================================================

Originator: Chris Fischer
Date: 12-11-1017
Tag: cime5.4.0-alpha.14
Answer Changes: None
Tests: code_checker, by-hand, scripts_regression_tests.py
       scripts_regression_tests.py (with python 3.6.2)

Dependencies:

Brief Summary:
    - No iteritems method in python3, use six compatibility library.
    - Fix couple mistakes introduced by ACME split, Pylint errors and timing problem for cesm.
    - Minor bugfix, root arugment was ignored.
    - Jgfouca/branch for acme split 12-08-2017.
    - Add debug print statements to describe current workload.
    - Fix issue in declaration.
    - Provide access functions for the setting of pio_rearranger variables.
    - Move GMAKE and GMAKE_J options to env_run so that changing them doesn't
      require a rebuild.
    - Fix processor overflow in create_test.
    - Miscellaneous tool improvement.
    - Add ability to customize CaseStatus success message for a phase.
    - DOCN mode fix.
    - Fix bug in compare namelists.
    - Fixes a memory leak in gptl.

User interface changes:
    - simple-py-prof sets PYTHONPATH for you, list_acme_tests assumes you want
      to list tests
    - jobid now added to CaseStatus case_submit entry.

PR summary: git log --oneline --first-parent [previous_tag]..master
f48881a Merge pull request #2130 from jedwards4b/py3_compatibility
90ffcf7 Merge pull request #2129 from ESMCI/jgfouca/fix_pylint_and_cesm_timing
036ac18 Merge pull request #2127 from ESMCI/jgfouca/xml_bugfix
9dfce92 Merge pull request #2126 from ESMCI/jgfouca/branch-for-acme-split-12-08-2017-pr
9c01c47 Merge pull request #2122 from ESMCI/jgfouca/create_test_add_workload_output
c0ce363 fix issue in declaration
f99b947 hot fix for pr 2121
bc6f180 Merge pull request #2120 from jedwards4b/mv_gmake_to_run
1dd0b61 Merge pull request #2119 from ESMCI/jgfouca/cime/fix_create_test_proc_overflow
0934a32 Merge pull request #2117 from ESMCI/jgfouca/misc_improve_tools
530c337 Merge pull request #2113 from ESMCI/jgfouca/custom_success_msg_case_status
cb0f58a Merge pull request #2114 from jedwards4b/DOCN_MODE_fix
148a8a9 Merge pull request #2111 from ESMCI/jgfouca/compare_nml_bugfix
2789236 Merge pull request #2110 from ESMCI/mfdeakin-sandia/gptl/memleak


Modified files: git diff --name-status [previous_tag]
M	.gitignore
M	ChangeLog
M	config/acme/allactive/config_compsets.xml
M	config/acme/allactive/config_pesall.xml
M	config/acme/config_grids.xml
A	config/acme/machines/Depends.summitdev.pgiacc
M	config/acme/machines/config_batch.xml
M	config/acme/machines/config_compilers.xml
M	config/acme/machines/config_machines.xml
M	config/acme/machines/config_pio.xml
A	config/acme/machines/syslog.theta
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/xml_schemas/config_machines.xsd
M	config/xml_schemas/config_machines_template.xml
M	doc/source/users_guide/porting-cime.rst
M	scripts/Tools/Makefile
M	scripts/Tools/cime_bisect
M	scripts/Tools/jenkins_generic_job
M	scripts/Tools/list_acme_tests
M	scripts/Tools/simple-py-prof
M	scripts/create_test
M	scripts/lib/CIME/SystemTests/homme.py
M	scripts/lib/CIME/XML/env_base.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/bless_test_results.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_submit.py
M	scripts/lib/CIME/compare_namelists.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/acme_cime_mgmt.py
M	scripts/lib/jenkins_generic_job.py
M	scripts/lib/update_acme_tests.py
M	scripts/tests/scripts_regression_tests.py
M	scripts/tests/user_mods_test3/shell_commands
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_acme.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/shr/seq_flds_mod.F90
M	src/share/timing/gptl.c
M	src/share/util/shr_pio_mod.F90
M	tools/cprnc/CMakeLists.txt

======================================================================

======================================================================

Originator: Chris Fischer
Date: 12-04-2017
Tag: cime5.4.0-alpha.13
Answer Changes: None
Tests: scripts_regression_tests.py, SMS_P8x2.f19_g16.X.yellowstone_intel
Dependencies:

Brief Summary:
    - BUILD_THREADED needs to be set if any nthrds > 1.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
307251e Merge pull request #2106 from jedwards4b/nthrds_sets_build_threaded


Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/case_setup.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 12-03-2017
Tag: cime5.4.0-alpha.12
Answer Changes: None
Tests: scripts_regression_tests.py
Dependencies:

Brief Summary:
    - Fix gptl threaded build, batch change for cheyenne.
    - Update CIME RST documentation.
    - Correct path for includes used in build.
    - Check for unicode in expect().
    - Separate liq and ice in glc2ocn mapping, and fix glc2ocn mapping bug.

User interface changes:
    -Splits GLC2OCN_RMAPNAME xml variable into
     GLC2OCN_LIQ_RMAPNAME and GLC2OCN_ICE_RMAPNAME, and similarly for
     GLC2OCN_RMAPTYPE

PR summary: git log --oneline --first-parent [previous_tag]..master
6dd6f09 Merge pull request #2105 from jedwards4b/gptl_threaded_build_fix
92f73e3 Merge pull request #2078 from bertinia/master
5dc7e19 Merge pull request #2101 from jedwards4b/mpiserial_bldfix
486efd6 Merge pull request #2097 from ESMCI/sarich/fix-buildexe-unicode
dd525f9 Merge pull request #2066 from billsacks/glc2ocn_separate_liq_ice

Modified files: git diff --name-status [previous_tag]
M	.gitignore
M	config/acme/config_grids.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_batch.xml
M	doc/source/conf.py
M	doc/source/data_models/data-ocean.rst
M	doc/source/index.rst
M	doc/source/misc_tools/index.rst
M	doc/source/users_guide/cloning-a-case.rst
M	doc/source/users_guide/introduction-and-overview.rst
M	doc/source/users_guide/optimizing-processor-layout.rst
M	doc/source/users_guide/porting-cime.rst
M	doc/source/users_guide/running-a-case.rst
M	doc/source/users_guide/testing.rst
M	doc/source/xml_files/acme.rst
M	doc/source/xml_files/drivers.rst
M	scripts/Tools/Makefile
M	scripts/lib/CIME/utils.py
M	src/build_scripts/buildlib.gptl
M	src/build_scripts/buildlib.mpi-serial
M	src/drivers/mct/cime_config/buildnml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/main/prep_ocn_mod.F90
M	src/drivers/mct/shr/seq_flds_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer
Date: 11-22-2017
Tag: cime5.4.0-alpha.11
Answer Changes: None
Tests: scripts_regression_tests.pr
Dependencies:

Brief Summary:
    - GPTL build threaded, makefile cleanup.
    - Changes in merged Makefile to satisfy dependancies thus making rebuild faster.
    - Fix run_sub_or_cmd in the case where a cmd is run and log is None.
    - Enable ldsta case.submit to be run twice.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
5ea8d6b Merge pull request #2092 from jedwards4b/gptl_build_threaded
4361a51 Merge pull request #2090 from jedwards4b/makefaster
ca4c1f9 Merge pull request #2086 from ESMCI/jgfouca/run_sub_no_log
5791d32 Merge pull request #2084 from ESMCI/mfdeakin-sandia/ldsta/rerun

Modified files: git diff --name-status [previous_tag]
M       scripts/Tools/Makefile
M       scripts/lib/CIME/SystemTests/ldsta.py
M       scripts/lib/CIME/build.py
M       scripts/lib/CIME/case_run.py
M       scripts/lib/CIME/preview_namelists.py
M       scripts/lib/CIME/utils.py
M       src/build_scripts/buildlib.gptl


======================================================================

======================================================================

Originator: Chris Fischer
Date: 11-17-2017
Tag: cime5.4.0-alpha.10
Answer Changes: None
Tests: cime_developer, scripts_regression_test
       code_checker, create_test cime_developer
       SMS.f09_g17.B1850.yellowstone_intel
       cime_tiny
Dependencies:

Brief Summary:
    - Add LDSTA to cime_developer test suite.
    - Major refactor of baseline handling.
    - Add bless logging capability.
    - Fix clm build.
    - Add function to ensure correct bld logging.
    - Short term archiver last date option test.
    - Redo mct and mpi-serial buildlib scripts in python.
    - Add a list of test types to the users guide.
    - Fix MCC test on master.
    - Fix csm_build, remove debug print statement.
    - Cleanup gptl build, replace perl buildlib.csm_share with python.
    - Convert buildlib.gptl to python and call it and the buildlib.pio as subroutines.
    - Run sub logging fixes.
    - Fix redirection for run_sub to include stderr.
    - Separate DATA_ASSIMILATION flag by component and add to Fortran infodata.
    - Add unit tests of compare_two's handling of pass/fail in comparison.
    - Fixes incorrect timer event name in data runoff model.
    - Update from ACME 11-13-2017.
    - Fix pylint issue.
    - Locked files handled BUILD_COMPLETE better.
    - Add optional COSTPES_PER_NODE.
    - Switch melvin to use officially supported pfunit.
    - USER_REQUESTED_ vars should go in env_batch.
    - Use_existing needs to set FAIL states back to PEND.
    - Add create_test options to config for user tuned defaults.
    - Jgfouca/branch for acme split 11-07-2017 pr.
    - Improve email handling.
    - Add retry capability to create_test.
    - Convert line to utf-8.
    - Change paths to case2 rundir and exeroot.

User interface changes:
    - Better defaults for bless_test_results and compare_test_results.
    - New bless_log file in baseline dirs.
    - Allow multiple -m args to case.submit. Allows user to put email settings in .cime/config.
    - New --retry option to create_test.

PR summary: git log --oneline --first-parent [previous_tag]..master
6dd002f Merge pull request #2074 from ESMCI/mfdeakin-sandia/cime_developer/ldsta
0c4ffa7 Merge pull request #2079 from ESMCI/jgfouca/major_baseline_refactor
5ac2f90 Merge pull request #2069 from ESMCI/jgfouca/add_bless_logs_2
c80333f Merge pull request #2076 from jedwards4b/clmbuildfix
09e6061 Merge pull request #2073 from ESMCI/jgfouca/fix_bld_logging
09aadd0 Merge pull request #2071 from ESMCI/mfdeakin-sandia/test_sta_last_date
8765c9c Merge pull request #2072 from jedwards4b/rebuildmct
92f74f8 Merge pull request #2062 from ESMCI/fischer/testtype_doc
690e7f7 fix MCC test on master
a3d1554 fix csm_build, remove debug print statement
71fbd56 Merge pull request #2067 from jedwards4b/rebuildlibs
27fbbbd Merge pull request #2065 from jedwards4b/run_sub_logging_demo
9bea9a4 Merge pull request #2064 from ESMCI/jgfouca/run_sub_logging_fixes
7e1c8b5 Merge pull request #2055 from ESMCI/jgfouca/run_sub_logging_fixes
53e1ddf Merge pull request #2039 from jedwards4b/data_assimilation_to_fortran_try1
559c50a Merge pull request #2060 from billsacks/compare_two_comparison_unit_tests
da29a73 Merge pull request #2054 from ESMCI/bishtgautam/drof
9442c93 Merge pull request #2052 from ESMCI/jgfouca/branch-for-acme-split-11-13-2017-pr
93461b6 fix pylint issue
52c1ad4 Merge pull request #2051 from jedwards4b/rebuild_after_error
d713717 Merge pull request #2050 from jedwards4b/COST_PER_NODE
134cb8f Merge pull request #2049 from ESMCI/jgfouca/switch_melvin_to_offical_pfunit
5de7b7e Merge pull request #2047 from jedwards4b/fix_for_user_requested_flags
04e56d2 Merge pull request #2045 from ESMCI/jgfouca/fix_use_existing
e091e2a Merge pull request #2042 from jedwards4b/create_test_options_in_config
c44fce4 Merge pull request #2033 from ESMCI/jgfouca/branch-for-acme-split-11-07-2017-pr
d03cde1 Merge pull request #2035 from ESMCI/jgfouca/improve_email_handling
426f61c Merge pull request #2034 from ESMCI/jgfouca/create_test_retry
7c54009 Merge pull request #2038 from jedwards4b/fix_dae_test
daee7ac Merge pull request #2036 from billsacks/compare2_fix_dirs


Modified files: git diff --name-status [previous_tag]
M	config/acme/allactive/config_pesall.xml
M	config/acme/config_archive.xml
M	config/acme/machines/Depends.cetus
M	config/acme/machines/Depends.intel
A	config/acme/machines/Depends.intel18
M	config/acme/machines/Depends.mira
M	config/acme/machines/Depends.summitdev.ibm
M	config/acme/machines/Depends.titan.pgi
M	config/acme/machines/Depends.titan.pgiacc
D	config/acme/machines/Makefile
M	config/acme/machines/config_batch.xml
M	config/acme/machines/config_compilers.xml
M	config/acme/machines/config_machines.xml
M	config/acme/machines/config_pio.xml
D	config/acme/machines/mkDepends
D	config/acme/machines/mkSrcfiles
M	config/acme/machines/syslog.cori-haswell
M	config/acme/machines/syslog.cori-knl
M	config/acme/machines/syslog.edison
M	config/acme/testmods_dirs/allactive/cam/cosplite/xmlchange_cmnds
D	config/cesm/machines/Makefile
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_machines.xml
D	config/cesm/machines/mkDepends
D	config/cesm/machines/mkSrcfiles
M	config/config_tests.xml
M	config/xml_schemas/config_batch.xsd
M	config/xml_schemas/config_machines.xsd
M	config/xml_schemas/env_mach_specific.xsd
M	doc/source/users_guide/testing.rst
A	scripts/Tools/Makefile
A	scripts/Tools/acme_cime_merge
M	scripts/Tools/acme_cime_split
M	scripts/Tools/bless_test_results
M	scripts/Tools/case.cmpgen_namelists
M	scripts/Tools/case.submit
M	scripts/Tools/case_diff
M	scripts/Tools/compare_test_results
A	scripts/Tools/mkDepends
A	scripts/Tools/mkSrcfiles
M	scripts/Tools/xmlchange
M	scripts/create_test
M	scripts/lib/CIME/SystemTests/dae.py
A	scripts/lib/CIME/SystemTests/ldsta.py
M	scripts/lib/CIME/SystemTests/pre.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/bless_test_results.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/case_submit.py
M	scripts/lib/CIME/check_lockedfiles.py
M	scripts/lib/CIME/compare_test_results.py
M	scripts/lib/CIME/get_timing.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
M	scripts/lib/CIME/tests/case_fake.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/CIME/wait_for_tests.py
A	scripts/lib/acme_cime_mgmt.py
M	scripts/lib/update_acme_tests.py
M	scripts/tests/run_acme_ctest/runAcmeTest_template.sh
M	scripts/tests/scripts_regression_tests.py
M	src/build_scripts/buildlib.csm_share
M	src/build_scripts/buildlib.gptl
M	src/build_scripts/buildlib.mct
M	src/build_scripts/buildlib.mpi-serial
M	src/build_scripts/buildlib.pio
M	src/components/data_comps/desp/cime_config/namelist_definition_desp.xml
M	src/components/data_comps/drof/drof_comp_mod.F90
M	src/drivers/mct/cime_config/buildnml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_acme.xml
M	src/drivers/mct/cime_config/config_compsets.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/main/cime_comp_mod.F90
M	src/drivers/mct/main/cime_driver.F90
M	src/drivers/mct/main/component_mod.F90
M	src/drivers/mct/shr/seq_comm_mct.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90
M	src/drivers/mct/shr/seq_timemgr_mod.F90
M	src/share/timing/ChangeLog
M	src/share/timing/Makefile
M	src/share/timing/f_wrappers.c
M	src/share/timing/gptl.c
M	src/share/timing/gptl.inc
M	src/share/timing/perf_mod.F90
M	src/share/timing/private.h
======================================================================

======================================================================

Originator: Chris Fischer
Date: 11-08-2017
Tag: cime5.4.0-alpha.09
Answer Changes: None
Tests: IRT.T62_g17.C1850ECO.yellowstone_intel.pop-default
       code_checker, seq by-hand and with re-run
Dependencies:

Brief Summary:
    - Allow undated history files to be archived.
    - Convert SEQ to use compare-two.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
ce40669 Merge pull request #2037 from jedwards4b/fix_for_undated_history_file_archiving
280e006 Merge pull request #2030 from ESMCI/jgfouca/seq_cmpr_two

Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/SystemTests/seq.py
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/case_st_archive.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 11-07-2017
Tag: cime5.4.0-alpha.08
Answer Changes: None
Tests: Hand test B1850
Dependencies:

Brief Summary:
    - Handle case when cmdargs is not a list

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
fc72203 Merge pull request #2032 from jedwards4b/cmdargs_fix

Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/utils.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 11-06-2017
Tag: cime5.4.0-alpha.07
Answer Changes: None
Tests: scripts_regression_tests.pr
       manual checks of mapping files generated with runoff_to_ocn tool and run of check_map.sh tool
       Tested runoff_map tool with a source file
       run_merge_mapping_files.sh
       code_checker
       tests with casename try+45
Dependencies:

Brief Summary:
    - Improve interface to external scripts PRERUN_SCRIPT, POSTRUN_SCRIPT, DATA_ASSIMILATION_SCRIPT.
    - Better error message for compsets.
    - For runoff map: fix mask_b and frac_b in nearest neighbor map.
    - If area units on source grid file are in sq deg, convert to sq radians.
    - Handle the case where no points are mapped to marginal seas.
    - Add function to rebuild dependencies.
    - Make srt change backward compatible.
    - Allow overrides in config batch.
    - Fix machines option to srt and unitialzed var.
    - Fix cprnc build on mac.
    - Add NLCOMP warning if comparison fails and RUN phase is complete.
    - Remove string formatting from code-path that checks python version.
    - Bluewaters update.
    - Fix for ACME MPAS builds.
    - Add support for selecting different driver.
    - Fix critical bug with py3 str handling.
    - Only report mem and tput errors once.
    - Fix slurm output fields.
    - Fix critical problems found during ACME/ESMCI integration.
    - Handle pattern match chars like + in casename.
    - Add check for a batch system when testing user prerequisites.
    - Fix batch prepend test.
    - py3 fixes
    - Fix COST_PES and TOTALPES for titan (aprun).
    - Add support for arbitrary prerequisites to case.submit.
    - Updates for NAS pleiades systems.

User interface changes:
    - Add --clean-depends to case.build, this argument can take a component list and will
      clean all components if one is not provided.
    - Some additional output from nl comp code in some cases
    - --driver added to create_newcase, new _V$driver testopt.


PR summary: git log --oneline --first-parent [previous_tag]..master
0027c84 Merge pull request #2005 from jedwards4b/external_process_interface
a84b875 Merge pull request #2027 from jedwards4b/better_errormsg_for_compsets
184d7de Merge pull request #2013 from billsacks/runoff_nn_fix_mask
28f74aa Merge pull request #2022 from billsacks/runoff_convert_sq_degrees
4793fd8 Merge pull request #2007 from billsacks/runoff_map_no_marginal_ocean
5e79775 Merge pull request #2026 from jedwards4b/clean_depends
2b79440 make srt change backward compatible
a5a6949 Merge pull request #2025 from jedwards4b/allow_overrides_in_config_batch
cd181bb Merge pull request #2023 from jedwards4b/fix_unitialized_var
2978605 Merge pull request #2021 from billsacks/fix_cprnc_make
2d39e61 Merge pull request #2016 from ESMCI/jgfouca/add_nl_comp_warning
32375b4 Merge pull request #2017 from ESMCI/jgfouca/fix_cime_for_old_python
f3493fa Merge pull request #2015 from jedwards4b/bluewaters_update1
33ddbe8 Merge pull request #2008 from ESMCI/jgfouca/fix_acme_mpas_builds
f99c174 Merge pull request #1988 from ESMCI/jgfouca/add_driver_selection_support
33597f4 Merge pull request #2003 from ESMCI/jgfouca/py3_str_unicode_confusion
9202dbb Merge pull request #1998 from ESMCI/jgfouca/only_report_memory_tput_errors_once
09b7b8e Merge pull request #2001 from ESMCI/jgfouca/fix_slurm_output_fields
e67caa2 Merge pull request #1999 from ESMCI/jgfouca/misc_fixes
abf1e91 Merge pull request #1997 from jedwards4b/handle_special_chars_in_casename
952c5fd Merge pull request #1996 from ESMCI/mfdeakin-sandia/case_submit_prereq/fix_test
ef08588 fix batch prepend test
4226f42 py3 fixes
e959bdc Merge pull request #1990 from ESMCI/jgfouca/titan_fixes_and_misc
5f7359b Merge pull request #1753 from ESMCI/mfdeakin-sandia/case_submit/prereq
b8190ea Merge pull request #1983 from ESMCI/jgfouca/merge_st_archive

Modified files: git diff --name-status [previous_tag]
M       config/acme/config_files.xml
M       config/acme/machines/Makefile
M       config/acme/machines/config_batch.xml
M       config/cesm/machines/Makefile
M       config/cesm/machines/config_batch.xml
M       config/cesm/machines/config_machines.xml
M       config/xml_schemas/config_batch.xsd
M       doc/source/users_guide/running-a-case.rst
M       scripts/Tools/case.build
M       scripts/Tools/case.submit
M       scripts/create_newcase
M       scripts/lib/CIME/SystemTests/dae.py
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M       scripts/lib/CIME/XML/component.py
M       scripts/lib/CIME/XML/entry_id.py
M       scripts/lib/CIME/XML/env_batch.py
M       scripts/lib/CIME/XML/env_mach_pes.py
M       scripts/lib/CIME/XML/generic_xml.py
M       scripts/lib/CIME/XML/machines.py
M       scripts/lib/CIME/aprun.py
M       scripts/lib/CIME/build.py
M       scripts/lib/CIME/buildlib.py
M       scripts/lib/CIME/case.py
M       scripts/lib/CIME/case_cmpgen_namelists.py
M       scripts/lib/CIME/case_run.py
M       scripts/lib/CIME/case_setup.py
M       scripts/lib/CIME/case_st_archive.py
M       scripts/lib/CIME/case_submit.py
M       scripts/lib/CIME/compare_namelists.py
M       scripts/lib/CIME/get_timing.py
M       scripts/lib/CIME/test_scheduler.py
M       scripts/lib/CIME/utils.py
M       scripts/query_config
M       scripts/tests/scripts_regression_tests.py
M       src/drivers/mct/cime_config/config_component.xml
M       src/drivers/mct/main/prep_ocn_mod.F90
M       tools/cprnc/Makefile
M       tools/mapping/check_maps/src/ESMF_RegridWeightGenCheck.F90
M       tools/mapping/gen_mapping_files/runoff_to_ocn/ncl/merge_mapping_files.ncl
M       tools/mapping/gen_mapping_files/runoff_to_ocn/src/main.F90
M       tools/mapping/gen_mapping_files/runoff_to_ocn/src/map_mod.F90


======================================================================

======================================================================

Originator: Chris Fischer
Date: 10-25-2017
Tag: cime5.4.0-alpha.06
Answer Changes: None
Tests: scripts_regression_tests.py
       cesm F cases
Dependencies:

Brief Summary:
    - Update mpt and pnetcdf on cheyenne.
    - Fix several data component issues.
    - Resolve compset issue.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
aac772f Merge pull request #1992 from jedwards4b/cheyenne_mpt_update
4e7bd64 Merge pull request #1987 from ESMCI/mvertens/fix_datacomps
dd2734a Merge pull request #1981 from jedwards4b/resolve_compset_issue

Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_files.xml
M       config/cesm/machines/config_machines.xml
M       scripts/lib/CIME/XML/archive.py
M       scripts/lib/CIME/XML/entry_id.py
M       scripts/lib/CIME/XML/files.py
M       scripts/lib/CIME/case_st_archive.py
M       src/build_scripts/buildlib.csm_share
M       src/components/data_comps/datm/cime_config/buildnml
M       src/components/data_comps/dice/cime_config/buildnml
M       src/components/data_comps/dlnd/cime_config/buildnml
M       src/components/data_comps/docn/cime_config/buildnml
M       src/components/data_comps/docn/docn_comp_mod.F90
M       src/components/data_comps/drof/cime_config/buildnml
D       src/components/data_comps/dshare/shr_dmodel_mod.F90
D       src/components/data_comps/dshare/shr_strdata_mod.F90
D       src/components/data_comps/dshare/shr_stream_mod.F90
D       src/components/data_comps/dshare/shr_tInterp_mod.F90
M       src/components/data_comps/dwav/cime_config/buildnml
M       src/drivers/mct/cime_config/buildnml
M       src/drivers/mct/cime_config/config_archive.xml
A       src/share/streams/shr_dmodel_mod.F90
A       src/share/streams/shr_strdata_mod.F90
A       src/share/streams/shr_stream_mod.F90
A       src/share/streams/shr_tInterp_mod.F90


======================================================================

======================================================================

Originator: Chris Fischer
Date: 10-25-2017
Tag: cime5.4.0-alpha.05
Answer Changes: None
Tests: scripts_regression_tests
       ne16_ne16_mg17 alias (compset QPC6)
       ERS.f09_g17.B1850.cheyenne_intel.allactive-defaultio
Dependencies:

Brief Summary:
    - Add mapping files for T42_T42_mg17.
    - Remove empty proxy tag from anlworkstation.
    - Updates for testreporter and remove AWAV from testlist.
    - Bring in E3SM cime changes for past 3 months.
    - Adjustments for new CAM-SE dycore.
    - Make sure user changes to wallclock/queue are not lost.
    - Minor cleanup of PEM test.
    - Add COMP_ROOT_DIR_ variables so that a component can be moved with the
      change of a single cime variable.
    - Set correct domain files for ne16np4.
    - Add LBL Machines.
    - Data model documentation edits.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
299f1ab Merge pull request #1991 from ESMCI/fischer/T42_T42_mg17
a8cd748 Merge pull request #1989 from ESMCI/dqwu/anlworkstation-remove-proxy-tag
de4df65 Merge pull request #1984 from ESMCI/fischer/TestReporter
0c1b306 Merge pull request #1970 from ESMCI/jgfouca/branch-for-acme-split-10-17-2017-pr
4f201fe Merge pull request #1979 from gold2718/seUpdates
3d509a2 Merge pull request #1978 from ESMCI/jgfouca/fix_custom_walltime
14d71e9 Merge pull request #1976 from billsacks/pem_cleanup
0e5cee1 Merge pull request #1968 from jedwards4b/add_comp_root_dir_vars
a1a2c14 Merge pull request #1973 from gold2718/seDomainFiles
48c6fa8 Merge pull request #1956 from ekluzek/addlblmachs
a915609 Merge pull request #1969 from billsacks/data_model_edits


Modified files: git diff --name-status [previous_tag]
M	config/acme/allactive/config_compsets.xml
M	config/acme/allactive/config_pesall.xml
M	config/acme/config_archive.xml
M	config/acme/config_files.xml
M	config/acme/config_grids.xml
D	config/acme/machines/Depends.corip1
M	config/acme/machines/Depends.intel
D	config/acme/machines/Depends.intel14
D	config/acme/machines/Depends.intelmic
D	config/acme/machines/Depends.intelmic14
A	config/acme/machines/Depends.summitdev.ibm
M	config/acme/machines/Makefile
M	config/acme/machines/config_batch.xml
M	config/acme/machines/config_compilers.xml
M	config/acme/machines/config_machines.xml
M	config/acme/machines/template.st_archive
A	config/acme/testmods_dirs/allactive/clm/bgcinterface/user_nl_clm
A	config/acme/testmods_dirs/allactive/clm/rd/user_nl_clm
A	config/acme/testmods_dirs/allactive/clm/vst/user_nl_clm
M	config/cesm/config_files.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.st_archive
M	config/config_tests.xml
M	config/xml_schemas/config_compilers_v2.xsd
M	config/xml_schemas/config_machines.xsd
M	config/xml_schemas/config_machines_template.xml
M	config/xml_schemas/env_mach_specific.xsd
M	doc/source/data_models/data-atm.rst
M	doc/source/data_models/data-lnd.rst
M	doc/source/data_models/data-model-science.rst
M	doc/source/data_models/data-ocean.rst
M	doc/source/data_models/data-river.rst
M	doc/source/data_models/data-seaice.rst
M	doc/source/data_models/data-wave.rst
M	doc/source/data_models/design-details.rst
M	doc/source/data_models/input-streams.rst
M	doc/source/data_models/introduction.rst
A	scripts/Tools/acme_cime_split
M	scripts/Tools/jenkins_generic_job
M	scripts/Tools/preview_run
M	scripts/Tools/testreporter.py
M	scripts/Tools/xmlchange
M	scripts/create_test
M	scripts/fortran_unit_testing/run_tests.py
M	scripts/lib/CIME/BuildTools/configure.py
M	scripts/lib/CIME/SystemTests/erp.py
M	scripts/lib/CIME/SystemTests/pem.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/XML/pes.py
M	scripts/lib/CIME/bless_test_results.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/test_status.py
M	scripts/lib/CIME/tests/case_fake.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/jenkins_generic_job.py
M	scripts/lib/update_acme_tests.py
A	scripts/tests/run_acme_ctest/CMakeLists.txt
A	scripts/tests/run_acme_ctest/CTestConfig.cmake
A	scripts/tests/run_acme_ctest/runAcmeTest_template.sh
M	scripts/tests/scripts_regression_tests.py
M	src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M	src/components/data_comps/docn/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_acme.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/drivers/mct/cime_config/testdefs/testlist_drv.xml
M	src/drivers/mct/main/cime_comp_mod.F90
M	src/drivers/mct/main/seq_diag_mct.F90
D	src/externals/pio1/tests/testpio/perl5lib/XML/man3/XML_Lite.3
D	src/externals/pio1/tests/testpio/perl5lib/XML/man3/XML_Lite_Element.3
D	src/externals/pio2/examples/basic/perl5lib/XML/man3/XML_Lite.3
D	src/externals/pio2/examples/basic/perl5lib/XML/man3/XML_Lite_Element.3
M	src/share/timing/GPTLget_memusage.c
M	src/share/timing/GPTLprint_memusage.c
M	src/share/util/shr_flux_mod.F90
M	src/share/util/shr_mem_mod.F90
M	src/share/util/shr_orb_mod.F90
M	src/share/util/shr_reprosum_mod.F90
M	utils/perl5lib/compilers_translation_tool.pl

======================================================================

======================================================================

Originator: Chris Fischer
Date: 10-16-2017
Tag: cime5.4.0-alpha.04
Answer Changes: None
Tests: scripts_regression_tests.py code_checker
Dependencies:

Brief Summary:
    - Cleanup of the compvar implementation.
    - Refactor CPLHIST mode and add DATM CPLHIST topo capability.
    - Fix py3 for erio test.
    - Fix some issues found in type conversion.
    - Port to python3 while maintaining compatibility with python 2.7
    - Remove developers table on README.md.
    - Load balancing tool mods.
    - Add auto-normalization to case_diff.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
af429bd Merge pull request #1965 from jedwards4b/iscompvar_cleanup
16adad1 Merge pull request #1950 from ESMCI/mvertens/cplhist_topo
02cc2fd Fix py3 for erio test
116e6e7 Merge pull request #1962 from jedwards4b/convert_to_string_fix
c5cf2af PR #1949 jedwards4b/py3_port_branch
c6cf37e Merge pull request #1926 from ESMCI/rljacob/update-readme
128625f Merge pull request #1942 from jedwards4b/load-balancing-tool-mods
6f43f73 Merge pull request #1958 from ESMCI/jgfouca/case_diff_auto_normalize


Modified files: git diff --name-status [previous_tag]
M	CMakeLists.txt
M	LICENSE.TXT
D	README
M	README.md
D	README.unit_testing
M	config/acme/allactive/config_compsets.xml
D	config/acme/allactive/config_compsets.xml.cime2
D	config/acme/allactive/config_pes.xml
D	config/acme/allactive/config_pes.xml.cime2
M	config/acme/allactive/config_pesall.xml
D	config/acme/allactive/testmods_dirs/cam/outfrq9s/shell_commands
D	config/acme/allactive/testmods_dirs/force_netcdf_pio/shell_commands
M	config/acme/config_archive.xml
M	config/acme/config_files.xml
M	config/acme/config_grids.xml
M	config/acme/machines/Makefile
M	config/acme/machines/config_batch.xml
M	config/acme/machines/config_batch.xsd
M	config/acme/machines/config_compilers.xml
D	config/acme/machines/config_lt_archive.xml
M	config/acme/machines/config_machines.xml
M	config/acme/machines/config_pio.xml
A	config/acme/machines/syslog.anvil
M	config/acme/machines/syslog.cetus
M	config/acme/machines/syslog.cori-haswell
M	config/acme/machines/syslog.cori-knl
M	config/acme/machines/syslog.edison
M	config/acme/machines/syslog.mira
M	config/acme/machines/syslog.titan
M	config/acme/machines/template.case.run
M	config/acme/machines/template.case.test
D	config/acme/machines/template.lt_archive
M	config/acme/machines/template.st_archive
M	config/acme/machines/userdefined_laptop_template/config_compilers.xml
M	config/acme/machines/userdefined_laptop_template/config_machines.xml
A	config/acme/testmods_dirs/allactive/cam/cosplite/user_nl_cam
A	config/acme/testmods_dirs/allactive/cam/cosplite/xmlchange_cmnds
A	config/acme/testmods_dirs/allactive/cam/cosplite_nhtfrq5/user_nl_cam
A	config/acme/testmods_dirs/allactive/cam/cosplite_nhtfrq5/xmlchange_cmnds
A	config/acme/testmods_dirs/allactive/cam/outfrq9s/xmlchange_cmnds
A	config/acme/testmods_dirs/allactive/cam/rtm_null/xmlchange_cmnds
A	config/acme/testmods_dirs/allactive/clm/betr/xmlchange_cmnds
A	config/acme/testmods_dirs/allactive/clm/eca/user_nl_clm
A	config/acme/testmods_dirs/allactive/clm/fates/user_nl_clm
A	config/acme/testmods_dirs/allactive/force_netcdf_pio/shell_commands
A	config/acme/testmods_dirs/allactive/force_netcdf_pio/xmlchange_cmnds
M	config/cesm/config_archive.xml
M	config/cesm/config_files.xml
M	config/cesm/config_grids.xml
D	config/cesm/machines/Depends.goldbach
M	config/cesm/machines/Makefile
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
D	config/cesm/machines/config_lt_archive.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/config_pio.xml
M	config/cesm/machines/template.case.run
M	config/cesm/machines/template.case.test
D	config/cesm/machines/template.lt_archive
M	config/cesm/machines/template.st_archive
M	config/cesm/machines/userdefined_laptop_template/README.md
M	config/cesm/machines/userdefined_laptop_template/config_compilers.xml
M	config/cesm/machines/userdefined_laptop_template/config_machines.xml
M	config/config_headers.xml
M	config/config_tests.xml
M	config/xml_schemas/config_batch.xsd
M	config/xml_schemas/config_compsets.xsd
M	config/xml_schemas/config_grids_v2.xsd
M	config/xml_schemas/config_machines.xsd
M	config/xml_schemas/config_machines_template.xml
M	config/xml_schemas/config_pes.xsd
M	config/xml_schemas/entry_id_base.xsd
A	config/xml_schemas/entry_id_base_version3.xsd
A	config/xml_schemas/entry_id_version3.xsd
A	config/xml_schemas/env_batch.xsd
A	config/xml_schemas/env_mach_pes.xsd
A	config/xml_schemas/env_mach_specific.xsd
A	doc/.gitignore
A	doc/Makefile
A	doc/README
A	doc/source/README
A	doc/source/Tools_user/index.rst.template
A	doc/source/_static
A	doc/source/build_cpl/adding-components.rst
A	doc/source/build_cpl/index.rst
A	doc/source/build_cpl/introduction.rst
A	doc/source/conf.py
A	doc/source/data_models/data-atm.rst
A	doc/source/data_models/data-lnd.rst
A	doc/source/data_models/data-model-science.rst
A	doc/source/data_models/data-ocean.rst
A	doc/source/data_models/data-river.rst
A	doc/source/data_models/data-seaice.rst
A	doc/source/data_models/data-wave.rst
A	doc/source/data_models/design-details.rst
A	doc/source/data_models/index.rst
A	doc/source/data_models/input-namelists.rst
A	doc/source/data_models/input-streams.rst
A	doc/source/data_models/introduction.rst
A	doc/source/driver_cpl/bit-for-bit-flag.rst
A	doc/source/driver_cpl/budgets.rst
A	doc/source/driver_cpl/cplug-02.1-figx1.jpg
A	doc/source/driver_cpl/design.rst
A	doc/source/driver_cpl/driver_threading_control.rst
A	doc/source/driver_cpl/grids.rst
A	doc/source/driver_cpl/history-and-restarts.rst
A	doc/source/driver_cpl/implementation.rst
A	doc/source/driver_cpl/index.rst
A	doc/source/driver_cpl/initialization-and-restart.rst
A	doc/source/driver_cpl/introduction.rst
A	doc/source/driver_cpl/multi-instance.rst
A	doc/source/driver_cpl/namelist-overview.rst
A	doc/source/driver_cpl/time-management.rst
A	doc/source/glossary/index.rst
A	doc/source/index.rst
A	doc/source/misc_tools/index.rst
A	doc/source/misc_tools/load-balancing-tool.rst
A	doc/source/users_guide/adding-cases.rst
A	doc/source/users_guide/building-a-case.rst
A	doc/source/users_guide/case-basics.rst
A	doc/source/users_guide/cime-internals.rst
A	doc/source/users_guide/cloning-a-case.rst
A	doc/source/users_guide/create-a-case.rst
A	doc/source/users_guide/customizing-a-case.rst
A	doc/source/users_guide/index.rst
A	doc/source/users_guide/introduction-and-overview.rst
A	doc/source/users_guide/multi-instance.rst
A	doc/source/users_guide/optimizing-processor-layout.rst
A	doc/source/users_guide/porting-cime.rst
A	doc/source/users_guide/running-a-case.rst
A	doc/source/users_guide/setting-up-a-case.rst
A	doc/source/users_guide/testing.rst
A	doc/source/users_guide/troubleshooting.rst
A	doc/source/users_guide/unit_testing.rst
A	doc/source/users_guide/use_cases/basics-a-basic-example.rst
A	doc/source/users_guide/use_cases/basics-mpi-example.rst
A	doc/source/users_guide/use_cases/basics-setting-up-a-branch-or-hybrid-run.rst
A	doc/source/users_guide/use_cases/use-cases.rst
A	doc/source/what_cime/index.rst
A	doc/source/xml_files/acme.rst
A	doc/source/xml_files/atmosphere.rst
A	doc/source/xml_files/cesm.rst
A	doc/source/xml_files/common.rst
A	doc/source/xml_files/components.rst
A	doc/source/xml_files/drivers.rst
A	doc/source/xml_files/esp.rst
A	doc/source/xml_files/index.rst
A	doc/source/xml_files/land.rst
A	doc/source/xml_files/landice.rst
A	doc/source/xml_files/ocean.rst
A	doc/source/xml_files/river.rst
A	doc/source/xml_files/seaice.rst
A	doc/source/xml_files/wave.rst
A	doc/tools_autodoc.cfg
A	doc/tools_autodoc.py
A	index.html
D	scripts/Tools/README.post_process
M	scripts/Tools/acme_check_env
D	scripts/Tools/archive_metadata.sh
M	scripts/Tools/bless_test_results
M	scripts/Tools/case.build
M	scripts/Tools/case.cmpgen_namelists
A	scripts/Tools/case.qstatus
M	scripts/Tools/case.setup
M	scripts/Tools/case.submit
M	scripts/Tools/case_diff
M	scripts/Tools/check_case
D	scripts/Tools/check_exactrestart.pl
M	scripts/Tools/check_input_data
M	scripts/Tools/check_lockedfiles
M	scripts/Tools/cime_bisect
M	scripts/Tools/cimeteststatus
M	scripts/Tools/code_checker
M	scripts/Tools/compare_namelists
M	scripts/Tools/compare_test_results
M	scripts/Tools/component_compare_baseline
M	scripts/Tools/component_compare_copy
M	scripts/Tools/component_compare_test
M	scripts/Tools/component_generate_baseline
D	scripts/Tools/create_train
D	scripts/Tools/cron_script
A	scripts/Tools/cs.status
D	scripts/Tools/cs_status
M	scripts/Tools/getTiming
M	scripts/Tools/jenkins_generic_job
M	scripts/Tools/jenkins_script
M	scripts/Tools/list_acme_tests
D	scripts/Tools/load.awk
D	scripts/Tools/lt_archive.sh
D	scripts/Tools/mdiag_reduce.csh
D	scripts/Tools/mdiag_reduce.pl
M	scripts/Tools/normalize_cases
M	scripts/Tools/pelayout
M	scripts/Tools/pointclm/makepointdata.py
M	scripts/Tools/pointclm/post_process.py
M	scripts/Tools/pointclm/site_fullrun.py
M	scripts/Tools/preview_namelists
A	scripts/Tools/preview_run
M	scripts/Tools/save_provenance
M	scripts/Tools/simple_compare
A	scripts/Tools/testreporter.py
M	scripts/Tools/update_acme_tests
M	scripts/Tools/wait_for_tests
M	scripts/Tools/xmlchange
M	scripts/Tools/xmlconvertors/config_pes_converter.py
M	scripts/Tools/xmlconvertors/grid_xml_converter.py
M	scripts/Tools/xmlquery
M	scripts/create_clone
M	scripts/create_newcase
M	scripts/create_test
A	scripts/fortran_unit_testing/Examples/circle_area/src/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/circle_area/src/circle.F90
A	scripts/fortran_unit_testing/Examples/circle_area/tests/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/circle_area/tests/CTest/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/circle_area/tests/CTest/test_driver.F90
A	scripts/fortran_unit_testing/Examples/circle_area/tests/pFUnit/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/circle_area/tests/pFUnit/test_circle.pf
A	scripts/fortran_unit_testing/Examples/interpolate_1d/src/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/interpolate_1d/src/interpolate_1d.F90
A	scripts/fortran_unit_testing/Examples/interpolate_1d/tests/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/interpolate_1d/tests/CTest/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/interpolate_1d/tests/CTest/test_driver.F90
A	scripts/fortran_unit_testing/Examples/interpolate_1d/tests/pFUnit/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/interpolate_1d/tests/pFUnit/test_interpolate_point.pf
A	scripts/fortran_unit_testing/Examples/test_list.xml
A	scripts/fortran_unit_testing/README
A	scripts/fortran_unit_testing/python/.gitignore
A	scripts/fortran_unit_testing/python/printer.py
A	scripts/fortran_unit_testing/python/test_xml_test_list.py
A	scripts/fortran_unit_testing/python/xml_test_list.py
A	scripts/fortran_unit_testing/run_tests.py
M	scripts/lib/CIME/BuildTools/cmakemacroswriter.py
M	scripts/lib/CIME/BuildTools/configure.py
M	scripts/lib/CIME/BuildTools/macrowriterbase.py
M	scripts/lib/CIME/SystemTests/dae.py
M	scripts/lib/CIME/SystemTests/eri.py
M	scripts/lib/CIME/SystemTests/erio.py
M	scripts/lib/CIME/SystemTests/erp.py
M	scripts/lib/CIME/SystemTests/err.py
A	scripts/lib/CIME/SystemTests/erri.py
M	scripts/lib/CIME/SystemTests/ers.py
A	scripts/lib/CIME/SystemTests/ers2.py
M	scripts/lib/CIME/SystemTests/homme.py
A	scripts/lib/CIME/SystemTests/irt.py
D	scripts/lib/CIME/SystemTests/lii.py
A	scripts/lib/CIME/SystemTests/mcc.py
M	scripts/lib/CIME/SystemTests/nck.py
M	scripts/lib/CIME/SystemTests/ncr.py
A	scripts/lib/CIME/SystemTests/nodefail.py
M	scripts/lib/CIME/SystemTests/pea.py
M	scripts/lib/CIME/SystemTests/pem.py
M	scripts/lib/CIME/SystemTests/pet.py
M	scripts/lib/CIME/SystemTests/pre.py
A	scripts/lib/CIME/SystemTests/restart_tests.py
M	scripts/lib/CIME/SystemTests/seq.py
D	scripts/lib/CIME/SystemTests/ssp.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/archive.py
M	scripts/lib/CIME/XML/batch.py
M	scripts/lib/CIME/XML/compilerblock.py
M	scripts/lib/CIME/XML/compilers.py
M	scripts/lib/CIME/XML/component.py
M	scripts/lib/CIME/XML/compsets.py
M	scripts/lib/CIME/XML/entry_id.py
M	scripts/lib/CIME/XML/env_archive.py
M	scripts/lib/CIME/XML/env_base.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_pes.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/env_run.py
M	scripts/lib/CIME/XML/env_test.py
M	scripts/lib/CIME/XML/files.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/XML/grids.py
D	scripts/lib/CIME/XML/lt_archive.py
M	scripts/lib/CIME/XML/machines.py
M	scripts/lib/CIME/XML/namelist_definition.py
M	scripts/lib/CIME/XML/pes.py
A	scripts/lib/CIME/XML/test_reporter.py
M	scripts/lib/CIME/XML/testlist.py
M	scripts/lib/CIME/XML/tests.py
M	scripts/lib/CIME/XML/testspec.py
A	scripts/lib/CIME/aprun.py
M	scripts/lib/CIME/bless_test_results.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/buildlib.py
M	scripts/lib/CIME/buildnml.py
M	scripts/lib/CIME/case.py
A	scripts/lib/CIME/case_clone.py
M	scripts/lib/CIME/case_cmpgen_namelists.py
D	scripts/lib/CIME/case_lt_archive.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/case_submit.py
M	scripts/lib/CIME/case_test.py
M	scripts/lib/CIME/check_input_data.py
M	scripts/lib/CIME/check_lockedfiles.py
M	scripts/lib/CIME/code_checker.py
M	scripts/lib/CIME/compare_namelists.py
M	scripts/lib/CIME/compare_test_results.py
M	scripts/lib/CIME/get_timing.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/namelist.py
M	scripts/lib/CIME/nmlgen.py
M	scripts/lib/CIME/preview_namelists.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/simple_compare.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/test_status.py
M	scripts/lib/CIME/test_utils.py
M	scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
M	scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two_link_to_case2_output.py
M	scripts/lib/CIME/tests/SystemTests/test_utils/test_user_nl_utils.py
M	scripts/lib/CIME/tests/case_fake.py
A	scripts/lib/CIME/tests/test_user_mod_support.py
M	scripts/lib/CIME/user_mod_support.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/CIME/wait_for_tests.py
M	scripts/lib/cs.status.template
M	scripts/lib/jenkins_generic_job.py
A	scripts/lib/six.py
A	scripts/lib/testreporter.template
M	scripts/lib/update_acme_tests.py
D	scripts/manage_case
M	scripts/manage_pes
A	scripts/query_config
M	scripts/query_testlists
M	scripts/tests/CMakeLists.txt
M	scripts/tests/CTestConfig.cmake
M	scripts/tests/list_tests
M	scripts/tests/scripts_regression_tests.py
A	scripts/tests/user_mods_test3/shell_commands
A	src/CMake/.gitignore
A	src/CMake/CESM_utils.cmake
A	src/CMake/CIME_initial_setup.cmake
A	src/CMake/CIME_utils.cmake
A	src/CMake/ChangeLog
A	src/CMake/Compilers.cmake
A	src/CMake/FindpFUnit.cmake
A	src/CMake/LICENSE
A	src/CMake/README.md
A	src/CMake/Sourcelist_utils.cmake
A	src/CMake/TryCSizeOf.f90
A	src/CMake/TryMPIIO.f90
A	src/CMake/TryMPIMod.f90
A	src/CMake/TryMPISERIAL.f90
A	src/CMake/TryPnetcdf_inc.f90
A	src/CMake/TryPnetcdf_mod.f90
A	src/CMake/genf90_utils.cmake
A	src/CMake/mpiexec.cmake
A	src/CMake/pFUnit_utils.cmake
M	src/build_scripts/buildlib.csm_share
M	src/build_scripts/buildlib.gptl
A	src/build_scripts/buildlib.internal_components
M	src/build_scripts/buildlib.mct
M	src/build_scripts/buildlib.mpi-serial
M	src/build_scripts/buildlib.pio
D	src/components/data_comps/datm/atm_comp_mct.F90
T	src/components/data_comps/datm/cime_config/buildlib
M	src/components/data_comps/datm/cime_config/buildnml
M	src/components/data_comps/datm/cime_config/config_archive.xml
M	src/components/data_comps/datm/cime_config/config_component.xml
M	src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M	src/components/data_comps/datm/datm_comp_mod.F90
M	src/components/data_comps/datm/datm_shr_mod.F90
A	src/components/data_comps/datm/mct/atm_comp_mct.F90
T	src/components/data_comps/desp/cime_config/buildlib
M	src/components/data_comps/desp/cime_config/buildnml
M	src/components/data_comps/desp/cime_config/config_component.xml
M	src/components/data_comps/desp/cime_config/namelist_definition_desp.xml
M	src/components/data_comps/desp/desp_comp_mod.F90
D	src/components/data_comps/desp/esp_comp_mct.F90
M	src/components/data_comps/desp/esp_utils.F90
A	src/components/data_comps/desp/mct/esp_comp_mct.F90
T	src/components/data_comps/dice/cime_config/buildlib
M	src/components/data_comps/dice/cime_config/buildnml
M	src/components/data_comps/dice/cime_config/config_archive.xml
M	src/components/data_comps/dice/cime_config/config_component.xml
M	src/components/data_comps/dice/cime_config/namelist_definition_dice.xml
M	src/components/data_comps/dice/dice_comp_mod.F90
A	src/components/data_comps/dice/dice_shr_mod.F90
D	src/components/data_comps/dice/ice_comp_mct.F90
A	src/components/data_comps/dice/mct/ice_comp_mct.F90
T	src/components/data_comps/dlnd/cime_config/buildlib
M	src/components/data_comps/dlnd/cime_config/buildnml
M	src/components/data_comps/dlnd/cime_config/config_archive.xml
M	src/components/data_comps/dlnd/cime_config/config_component.xml
M	src/components/data_comps/dlnd/cime_config/namelist_definition_dlnd.xml
M	src/components/data_comps/dlnd/dlnd_comp_mod.F90
A	src/components/data_comps/dlnd/dlnd_shr_mod.F90
D	src/components/data_comps/dlnd/lnd_comp_mct.F90
A	src/components/data_comps/dlnd/mct/lnd_comp_mct.F90
T	src/components/data_comps/docn/cime_config/buildlib
M	src/components/data_comps/docn/cime_config/buildnml
M	src/components/data_comps/docn/cime_config/config_archive.xml
M	src/components/data_comps/docn/cime_config/config_component.xml
M	src/components/data_comps/docn/cime_config/namelist_definition_docn.xml
M	src/components/data_comps/docn/docn_comp_mod.F90
A	src/components/data_comps/docn/docn_shr_mod.F90
A	src/components/data_comps/docn/mct/ocn_comp_mct.F90
D	src/components/data_comps/docn/ocn_comp_mct.F90
T	src/components/data_comps/drof/cime_config/buildlib
M	src/components/data_comps/drof/cime_config/buildnml
M	src/components/data_comps/drof/cime_config/config_archive.xml
M	src/components/data_comps/drof/cime_config/config_component.xml
M	src/components/data_comps/drof/cime_config/namelist_definition_drof.xml
M	src/components/data_comps/drof/drof_comp_mod.F90
A	src/components/data_comps/drof/drof_shr_mod.F90
A	src/components/data_comps/drof/mct/rof_comp_mct.F90
D	src/components/data_comps/drof/rof_comp_mct.F90
A	src/components/data_comps/dshare/shr_dmodel_mod.F90
A	src/components/data_comps/dshare/shr_strdata_mod.F90
A	src/components/data_comps/dshare/shr_stream_mod.F90
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D	tools/load_balancing_tool/code/neos.py
D	tools/load_balancing_tool/global_variables.csh
A	tools/load_balancing_tool/layouts.py
A	tools/load_balancing_tool/load_balancing_solve.py
A	tools/load_balancing_tool/load_balancing_submit.py
A	tools/load_balancing_tool/optimize_model.py
D	tools/load_balancing_tool/run_first.csh
D	tools/load_balancing_tool/run_second.csh
A	tools/load_balancing_tool/tests/__init__.py
A	tools/load_balancing_tool/tests/atm_lnd.py
A	tools/load_balancing_tool/tests/example.json
A	tools/load_balancing_tool/tests/load_balancing_test.py
A	tools/load_balancing_tool/tests/test.xml
A	tools/load_balancing_tool/tests/timing/timing_1
A	tools/load_balancing_tool/tests/timing/timing_2
A	tools/load_balancing_tool/tests/timing/timing_3
M	tools/mapping/check_maps/.gitignore
M	tools/mapping/check_maps/README
M	tools/mapping/check_maps/src/ESMF_RegridWeightGenCheck.F90
M	tools/mapping/check_maps/src/Makefile
M	tools/mapping/gen_domain_files/INSTALL
M	tools/mapping/gen_domain_files/src/Makefile
M	tools/mapping/gen_mapping_files/README
A	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/.gitignore
M	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/README
M	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/create_ESMF_map.sh
M	tools/mapping/gen_mapping_files/runoff_to_ocn/INSTALL
M	tools/mapping/gen_mapping_files/runoff_to_ocn/README
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_r05_to_gx1v6_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_r05_to_gx1v7_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_r05_to_gx3v7_nnsm_e1000r500.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_rx1_to_gx1v6_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_rx1_to_gx1v7_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_rx1_to_gx3v7_nnsm_e1000r500.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_wr50a_to_ar9v4_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_wr50a_to_gx3v7_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/maps/.gitignore
A	tools/mapping/gen_mapping_files/runoff_to_ocn/ncl/merge_mapping_files.ncl
A	tools/mapping/gen_mapping_files/runoff_to_ocn/run_merge_mapping_files.sh
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map.nml
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map_r05_gx3v7.nml
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map_rx1_gx1v6.nml
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map_tx01.nml
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map_wr50a_ar9v4.nml
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map_wr50a_gx3v7.nml
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/Makefile
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/fixroff_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/kind_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/main.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/map_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/mapsort_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/shr_kind_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/shr_sys_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/shr_timer_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/smooth_mod.F90
M	tools/mapping/map_field/INSTALL
M	tools/mapping/map_field/src/Makefile
M	tools/mapping/map_field/src/map_field.F90
A	tools/statistical_ensemble_test/README
M	tools/statistical_ensemble_test/ensemble.sh
D	tools/statistical_ensemble_test/ncl_library/Zscore.ncl
D	tools/statistical_ensemble_test/ncl_library/area_avg.ncl
D	tools/statistical_ensemble_test/ncl_library/create_ensemble.ncl
D	tools/statistical_ensemble_test/ncl_library/global.ncl
D	tools/statistical_ensemble_test/ncl_library/plot_rmsz.ncl
D	tools/statistical_ensemble_test/ncl_library/print.ncl
D	tools/statistical_ensemble_test/ncl_library/rmsz.ncl
D	tools/statistical_ensemble_test/ncl_library/vinterp.ncl
M	tools/statistical_ensemble_test/pyCECT/pyCECT.py
M	tools/statistical_ensemble_test/pyCECT/pyEnsLib.py
M	tools/statistical_ensemble_test/pyCECT/pyEnsSum.py
M	tools/statistical_ensemble_test/pyCECT/pyEnsSumPop.py
M	tools/statistical_ensemble_test/single_run.sh
D	tools/statistical_ensemble_test/test_run_against_ensemble.ncl
D	tools/statistical_ensemble_test/validation_test.sh
D	tools/unit_testing/Examples/circle_area/src/CMakeLists.txt
D	tools/unit_testing/Examples/circle_area/src/circle.F90
D	tools/unit_testing/Examples/circle_area/tests/CMakeLists.txt
D	tools/unit_testing/Examples/circle_area/tests/CTest/CMakeLists.txt
D	tools/unit_testing/Examples/circle_area/tests/CTest/test_driver.F90
D	tools/unit_testing/Examples/circle_area/tests/pFUnit/CMakeLists.txt
D	tools/unit_testing/Examples/circle_area/tests/pFUnit/test_circle.pf
D	tools/unit_testing/Examples/interpolate_1d/src/CMakeLists.txt
D	tools/unit_testing/Examples/interpolate_1d/src/interpolate_1d.F90
D	tools/unit_testing/Examples/interpolate_1d/tests/CMakeLists.txt
D	tools/unit_testing/Examples/interpolate_1d/tests/CTest/CMakeLists.txt
D	tools/unit_testing/Examples/interpolate_1d/tests/CTest/test_driver.F90
D	tools/unit_testing/Examples/interpolate_1d/tests/pFUnit/CMakeLists.txt
D	tools/unit_testing/Examples/interpolate_1d/tests/pFUnit/test_interpolate_point.pf
D	tools/unit_testing/Examples/test_list.xml
D	tools/unit_testing/README
D	tools/unit_testing/python/.gitignore
D	tools/unit_testing/python/comparable.py
D	tools/unit_testing/python/environment.py
D	tools/unit_testing/python/machine_setup.py
D	tools/unit_testing/python/printer.py
D	tools/unit_testing/python/test_environment.py
D	tools/unit_testing/python/test_xml_test_list.py
D	tools/unit_testing/python/test_xml_utils.py
D	tools/unit_testing/python/xml_test_list.py
D	tools/unit_testing/python/xml_utils.py
D	tools/unit_testing/run_tests.py
M	tools/utils/find_circular_dependency.py
M	utils/perl5lib/Build/Namelist.pm

======================================================================

======================================================================

Originator: Chris Fischer
Date: 10-9-2017
Tag: cime5.4.0-alpha.03
Answer Changes: None
Tests: scripts_regression_tests.pr
       manual test of create_clone
Dependencies:

Brief Summary:
    - Fix SE domain files.
    - Use keyword-value pairs for create_clone call.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
55d2dbe Merge pull request #1957 from billsacks/create_clone_args
443312c Merge pull request #1951 from gold2718/seDomainFiles


Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_grids.xml
M       scripts/create_clone
M       src/drivers/mct/cime_config/config_component_cesm.xml

======================================================================

======================================================================

Originator: Chris Fischer
Date: 10-6-2017
Tag: cime5.4.0-alpha.02
Answer Changes: None
Tests: scripts_regression_tests.py SMS_Ln9.f19_f19_mg17.F2000_DEV.yellowstone_intel.cam-cosp
       IRT_Ld7.T31_g37.B1850C5L45BGCR.cheyenne_intel
       hand testing tools/load_balancing_tool/test/test_load_balancing_tool.py
       load_balancing_test.py
Dependencies:

Brief Summary:
    - Fix cosp build instructions.
    - Pio update branch.
    - Refactor args to submit scripts.
    - Archive pop tavg rpointer file.
    - Add option to define test types in query_testlists.
    - Fix tests for small systems.
    - Only run driver build namelist after first day cycle.
    - Load balancing tool mods.
    - Use local baseline directory for testing.
    - Add ability to cancel batch jobs to the system.
    - A port to a generic Linux workstation.
    - Fix pylint issue.
    - Fix st_archive.
    - Document uniqueness requirement for test-id.
    - Add Argonne copyright statement.
    - Rewrite of the load balancing tool.
    - Imported mpi-serial changes from MCSclimate/mpi-serial.

User interface changes:
    - New batch_env optional entry in config_batch.
    - Add --baseline-root argument to case.cmpgen_baselines.
    - new batch_cancel field in config_batch.

PR summary: git log --oneline --first-parent [previous_tag]..master
a2f0979 Merge pull request #1947 from jedwards4b/cosp_build_fix
1655800 Merge pull request #1948 from jedwards4b/pio_update_branch
d590c55 Merge pull request #1945 from ESMCI/jgfouca/refactor_args_to_submit_scripts
7f44f80 Merge pull request #1944 from jedwards4b/pop_tavg_archive
c7cf4eb Merge pull request #1930 from billsacks/query_testtypes
0742931 Merge pull request #1943 from jedwards4b/small_systems
34522a3 Merge pull request #1941 from jedwards4b/da_optimization
be3bf2e Merge pull request #1923 from jedwards4b/load-balancing-tool-mods
2d2ab96 Merge pull request #1939 from jedwards4b/srt_baselines
4e0e02e Merge pull request #1932 from ESMCI/jgfouca/add_job_cancel
d3a2da4 Merge pull request #1936 from jedwards4b/centos7_linux
bc35e32 fix pylint issue
874dc10 Merge pull request #1916 from ESMCI/kdraeder/fix_st_archive
7672387 Merge pull request #1934 from billsacks/document_testids
202e9a0 Merge pull request #1925 from ESMCI/rljacob/add-anl-copyright
b8b9f9e Merge pull request #1902 from ESMCI/sarich/tools/load-balancing-tool
4489a90 Merge pull request #1922 from gold2718/mpiserial_update



Modified files: git diff --name-status [previous_tag]
M	LICENSE.TXT
M	config/acme/machines/config_batch.xml
M	config/acme/machines/template.case.run
M	config/acme/machines/template.case.test
M	config/cesm/config_archive.xml
M	config/cesm/machines/Makefile
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.case.run
M	config/cesm/machines/template.case.test
M	config/config_tests.xml
M	config/xml_schemas/config_batch.xsd
M	doc/source/misc_tools/index.rst
A	doc/source/misc_tools/load-balancing-tool.rst
M	scripts/Tools/case.cmpgen_namelists
M	scripts/create_test
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/tests.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/CIME/wait_for_tests.py
M	scripts/lib/jenkins_generic_job.py
M	scripts/lib/update_acme_tests.py
M	scripts/query_testlists
M	scripts/tests/scripts_regression_tests.py
M	src/externals/mct/mpi-serial/Makefile
M	src/externals/mct/mpi-serial/mpi.c
M	src/externals/mct/mpi-serial/mpif.h
M	src/externals/mct/mpi-serial/tests/ftest.F90
M	src/externals/mct/mpi-serial/tests/ftest_old.F90
M	src/externals/mct/mpi-serial/type.c
M	src/externals/pio1/pio/CMakeLists.txt
M	src/externals/pio1/pio/pionfput_mod.F90.in
M	src/externals/pio1/tests/testpio/perl5lib/ChangeLog
M	src/externals/pio1/tests/testpio/perl5lib/XML/Changes
M	src/externals/pio1/tests/testpio/perl5lib/XML/Lite.pm
M	src/externals/pio1/tests/testpio/perl5lib/XML/Lite/Element.pm
M	src/externals/pio1/tests/testpio/perl5lib/XML/README
D	src/externals/pio1/tests/testpio/perl5lib/XML/man3/XML::Lite.3
D	src/externals/pio1/tests/testpio/perl5lib/XML/man3/XML::Lite::Element.3
A	src/externals/pio1/tests/testpio/perl5lib/XML/man3/XML_Lite.3
A	src/externals/pio1/tests/testpio/perl5lib/XML/man3/XML_Lite_Element.3
M	src/externals/pio1/timing/COPYING
M	src/externals/pio2/.gitignore
M	src/externals/pio2/CMakeLists.txt
M	src/externals/pio2/CTestScript.cmake
A	src/externals/pio2/Makefile.am
A	src/externals/pio2/cmake_config.h.in
A	src/externals/pio2/configure.ac
M	src/externals/pio2/ctest/CTestEnvironment-cgd.cmake
M	src/externals/pio2/ctest/runcdash-cgd-gnu-openmpi.sh
M	src/externals/pio2/doc/source/Decomp.txt
M	src/externals/pio2/doc/source/base.txt
M	src/externals/pio2/doc/source/contributing_code.txt
M	src/externals/pio2/doc/source/mach_walkthrough.txt
D	src/externals/pio2/examples/basic/perl5lib/XML/man3/XML::Lite.3
D	src/externals/pio2/examples/basic/perl5lib/XML/man3/XML::Lite::Element.3
A	src/externals/pio2/examples/basic/perl5lib/XML/man3/XML_Lite.3
A	src/externals/pio2/examples/basic/perl5lib/XML/man3/XML_Lite_Element.3
M	src/externals/pio2/examples/c/CMakeLists.txt
M	src/externals/pio2/scripts/prune_decomps.pl
A	src/externals/pio2/src/Makefile.am
M	src/externals/pio2/src/clib/CMakeLists.txt
A	src/externals/pio2/src/clib/Makefile.am
D	src/externals/pio2/src/clib/config.h.in
D	src/externals/pio2/src/clib/dtypes.h
M	src/externals/pio2/src/clib/pio.h
M	src/externals/pio2/src/clib/pio_darray.c
M	src/externals/pio2/src/clib/pio_darray_int.c
M	src/externals/pio2/src/clib/pio_file.c
M	src/externals/pio2/src/clib/pio_get_nc.c
M	src/externals/pio2/src/clib/pio_getput_int.c
M	src/externals/pio2/src/clib/pio_internal.h
M	src/externals/pio2/src/clib/pio_lists.c
M	src/externals/pio2/src/clib/pio_msg.c
M	src/externals/pio2/src/clib/pio_nc.c
M	src/externals/pio2/src/clib/pio_nc4.c
M	src/externals/pio2/src/clib/pio_put_nc.c
M	src/externals/pio2/src/clib/pio_rearrange.c
M	src/externals/pio2/src/clib/pio_spmd.c
M	src/externals/pio2/src/clib/pio_varm.c
M	src/externals/pio2/src/clib/pioc.c
M	src/externals/pio2/src/clib/pioc_sc.c
M	src/externals/pio2/src/clib/pioc_support.c
M	src/externals/pio2/src/flib/piolib_mod.F90
M	src/externals/pio2/src/gptl/COPYING
A	src/externals/pio2/tests/Makefile.am
M	src/externals/pio2/tests/cunit/CMakeLists.txt
A	src/externals/pio2/tests/cunit/Makefile.am
M	src/externals/pio2/tests/cunit/pio_tests.h
A	src/externals/pio2/tests/cunit/run_tests.sh
M	src/externals/pio2/tests/cunit/test_async_3proc.c
M	src/externals/pio2/tests/cunit/test_async_4proc.c
A	src/externals/pio2/tests/cunit/test_async_manyproc.c
A	src/externals/pio2/tests/cunit/test_async_mpi.c
A	src/externals/pio2/tests/cunit/test_async_multi2.c
A	src/externals/pio2/tests/cunit/test_async_multicomp.c
M	src/externals/pio2/tests/cunit/test_async_simple.c
M	src/externals/pio2/tests/cunit/test_common.c
M	src/externals/pio2/tests/cunit/test_darray.c
M	src/externals/pio2/tests/cunit/test_darray_1d.c
A	src/externals/pio2/tests/cunit/test_darray_2sync.c
M	src/externals/pio2/tests/cunit/test_darray_3d.c
A	src/externals/pio2/tests/cunit/test_darray_async.c
A	src/externals/pio2/tests/cunit/test_darray_async_many.c
A	src/externals/pio2/tests/cunit/test_darray_async_simple.c
A	src/externals/pio2/tests/cunit/test_darray_frame.c
M	src/externals/pio2/tests/cunit/test_darray_multi.c
M	src/externals/pio2/tests/cunit/test_darray_multivar.c
M	src/externals/pio2/tests/cunit/test_darray_multivar2.c
A	src/externals/pio2/tests/cunit/test_darray_multivar3.c
M	src/externals/pio2/tests/cunit/test_decomp_uneven.c
M	src/externals/pio2/tests/cunit/test_decomps.c
M	src/externals/pio2/tests/cunit/test_intercomm2.c
M	src/externals/pio2/tests/cunit/test_iosystem2.c
M	src/externals/pio2/tests/cunit/test_iosystem2_simple.c
M	src/externals/pio2/tests/cunit/test_iosystem2_simple2.c
M	src/externals/pio2/tests/cunit/test_iosystem3.c
M	src/externals/pio2/tests/cunit/test_iosystem3_simple.c
M	src/externals/pio2/tests/cunit/test_iosystem3_simple2.c
M	src/externals/pio2/tests/cunit/test_pioc.c
M	src/externals/pio2/tests/cunit/test_pioc_fill.c
M	src/externals/pio2/tests/cunit/test_pioc_putget.c
M	src/externals/pio2/tests/cunit/test_pioc_unlim.c
M	src/externals/pio2/tests/cunit/test_rearr.c
M	src/externals/pio2/tests/cunit/test_shared.c
M	src/externals/pio2/tests/cunit/test_spmd.c
M	src/externals/pio2/tests/general/CMakeLists.txt
M	src/externals/pio2/tests/general/ncdf_simple_tests.F90.in
M	src/externals/pio2/tests/general/pio_decomp_fillval.F90.in
M	src/externals/pio2/tests/general/pio_decomp_frame_tests.F90.in
M	src/externals/pio2/tests/general/util/pio_tutil.F90
M	tools/load_balancing_tool/README
D	tools/load_balancing_tool/code/cesm_scaling.gplot
D	tools/load_balancing_tool/code/create_dataFile.pl
D	tools/load_balancing_tool/code/f02_peList.txt
D	tools/load_balancing_tool/code/f05_peList.txt
D	tools/load_balancing_tool/code/f09_peList.txt
D	tools/load_balancing_tool/code/f19_peList.txt
D	tools/load_balancing_tool/code/fv_model.mod
D	tools/load_balancing_tool/code/fv_model.run
D	tools/load_balancing_tool/code/fv_second_pass.pl
D	tools/load_balancing_tool/code/get_cesm_times.pl
D	tools/load_balancing_tool/code/load_balance.pl
D	tools/load_balancing_tool/code/merge.py
D	tools/load_balancing_tool/code/model.data
D	tools/load_balancing_tool/code/model.mod
D	tools/load_balancing_tool/code/model.run
D	tools/load_balancing_tool/code/neos.py
D	tools/load_balancing_tool/global_variables.csh
A	tools/load_balancing_tool/layouts.py
A	tools/load_balancing_tool/load_balancing_solve.py
A	tools/load_balancing_tool/load_balancing_submit.py
A	tools/load_balancing_tool/optimize_model.py
D	tools/load_balancing_tool/run_first.csh
D	tools/load_balancing_tool/run_second.csh
A	tools/load_balancing_tool/tests/__init__.py
A	tools/load_balancing_tool/tests/atm_lnd.py
A	tools/load_balancing_tool/tests/example.json
A	tools/load_balancing_tool/tests/load_balancing_test.py
A	tools/load_balancing_tool/tests/test.xml
A	tools/load_balancing_tool/tests/timing/timing_1
A	tools/load_balancing_tool/tests/timing/timing_2
A	tools/load_balancing_tool/tests/timing/timing_3

======================================================================

Originator: Chris Fischer
Date: 9-25-2017
Tag: cime5.4.0-alpha.01
Answer Changes: None
Tests:
Dependencies:

Brief Summary:
    - Update version to cime5.3.0-alpha.01

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master

Modified files: git diff --name-status [previous_tag]

======================================================================

======================================================================

Originator: Chris Fischer
Date: 9-25-2017
Tag: cime5.3.0-alpha.36
Answer Changes: None
Tests:  scripts_regression_tests
Dependencies:

Brief Summary:
    - Big refactor to queue selection.
    - Shorter paths for case2 using system_tests_compare_two.
    - Update atm coupling frequency for high-resolution grids.
    - Add '-framework Accelerate' to LDFLAGS on a mac.
    - Fix E3SM idmap check.
    - Fix pylint issues.
    - ERR test rework.
    - New error trap if invalid "idmap" file is present in seq_maps.rc.
    - Yellowstone tasps per node correction.
    - Added new CAM-SE FVM grids and removed incorrect aliases.
    - Fix generate and compare baseline functions.
    - Add a derived variable NTASKS_PER_INST_COMP where COMP is the component
      name (ATM, LND, etc)
    - Don't check_if_comp_var to return a new vid if it's not a comp var.

User interface changes:
    - jobmin and jobmax gone from config_batch.xml
    - All CAM-SE grid aliases for data ocean models require a mask.


PR summary: git log --oneline --first-parent [previous_tag]..master
6049c79 Merge pull request #1918 from ESMCI/jgfouca/queue_selection_refactor_2
56d71c5 Merge pull request #1919 from billsacks/compare_two_shorter_path
e1b549d Merge pull request #1921 from gold2718/atm_ncpl_mods
f5ac341 Merge pull request #1906 from billsacks/mac_lapack
c15c0ad Merge pull request #1917 from ESMCI/mvertens/fix_acme_idmapcheck
f722595 fix pylint issues
19922e1 Merge pull request #1912 from jedwards4b/err_test_rework
b1d1b9b Merge pull request #1893 from ESMCI/mvertens/trip_invalid_idmap
c330b46 Merge pull request #1911 from jedwards4b/yellowstone_tpn_correction
0136051 Merge pull request #1896 from gold2718/fix_camse_grids
e036093 Merge pull request #1904 from jedwards4b/fix_gen_and_comp
f0522a6 Merge pull request #1900 from jedwards4b/NTASKS_PER_INST_XXX
f5aafff Merge pull request #1901 from ESMCI/jgfouca/xmlquery_minor_fix
2daf8aa Minor pylint fix, make get_queue_specs public


Modified files: git diff --name-status [previous_tag]
M	config/acme/machines/config_batch.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/config_headers.xml
M	config/config_tests.xml
M	config/xml_schemas/config_batch.xsd
M	config/xml_schemas/env_batch.xsd
M	scripts/create_test
M	scripts/lib/CIME/SystemTests/err.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/env_base.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_pes.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/buildlib.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_clone.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/namelist.py
M	scripts/lib/CIME/nmlgen.py
M	scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
M	scripts/lib/CIME/tests/case_fake.py
M	scripts/lib/CIME/utils.py
M	scripts/tests/scripts_regression_tests.py
M	src/build_scripts/buildlib.csm_share
M	src/drivers/mct/cime_config/buildnml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml

======================================================================

======================================================================

Originator: Chris Fischer
Date: 9-19-2017
Tag: cime5.3.0-alpha.35
Answer Changes: None
Tests: scripts_regression_tests.py, PEM_Ln9.f19_g16_rx1.A.yellowstone_intel
Dependencies:

Brief Summary:
    - Test fixes.
    - Can test single-submit on chama in addition to skybridge.
    - Fix single submit option to create_test.
    - Rename PES_PER_NODE to MAX_MPITASKS_PER_NODE.
    - New git pelayout doc.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
e1e5e79 Merge pull request #1895 from jedwards4b/test_fixes
a3349ed Merge pull request #1899 from ESMCI/jgfouca/fix_single_submit
40e4b7b Merge pull request #1898 from ESMCI/jgfouca/fix_single_submit
5ba192b Merge pull request #1891 from jedwards4b/rename_pes_per_node
eb59169 Merge pull request #1888 from ESMCI/mvertens/new_pelayout_doc

Modified files: git diff --name-status [previous_tag]
M	config/acme/allactive/config_pesall.xml
M	config/acme/machines/config_batch.xml
M	config/acme/machines/config_machines.xml
M	config/acme/machines/config_pio.xml
M	config/acme/machines/userdefined_laptop_template/config_machines.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/config_pio.xml
M	config/cesm/machines/userdefined_laptop_template/config_machines.xml
M	config/config_headers.xml
M	config/config_tests.xml
M	config/xml_schemas/config_machines.xsd
M	config/xml_schemas/config_machines_template.xml
M	config/xml_schemas/config_pes.xsd
M	doc/source/users_guide/customizing-a-case.rst
M	doc/source/users_guide/porting-cime.rst
M	scripts/create_test
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/XML/env_mach_pes.py
M	scripts/lib/CIME/XML/machines.py
M	scripts/lib/CIME/aprun.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/get_timing.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/query_config
M	scripts/tests/scripts_regression_tests.py
M	src/components/data_comps/docn/docn_shr_mod.F90
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/main/cime_comp_mod.F90

======================================================================

======================================================================

Originator: Chris Fischer
Date: 9-13-2017
Tag: cime5.3.0-alpha.34
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:

Brief Summary:
    - Fix T31_g37 grid match in config_grids.
    - Add a timeout option to wait_for_tests.
    - Minor update to sphinx documentation.
    - Allow queue selection by node count instead of task count.
    - Get chama working (able to run scripts_regression_tests).
    - Case clone move fix.
    - Move case clone to its own file.
    - Error check compset name.
    - Improve error check for non-python sub processes.
    - Add new user-mods option to create_clone.
    - Fix 2-to-3 conversion errors in cime_bisect.
    - Implementation of multiple drivers.
    - Make sure file exists.
    - Get log file from logdir instead of rundir.
    - Add more unit tests of system_tests_compare_two, fix multisubmit bug.
    - Merge new erp test into new restart_tests abstract class.

User interface changes:
    - New --timeout flag for wait_for_tests
    - New ways to select queue in config_batch.xml
    - New argument to create_clone.

PR summary: git log --oneline --first-parent [previous_tag]..master
7efc1f5 Merge pull request #1886 from ESMCI/fischer/T41_g37_fix
6a6b5e8 Merge pull request #1884 from ESMCI/jgfouca/add_timeout_for_wait_for_tests
c848b17 Merge pull request #1883 from bertinia/master
766899e Merge pull request #1878 from ESMCI/jgfouca/queue_selection_based_on_nodes
d89064b Merge pull request #1881 from ESMCI/jgfouca/get_chama_working
b1ce54a Merge pull request #1880 from jedwards4b/case_clone
947e533 Merge pull request #1879 from jedwards4b/case_clone
2b1e151 Merge pull request #1873 from jedwards4b/error_check_compset_name
a72e5a0 Merge pull request #1875 from jedwards4b/improve_nonpy_subproc_handling
0b3dfca Merge pull request #1866 from ESMCI/mvertens/clone_with_usermods
cbe26ae Merge pull request #1876 from ESMCI/jgfouca/fix_2_to_3_conversion_errors_in_cime_bisect
c7efee1 Implementation of multiple drivers
4d9a8d7 Merge pull request #1868 from jedwards4b/is_python_a_file
7f34aa0 Merge pull request #1863 from jedwards4b/log_file_generate
230f7dd Merge pull request #1858 from billsacks/comparetwo_multisubmit_fix
14d138d Merge pull request #1857 from jedwards4b/erp_to_restart_tests


Modified files: git diff --name-status [previous_tag]
M	config/acme/machines/config_batch.xml
M	config/acme/machines/config_machines.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_batch.xml
M	config/config_tests.xml
M	config/xml_schemas/config_batch.xsd
M	config/xml_schemas/env_batch.xsd
M	doc/Makefile
D	doc/source/glossary.rst
M	doc/source/index.rst
M	doc/source/users_guide/cloning-a-case.rst
M	doc/source/users_guide/index.rst
M	doc/source/users_guide/multi-instance.rst
M	doc/source/xml_files/cesm.rst
D	scripts/Tools/archive_metadata.sh
M	scripts/Tools/check_case
M	scripts/Tools/check_lockedfiles
M	scripts/Tools/cime_bisect
M	scripts/Tools/wait_for_tests
M	scripts/create_clone
M	scripts/create_newcase
M	scripts/lib/CIME/SystemTests/erp.py
A	scripts/lib/CIME/SystemTests/mcc.py
M	scripts/lib/CIME/SystemTests/pre.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/entry_id.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_pes.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/buildnml.py
M	scripts/lib/CIME/case.py
A	scripts/lib/CIME/case_clone.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/case_submit.py
M	scripts/lib/CIME/check_lockedfiles.py
M	scripts/lib/CIME/get_timing.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/preview_namelists.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
M	scripts/lib/CIME/tests/test_user_mod_support.py
M	scripts/lib/CIME/user_mod_support.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/CIME/wait_for_tests.py
M	scripts/lib/update_acme_tests.py
M	scripts/tests/scripts_regression_tests.py
A	scripts/tests/user_mods_test3/shell_commands
M	src/build_scripts/buildlib.csm_share
M	src/components/data_comps/desp/cime_config/buildnml
M	src/components/data_comps/desp/desp_comp_mod.F90
M	src/components/xcpl_comps/xshare/dead_mod.F90
M	src/drivers/mct/cime_config/buildnml
M	src/drivers/mct/cime_config/config_archive.xml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/cime_config/testdefs/testlist_drv.xml
M	src/drivers/mct/main/cime_comp_mod.F90
M	src/drivers/mct/main/seq_hist_mod.F90
M	src/drivers/mct/main/seq_rest_mod.F90
M	src/drivers/mct/shr/seq_comm_mct.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90
M	src/drivers/mct/unit_test/utils/mct_wrapper_mod.F90
M	src/externals/mct/mct/m_MCTWorld.F90

======================================================================

======================================================================

Originator: Chris Fischer
Date: 9-01-2017
Tag: cime5.3.0-alpha.33
Answer Changes: None
Tests:  scripts_regression_tests.py N_TestUnitTest
        cime_developer using pio1 and latest pio2 develop code
Dependencies:

Brief Summary:
    - Rewrite ERP with SystemTestsCompareTwo.
    - Convert the ERR and ERRI test to the compare2 framework.
    - Get PFUnit working on melvin.
    - Do not print message about leaving case directory if the directory was
      never created.
    - Allow user to adjust ulimits.
    - Fix runtime issues with latest pio2 development.
    - Preserve test order in test_scheduler.
    - Update README
    - Documentation tool updates and st_archive fix.
    - Make the unsupported warning from create_newcase more prominent in the
      output.
    - Add irt test.
    - Move inputdata location on pleiades.
    - Fix issue with clone to new user.
    - Fix for cime_output_root doesnt exist.
    - Compare two test case names match.
    - Fix Cmake path in fortran unit tests.
    - Fix typo in config_machines.xml.
    - Fix race condition for updated test_schedule use_existing test.
    - Homebrew generic mac port.
    - Add valid_lists for some of the *_OPTION entries that lacked them.
    - Move from cime/src/externals/CMake to cime/src/CMake.
    - Add message at end of successful build.
    - Upgrade build system.
    - Fix issue with update and alternate compiler.
    - Fix use-existing feature for create_test.


User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
c3459de Merge pull request #1855 from billsacks/erp2systemcomparetwo_refactor
a3bcaa0 Merge pull request #1852 from jedwards4b/err_2_compare_two
751fd7a Merge pull request #1844 from ESMCI/jgfouca/get_pfunit_working_on_melvin
0b8afd9 Merge pull request #1850 from jedwards4b/fix_error_message
dd04e87 Merge pull request #1847 from jedwards4b/user_resource_setting
65ac258 Merge pull request #1842 from jedwards4b/pio2_fix
33113cb Merge pull request #1843 from ESMCI/jgfouca/create_test_preserve_test_order
591c51b Update README
8b2c8a1 Merge pull request #1838 from bertinia/master
fef051e Merge pull request #1840 from jedwards4b/enhance_warning
fab7ccd Merge pull request #1837 from jedwards4b/add_irt_test
994d884 Merge pull request #1836 from fvitt/pleiades_inputdata
8545d9c Merge pull request #1835 from jedwards4b/clone_new_user_fix
3523743 fix for cime_output_root doesnt exist
00ac08a Merge pull request #1832 from jedwards4b/match_names_in_cases
7be7fb3 fix Cmake path in fortran unit tests
3dcdcb2 fix typo in config_machines.xml
730ed8b Merge pull request #1829 from ESMCI/jgfouca/fixes_for_test_scheduler_tests
9ec6020 Merge pull request #1820 from jedwards4b/homebrew_port
c4efac7 Merge pull request #1831 from ESMCI/jgfouca/add_valid_lists_for_options
33b8378 Merge pull request #1828 from ESMCI/jgfouca/move_cmake_stuff
02a9486 Merge pull request #1826 from billsacks/successful_build
2f9eacb Merge pull request #1823 from ESMCI/jgfouca/build_system_upgrades
8db85c7 fix issue with update and alternate compiler
356501d Merge pull request #1822 from ESMCI/jgfouca/fix_use_existing


Modified files: git diff --name-status [previous_tag]
M	config/acme/config_archive.xml
M	config/acme/machines/Makefile
M	config/acme/machines/config_compilers.xml
M	config/acme/machines/config_machines.xml
M	config/cesm/config_archive.xml
M	config/cesm/config_files.xml
M	config/cesm/machines/Makefile
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/config_tests.xml
M	config/xml_schemas/config_machines.xsd
M	config/xml_schemas/config_machines_template.xml
M	config/xml_schemas/env_mach_specific.xsd
M	doc/README
A	doc/source/glossary.rst
M	doc/source/index.rst
M	doc/source/users_guide/index.rst
M	doc/source/what_cime/index.rst
M	scripts/Tools/case.build
M	scripts/create_test
M	scripts/fortran_unit_testing/run_tests.py
M	scripts/lib/CIME/BuildTools/configure.py
M	scripts/lib/CIME/BuildTools/macrowriterbase.py
M	scripts/lib/CIME/SystemTests/erp.py
M	scripts/lib/CIME/SystemTests/err.py
M	scripts/lib/CIME/SystemTests/erri.py
A	scripts/lib/CIME/SystemTests/irt.py
A	scripts/lib/CIME/SystemTests/restart_tests.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/compsets.py
M	scripts/lib/CIME/XML/env_archive.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/grids.py
M	scripts/lib/CIME/XML/machines.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
M	scripts/lib/CIME/tests/case_fake.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/update_acme_tests.py
M	scripts/query_config
M	scripts/tests/scripts_regression_tests.py
A	src/CMake/.gitignore
A	src/CMake/CESM_utils.cmake
A	src/CMake/CIME_initial_setup.cmake
A	src/CMake/CIME_utils.cmake
A	src/CMake/ChangeLog
A	src/CMake/Compilers.cmake
A	src/CMake/FindpFUnit.cmake
A	src/CMake/LICENSE
A	src/CMake/README.md
A	src/CMake/Sourcelist_utils.cmake
A	src/CMake/TryCSizeOf.f90
A	src/CMake/TryMPIIO.f90
A	src/CMake/TryMPIMod.f90
A	src/CMake/TryMPISERIAL.f90
A	src/CMake/TryPnetcdf_inc.f90
A	src/CMake/TryPnetcdf_mod.f90
A	src/CMake/genf90_utils.cmake
A	src/CMake/mpiexec.cmake
A	src/CMake/pFUnit_utils.cmake
M	src/components/data_comps/datm/cime_config/config_archive.xml
M	src/components/data_comps/desp/esp_utils.F90
M	src/components/data_comps/dice/cime_config/config_archive.xml
M	src/components/data_comps/dlnd/cime_config/config_archive.xml
M	src/components/data_comps/docn/cime_config/config_archive.xml
M	src/components/data_comps/drof/cime_config/config_archive.xml
M	src/components/data_comps/dwav/cime_config/config_archive.xml
M	src/drivers/mct/cime_config/config_archive.xml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_acme.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
D	src/drivers/mct/doc/bookinfo.xml
D	src/drivers/mct/doc/chap1.xml
D	src/drivers/mct/doc/chap2.xml
D	src/drivers/mct/doc/figx1.jpg
D	src/drivers/mct/doc/namelist.xml
D	src/drivers/mct/doc/rundocbook.csh
D	src/drivers/mct/doc/stylesheet.dsl
D	src/drivers/mct/doc/ug.xml
D	src/externals/CMake/.gitignore
D	src/externals/CMake/CESM_utils.cmake
D	src/externals/CMake/CIME_initial_setup.cmake
D	src/externals/CMake/CIME_utils.cmake
D	src/externals/CMake/ChangeLog
D	src/externals/CMake/Compilers.cmake
D	src/externals/CMake/FindpFUnit.cmake
D	src/externals/CMake/LICENSE
D	src/externals/CMake/README.md
D	src/externals/CMake/Sourcelist_utils.cmake
D	src/externals/CMake/TryCSizeOf.f90
D	src/externals/CMake/TryMPIIO.f90
D	src/externals/CMake/TryMPIMod.f90
D	src/externals/CMake/TryMPISERIAL.f90
D	src/externals/CMake/TryPnetcdf_inc.f90
D	src/externals/CMake/TryPnetcdf_mod.f90
D	src/externals/CMake/genf90_utils.cmake
D	src/externals/CMake/mpiexec.cmake
D	src/externals/CMake/pFUnit_utils.cmake
M	src/share/util/shr_pcdf_mod.F90
M	tools/cprnc/CMakeLists.txt

======================================================================

======================================================================

Originator: Chris Fischer
Date: 8-16-2017
Tag: cime5.3.0-alpha.32
Answer Changes: None
Tests: scripts_regression_tests.py, f19_f19 and f09_f09 ADESP tests on hobart
       cesm2 prealpha tests on cheyenne
       scripts_regression_tests.py --compiler gnu --mpilib openmpi on cheyenne
Dependencies:

Brief Summary:
    - Remove untested/unused scripts in Tools directory.
    - Remove mask specification for test using DOCN%SOMAQP.
    - Improve error messages from xmlchange.
    - seq_comm_mct code cleanup.
    - Refactor how spare nodes get computed.
    - Fix SEQ test on skybridge.
    - Get melvin scripts_regression_tests working again.
    - Merge configuration changes from ACME to CIME.
    - Allow running infnan unit tests even in DEBUG mode.
    - Add -Og -fbacktrace to gnu debug flags.
    - Allow --compiler and --mpilib
    - Add a --compiler and --mpilib options to scripts_regression_tests.py.

User interface changes:
    - Yes, new case variables controlling spare nodes
    - Yes scripts_regression_tests.py now has --compiler and --mpilibs option.

PR summary: git log --oneline --first-parent [previous_tag]..master
1be3c17 Merge pull request #1751 from jedwards4b/tools_cleanup
30a17eb Merge pull request #1819 from ESMCI/fischer/ADESP_test_fix
37909bd Merge pull request #1818 from ESMCI/jgfouca/xmlchange_improve_error
8e9a554 Merge pull request #1805 from jedwards4b/seq_comm_mct_refactor
aa917ee Merge pull request #1816 from ESMCI/jgfouca/refactor_spare_nodes
b5ba1e8 Merge pull request #1817 from ESMCI/jgfouca/fix_seq_on_skybridge
bc0e1f1 Merge pull request #1815 from ESMCI/jgfouca/get_melvin_working_again
8032624 Merge pull request #1812 from ESMCI/mfdeakin-sandia/configuration_changes
f814ef3 Merge pull request #1810 from billsacks/infnan_unit_test
d3bcd58 Merge pull request #1808 from billsacks/gnu_debug_flags
7f91804 Merge pull request #1804 from jedwards4b/allow_new_opts_ctest
ab8f58b Merge pull request #1789 from jedwards4b/srt_compiler_option


Modified files: git diff --name-status [previous_tag]
M       config/acme/machines/config_machines.xml
M       config/cesm/machines/config_compilers.xml
M       config/config_tests.xml
M       config/xml_schemas/config_machines_template.xml
M       config/xml_schemas/env_mach_pes.xsd
M       config/xml_schemas/env_mach_specific.xsd
D       scripts/Tools/check_exactrestart.pl
D       scripts/Tools/create_train
D       scripts/Tools/load.awk
D       scripts/Tools/mdiag_reduce.csh
D       scripts/Tools/mdiag_reduce.pl
M       scripts/Tools/xmlchange
M       scripts/lib/CIME/SystemTests/seq.py
M       scripts/lib/CIME/XML/env_mach_pes.py
M       scripts/lib/CIME/XML/machines.py
M       scripts/lib/CIME/case_setup.py
M       scripts/tests/CMakeLists.txt
M       scripts/tests/CTestConfig.cmake
M       scripts/tests/scripts_regression_tests.py
M       src/drivers/mct/cime_config/config_component.xml
M       src/drivers/mct/cime_config/namelist_definition_drv.xml
M       src/drivers/mct/cime_config/testdefs/testlist_drv.xml
M       src/drivers/mct/main/cime_comp_mod.F90
M       src/drivers/mct/main/component_mod.F90
M       src/drivers/mct/shr/seq_comm_mct.F90
M       src/share/test/unit/shr_infnan_test/CMakeLists.txt
M       src/share/test/unit/shr_infnan_test/test_infnan.F90


======================================================================

Originator: Chris Fischer
Date: 8-08-2017
Tag: cime5.3.0-alpha.31
Answer Changes: [None, Round Off, Climate Changing]
Tests: spcam test, scripts_regression_tests.py
       ERP.f09_f09_mg17.F2000_DEV
Dependencies:

Brief Summary:
    - Updates for cheyenne.
    - Broadcast comp_layout value from master after namelist read.
    - Update CONTINUE_RUN before case.setup is run in erp test.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
c9c1fb9 Merge pull request #1800 from jedwards4b/cheyenne_updates
dce137b Merge pull request #1799 from jedwards4b/broadcast_layout
7b845d2 Merge pull request #1797 from jedwards4b/hybrid_erp_test_fix

Modified files: git diff --name-status [previous_tag]
M       config/cesm/machines/config_compilers.xml
M       config/cesm/machines/config_machines.xml
M       scripts/lib/CIME/SystemTests/erp.py
M       scripts/lib/CIME/check_input_data.py
M       src/drivers/mct/shr/seq_comm_mct.F90


======================================================================
Originator: Chris Fischer
Date: 8-07-2017
Tag: cime5.3.0-alpha.30
Answer Changes: None
Tests: scripts_regression_tests.pr
       SMS_D_Ln9.f19_g16_rx1.A.hobart_intel
       PFS.f19_g17.B1850.cheyenne_intel
       I compset
       PET_Ln9.f09_f09_mg17.F2000_DEV.cheyenne_intel.cam-outfrq9s
       ERS.f09_g17.AIAF.cheyenne_intel
       ERS.f09_g17.B1850Ws.cheyenne_intel.allactive-defaultio
       ERS_D.T62_t12.DTEST.cheyenne_intel.cice-default
       WACCMX smoke tests on pleiades
Dependencies:

Brief Summary:
    - Stage the refcase before calling buildnml.
    - Add more default logging to desp.
    - Revert to netcdf 4.3.3.1 on yellowstone.
    - Fix to get PRE test working on ADESP_TEST on Cheyenne.
    - Update cori-knl batch and fix xsd error.
    - Updates for NAS pleiades systems.
    - Fix long line.
    - Refactored datamodels.
    - Documentation updates.
    - Update IO_format for data models.
    - Don't use Machines object to get DIN_LOC_ROOT.
    - Fix uninitialized variable.
    - Replace cdf64 logical with PIO_NETCDF_FORMAT character variable.
    - Fix documentation error.
    - Machine and grid updates.
    - Check flds for nan.
    - Facilitate expected error unit tests.
    - Revert the netcdf update on yellowstone for gnu and pgi compilers.
    - Remove misleading text from the dependency string in config_batch.xml.
    - Add new case.qstatus script.
    - Removing extraneous whitespace from the mct driver code.
    - Fix issues with ensemble.sh.
    - Yellowstone update netcdf module for compatibility with cdf5
    - Fix print statement in find_circular_dependecy.py.
    - Documentation updates.
    - More documentation updates.
    - Implement NCR with SystemTestsCompareTwo.
    - Fix pylint issue
    - Clean up caseroot directory upon failed creation.
    - Make xmlquery, xmlchange work with entry_id variables in the
      env_mach_specific.xml file.
    - Need to add description fields for new datasets.
    - get_tasks_per_node should never return 0.
    - Start a section on adding new components to cime.
    - Cleanup botched rebase for config_batch.xml.
    - Couple trivial changes to satisfy pylint.
    - Add Support for Email Options.
    - System tests compare two stage two.
    - Add --pesfile option to create_test.
    - Fix melvin.
    - Update netcdf version for ACME.
    - fix of test IME.tests.SystemTests.test_system_tests_compare_two.TestSystemTestsCompareTwo
    - Change SIAF compset name in dice to IAF to be consistent with other components.
    - Fix PRE test with the ADESP and ADESP_TEST compsets
    - datm updates for clm.
    - Build scripts in source mods.
    - Update for hobart out-of-the-box support
    - Eleminate --user-compset, allow longname in tests.
    - Fix error in path to env_mach_specific.xml file.
    - Apply OCN_NCPL setting to any version of CLM.
    - Fix of PRE test failing in cdash.
    - Avoids an error if the forcing description is missing from
      config_compsets_cesm.xml.
    - lcdf4 flag does apply to pnetcdf.
    - Fix an issue with pio_numtasks setting and make sure that external
      scripts are syncd with case.
    - Remove cesm refs from cime driver.
    - Description field error check of user compsets.
    - Introduce version 3.0 schema for entry_id files
    - Fix bug in case.run where arg skip-preview-namelist is out of sequence.

User interface changes:
    - New case.qstatus tool.
    - Autodeletion of broken case dirs.
    - Add --mail-user and --mail-type to case.submit.
    - Add --pesfile option to create_test.
    - Remove --user-compset from create_newcase, allow compset longname in
      testname argument to create_test.

PR summary: git log --oneline --first-parent [previous_tag]..master
6db1569 Merge pull request #1795 from jedwards4b/stage_refcase
2815ea6 Merge pull request #1790 from gold2718/PreFix
c465923 Merge pull request #1791 from jedwards4b/yellowstone_netcdf_revert
c4d50cc Merge pull request #1787 from gold2718/PreFix
b65bfd6 Merge pull request #1784 from jedwards4b/misc_fixes
05e576d Merge pull request #1783 from fvitt/pleiades_cime5.3.0-alpha.29
397a62e Merge pull request #1786 from jedwards4b/fix_long_line
38a88f1 Merge pull request #1767 from ESMCI/mvertens/refactored_datamodels
b4c5cf7 Merge pull request #1782 from ESMCI/bertinia/doc
a650e47 Merge pull request #1778 from jedwards4b/update_dmodel_ioformat
999abc1 Merge pull request #1776 from jedwards4b/no_machines_in_check_input_data
d5f0db6 Merge pull request #1780 from jedwards4b/fix_uninitialized_var
919aee3 Merge pull request #1777 from jedwards4b/pio_netcdf_format
2f9fa03 Fix documentation error
32f9801 Merge pull request #1775 from ESMCI/fischer/machine_grid_updates
9217c9b Merge pull request #1765 from jedwards4b/check_flds_for_nan
8c61ea2 Merge pull request #1771 from billsacks/unittest_throw_exception
25d82e6 Merge pull request #1772 from jedwards4b/revert_netcdf_for_secondary_compilers_yellowstone
7a671be Merge pull request #1768 from ESMCI/mfdeakin-sandia/config_batch/remove_misleading_text
df44c12 Merge pull request #1758 from ESMCI/jgfouca/case_qstatus
bb1aec9 Merge pull request #1766 from jedwards4b/remove_whitespace_mct_driver
b4419ef Merge pull request #1761 from allibco/master
84aafd5 Merge pull request #1759 from jedwards4b/yellowstone_updates
bdad4d9 Fixed print statement in find_circular_dependecy.py
bb9c6f0 Merge pull request #1756 from ESMCI/bertinia/doc
2e46704 Merge pull request #1752 from ESMCI/bertinia/doc
e1db2f1 Merge pull request #1744 from ESMCI/mfdeakin-sandia/systemtestscomparetwo/ncr
89fbd14 fix pylint issue
154db7b Merge pull request #1750 from ESMCI/jgfouca/cleanup_caseroot_upon_failed_creation
ffd327a Merge pull request #1748 from jedwards4b/run_exe_xmlquery
37a6807 Merge pull request #1745 from jedwards4b/clm_datm_changesv3
8652190 Merge pull request #1746 from ESMCI/jgfouca/fix_small_machines
808774d Merge pull request #1742 from jedwards4b/adding_components
1afee01 Cleanup botched rebase for config_batch.xml
550ccc9 Couple trivial changes to satisfy pylint
7a2739f Merge pull request #1719 from ESMCI/erichlf/batch/email
16070a4 Merge pull request #1738 from jedwards4b/system_tests_compare_two_stage_two
469156f Merge pull request #1735 from jedwards4b/add_pesfile_to_create_test
eceeaeb Merge pull request #1740 from ESMCI/jgfouca/update_netcdf_for_sandia_machines
8c4828b Merge pull request #1739 from ESMCI/jgfouca/update_netcdf_for_sandia_machines
d5a9d61 hot fix of test IME.tests.SystemTests.test_system_tests_compare_two.TestSystemTestsCompareTwo
d5b7c48 Merge pull request #1736 from jedwards4b/dice_compset_fix
fecd52e Merge pull request #1734 from gold2718/PreFix
1fd77e8 Merge pull request #1728 from ESMCI/sacks/updates_for_clm_v2
69f0128 Merge pull request #1730 from jedwards4b/build_scripts_in_SourceMods
29d87f0 Merge pull request #1729 from bertinia/master
095e84c Merge pull request #1721 from jedwards4b/remove_user_compset_arg
a26d8b1 Merge pull request #1725 from jedwards4b/env_mach_specific_path_correction
3d40552 Merge pull request #1688 from billsacks/ocn_ncpl_clm5
e9c2f45 hot fix of PRE test failing in cdash
a8d0993 Merge pull request #1716 from jedwards4b/missing_forcing_fix
a170957 Merge pull request #1705 from jedwards4b/cpl_hist_64bit_mode
2732eda Merge pull request #1712 from jedwards4b/pio_namelist_and_externals_fix
02608e4 Merge pull request #1708 from ESMCI/rljacob/drv/de-cesmify
fb3a6c5 Merge pull request #1697 from jedwards4b/description_field
4b116ba Merge pull request #1703 from ESMCI/sarich/scripts/fix-skip-preview-namelist-parsing-order


Modified files: git diff --name-status [previous_tag]
M	CMakeLists.txt
M	config/acme/config_files.xml
M	config/acme/machines/Makefile
M	config/acme/machines/config_batch.xml
M	config/acme/machines/config_batch.xsd
M	config/acme/machines/config_machines.xml
M	config/acme/machines/template.case.run
M	config/cesm/config_files.xml
M	config/cesm/config_grids.xml
D	config/cesm/machines/Depends.goldbach
M	config/cesm/machines/Makefile
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/config_tests.xml
M	config/xml_schemas/config_batch.xsd
M	config/xml_schemas/entry_id_base.xsd
A	config/xml_schemas/entry_id_base_version3.xsd
A	config/xml_schemas/entry_id_version3.xsd
M	config/xml_schemas/env_mach_specific.xsd
A	doc/.gitignore
M	doc/Makefile
A	doc/README
A	doc/source/README
A	doc/source/Tools_user/index.rst.template
A	doc/source/build_cpl/adding-components.rst
M	doc/source/build_cpl/index.rst
M	doc/source/build_cpl/introduction.rst
M	doc/source/conf.py
D	doc/source/conf.py_old
M	doc/source/driver_cpl/time-management.rst
A	doc/source/glossary/index.rst
M	doc/source/index.rst
M	doc/source/users_guide/adding-cases.rst
M	doc/source/users_guide/create-a-case.rst
M	doc/source/users_guide/index.rst
M	doc/source/users_guide/introduction-and-overview.rst
M	doc/source/users_guide/running-a-case.rst
M	doc/source/what_cime/index.rst
A	doc/source/xml_files/acme.rst
A	doc/source/xml_files/atmosphere.rst
A	doc/source/xml_files/cesm.rst
A	doc/source/xml_files/common.rst
A	doc/source/xml_files/components.rst
A	doc/source/xml_files/drivers.rst
A	doc/source/xml_files/esp.rst
A	doc/source/xml_files/index.rst
A	doc/source/xml_files/land.rst
A	doc/source/xml_files/landice.rst
A	doc/source/xml_files/ocean.rst
A	doc/source/xml_files/river.rst
A	doc/source/xml_files/seaice.rst
A	doc/source/xml_files/wave.rst
A	doc/tools_autodoc.cfg
A	doc/tools_autodoc.py
M	scripts/Tools/case.build
A	scripts/Tools/case.qstatus
M	scripts/Tools/case.submit
M	scripts/Tools/check_input_data
M	scripts/Tools/normalize_cases
M	scripts/Tools/xmlquery
M	scripts/create_newcase
M	scripts/create_test
M	scripts/lib/CIME/SystemTests/dae.py
M	scripts/lib/CIME/SystemTests/ncr.py
M	scripts/lib/CIME/SystemTests/pre.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/component.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_pes.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/env_run.py
M	scripts/lib/CIME/XML/files.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/buildlib.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_submit.py
M	scripts/lib/CIME/check_input_data.py
M	scripts/lib/CIME/preview_namelists.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
M	scripts/lib/CIME/tests/case_fake.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/update_acme_tests.py
M	scripts/manage_pes
M	scripts/query_config
M	scripts/tests/scripts_regression_tests.py
M	src/build_scripts/buildlib.csm_share
A	src/build_scripts/buildlib.internal_components
M	src/build_scripts/buildlib.mct
M	src/build_scripts/buildlib.mpi-serial
D	src/components/data_comps/datm/atm_comp_mct.F90
T	src/components/data_comps/datm/cime_config/buildlib
M	src/components/data_comps/datm/cime_config/config_component.xml
M	src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M	src/components/data_comps/datm/datm_comp_mod.F90
M	src/components/data_comps/datm/datm_shr_mod.F90
A	src/components/data_comps/datm/mct/atm_comp_mct.F90
T	src/components/data_comps/desp/cime_config/buildlib
M	src/components/data_comps/desp/cime_config/buildnml
M	src/components/data_comps/desp/cime_config/config_component.xml
M	src/components/data_comps/desp/cime_config/namelist_definition_desp.xml
M	src/components/data_comps/desp/desp_comp_mod.F90
D	src/components/data_comps/desp/esp_comp_mct.F90
M	src/components/data_comps/desp/esp_utils.F90
A	src/components/data_comps/desp/mct/esp_comp_mct.F90
T	src/components/data_comps/dice/cime_config/buildlib
M	src/components/data_comps/dice/cime_config/config_component.xml
M	src/components/data_comps/dice/dice_comp_mod.F90
A	src/components/data_comps/dice/dice_shr_mod.F90
D	src/components/data_comps/dice/ice_comp_mct.F90
A	src/components/data_comps/dice/mct/ice_comp_mct.F90
T	src/components/data_comps/dlnd/cime_config/buildlib
M	src/components/data_comps/dlnd/cime_config/config_component.xml
M	src/components/data_comps/dlnd/cime_config/namelist_definition_dlnd.xml
M	src/components/data_comps/dlnd/dlnd_comp_mod.F90
A	src/components/data_comps/dlnd/dlnd_shr_mod.F90
D	src/components/data_comps/dlnd/lnd_comp_mct.F90
A	src/components/data_comps/dlnd/mct/lnd_comp_mct.F90
T	src/components/data_comps/docn/cime_config/buildlib
M	src/components/data_comps/docn/cime_config/config_component.xml
M	src/components/data_comps/docn/docn_comp_mod.F90
A	src/components/data_comps/docn/docn_shr_mod.F90
A	src/components/data_comps/docn/mct/ocn_comp_mct.F90
D	src/components/data_comps/docn/ocn_comp_mct.F90
T	src/components/data_comps/drof/cime_config/buildlib
M	src/components/data_comps/drof/cime_config/config_component.xml
M	src/components/data_comps/drof/drof_comp_mod.F90
A	src/components/data_comps/drof/drof_shr_mod.F90
A	src/components/data_comps/drof/mct/rof_comp_mct.F90
D	src/components/data_comps/drof/rof_comp_mct.F90
A	src/components/data_comps/dshare/shr_dmodel_mod.F90
A	src/components/data_comps/dshare/shr_strdata_mod.F90
A	src/components/data_comps/dshare/shr_stream_mod.F90
A	src/components/data_comps/dshare/shr_tInterp_mod.F90
T	src/components/data_comps/dwav/cime_config/buildlib
M	src/components/data_comps/dwav/cime_config/config_component.xml
M	src/components/data_comps/dwav/dwav_comp_mod.F90
A	src/components/data_comps/dwav/dwav_shr_mod.F90
A	src/components/data_comps/dwav/mct/wav_comp_mct.F90
D	src/components/data_comps/dwav/wav_comp_mct.F90
T	src/components/stub_comps/satm/cime_config/buildlib
M	src/components/stub_comps/satm/cime_config/buildnml
M	src/components/stub_comps/satm/cime_config/config_component.xml
T	src/components/stub_comps/sesp/cime_config/buildlib
M	src/components/stub_comps/sesp/cime_config/buildnml
M	src/components/stub_comps/sesp/cime_config/config_component.xml
T	src/components/stub_comps/sglc/cime_config/buildlib
M	src/components/stub_comps/sglc/cime_config/buildnml
M	src/components/stub_comps/sglc/cime_config/config_component.xml
T	src/components/stub_comps/sice/cime_config/buildlib
M	src/components/stub_comps/sice/cime_config/buildnml
M	src/components/stub_comps/sice/cime_config/config_component.xml
T	src/components/stub_comps/slnd/cime_config/buildlib
M	src/components/stub_comps/slnd/cime_config/buildnml
M	src/components/stub_comps/slnd/cime_config/config_component.xml
T	src/components/stub_comps/socn/cime_config/buildlib
M	src/components/stub_comps/socn/cime_config/buildnml
T	src/components/stub_comps/srof/cime_config/buildlib
M	src/components/stub_comps/srof/cime_config/buildnml
T	src/components/stub_comps/swav/cime_config/buildlib
M	src/components/stub_comps/swav/cime_config/buildnml
M	src/components/stub_comps/swav/cime_config/config_component.xml
T	src/components/xcpl_comps/xatm/cime_config/buildlib
M	src/components/xcpl_comps/xatm/cime_config/config_component.xml
T	src/components/xcpl_comps/xglc/cime_config/buildlib
M	src/components/xcpl_comps/xglc/cime_config/config_component.xml
T	src/components/xcpl_comps/xice/cime_config/buildlib
M	src/components/xcpl_comps/xice/cime_config/config_component.xml
T	src/components/xcpl_comps/xlnd/cime_config/buildlib
M	src/components/xcpl_comps/xlnd/cime_config/config_component.xml
T	src/components/xcpl_comps/xocn/cime_config/buildlib
M	src/components/xcpl_comps/xocn/cime_config/config_component.xml
T	src/components/xcpl_comps/xrof/cime_config/buildlib
M	src/components/xcpl_comps/xrof/cime_config/config_component.xml
T	src/components/xcpl_comps/xwav/cime_config/buildlib
M	src/components/xcpl_comps/xwav/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_acme.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/drivers/mct/cime_config/config_compsets.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/cime_config/namelist_definition_modelio.xml
M	src/drivers/mct/cime_config/testdefs/testlist_drv.xml
A	src/drivers/mct/cime_config/testdefs/testmods_dirs/drv/som/shell_commands
M	src/drivers/mct/main/CMakeLists.txt
D	src/drivers/mct/main/cesm_comp_mod.F90
D	src/drivers/mct/main/cesm_driver.F90
A	src/drivers/mct/main/cime_comp_mod.F90
A	src/drivers/mct/main/cime_driver.F90
M	src/drivers/mct/main/component_mod.F90
M	src/drivers/mct/main/component_type_mod.F90
M	src/drivers/mct/main/map_glc2lnd_mod.F90
M	src/drivers/mct/main/map_lnd2glc_mod.F90
M	src/drivers/mct/main/mrg_mod.F90
M	src/drivers/mct/main/prep_aoflux_mod.F90
M	src/drivers/mct/main/prep_atm_mod.F90
M	src/drivers/mct/main/prep_glc_mod.F90
M	src/drivers/mct/main/prep_ice_mod.F90
M	src/drivers/mct/main/prep_ocn_mod.F90
M	src/drivers/mct/main/seq_diag_mct.F90
M	src/drivers/mct/main/seq_domain_mct.F90
M	src/drivers/mct/main/seq_flux_mct.F90
M	src/drivers/mct/main/seq_hist_mod.F90
M	src/drivers/mct/main/seq_io_mod.F90
M	src/drivers/mct/main/seq_rest_mod.F90
M	src/drivers/mct/shr/CMakeLists.txt
M	src/drivers/mct/shr/glc_elevclass_mod.F90
M	src/drivers/mct/shr/seq_flds_mod.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90
M	src/drivers/mct/shr/seq_timemgr_mod.F90
M	src/drivers/mct/shr/shr_ndep_mod.F90
M	src/drivers/mct/unit_test/CMakeLists.txt
A	src/drivers/mct/unit_test/check_fields_test/CMakeLists.txt
A	src/drivers/mct/unit_test/check_fields_test/test_check_fields.pf
M	src/drivers/mct/unit_test/utils/create_mapper_mod.F90
M	src/externals/CMake/CIME_utils.cmake
M	src/share/test/unit/CMakeLists.txt
A	src/share/test/unit/mock/README
M	src/share/test/unit/mock/shr_sys_mod.nompi_abortthrows.F90
A	src/share/test/unit/shr_abort_test/CMakeLists.txt
A	src/share/test/unit/shr_abort_test/README
A	src/share/test/unit/shr_abort_test/test_shr_abort.pf
M	src/share/test/unit/shr_assert_test/CMakeLists.txt
M	src/share/test/unit/shr_spfn_test/CMakeLists.txt
M	src/share/test/unit/shr_string_test/CMakeLists.txt
M	src/share/unit_test_stubs/README
A	src/share/unit_test_stubs/util/CMakeLists.txt
A	src/share/unit_test_stubs/util/README
A	src/share/unit_test_stubs/util/shr_abort_mod.abortthrows.F90
M	src/share/util/CMakeLists.txt
A	src/share/util/shr_abort_mod.F90
D	src/share/util/shr_dmodel_mod.F90
M	src/share/util/shr_mct_mod.F90
M	src/share/util/shr_pcdf_mod.F90
M	src/share/util/shr_pio_mod.F90
D	src/share/util/shr_strdata_mod.F90
D	src/share/util/shr_stream_mod.F90
M	src/share/util/shr_sys_mod.F90
D	src/share/util/shr_tInterp_mod.F90
M	tools/cprnc/README
M	tools/statistical_ensemble_test/ensemble.sh
M	tools/statistical_ensemble_test/single_run.sh
M	tools/utils/find_circular_dependency.py


======================================================================

======================================================================

Originator: Chris Fischer
Date: 6-22-2017
Tag: cime5.3.0-alpha.29
Answer Changes: None
Tests: Hand tested AIAF creation for acme and cesm models
Dependencies:

Brief Summary:
    - Back up datm tintalgo for AIAF to cesm default for just cesm.
    - Update copyright, authors and section 6.4 content.
    - Correct faq to point to use_cases.
    - Merge doc branch from bjsmith

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
5921fff Merge pull request #1702 from ESMCI/mvertens/fix_datm_tintalgo
18faea2 Merge pull request #1700 from bertinia/master
d29cd98 Merge pull request #1698 from bertinia/master
00989ab Merge branch 'bjsmith2014-master'


Modified files: git diff --name-status [previous_tag]
M       doc/source/conf.py
M       doc/source/users_guide/adding-cases.rst
M       doc/source/users_guide/case-basics.rst
M       doc/source/users_guide/create-a-case.rst
D       doc/source/users_guide/faq/basics-a-basic-example.rst
D       doc/source/users_guide/faq/basics-mpi-example.rst
D       doc/source/users_guide/faq/basics-setting-up-a-branch-or-hybrid-run.rst
D       doc/source/users_guide/faq/faq.rst
M       doc/source/users_guide/index.rst
M       doc/source/users_guide/running-a-case.rst
A       doc/source/users_guide/use_cases/basics-a-basic-example.rst
A       doc/source/users_guide/use_cases/basics-mpi-example.rst
A       doc/source/users_guide/use_cases/basics-setting-up-a-branch-or-hybrid-run.rst
A       doc/source/users_guide/use_cases/use-cases.rst
M       src/components/data_comps/datm/cime_config/buildnml
M       src/components/data_comps/datm/cime_config/namelist_definition_datm.xml


======================================================================

======================================================================

Originator: Chris Fischer
Date: 6-15-2017
Tag: cime5.3.0-alpha.28
Answer Changes: None
Tests:  scripts_regression_tests.py
Dependencies:

Brief Summary:
    - Change typo PCLHIST to CPLHIST in datm.
    - Remove empty proxy tag from anlworkstation.
    - Create PULL_REQUEST_TEMPLATE.
    - Updating CIME users guide.
    - Adds support for data model to read multiple time slices at once.
    - Fix xmlquery issues.
    - Merge last 3 months of ACME work.
    - Backward compatible change to allow more than one mach for each grid.

User interface changes:
    - new xml variable, readmode
    - xmlquery --group has been changed go xmlquery --get-group

PR summary: git log --oneline --first-parent [previous_tag]..master
f449794 Merge pull request #1696 from ESMCI/fischer/cplhist
547f68b Merge pull request #1689 from ESMCI/dqwu/anlworkstation-remove-proxy-tag
160a6e7 Create PULL_REQUEST_TEMPLATE
9b5ef51 Merge pull request #1686 from bjsmith2014/master 7efcbcf hot fix for pylint error
002df11 Merge pull request #1418 from bishtgautam/bishtgautam/data-model c7c79fe
813683d Merge pull request #1684 from ESMCI/mvertens/fixing_xmlquery
47a559a Merge pull request #1634 from ESMCI/jgfouca/acme_merge_06_01_2017
b795c3e Merge pull request #1680 from jedwards4b/config_pes_xsd_correction


Modified files: git diff --name-status [previous_tag]
M	.github/PULL_REQUEST_TEMPLATE
M	config/acme/allactive/config_compsets.xml
D	config/acme/allactive/config_compsets.xml.cime2
D	config/acme/allactive/config_pes.xml
D	config/acme/allactive/config_pes.xml.cime2
M	config/acme/allactive/config_pesall.xml
D	config/acme/allactive/testmods_dirs/cam/outfrq9s/shell_commands
D	config/acme/allactive/testmods_dirs/force_netcdf_pio/shell_commands
M	config/acme/config_archive.xml
M	config/acme/config_grids.xml
M	config/acme/machines/Makefile
M	config/acme/machines/config_batch.xml
M	config/acme/machines/config_compilers.xml
M	config/acme/machines/config_machines.xml
M	config/acme/machines/config_pio.xml
M	config/acme/machines/syslog.anvil
M	config/acme/machines/syslog.cetus
M	config/acme/machines/syslog.cori-haswell
M	config/acme/machines/syslog.cori-knl
M	config/acme/machines/syslog.edison
M	config/acme/machines/syslog.mira
M	config/acme/machines/syslog.titan
M	config/acme/machines/template.case.run
M	config/acme/machines/template.st_archive
A	config/acme/testmods_dirs/allactive/cam/cosplite/user_nl_cam
A	config/acme/testmods_dirs/allactive/cam/cosplite/xmlchange_cmnds
A	config/acme/testmods_dirs/allactive/cam/cosplite_nhtfrq5/user_nl_cam
A	config/acme/testmods_dirs/allactive/cam/cosplite_nhtfrq5/xmlchange_cmnds
M	config/acme/testmods_dirs/allactive/cam/outfrq9s/xmlchange_cmnds
A	config/acme/testmods_dirs/allactive/cam/rtm_null/xmlchange_cmnds
A	config/acme/testmods_dirs/allactive/clm/betr/xmlchange_cmnds
A	config/acme/testmods_dirs/allactive/clm/eca/user_nl_clm
A	config/acme/testmods_dirs/allactive/clm/fates/user_nl_clm
M	config/cesm/machines/template.st_archive
M	config/config_tests.xml
M	config/xml_schemas/config_pes.xsd
M	doc/source/users_guide/adding-cases.rst
M	doc/source/users_guide/multi-instance.rst
M	doc/source/users_guide/unit_testing.rst
D	scripts/Tools/cron_script
M	scripts/Tools/jenkins_generic_job
M	scripts/Tools/jenkins_script
M	scripts/Tools/xmlquery
A	scripts/lib/CIME/SystemTests/erri.py
M	scripts/lib/CIME/SystemTests/homme.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/aprun.py
M	scripts/lib/CIME/bless_test_results.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_cmpgen_namelists.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/check_input_data.py
M	scripts/lib/CIME/code_checker.py
M	scripts/lib/CIME/compare_test_results.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/test_status.py
M	scripts/lib/jenkins_generic_job.py
M	scripts/lib/update_acme_tests.py
M	scripts/tests/scripts_regression_tests.py
M	src/components/data_comps/datm/cime_config/config_component.xml
M	src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M	src/components/data_comps/dice/cime_config/namelist_definition_dice.xml
M	src/components/data_comps/dlnd/cime_config/namelist_definition_dlnd.xml
M	src/components/data_comps/docn/cime_config/config_component.xml
M	src/components/data_comps/docn/cime_config/namelist_definition_docn.xml
M	src/components/data_comps/drof/cime_config/namelist_definition_drof.xml
M	src/components/data_comps/dwav/cime_config/namelist_definition_dwav.xml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_acme.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/drivers/mct/cime_config/config_pes.xml
M	src/externals/mct/mct/Makefile
M	src/externals/mct/mct/m_AttrVect.F90
M	src/externals/mct/mct/m_GlobalSegMap.F90
M	src/externals/mct/mct/m_MatAttrVectMul.F90
M	src/externals/mct/mct/m_Rearranger.F90
M	src/externals/mct/mct/m_Router.F90
A	src/externals/mct/mct/m_SPMDutils.F90
M	src/externals/mct/mpeu/m_FcComms.F90
D	src/externals/mct/mpi-serial/NOTES
M	src/externals/mct/testsystem/testall/ReadSparseMatrixAsc.F90
M	src/externals/mct/testsystem/testall/cpl.F90
M	src/externals/pio1/pio/pio_types.F90
M	src/externals/pio1/pio/piolib_mod.F90
M	src/externals/pio1/pio/pionfput_mod.F90.in
M	src/share/util/shr_dmodel_mod.F90
M	src/share/util/shr_strdata_mod.F90
M	tools/cprnc/CMakeLists.txt

======================================================================

======================================================================

Originator: Bill Sacks
Date: 6-13-2017
Tag: cime5.3.0-alpha.27
Answer Changes: None
Tests: scripts_regression_tests on most PRs
Dependencies: CLM now needs to define its own LII and SSP tests

Brief Summary:
    - Allow for distributed config_tests.xml file and move LII and SSP
      tests out of cime. Also an unrelated minor bug fix in case.py
    - Updates to CIME User Guide
    - Fix XML schemas error for ALCF's Mira/Cetus
    - Do not add empty user mods
    - Clean up help text for query_testlists

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
d8ae575 Merge pull request #1682 from jedwards4b/config_tests_distribution
08cfb55 Merge pull request #1681 from bjsmith2014/master
d0d6648 Merge pull request #1679 from ESMCI/dqwu/fix_xml_schemas_alcf
876b6fe Merge pull request #1675 from billsacks/do_not_add_empty_user_mods
fdcac68 Merge pull request #1669 from billsacks/query_testlists_help
15768a0 Merge pull request #1671 from bjsmith2014/master

Modified files: git diff --name-status [previous_tag]
M       config/acme/machines/config_machines.xml
M       config/cesm/config_files.xml
M       config/config_tests.xml
M       doc/source/users_guide/multi-instance.rst
M       doc/source/users_guide/unit_testing.rst
D       scripts/lib/CIME/SystemTests/lii.py
D       scripts/lib/CIME/SystemTests/ssp.py
M       scripts/lib/CIME/XML/tests.py
M       scripts/lib/CIME/case.py
M       scripts/lib/CIME/utils.py
M       scripts/query_testlists

======================================================================

======================================================================

Originator: Chris Fischer
Date: 6-10-2017
Tag: cime5.3.0-alpha.26
Answer Changes: None
Tests:  scripts_regression_tests.py J_TestCreateNewcase
        scripts_regression_tests
Dependencies:

Brief Summary:
    - Provides better description of CCSM_BGC xml variable for both ACME and
      CESM
    - Add a test to scripts_regression_tests.py to assure that instantiating a
      case does not invoke a flush command.
    - User compset fixes.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
f8eb8b4 Merge pull request #1670 from ESMCI/mvertens/fix_ccsm_bgc_desc
8ea2801 Merge pull request #1666 from jedwards4b/case_instantiate_test
383c1f5 Merge pull request #1667 from billsacks/user_compset_fixes


Modified files: git diff --name-status [previous_tag]
M       scripts/create_newcase
M       scripts/lib/CIME/case.py
M       scripts/tests/scripts_regression_tests.py
M       src/drivers/mct/cime_config/config_component_acme.xml
M       src/drivers/mct/cime_config/config_component_cesm.xml
M       src/drivers/mct/cime_config/namelist_definition_drv.xml

======================================================================

======================================================================

Originator: Chris Fischer
Date: 6-8-2017
Tag: cime5.3.0-alpha.25
Answer Changes: None
Tests:  scripts_regression_tests.py, SMS_D.f19_f19.F1850.cori-knl_intel
        create_test cime_developer
Dependencies:

Brief Summary:
    - Remove COMP_INTERFACE references to esmf and downcase the value.
    - Make Flgl_qice attname consistent with name.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
aadee35 Merge pull request #1663 from jedwards4b/comp_interface_fix
f8f6221 Merge pull request #1662 from billsacks/fix_flgl


Modified files: git diff --name-status [previous_tag]
M       config/acme/machines/Makefile
M       config/cesm/machines/Makefile
M       scripts/lib/CIME/build.py
M       scripts/lib/CIME/test_scheduler.py
M       src/drivers/mct/cime_config/config_component.xml
M       src/drivers/mct/shr/seq_flds_mod.F90


======================================================================

======================================================================

Originator: Chris Fischer
Date: 6-8-2017
Tag: cime5.3.0-alpha.24
Answer Changes: None
Tests: scripts_regression_tests.py
Dependencies:

Brief Summary:
    - Convert user_mods_dir to abspath earlier.
    - Update gnu modules on cheyenne to use openmpi.
    - Fix failing builds on CIME master.
    - Update cime users guide.
    - Cleanup and fixes addressing running scripts_regression_tests.py on a mac.
    - Update contents after create_case.
    - Define out-of-the-box.
    - Update case-basics
    - Replace manage_case with query_case.
    - Updates modules for cori-knl in cesm.
    - Update cime users guide.
    - Add a grid alias and new test to mct driver testlist.
    - Merge of bjsmith changes to cime users guide.
    - New match attribute that can be 'last' or 'first' for values match in
      component.py

User interface changes:
    - New match attribute elements that are children of <entry> nodes.

PR summary: git log --oneline --first-parent [previous_tag]..master
72198f2 Merge pull request #1657 from billsacks/usermods_relative_path
9ae4f31 Merge pull request #1661 from ESMCI/fischer/gnu_cheyenne
9a43e4b hot fix for issue 1656
75c1967 Merge pull request #1652 from bjsmith2014/master
86912da Merge pull request #1645 from jedwards4b/macport_issues
8517405 Update contents after create_case
435b426 Define out-of-the-box
cb41c58 Update case-basics
6e72a7b replace manage_case with query_case
19a4641 Merge pull request #1649 from jedwards4b/cori_update
543629e Merge pull request #1648 from bjsmith2014/master
0ab580e Merge pull request #1646 from ESMCI/fischer/TestGridUpdate
c26ec40 Merge pull request #1641 from bjsmith2014/master
0d1bbd8 Merge pull request #1636 from ESMCI/mvertens/new_component_matches
3b238a8 Merge pull request #1635 from bjsmith2014/master

Modified files: git diff --name-status [previous_tag]
M       config/acme/machines/Makefile
M       config/cesm/config_grids.xml
M       config/cesm/machines/Makefile
M       config/cesm/machines/config_machines.xml
M       config/xml_schemas/config_compsets.xsd
M       doc/source/users_guide/building-a-case.rst
M       doc/source/users_guide/case-basics.rst
M       doc/source/users_guide/cime-internals.rst
M       doc/source/users_guide/cloning-a-case.rst
M       doc/source/users_guide/create-a-case.rst
M       doc/source/users_guide/customizing-a-case.rst
M       doc/source/users_guide/introduction-and-overview.rst
M       doc/source/users_guide/optimizing-processor-layout.rst
M       doc/source/users_guide/porting-cime.rst
M       doc/source/users_guide/running-a-case.rst
M       doc/source/users_guide/setting-up-a-case.rst
M       doc/source/users_guide/troubleshooting.rst
M       scripts/create_newcase
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/XML/component.py
M       scripts/lib/CIME/XML/entry_id.py
M       scripts/lib/CIME/XML/machines.py
M       src/build_scripts/buildlib.csm_share
M       src/components/data_comps/datm/cime_config/config_component.xml
M       src/components/data_comps/desp/cime_config/config_component.xml
M       src/components/data_comps/dice/cime_config/config_component.xml
M       src/components/data_comps/dlnd/cime_config/config_component.xml
M       src/components/data_comps/docn/cime_config/config_component.xml
M       src/components/data_comps/drof/cime_config/config_component.xml
M       src/components/data_comps/dwav/cime_config/config_component.xml
M       src/drivers/mct/cime_config/config_component.xml
M       src/drivers/mct/cime_config/config_component_acme.xml
M       src/drivers/mct/cime_config/config_component_cesm.xml
M       src/drivers/mct/cime_config/testdefs/testlist_drv.xml


======================================================================

======================================================================

Originator: Chris Fischer
Date: 6-4-2017
Tag: cime5.3.0-alpha.23
Answer Changes: None
Tests: scripts_regression_tests
       pylint, unit-tests
Dependencies:

Brief Summary:
    - Fixes a critical error for ERP tests.
    - Change run_cmd_no_fail doctest to not match directory.
    - Bring bless_test_results behavior into an exact match with create_test -g.
    - Merge and update CIME users guide rst source.
    - Fix a critical problem in code_checker that caused it to filter too many files.
    - Copied doc dir into master in order to create a gh-pages orphan branch.
    - Fix race condition with case XML files when using set_file and some other unrelated bugs.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
4525e19 Merge pull request #1639 from ESMCI/mvertens/python3string_fixes
4775d9a Change run_cmd_no_fail doctest to not match directory
4db9834 Merge pull request #1632 from ESMCI/jgfouca/generate_baseline_should_include_logs
4ba0b44 Merge pull request #1631 from bjsmith2014/master
37e4ed7 Merge pull request #1629 from ESMCI/jgfouca/pylint_fixes_and_more
6a7ffc2 Merge pull request #1623 from bertinia/master
65bd395 Merge pull request #1616 from ESMCI/jgfouca/fix_race


Modified files: git diff --name-status [previous_tag]
M	.gitignore
A	.nojekyll
M	LICENSE.TXT
A	doc/Makefile
A	doc/source/_static
A	doc/source/build_cpl/index.rst
A	doc/source/build_cpl/introduction.rst
A	doc/source/conf.py
A	doc/source/conf.py_old
A	doc/source/data_models/data-atm.rst
A	doc/source/data_models/data-lnd.rst
A	doc/source/data_models/data-model-science.rst
A	doc/source/data_models/data-ocean.rst
A	doc/source/data_models/data-river.rst
A	doc/source/data_models/data-seaice.rst
A	doc/source/data_models/data-wave.rst
A	doc/source/data_models/design-details.rst
A	doc/source/data_models/index.rst
A	doc/source/data_models/input-streams.rst
A	doc/source/data_models/introduction.rst
A	doc/source/driver_cpl/bit-for-bit-flag.rst
A	doc/source/driver_cpl/budgets.rst
A	doc/source/driver_cpl/cplug-02.1-figx1.jpg
A	doc/source/driver_cpl/design.rst
A	doc/source/driver_cpl/driver_threading_control.rst
A	doc/source/driver_cpl/grids.rst
A	doc/source/driver_cpl/history-and-restarts.rst
A	doc/source/driver_cpl/implementation.rst
A	doc/source/driver_cpl/index.rst
A	doc/source/driver_cpl/initialization-and-restart.rst
A	doc/source/driver_cpl/introduction.rst
A	doc/source/driver_cpl/multi-instance.rst
A	doc/source/driver_cpl/namelist-overview.rst
A	doc/source/driver_cpl/time-management.rst
A	doc/source/index.rst
A	doc/source/misc_tools/index.rst
A	doc/source/users_guide/adding-cases.rst
A	doc/source/users_guide/building-a-case.rst
A	doc/source/users_guide/case-basics.rst
A	doc/source/users_guide/cime-internals.rst
A	doc/source/users_guide/cloning-a-case.rst
A	doc/source/users_guide/create-a-case.rst
A	doc/source/users_guide/customizing-a-case.rst
A	doc/source/users_guide/faq/basics-a-basic-example.rst
A	doc/source/users_guide/faq/basics-mpi-example.rst
A	doc/source/users_guide/faq/basics-setting-up-a-branch-or-hybrid-run.rst
A	doc/source/users_guide/faq/faq.rst
A	doc/source/users_guide/index.rst
A	doc/source/users_guide/introduction-and-overview.rst
A	doc/source/users_guide/multi-instance.rst
A	doc/source/users_guide/optimizing-processor-layout.rst
A	doc/source/users_guide/porting-cime.rst
A	doc/source/users_guide/running-a-case.rst
A	doc/source/users_guide/setting-up-a-case.rst
A	doc/source/users_guide/testing.rst
A	doc/source/users_guide/troubleshooting.rst
A	doc/source/users_guide/unit_testing.rst
A	doc/source/what_cime/index.rst
A	index.html
M	scripts/Tools/normalize_cases
M	scripts/lib/CIME/SystemTests/erp.py
M	scripts/lib/CIME/SystemTests/homme.py
M	scripts/lib/CIME/SystemTests/ncr.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/XML/machines.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/code_checker.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/CIME/wait_for_tests.py
M	scripts/tests/scripts_regression_tests.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 5-28-2017
Tag: cime5.3.0-alpha.22
Answer Changes: Climate Changing for active two-way coupled GLC
Tests: Ran gnu TG smoke tests
       aux_clm45 yellowstone_gnu
       create_test cime_developer --queue long
       scripts_regression_tests.py --fast
       code_checker and scripts_regressions_tests.pr
       CECO.hobart_pgi build

Dependencies:

Brief Summary:
    - Remove no-longer-needed CISM_GNU setting.
    - Add more error-checking with gnu in debug mode.
    - Map SMB from lnd to glc using bilinear mapping with a conservation
      correction.
    - Do not eval words - only strings with whitespace.
    - Change all python2 style strings to python3 style strings.
    - Update the user_defined template.
    - Update testreporter and change hobart queue to medium.
    - Improve handling of hist comparisons in TestStatus.log.
    - Update PGI compiler to 17.04 on hobart.
    - Downscale build parellism on small machines.

User interface changes:
    - New drv_in namelist variable: 'glc_renormalize_smb'
    - Contents of TestStatus.log.
    - Automatic downscale of builds.

PR summary: git log --oneline --first-parent [previous_tag]..master
2f6e683 Merge pull request #1620 from billsacks/remove_cism_gnu
4f08bb0 Merge pull request #1618 from billsacks/gnu_debug_flags
7a5242d Merge pull request #1609 from billsacks/lnd2glc_bilinear
21f2a20 Merge pull request #1614 from jedwards4b/eval_fix
2890518 Merge pull request #1608 from ESMCI/erichlf/3strings
fb3f533 Merge pull request #1611 from jedwards4b/update_user_defined
162ba85 Merge pull request #1610 from ESMCI/fischer/testreporter_fix
a9cc09c Merge pull request #1606 from ESMCI/jgfouca/improve_logs_for_compares
2deb949 Merge pull request #1602 from mnlevy1981/machines/hobart_pgi_ver
0b55ea3 Merge pull request #1605 from ESMCI/jgfouca/downscale_builds_on_small_machs


Modified files: git diff --name-status [previous_tag]
M	config/acme/machines/template.st_archive
M	config/cesm/machines/Makefile
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.st_archive
M	config/cesm/machines/userdefined_laptop_template/README.md
M	config/cesm/machines/userdefined_laptop_template/config_compilers.xml
M	config/cesm/machines/userdefined_laptop_template/config_machines.xml
M	scripts/Tools/acme_check_env
M	scripts/Tools/bless_test_results
M	scripts/Tools/case.build
M	scripts/Tools/case.cmpgen_namelists
M	scripts/Tools/case.setup
M	scripts/Tools/case_diff
M	scripts/Tools/check_case
M	scripts/Tools/check_input_data
M	scripts/Tools/check_lockedfiles
M	scripts/Tools/cime_bisect
M	scripts/Tools/code_checker
M	scripts/Tools/compare_namelists
M	scripts/Tools/compare_test_results
M	scripts/Tools/component_compare_baseline
M	scripts/Tools/component_compare_copy
M	scripts/Tools/component_compare_test
M	scripts/Tools/component_generate_baseline
M	scripts/Tools/cs.status
M	scripts/Tools/jenkins_generic_job
M	scripts/Tools/list_acme_tests
M	scripts/Tools/normalize_cases
M	scripts/Tools/pelayout
M	scripts/Tools/pointclm/makepointdata.py
M	scripts/Tools/pointclm/post_process.py
M	scripts/Tools/pointclm/site_fullrun.py
M	scripts/Tools/preview_run
M	scripts/Tools/save_provenance
M	scripts/Tools/simple_compare
M	scripts/Tools/testreporter.py
M	scripts/Tools/update_acme_tests
M	scripts/Tools/xmlconvertors/config_pes_converter.py
M	scripts/Tools/xmlconvertors/grid_xml_converter.py
M	scripts/create_newcase
M	scripts/fortran_unit_testing/python/printer.py
M	scripts/fortran_unit_testing/run_tests.py
M	scripts/lib/CIME/BuildTools/configure.py
M	scripts/lib/CIME/BuildTools/macrowriterbase.py
M	scripts/lib/CIME/SystemTests/dae.py
M	scripts/lib/CIME/SystemTests/eri.py
M	scripts/lib/CIME/SystemTests/erio.py
M	scripts/lib/CIME/SystemTests/erp.py
M	scripts/lib/CIME/SystemTests/err.py
M	scripts/lib/CIME/SystemTests/ers.py
M	scripts/lib/CIME/SystemTests/ers2.py
M	scripts/lib/CIME/SystemTests/homme.py
M	scripts/lib/CIME/SystemTests/nck.py
M	scripts/lib/CIME/SystemTests/ncr.py
M	scripts/lib/CIME/SystemTests/nodefail.py
M	scripts/lib/CIME/SystemTests/pea.py
M	scripts/lib/CIME/SystemTests/pem.py
M	scripts/lib/CIME/SystemTests/pet.py
M	scripts/lib/CIME/SystemTests/pre.py
M	scripts/lib/CIME/SystemTests/seq.py
M	scripts/lib/CIME/SystemTests/ssp.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/archive.py
M	scripts/lib/CIME/XML/batch.py
M	scripts/lib/CIME/XML/compilerblock.py
M	scripts/lib/CIME/XML/compilers.py
M	scripts/lib/CIME/XML/component.py
M	scripts/lib/CIME/XML/compsets.py
M	scripts/lib/CIME/XML/entry_id.py
M	scripts/lib/CIME/XML/env_archive.py
M	scripts/lib/CIME/XML/env_base.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_pes.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/env_test.py
M	scripts/lib/CIME/XML/files.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/XML/grids.py
M	scripts/lib/CIME/XML/machines.py
M	scripts/lib/CIME/XML/namelist_definition.py
M	scripts/lib/CIME/XML/pes.py
M	scripts/lib/CIME/XML/test_reporter.py
M	scripts/lib/CIME/XML/testlist.py
M	scripts/lib/CIME/XML/tests.py
M	scripts/lib/CIME/XML/testspec.py
M	scripts/lib/CIME/aprun.py
M	scripts/lib/CIME/bless_test_results.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/buildlib.py
M	scripts/lib/CIME/buildnml.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_cmpgen_namelists.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/case_test.py
M	scripts/lib/CIME/check_input_data.py
M	scripts/lib/CIME/check_lockedfiles.py
M	scripts/lib/CIME/compare_namelists.py
M	scripts/lib/CIME/compare_test_results.py
M	scripts/lib/CIME/get_timing.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/namelist.py
M	scripts/lib/CIME/nmlgen.py
M	scripts/lib/CIME/preview_namelists.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/simple_compare.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/test_status.py
M	scripts/lib/CIME/test_utils.py
M	scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two.py
M	scripts/lib/CIME/tests/SystemTests/test_system_tests_compare_two_link_to_case2_output.py
M	scripts/lib/CIME/tests/test_user_mod_support.py
M	scripts/lib/CIME/user_mod_support.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/CIME/wait_for_tests.py
M	scripts/lib/jenkins_generic_job.py
M	scripts/lib/update_acme_tests.py
M	scripts/tests/list_tests
M	scripts/tests/scripts_regression_tests.py
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/main/CMakeLists.txt
M	src/drivers/mct/main/map_lnd2glc_mod.F90
M	src/drivers/mct/main/prep_glc_mod.F90
M	src/drivers/mct/main/prep_lnd_mod.F90
D	src/drivers/mct/main/vertical_gradient_calculator_2nd_order.F90
D	src/drivers/mct/main/vertical_gradient_calculator_base.F90
D	src/drivers/mct/main/vertical_gradient_calculator_factory.F90
M	src/drivers/mct/shr/glc_elevclass_mod.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90
M	src/drivers/mct/unit_test/CMakeLists.txt
M	src/drivers/mct/unit_test/glc_elevclass_test/test_glc_elevclass.pf
D	src/drivers/mct/unit_test/map_lnd2glc_test/CMakeLists.txt
D	src/drivers/mct/unit_test/map_lnd2glc_test/test_map_lnd2glc.pf
M	src/drivers/mct/unit_test/stubs/CMakeLists.txt
D	src/drivers/mct/unit_test/stubs/vertical_gradient_calculator_constant.F90
D	src/drivers/mct/unit_test/vertical_gradient_calculator_test/CMakeLists.txt
D	src/drivers/mct/unit_test/vertical_gradient_calculator_test/README
D	src/drivers/mct/unit_test/vertical_gradient_calculator_test/gradient_example.txt
D	src/drivers/mct/unit_test/vertical_gradient_calculator_test/plot_gradient
D	src/drivers/mct/unit_test/vertical_gradient_calculator_test/test_vertical_gradient_calculator_2nd_order.pf
D	src/drivers/mct/unit_test/vertical_gradient_calculator_test/test_vertical_gradient_calculator_factory.pf
M	src/share/test/unit/shr_string_test/test_shr_string.pf
M	src/share/util/shr_string_mod.F90
M	tools/load_balancing_tool/code/merge.py
M	tools/load_balancing_tool/code/neos.py
M	tools/statistical_ensemble_test/pyCECT/pyCECT.py
M	tools/statistical_ensemble_test/pyCECT/pyEnsLib.py
M	tools/statistical_ensemble_test/pyCECT/pyEnsSum.py
M	tools/statistical_ensemble_test/pyCECT/pyEnsSumPop.py
M	tools/utils/find_circular_dependency.py

======================================================================

======================================================================
Originator: Chris Fischer
Date: 5-24-2017
Tag: cime5.3.0-alpha.21
Answer Changes: None
Tests: scripts_regression_tests.py
Dependencies:

Brief Summary:
    - Fixed issue with GET_REFCASE not being set correctly.
    - Don't ignore attributes for Compilers.get_value.
    - Add ability for create_test to infer non-default machine from tests.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
25a7f27 Merge pull request #1604 from jedwards4b/refcase_fix
56fd28c Merge pull request #1598 from ESMCI/jgfouca/compiler_use_attribute
7003fe2 Merge pull request #1597 from ESMCI/jgfouca/infer_machine_from_tests

Modified files: git diff --name-status [previous_tag]
M       scripts/create_test
M       scripts/lib/CIME/XML/compilers.py
M       scripts/lib/CIME/case.py
M       scripts/lib/update_acme_tests.py
M       scripts/tests/scripts_regression_tests.py


======================================================================
Originator: Chris Fischer
Date: 5-24-2017
Tag: cime5.3.0-alpha.20
Answer Changes: None
Tests:
Dependencies:

Brief Summary:
    - Add the f19_g17 maps, as wall as the ww3 <-> tx1v1 maps.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
0e9a1e0 Merge pull request #1594 from mnlevy1981/maps/update_ocean_maps

Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_grids.xml

======================================================================
Originator: Chris Fischer
Date: 5-24-2017
Tag: cime5.3.0-alpha.19
Answer Changes: None
Tests: scripts_regression_tests --fast
Dependencies:

Brief Summary:
    - Revert "Updated grid aliases in cesm/config_grids.xml"
    - Build failures should not dump a full stacktracesince a code problem is
      not the fault of CIME infrastructure.
      Also, deprecate shell calls to date in favor of python interface to get
      timestamp.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
0817502 Merge pull request #1596 from ESMCI/revert-1585-master
0ee6cb7 Merge pull request #1595 from ESMCI/jgfouca/improve_build_fail_msg


Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_grids.xml
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/build.py
M       src/drivers/mct/cime_config/buildnml


======================================================================
Originator: Chris Fischer
Date: 5-23-2017
Tag: cime5.3.0-alpha.18
Answer Changes: None
Tests: scripts_regression_tests.py, hand test xmlquery
       ERS.f19_g16.X.yellowstone_intel
       1850_DATM%CPLHIST_SLND_CICE_POP2%ECO_DROF%CPLHIST_SGLC_WW3
       SMS_D_Mmpi-serial_Ld1.T42_T42.FSCM5A97.hobart_nag

Dependencies:

Brief Summary:
    - Updated grid aliases in cesm/config_grids.xml.
    - Fix logic in st_archive wrt DOUT_S_SAVE_INTERIM_RESTART_FILES.
    - Improve comment for BASELINE status in TestStatus.
    - Fix an issue with xmlquery when the --file and --listall flags are used
      together.
    - Remove grid attribute from compset elements.
    - Update cime to support full X configuration.
    - Remove empty <Proxy> tag from anlworkstation.
    - DOCN aquaplanet from file and new A compsets with DOCN modes.
    - Use %CPLHIST for DATM coupler hist forcing.
    - Point to gx1v7 domain files that exist.
    - Merged recent changes from MCSclimate/mpi-serial into CIME.
      Includes new hvector functions.

User interface changes:
    - TestStatus changes

PR summary: git log --oneline --first-parent [previous_tag]..master
e9a944c Merge pull request #1585 from alperaltuntas/master
568938d Merge pull request #1573 from jedwards4b/sta_fix
a4352db Merge pull request #1591 from ESMCI/jgfouca/improve_baseline_teststatus_comment
b4182ec Merge pull request #1593 from jedwards4b/xmlquery_and_config_compset
3189a86 Merge pull request #1592 from billsacks/compset_no_grid_attribute
7f6004f Merge pull request #1586 from apcraig/xcase
1ee8025 Merge pull request #1590 from ESMCI/sarich/anlworkstation-remove-proxy-tag
09c5136 Merge pull request #1582 from ESMCI/mvertens/docnmods
8657a18 Merge pull request #1578 from ESMCI/mvertens/datm_cplhist_mod
f109d77 Merge pull request #1567 from mnlevy1981/grids/fix_gx1v7_domain_datestamps
a8cc1a2 Merge pull request #1568 from gold2718/mpi-serial-import


Modified files: git diff --name-status [previous_tag]
M       config/acme/machines/config_machines.xml
M       config/cesm/config_grids.xml
M       config/cesm/machines/config_machines.xml
M       config/xml_schemas/config_compsets.xsd
M       scripts/Tools/xmlquery
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/case_st_archive.py
M       src/components/data_comps/datm/cime_config/config_component.xml
M       src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M       src/components/data_comps/docn/cime_config/config_component.xml
M       src/components/data_comps/docn/cime_config/namelist_definition_docn.xml
M       src/components/data_comps/docn/docn_comp_mod.F90
M       src/components/data_comps/drof/cime_config/namelist_definition_drof.xml
M       src/components/xcpl_comps/xshare/dead_mct_mod.F90
M       src/drivers/mct/cime_config/config_component_cesm.xml
M       src/drivers/mct/cime_config/config_compsets.xml
A       src/drivers/mct/cime_config/testdefs/testmods_dirs/drv/default/shell_commands
M       src/externals/mct/mpi-serial/Makefile
M       src/externals/mct/mpi-serial/README
M       src/externals/mct/mpi-serial/collective.c
A       src/externals/mct/mpi-serial/error.c
A       src/externals/mct/mpi-serial/ic_merge.c
M       src/externals/mct/mpi-serial/mpi.h
M       src/externals/mct/mpi-serial/mpif.h
M       src/externals/mct/mpi-serial/tests/ftest_old.F90
M       src/externals/mct/mpi-serial/type.c


======================================================================


Originator: Chris Fischer
Date: 5-18-2017
Tag: cime5.3.0-alpha.17
Answer Changes: None
Tests: ERI.f09_g17.B1850.cheyenne_intel.allactive-defaultio
       scripts_regression_test.py
Dependencies:

Brief Summary:
    - Rearranges code for lookups a little in case.py.
    - Undo recent change to land domain.
    - Fix config pes converter.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
d33bc68 Merge pull request #1561 from jedwards4b/lookups_cleanup
3cc8bac Merge pull request #1560 from jedwards4b/undo_land_domain_change
c3458a8 Merge pull request #1557 from ESMCI/sarich/fix-config-pes-converter


Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_grids.xml
M       scripts/Tools/xmlconvertors/config_pes_converter.py
M       scripts/Tools/xmlconvertors/grid_xml_converter.py
M       scripts/lib/CIME/case.py


======================================================================

======================================================================
Originator: Chris Fischer
Date: 5-17-2017
Tag: cime5.3.0-alpha.16
Answer Changes: None
Tests: scripts_reggression_tests.py
Dependencies:

Brief Summary:
    - Fix bug which was preventing config_compsets from modifying xml
      variables.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
d4e9285 Merge pull request #1559 from jedwards4b/compset_var_settings

Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_grids.xml
M       scripts/lib/CIME/case.py



======================================================================
Originator: Jim Edwards
Date: 5-17-2017
Tag: cime5.3.0-alpha.15
Answer Changes: None
Tests: scripts_regression_tests.py
d581e52 (HEAD, origin/master, origin/HEAD, master) Merge pull request #1554 from jedwards4b/eri_histfile_cleanup
906c88a Merge pull request #1556 from ESMCI/mvertens/fix_usermods
d404d35 Merge pull request #1551 from jedwards4b/multi_component_user_mods
7355f9d Merge pull request #1547 from ESMCI/mvertens/convert_stream_tabs
99c59b4 Merge pull request #1552 from jedwards4b/user_compset_message_change
7aebc3e Merge pull request #1553 from jedwards4b/memory_usage_correction
9e81110 Merge pull request #1548 from jedwards4b/improve_user_compset_error_checking
98d386f Merge pull request #1546 from jedwards4b/improve_user_compset_error_checking
980f15d Merge pull request #1542 from jedwards4b/fix_env_run_check_in_tests



======================================================================
Originator: Chris Fischer
Date: 5-15-2017
Tag: cime5.3.0-alpha.14
Answer Changes: None
Tests: scripts_regression_tests.py
       hand test 2000_CAM50_SLND_SICE_DOCN%AQP3_SROF_SGLC_SWAV
       ERR.f09_g16.B1850.cheyenne_intel.allactive-defaultio

Dependencies:

Brief Summary:
    - Update mct testlist from yellowstone to cheyenne.
    - Remove xrof_flood_mode from config_grids assure exactly two grids.
    - Add ability to remove tabs in shr_string_lalign.
    - Timing should use largest ncpl value not atm value.
    - Remove user_mods support from the config_compsets.xml file and adds it
      to the config_component.xml file.
    - Define the list of expected attributes to the mpirun command so that the
      all do not need to be passed in.
    - Avoid defining non-existant variable MASK_DOMAIN_FILE.
    - Make sure that case.set_value is setting a valid variable and error out
      if it is not.
    - Improve error message for incorrect grid alias.
    - Add a case.test --reset option to manually reset a test to initial
      conditions.
    - Improve error messages for modify_via_xml and cannot_modify_by_user_nl.
    - Only create rest directories if they are going to be populated.
    - Allow the user the option of skipping the xmllint validation of cime xml
      files.

User interface changes:
    - Add --reset option to case.test.

PR summary: git log --oneline --first-parent [previous_tag]..master
71b8edb Merge pull request #1537 from ESMCI/fischer/testlist_cheyenne
7494139 Merge pull request #1535 from jedwards4b/xrof_flood_mode_fixagain
5894c4d Merge pull request #1531 from ESMCI/mvertens/remove_stream_tabs
9f92bf0 Merge pull request #1524 from jedwards4b/correct_ncpl_in_timing
62fa492 Merge pull request #1523 from jedwards4b/user_mods_in_component
a5e9bc0 Merge pull request #1521 from jedwards4b/define_expected_attributes
cecbbd5 Merge pull request #1518 from jedwards4b/no_mask_domain
1bbbfc2 Merge pull request #1517 from jedwards4b/set_value_valid
3bcfbe4 Merge pull request #1515 from jedwards4b/grid_alais_message
94455fc Merge pull request #1502 from jedwards4b/reset_test_case
6ebd989 Merge pull request #1514 from billsacks/modify_via_xml_error_msg
9d865d5 Merge pull request #1511 from jedwards4b/no_interum_dirs
144cc38 Merge pull request #1509 from jedwards4b/allowed_schema_skip


Modified files: git diff --name-status [previous_tag]
M       config/acme/machines/template.case.test
M       config/cesm/config_grids.xml
M       config/cesm/machines/template.case.test
M       config/xml_schemas/config_compsets.xsd
M       config/xml_schemas/env_mach_specific.xsd
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/XML/compsets.py
M       scripts/lib/CIME/XML/env_mach_specific.py
M       scripts/lib/CIME/XML/grids.py
M       scripts/lib/CIME/XML/namelist_definition.py
M       scripts/lib/CIME/XML/pes.py
M       scripts/lib/CIME/case.py
M       scripts/lib/CIME/case_st_archive.py
M       scripts/lib/CIME/case_submit.py
M       scripts/lib/CIME/case_test.py
M       scripts/lib/CIME/get_timing.py
M       src/build_scripts/buildlib.mct
M       src/drivers/mct/cime_config/testdefs/testlist_drv.xml
M       src/share/test/unit/shr_string_test/test_shr_string.pf
M       src/share/util/shr_string_mod.F90


======================================================================

======================================================================

Originator: Chris Fischer
Date: 5-10-2017
Tag: cime5.3.0-alpha.13
Answer Changes:  Round Off
Tests: aux_glc test suite
Dependencies:

Brief Summary:
    - New CISM mapping files.
    - Fix pylint issues.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
67c14ca Merge pull request #1478 from billsacks/cism_new_mapping_files
affab50 fix pylint issue


Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_grids.xml
M       scripts/lib/CIME/case.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 5-9-2017
Tag: cime5.3.0-alpha.12
Answer Changes: None
Tests: scripts_regression_tests.py
       hand test of xmlquery
       ERR.f09_g16.B1850
       code_checker
       create_test cime_developer
       SMS.ne30z60_ne30.F1850
       ERS2 test
       SMS_Mmpi-serial.f19_g17.X.hobart_intel
Dependencies:

Brief Summary:
    - Fixes building when certain path variables have a trailing /
    - xmlquery options --file and --listall were not working together, now
      they are.
    - Fix for SOM bug introduced in PR #1451
    - Add new grid aliases for gx3v7 and usgs masks.
    - Improve ERR by removing rundir files and recopying from sta rest
      directory.
    - Change allows the user to specify a file in either the config_pes.xml
      or the env_mach_pes.xml format.
    - Add skip-preview-namelist to case.submit and case_run.
    - Simplify settings in CCSM_CO2_PPMV in config_components_cesm.xml.
    - Fix force queue.
    - Fix pylint errors.
    - Fix bug where file drv_flds_in wasn't being closed after being opened.
    - Add missing term for NET WATER BUDGET tables.
    - Add some major NCAR contributors to cime.
    - Fixes for zlev problem.
    - Renamed manage_case to query_config.
    - Make alternative implementation for ERS.
    - Remove empty mpi-serial settings from config_machines.xml.
    - Only warning for single dash.
    - Additional fields needed for environment_variables.
    - Template files were not correctly upgraded to the new argument oarsing.
    - Fix ACME config_machines.xml format.
    - Add new runoff -> gx1v6 maps.
    - Removed old ncl utilities. Changed the random pertlim generator to allow
      more (and flexible) number of ensemble members. Added the capability to
      generate 9 time step ensembles for UF-CAM-ECT.

User interface changes:
    - xmlquery --file and --listall can now be used together.
    - --pesfile argument in create_newcase
    - Added --skip-preview-namelist to case.build and
      template.case.run
    - manage_case -> query_config
      --compset -> --compsets
      --machine -> --machines
      added 'all' option for --compsets
      added 'current' and to --machines
    - New ERS2 test type.
    - Print a warning to stdout if single dash used with multi-char arg.

PR summary: git log --oneline --first-parent [previous_tag]..master
56f5df26 Merge pull request #1495 from ESMCI/mfdeakin-sandia/fix_build_paths
e234bc6e Merge pull request #1504 from jedwards4b/xmlquery_again
10fbc430 Merge pull request #1501 from ESMCI/mvertens/somfix
3beac4ab Merge pull request #1500 from ESMCI/fischer/grid_mask
1ca58a07 Merge pull request #1499 from jedwards4b/err_test_improvement1
18112d92 Merge pull request #1494 from jedwards4b/pesfile_usage
cdcb096b Merge pull request #1471 from ESMCI/erichlf/case_submit/skip_pnl
5684406d Merge pull request #1487 from ESMCI/mvertens/fix_ccsm_co2_ppmv
99f1f5ba Merge pull request #1496 from ESMCI/jgfouca/fix_force_queue
93a452a9 Merge pull request #1490 from ESMCI/jgfouca/fix_pylint_errs
cf204753 Merge pull request #1491 from ESMCI/fischer/readnl_close
0847f8df Merge pull request #1427 from jtruesdal/water_budget
893a6135 Merge pull request #1458 from billsacks/ncar_credits
653dd297 Merge pull request #1469 from ESMCI/mvertens/fixzlev
68f4b5d7 Merge pull request #1388 from ESMCI/erichlf/manage_case
b661f5bd Merge branch 'jgfouca/alternative_impl_for_ers' (PR #1482)
ef7d0fe9 Merge pull request #1482 from ESMCI/jgfouca/alternative_impl_for_ers
7aadd49b Merge pull request #1454 from jedwards4b/mpi-serial-cleanup
4d4281f2 Merge pull request #1474 from jedwards4b/no_error_warning
34d00048 Minor hotfix for ACME config_machines.xml
71064281 Merge pull request #1477 from jedwards4b/env_vars_attributes
9c463bf9 Merge pull request #1476 from ESMCI/jgfouca/fix_acme_template_files
25ce0223 Merge pull request #1475 from
ESMCI/jgfouca/fix_acme_config_mach_xml_format
baaa2cc3 Merge pull request #1472 from mnlevy1981/mapping/runoff_to_gx1v6
00c22c0c Merge pull request #1457 from allibco/master


Modified files: git diff --name-status [previous_tag]
M	README.md
M	config/acme/machines/config_machines.xml
M	config/acme/machines/template.case.run
M	config/acme/machines/template.case.test
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/template.case.run
M	config/config_tests.xml
M	config/xml_schemas/env_mach_specific.xsd
M	scripts/Tools/case.submit
M	scripts/Tools/xmlquery
M	scripts/create_newcase
M	scripts/create_test
M	scripts/lib/CIME/SystemTests/err.py
A	scripts/lib/CIME/SystemTests/ers2.py
M	scripts/lib/CIME/XML/component.py
M	scripts/lib/CIME/XML/compsets.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_pes.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/generic_xml.py
M	scripts/lib/CIME/XML/grids.py
M	scripts/lib/CIME/XML/machines.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_submit.py
M	scripts/lib/CIME/code_checker.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/utils.py
D	scripts/manage_case
A	scripts/query_config
M	scripts/tests/scripts_regression_tests.py
M	src/build_scripts/buildlib.gptl
M	src/components/data_comps/docn/cime_config/config_component.xml
M	src/components/data_comps/docn/docn_comp_mod.F90
M	src/components/stub_comps/satm/cime_config/config_component.xml
M	src/components/stub_comps/sesp/cime_config/config_component.xml
M	src/components/stub_comps/sglc/cime_config/config_component.xml
M	src/components/stub_comps/sice/cime_config/config_component.xml
M	src/components/stub_comps/slnd/cime_config/config_component.xml
M	src/components/stub_comps/socn/cime_config/config_component.xml
M	src/components/stub_comps/srof/cime_config/config_component.xml
M	src/components/stub_comps/swav/cime_config/config_component.xml
M	src/components/xcpl_comps/xatm/cime_config/config_component.xml
M	src/components/xcpl_comps/xglc/cime_config/config_component.xml
M	src/components/xcpl_comps/xice/cime_config/config_component.xml
M	src/components/xcpl_comps/xlnd/cime_config/config_component.xml
M	src/components/xcpl_comps/xocn/cime_config/config_component.xml
M	src/components/xcpl_comps/xrof/cime_config/config_component.xml
M	src/components/xcpl_comps/xwav/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/drivers/mct/main/seq_diag_mct.F90
M	src/drivers/mct/shr/seq_drydep_mod.F90
M	src/drivers/mct/shr/shr_ndep_mod.F90
M	tools/Readme.configure
M	tools/configure
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_r05_to_gx1v6_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_rx1_to_gx1v6_nnsm_e1000r300.nml
A	tools/statistical_ensemble_test/README
M	tools/statistical_ensemble_test/ensemble.sh
D	tools/statistical_ensemble_test/ncl_library/Zscore.ncl
D	tools/statistical_ensemble_test/ncl_library/area_avg.ncl
D	tools/statistical_ensemble_test/ncl_library/create_ensemble.ncl
D	tools/statistical_ensemble_test/ncl_library/global.ncl
D	tools/statistical_ensemble_test/ncl_library/plot_rmsz.ncl
D	tools/statistical_ensemble_test/ncl_library/print.ncl
D	tools/statistical_ensemble_test/ncl_library/rmsz.ncl
D	tools/statistical_ensemble_test/ncl_library/vinterp.ncl
M	tools/statistical_ensemble_test/single_run.sh
D	tools/statistical_ensemble_test/test_run_against_ensemble.ncl
D	tools/statistical_ensemble_test/validation_test.sh

======================================================================

======================================================================

Originator: Chris Fischer
Date: 5-3-2017
Tag: cime5.3.0-alpha.11
Answer Changes: None
Tests:
       - scrtips_regression_tests.py
       - ./xmlchange --id CLM_BLDNML_OPTS --val "-bgc bgc -crop -irrig=.true."
       - ERP_D.f45_g37_rx1.A.hobart_nag
       - one off tests to make sure the new datasets are being run for the gx1v7
         but not for other resolutions.
Dependencies:

Brief Summary:
    - Update to env_mach_specific.xsd schema for unit_testing attribute and
      arguments and arg elements.
    - Remove all references to lt_archive which will not be supported in
      CESM2.0.
    - env_mach_specific.xsd schema was incomplete
    - Remove TOTAL_CORES as it was inaccurate in many cases.
    - in _check_for_invalid_args ignore quoted strings.
    - Add schemas for the 3 remaining case xml files.
    - NAG compiler needs an integer width on this read statement
    - Update queue selection to take walltime into account.
    - Add new CESM gx1v7 runoff maps for use with estuary parameterization.
    - Add a --script-root option to create_newcase.

User interface changes:
    - Removes TOTAL_CORES
    - Changes in how walltime is handled.

PR summary: git log --oneline --first-parent [previous_tag]..master
b255a7c resolve merge conflict
26dcbc4 update to env_mach_specific.xsd schema for unit_testing attribute and arguments and arg elements
3d09285 remove all references to lt_archive which will not be supported in CESM2.0
9900f32 Merge pull request #1467 from jedwards4b/schema_fix
7043e29 Merge branch 'jgfouca/remove_total_cores'
965f63e Merge pull request #1464 from ESMCI/jgfouca/remove_total_cores
6b15377 Merge pull request #1462 from jedwards4b/fix_for_quoted_args
cc323c2 Merge pull request #1461 from jedwards4b/more_schema_definitions
15297cd Merge pull request #1453 from jedwards4b/nag_aquap_fix
ce52822 Merge pull request #1450 from ESMCI/jgfouca/upgrade_queue_selection
5619a82 Merge pull request #1455 from jtruesdal/newmaps
a5da759 Merge pull request #1438 from ESMCI/mfdeakin-sandia/script_root_option


Modified files: git diff --name-status [previous_tag]
M       config/acme/config_files.xml
M       config/acme/machines/config_batch.xml
D       config/acme/machines/config_lt_archive.xml
M       config/acme/machines/config_machines.xml
D       config/acme/machines/template.lt_archive
M       config/acme/machines/userdefined_laptop_template/config_machines.xml
M       config/cesm/config_files.xml
M       config/cesm/config_grids.xml
M       config/cesm/machines/config_batch.xml
D       config/cesm/machines/config_lt_archive.xml
M       config/cesm/machines/config_machines.xml
D       config/cesm/machines/template.lt_archive
M       config/cesm/machines/userdefined_laptop_template/config_machines.xml
M       config/config_tests.xml
M       config/xml_schemas/config_batch.xsd
M       config/xml_schemas/config_machines.xsd
M       config/xml_schemas/config_machines_template.xml
A       config/xml_schemas/env_batch.xsd
A       config/xml_schemas/env_mach_pes.xsd
A       config/xml_schemas/env_mach_specific.xsd
D       scripts/Tools/README.post_process
D       scripts/Tools/lt_archive.sh
M       scripts/create_newcase
M       scripts/create_test
M       scripts/lib/CIME/XML/env_batch.py
M       scripts/lib/CIME/XML/env_mach_pes.py
M       scripts/lib/CIME/XML/env_mach_specific.py
D       scripts/lib/CIME/XML/lt_archive.py
M       scripts/lib/CIME/case.py
D       scripts/lib/CIME/case_lt_archive.py
M       scripts/lib/CIME/case_setup.py
M       scripts/lib/CIME/test_scheduler.py
M       scripts/lib/CIME/utils.py
M       scripts/tests/scripts_regression_tests.py
M       src/components/data_comps/docn/docn_comp_mod.F90
M       src/drivers/mct/cime_config/config_component.xml
======================================================================

======================================================================

Originator: Chris Fischer
Date: 5-2-207
Tag: cime5.3.0-alpha.10
Answer Changes: [None, Round Off, Climate Changing]
Tests: scripts_regression_tests.py with PIO_VERSION set to 2 in driver config_components.xml
       scripts_regression test
       ERP_Ln9.f09_f09.F1850_DONOTUSE.yellowstone_intel.cam-outfrq9s_clm5
       summarize_cprnc_diffs by hand
       code-checker
Dependencies:

Brief Summary:
    - Update to version 2.2.1 of the pio external.
    - Update the top-level READMEs.
    - New optional ndep stream from atm.
    - Creation of new aquaplanet capability in DOCN.
    - Fix typo in parse_args.
    - All command line arguments should conform. Allowed for one exception, the -value option to xmlquery.
    - ERP fix again.
    - Pick up multi-instance cprnc.out files in summarize_cprnc_diffs.
    - Fix an issue with pio1 determining if netcdf4 is available and removes a debug print statement.
    - Improve error message when config_files.xml is not found.
    - Fix pylint error.
    - Put explicit dot in paths in some instructions.
    - Remove scripts adjustment of pio settings.


User interface changes:
    - Now accepting only conforming command line arguments.

PR summary: git log --oneline --first-parent [previous_tag]..master
0dcd36c Merge pull request #1447 from jedwards4b/pio2_external_update
357ad45 Merge pull request #1432 from ESMCI/rljacob/README-cleanup
c76d946 Merge pull request #1448 from ESMCI/mvertens/ndep
e5f144d Merge pull request #1451 from ESMCI/mvertens/aquap
d4dfbf1 Merge pull request #1452 from jedwards4b/acme_run_template_fix
505ce67 Merge pull request #1393 from jedwards4b/test_cli
c1e5a38 Merge pull request #1445 from jedwards4b/erp_fix_again
f6c05d1 Merge pull request #1442 from billsacks/summarize_cprnc_multiinst
71cc74e Merge pull request #1425 from jedwards4b/pio1_fixes
aa9018a Merge pull request #1440 from jedwards4b/better_msg_for_config_files_not_found
1089e53 Merge pull request #1446 from ESMCI/jgfouca/fix_pylint_err_nml
3a498d2 Merge pull request #1371 from billsacks/source_file_from_path
ae2a5ca Add Sandia Corporation to CIME LICENSE.TXT
7692745 Merge pull request #1441 from jedwards4b/pio_default_settings


Modified files: git diff --name-status [previous_tag]

M	LICENSE.TXT
D	README
M	README.md
M	config/acme/machines/template.case.run
M	config/acme/machines/template.case.test
M	config/acme/machines/template.lt_archive
M	config/acme/machines/template.st_archive
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/template.case.run
M	config/cesm/machines/template.case.test
M	config/cesm/machines/template.lt_archive
M	config/cesm/machines/template.st_archive
M	scripts/Tools/acme_check_env
M	scripts/Tools/bless_test_results
M	scripts/Tools/case.build
M	scripts/Tools/case.cmpgen_namelists
M	scripts/Tools/case.setup
M	scripts/Tools/case.submit
M	scripts/Tools/case_diff
M	scripts/Tools/check_case
M	scripts/Tools/check_input_data
M	scripts/Tools/check_lockedfiles
M	scripts/Tools/cime_bisect
M	scripts/Tools/code_checker
M	scripts/Tools/compare_namelists
M	scripts/Tools/compare_test_results
M	scripts/Tools/component_compare_baseline
M	scripts/Tools/component_compare_copy
M	scripts/Tools/component_compare_test
M	scripts/Tools/component_generate_baseline
M	scripts/Tools/getTiming
M	scripts/Tools/jenkins_generic_job
M	scripts/Tools/list_acme_tests
M	scripts/Tools/normalize_cases
M	scripts/Tools/pelayout
M	scripts/Tools/preview_namelists
M	scripts/Tools/save_provenance
M	scripts/Tools/simple_compare
M	scripts/Tools/testreporter.py
M	scripts/Tools/update_acme_tests
M	scripts/Tools/wait_for_tests
M	scripts/Tools/xmlchange
M	scripts/Tools/xmlconvertors/config_pes_converter.py
M	scripts/Tools/xmlconvertors/grid_xml_converter.py
M	scripts/Tools/xmlquery
M	scripts/create_clone
M	scripts/create_newcase
M	scripts/create_test
M	scripts/fortran_unit_testing/run_tests.py
M	scripts/lib/CIME/SystemTests/erp.py
M	scripts/lib/CIME/SystemTests/seq.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/files.py
M	scripts/lib/CIME/buildlib.py
M	scripts/lib/CIME/buildnml.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/namelist.py
M	scripts/lib/CIME/utils.py
M	scripts/manage_case
M	scripts/manage_pes
M	scripts/query_testlists
M	scripts/tests/scripts_regression_tests.py
M	src/build_scripts/buildlib.gptl
M	src/build_scripts/buildlib.pio
M	src/components/data_comps/docn/cime_config/buildnml
M	src/components/data_comps/docn/cime_config/config_component.xml
M	src/components/data_comps/docn/cime_config/namelist_definition_docn.xml
M	src/components/data_comps/docn/docn_comp_mod.F90
M	src/drivers/mct/cime_config/namelist_definition_drv_flds.xml
M	src/drivers/mct/shr/seq_flds_mod.F90
A	src/drivers/mct/shr/shr_ndep_mod.F90
M	src/externals/pio1/pio/CMakeLists.txt
M	src/externals/pio1/pio/pionfput_mod.F90.in
M	src/externals/pio2/CMakeLists.txt
M	src/externals/pio2/CTestScript.cmake
M	src/externals/pio2/ctest/CTestEnvironment-anlworkstation.cmake
M	src/externals/pio2/ctest/CTestEnvironment-nwsc.cmake
A	src/externals/pio2/ctest/runcdash-cgd-gnu-openmpi.sh
M	src/externals/pio2/ctest/runcdash-cgd-nag.sh
M	src/externals/pio2/ctest/runcdash-nwsc-intel-mpiserial.sh
M	src/externals/pio2/ctest/runcdash-nwscla-intel.sh
M	src/externals/pio2/ctest/runctest-cgd.sh
M	src/externals/pio2/ctest/runctest-nwscla.sh
M	src/externals/pio2/doc/source/contributing_code.txt
M	src/externals/pio2/examples/c/CMakeLists.txt
A	src/externals/pio2/examples/c/darray_async.c
A	src/externals/pio2/examples/c/darray_no_async.c
M	src/externals/pio2/examples/c/example1.c
M	src/externals/pio2/src/clib/CMakeLists.txt
M	src/externals/pio2/src/clib/bget.c
M	src/externals/pio2/src/clib/config.h.in
M	src/externals/pio2/src/clib/pio.h
M	src/externals/pio2/src/clib/pio_darray.c
M	src/externals/pio2/src/clib/pio_darray_int.c
M	src/externals/pio2/src/clib/pio_file.c
M	src/externals/pio2/src/clib/pio_get_nc.c
M	src/externals/pio2/src/clib/pio_getput_int.c
M	src/externals/pio2/src/clib/pio_internal.h
M	src/externals/pio2/src/clib/pio_lists.c
M	src/externals/pio2/src/clib/pio_msg.c
M	src/externals/pio2/src/clib/pio_nc.c
M	src/externals/pio2/src/clib/pio_nc4.c
M	src/externals/pio2/src/clib/pio_put_nc.c
M	src/externals/pio2/src/clib/pio_rearrange.c
M	src/externals/pio2/src/clib/pio_spmd.c
M	src/externals/pio2/src/clib/pio_varm.c
M	src/externals/pio2/src/clib/pioc.c
M	src/externals/pio2/src/clib/pioc_sc.c
M	src/externals/pio2/src/clib/pioc_support.c
M	src/externals/pio2/tests/cunit/CMakeLists.txt
M	src/externals/pio2/tests/cunit/pio_tests.h
D	src/externals/pio2/tests/cunit/test_async_2comp.c
M	src/externals/pio2/tests/cunit/test_async_3proc.c
M	src/externals/pio2/tests/cunit/test_async_4proc.c
M	src/externals/pio2/tests/cunit/test_async_simple.c
M	src/externals/pio2/tests/cunit/test_darray_1d.c
M	src/externals/pio2/tests/cunit/test_darray_3d.c
A	src/externals/pio2/tests/cunit/test_darray_multi.c
M	src/externals/pio2/tests/cunit/test_darray_multivar.c
A	src/externals/pio2/tests/cunit/test_darray_multivar2.c
A	src/externals/pio2/tests/cunit/test_decomp_uneven.c
M	src/externals/pio2/tests/cunit/test_decomps.c
M	src/externals/pio2/tests/cunit/test_intercomm2.c
M	src/externals/pio2/tests/cunit/test_iosystem2_simple.c
M	src/externals/pio2/tests/cunit/test_pioc.c
M	src/externals/pio2/tests/cunit/test_pioc_fill.c
A	src/externals/pio2/tests/cunit/test_rearr.c
M	src/externals/pio2/tests/cunit/test_shared.c
M	src/externals/pio2/tests/cunit/test_spmd.c
M	src/externals/pio2/tests/general/ncdf_get_put.F90.in
M	src/externals/pio2/tests/general/pio_decomp_frame_tests.F90.in
M	src/externals/pio2/tests/general/util/pio_tutil.F90
M	src/share/util/shr_pio_mod.F90
M	src/share/util/shr_strdata_mod.F90
M	tools/configure
M	tools/cprnc/README
M	tools/cprnc/summarize_cprnc_diffs
M	tools/mapping/check_maps/.gitignore
M	tools/mapping/check_maps/README
M	tools/mapping/check_maps/src/ESMF_RegridWeightGenCheck.F90
M	tools/mapping/check_maps/src/Makefile
M	tools/mapping/gen_domain_files/INSTALL
M	tools/mapping/gen_domain_files/src/Makefile
M	tools/mapping/gen_mapping_files/README
A	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/.gitignore
M	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/README
M	tools/mapping/gen_mapping_files/gen_ESMF_mapping_file/create_ESMF_map.sh
M	tools/mapping/gen_mapping_files/runoff_to_ocn/INSTALL
M	tools/mapping/map_field/INSTALL
M	tools/mapping/map_field/src/Makefile

======================================================================

======================================================================

Originator: Chris Fischer
Date: 4-30-2017
Tag: cime5.3.0-alpha.09
Answer Changes: None
Tests: ERP_Ln9.f09_f09.F1850_DONOTUSE.yellowstone_intel.cam-outfrq9s_clm5
       scripts_regression_tests.py --fast, hand test xmlchange and xmlquery
Dependencies:

Brief Summary:
    - Fix erp test build.
    - Add Support for '+=' in Namelists.
    - Add --component Option to preview_namelist.
    - Add --file option to xmlquery and enable option in xmlchange.

User interface changes:
    - Added support for '+=' to namelist parser.
    - Added --component option to preview_namelist.
    - New --file option in xmlquery.

PR summary: git log --oneline --first-parent [previous_tag]..master
6d8b24b Merge pull request #1444 from jedwards4b/erp_test_fix
84b7bde Merge pull request #1389 from ESMCI/erichlf/namelist/plusEqual
45af658 Merge pull request #1436 from ESMCI/erichlf/preview_namelists/component
c4d4437 Merge pull request #1419 from jedwards4b/xmlcq_fileoption


Modified files: git diff --name-status [previous_tag]

M       scripts/Tools/preview_namelists
M       scripts/Tools/xmlchange
M       scripts/Tools/xmlquery
M       scripts/lib/CIME/SystemTests/erp.py
M       scripts/lib/CIME/XML/env_mach_specific.py
M       scripts/lib/CIME/XML/env_test.py
M       scripts/lib/CIME/XML/generic_xml.py
M       scripts/lib/CIME/case.py
M       scripts/lib/CIME/namelist.py
M       scripts/lib/CIME/preview_namelists.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 4-28-2017
Tag: cime5.3.0-alpha.08
Answer Changes: [None, Round Off, Climate Changing]
Tests: scripts_regression_tests, SMS_D_Ld3.f45_g37_rx1.A.hobart_nag,
        ERS_Ln9.T62_g37.DTEST.yellowstone_intel, CESM prealpha on hobart_nag
Dependencies: cime_config0.0.1.alpha.07, cism2_1_30, clm4_5_15_r235

Brief Summary:
    - Use ESMF7 on yellowstone and cheyenne.
    - Pass annual-average fields to GLC.
    - Give users more info and control over key run commands.
    - Moves unit testing infrastructure from tools/unit_testing to
      scripts/fortran_unit_testing.
    - There were tabs in create_newcase. None prevented the script from
      running, but should be removed for consistency.
    - nag compliler needs an additional library flag when built with debug.
    - Update case members in case_setup.
    - Handle the case when executable is None.
    - Fix big mistake in scripts_regression_tests.
    - Minor changes to xmlchange.
    - Fix minor bug in test_scheduler.
    - Rewrite testreporter into python.
    - Print time built per model.
    - Add input-dir to create_newcase.
    - Get unit test build and run working with serial or parallel pFUnit.
    - Add Support of true and false in Namelist.
    - Remove the cprnc.out files prior to running tests.
    - Fix bug where LockedFiles weren't checked if there was a dot in
      filepath.
    - Addition of new dwav and dlnd compsets and functionality.
    - Errput may be empty string or None.
    - Return aprun args but use executable string from xml.
    - Add illegal char : to check_name test.
    - Simplify netcdf lib args on hobart.
    - Bug fix for DART in case_st_archive.py.
    - Get Fortran unit tests working on cheyenne.
    - Two changes to fix the Fortran unit tests that had gotten broken
      recently.
    - Improve create_test output by dumping case errors directly to screen.
    - Fix NODEFAIL test on cheyenne.
    - Fix indentation problem in case_setup.
    - Allow user_mods directory in compset definition.
    - Fix typo in cori-knl bind command.
    - Big cs.status upgrade.
    - Force user to always go through case.submit.
    - Promote to warning if machine doesn't match probed machine.
    - Make Machines.get_value more likely to return values of the correct
      type.
    - Remove conditional pio1 code.
    - Fixes for PRE test.
    - Set rearr opts using a pio interface.
    - Bring in latest version of PIO1 to CIME.

User interface changes:
    - Moves run_tests.py to scripts/fortran_unit_testing.
    - Adds PET test to cime_developer, PET behavior change.
    - Output time per built component.
    - config_compilers should now give MPILIB and compile_threaded
      attributes for PFUNIT.
    - The default mode of operation for run_tests.py is now serial.
    - Other components that have unit tests (CLM and CAM) will need to
      rework their top-level CMakeLists.txt file slightly.
    - Do not allow ':' in testid or case name.
    - Output changes for create_test.
    - Significant to cs.status.
    - Minor output changes to create_newcase.
    - New PIO1 interface to set rearranger options.
    - Signficant: new preview_run tool and new XML variables.


PR summary: git log --oneline --first-parent [previous_tag]..master
6d8ccb3 Merge pull request #1403 from fvitt/esmf
fe82bd6 Merge pull request #1413 from billsacks/billsacks/glc_tavg_v2
dc29942 Merge pull request #1359 from ESMCI/jgfouca/new_query_tools
9c5b1aa Merge pull request #1428 from billsacks/move_unit_tests
c726ded Merge pull request #1435 from ESMCI/erichlf/create_newcase/tabs2spaces
8924bb3 Merge pull request #1421 from jedwards4b/hobart_nag_fix
f59dd4d Merge pull request #1414 from ESMCI/jgfouca/pet_fix_plus_coverage
67b1be7 Merge pull request #1410 from jedwards4b/executable_none_fix
0fe9e3d Merge pull request #1412 from ESMCI/jgfouca/fix_scripts_regr_test_rc
7c28d90 Merge pull request #1405 from ESMCI/jgfouca/xmlchange_append_add_space
68ab80b Merge pull request #1406 from ESMCI/jgfouca/test_sched_bugfix
da9d3b8 Merge pull request #1299 from ESMCI/fischer/testreporter_rewrite_python
f8f0fec Merge pull request #1402 from ESMCI/jgfouca/show_build_time_per_component
dc1a7ce Merge pull request #1401 from ESMCI/jgfouca/add_input_dir_to_create_newcase
962b20b Merge pull request #1396 from billsacks/compiler_from_macros
af32abd Merge pull request #1395 from ESMCI/erichlf/Build/Namelist.pm
9f5d489 Merge pull request #1394 from jedwards4b/system_test_rerun_improvement
1db632a Merge pull request #1391 from ESMCI/sarich/fix_bug_in_check_lockedfiles
5cda778 Merge pull request #1365 from ESMCI/mvertens/data_wave
2742c17 Merge pull request #1390 from ESMCI/jgfouca/fix_bug_in_errput_run_cmd
6dd85dd Merge pull request #1385 from jedwards4b/aprun_fix
4fb16a1 Merge pull request #1383 from jedwards4b/new_illegal_char
40a6017 Merge pull request #1386 from jedwards4b/hobart_netcdf_slib_fix
5a141f8 Merge pull request #1375 from ESMCI/bertinia/st_archive
06c5645 Merge pull request #1381 from billsacks/cheyenne_unit_tests
9629886 Merge pull request #1378 from jedwards4b/funit_test_fix
d79922e Merge pull request #1377 from ESMCI/jgfouca/improve_create_test_output
9d9f09c Merge pull request #1370 from ESMCI/jgfouca/minor_fix_for_cheyenne
a99eab3 Merge pull request #1373 from jedwards4b/pio_adjust_indentation_fix
ca289d9 Merge pull request #1366 from ESMCI/mvertens/usermods_in_compset
aaee38a Merge pull request #1369 from jedwards4b/cori-knlfix
d0e277d Merge pull request #1363 from ESMCI/jgfouca/big_cs_status_upgrade
dd5a30b Merge pull request #1362 from ESMCI/jgfouca/force_resubmit_to_use_submit
8282a8f Merge pull request #1361 from ESMCI/jgfouca/inform_user_of_machine
2530c66 Merge pull request #1360 from ESMCI/jgfouca/machine_get_value_type
1335a62 Merge pull request #1357 from ESMCI/jayeshkrishna/rem_cond_pio1_code
9903472 Merge pull request #1350 from gold2718/pausePOP
9f9da67 Merge pull request #1354 from ESMCI/jayeshkrishna/pio_use_set_rearr_opts
be0f9a4 Merge pull request #1352 from ESMCI/jayeshkrishna/bring_latest_pio1


Modified files: git diff --name-status [previous_tag]

M	CMakeLists.txt
D	README.unit_testing
M	config/acme/machines/config_compilers.xml
M	config/acme/machines/userdefined_laptop_template/config_compilers.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/userdefined_laptop_template/config_compilers.xml
M	config/config_tests.xml
M	config/xml_schemas/config_compsets.xsd
M	config/xml_schemas/config_grids_v2.xsd
M	config/xml_schemas/config_machines.xsd
A	scripts/Tools/cs.status
D	scripts/Tools/cs_status
A	scripts/Tools/preview_run
A	scripts/Tools/testreporter.py
M	scripts/Tools/xmlchange
M	scripts/create_newcase
M	scripts/create_test
A	scripts/fortran_unit_testing/Examples/circle_area/src/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/circle_area/src/circle.F90
A	scripts/fortran_unit_testing/Examples/circle_area/tests/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/circle_area/tests/CTest/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/circle_area/tests/CTest/test_driver.F90
A	scripts/fortran_unit_testing/Examples/circle_area/tests/pFUnit/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/circle_area/tests/pFUnit/test_circle.pf
A	scripts/fortran_unit_testing/Examples/interpolate_1d/src/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/interpolate_1d/src/interpolate_1d.F90
A	scripts/fortran_unit_testing/Examples/interpolate_1d/tests/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/interpolate_1d/tests/CTest/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/interpolate_1d/tests/CTest/test_driver.F90
A	scripts/fortran_unit_testing/Examples/interpolate_1d/tests/pFUnit/CMakeLists.txt
A	scripts/fortran_unit_testing/Examples/interpolate_1d/tests/pFUnit/test_interpolate_point.pf
A	scripts/fortran_unit_testing/Examples/test_list.xml
A	scripts/fortran_unit_testing/README
A	scripts/fortran_unit_testing/python/.gitignore
A	scripts/fortran_unit_testing/python/printer.py
A	scripts/fortran_unit_testing/python/test_xml_test_list.py
A	scripts/fortran_unit_testing/python/xml_test_list.py
A	scripts/fortran_unit_testing/run_tests.py
M	scripts/lib/CIME/BuildTools/cmakemacroswriter.py
M	scripts/lib/CIME/BuildTools/configure.py
M	scripts/lib/CIME/SystemTests/nck.py
M	scripts/lib/CIME/SystemTests/nodefail.py
M	scripts/lib/CIME/SystemTests/pre.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/XML/compsets.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/machines.py
A	scripts/lib/CIME/XML/test_reporter.py
M	scripts/lib/CIME/aprun.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/case_test.py
M	scripts/lib/CIME/check_lockedfiles.py
M	scripts/lib/CIME/code_checker.py
M	scripts/lib/CIME/nmlgen.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/test_status.py
A	scripts/lib/CIME/tests/test_user_mod_support.py
M	scripts/lib/CIME/user_mod_support.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/cs.status.template
A	scripts/lib/testreporter.template
M	scripts/lib/update_acme_tests.py
M	scripts/tests/scripts_regression_tests.py
M	src/components/data_comps/datm/cime_config/config_component.xml
M	src/components/data_comps/datm/cime_config/namelist_definition_datm.xml
M	src/components/data_comps/datm/datm_comp_mod.F90
M	src/components/data_comps/desp/desp_comp_mod.F90
M	src/components/data_comps/desp/esp_comp_mct.F90
M	src/components/data_comps/dice/cime_config/config_component.xml
M	src/components/data_comps/dice/cime_config/namelist_definition_dice.xml
M	src/components/data_comps/dice/dice_comp_mod.F90
M	src/components/data_comps/dlnd/cime_config/buildnml
M	src/components/data_comps/dlnd/cime_config/config_component.xml
M	src/components/data_comps/docn/cime_config/config_component.xml
M	src/components/data_comps/docn/cime_config/namelist_definition_docn.xml
M	src/components/data_comps/docn/docn_comp_mod.F90
M	src/components/data_comps/drof/cime_config/namelist_definition_drof.xml
M	src/components/data_comps/drof/drof_comp_mod.F90
M	src/components/data_comps/dwav/cime_config/buildnml
M	src/components/data_comps/dwav/cime_config/config_component.xml
M	src/components/data_comps/dwav/cime_config/namelist_definition_dwav.xml
M	src/components/data_comps/dwav/dwav_comp_mod.F90
M	src/drivers/mct/cime_config/buildexe
M	src/drivers/mct/cime_config/buildnml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_acme.xml
M	src/drivers/mct/cime_config/config_component_cesm.xml
M	src/drivers/mct/cime_config/config_compsets.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
M	src/drivers/mct/main/cesm_comp_mod.F90
M	src/drivers/mct/main/prep_glc_mod.F90
M	src/drivers/mct/main/seq_io_mod.F90
M	src/drivers/mct/main/seq_rest_mod.F90
M	src/drivers/mct/shr/seq_comm_mct.F90
M	src/drivers/mct/shr/seq_infodata_mod.F90
M	src/drivers/mct/shr/seq_timemgr_mod.F90
M	src/drivers/mct/unit_test/CMakeLists.txt
M	src/drivers/mct/unit_test/stubs/CMakeLists.txt
A	src/drivers/mct/unit_test/stubs/seq_timemgr_mod.F90
A	src/externals/CMake/CIME_initial_setup.cmake
M	src/externals/CMake/CIME_utils.cmake
M	src/externals/CMake/README.md
M	src/externals/CMake/pFUnit_utils.cmake
M	src/externals/pio1/pio/CMakeLists.txt
M	src/externals/pio1/pio/pio.F90
M	src/externals/pio1/pio/piolib_mod.F90
M	src/share/unit_test_stubs/pio/pio.F90.in
M	src/share/util/shr_pio_mod.F90
D	tools/unit_testing/Examples/circle_area/src/CMakeLists.txt
D	tools/unit_testing/Examples/circle_area/src/circle.F90
D	tools/unit_testing/Examples/circle_area/tests/CMakeLists.txt
D	tools/unit_testing/Examples/circle_area/tests/CTest/CMakeLists.txt
D	tools/unit_testing/Examples/circle_area/tests/CTest/test_driver.F90
D	tools/unit_testing/Examples/circle_area/tests/pFUnit/CMakeLists.txt
D	tools/unit_testing/Examples/circle_area/tests/pFUnit/test_circle.pf
D	tools/unit_testing/Examples/interpolate_1d/src/CMakeLists.txt
D	tools/unit_testing/Examples/interpolate_1d/src/interpolate_1d.F90
D	tools/unit_testing/Examples/interpolate_1d/tests/CMakeLists.txt
D	tools/unit_testing/Examples/interpolate_1d/tests/CTest/CMakeLists.txt
D	tools/unit_testing/Examples/interpolate_1d/tests/CTest/test_driver.F90
D	tools/unit_testing/Examples/interpolate_1d/tests/pFUnit/CMakeLists.txt
D	tools/unit_testing/Examples/interpolate_1d/tests/pFUnit/test_interpolate_point.pf
D	tools/unit_testing/Examples/test_list.xml
D	tools/unit_testing/README
D	tools/unit_testing/python/.gitignore
D	tools/unit_testing/python/comparable.py
D	tools/unit_testing/python/environment.py
D	tools/unit_testing/python/machine_setup.py
D	tools/unit_testing/python/printer.py
D	tools/unit_testing/python/test_environment.py
D	tools/unit_testing/python/test_xml_test_list.py
D	tools/unit_testing/python/test_xml_utils.py
D	tools/unit_testing/python/xml_test_list.py
D	tools/unit_testing/python/xml_utils.py
D	tools/unit_testing/run_tests.py
M	utils/perl5lib/Build/Namelist.pm
======================================================================

======================================================================

Originator: Chris Fischer
Date: 4-14-2017
Tag: cime5.3.0-alpha.07
Answer Changes: None
Tests on various PRs: by-hand, code_checker, pylint, scripts_regression_tests,
       cime_developer with gnu compiler on cheyenne, All gnu debug tests in CESM
       test suites, create B compset with ww3 at T31 resolution,
       J_TestCreateNewcase, some cesm tests on cori-knl
Dependencies:

Brief Summary:
	-Updates to get going on cori-knl
	-Update domain_b in nnsm map
	-Fix bug where create_test was not handling user-selected projects correctly
	 in the case where the test_root depended on PROJECT.
	-HOMME Improvement
	-Unit testing: Determine machine-specific settings automatically
	-Mapping/update runoff to ocn
	-Fixes an issue with --user-compset flag
	-Fixes for cheyenne issue
	-Validate the case and test_id arguments
	-Add more checks for gnu in debug mode.
	-Avoid a problem with pio_typename in clone with keepexe.
	-Fix blues NETCDFROOT unresolved error.
	-Fix TOTAL_CORES.
	-Refactor BUILD_THREADED to match documentation.
	-Refactor run_cmd to handle file output streams more easily.
	-More-robust way of getting path to create_test.
	-Better content in TestStatus.log file.
	-Improved formatting/content of TestStatus.log
	-Better handling of poorly implemented batch systems.
	-Fix atm grid match for T31 atm2wav map.
	-Change flag for answer to create_newcase
	-Fix bug in xmlquery, add regr test to catch in future
	-Improve error message when user forgets --user-compset.
	-Cleanup TEST_ROOT if everything works.
	-Reduce newlines in CaseStatus.

User interface changes:
	-BUILD_THREADED behaves differently
	-for create_newcase, --answer becomes --handle-preexisting-dirs
	-Formatting changes to CaseStatus

PR summary: git log --oneline --first-parent [previous_tag]..master
30243ac Merge pull request #1351 from jedwards4b/cori_update
1f4c4e9 Merge pull request #1349 from mnlevy1981/mapping/runoff_metadata_bugfix
7664249 Merge pull request #1348 from ESMCI/jgfouca/fix_custom_proj_test_root
6156e0a Merge pull request #1346 from ESMCI/jgfouca/homme_improvement
3779ec1 Merge pull request #1343 from billsacks/run_tests_defaults
5074c4a Merge pull request #1280 from mnlevy1981/mapping/update_runoff_to_ocn
60bfc01 Merge pull request #1341 from jedwards4b/user-compset
5e79b04 Merge pull request #1340 from jedwards4b/cheyenne_fixes
37aac0f Merge pull request #1337 from jedwards4b/validate_case_and_test_id_args
5edf3fa Merge pull request #1339 from billsacks/gnu_debug_checks
82b6181 Merge pull request #1305 from jedwards4b/clone_keepexe_and_pio_typename
4d62d80 Merge pull request #1333 from ESMCI/sarich/fix-blues-netcdfroot
12bc9b3 Merge pull request #1336 from ESMCI/jgfouca/fix_total_cores
1adf8d1 Merge pull request #1335 from ESMCI/jgfouca/cleanup_build_threaded
315e849 Merge pull request #1326 from ESMCI/jgfouca/refactor_run_cmd
997ec60 Merge pull request #1321 from ESMCI/jgfouca/cime_bisect_robustness
cb7bd10 Merge pull request #1317 from ESMCI/jgfouca/better_testlog_content
7fb258b Merge pull request #1316 from ESMCI/jgfouca/handle_titan_batch_errs
2b4f7fe Merge pull request #1320 from billsacks/t31_wav_map
7370b02 Merge pull request #1311 from ESMCI/jgfouca/better_name_for_answer
b14ebe0 Merge pull request #1312 from ESMCI/jgfouca/fix_xmlquery_listall
f741180 Merge pull request #1314 from billsacks/user_compset_errmsg
243fafa Merge pull request #1310 from ESMCI/jgfouca/better_regr_cleanup
a4c7ab7 Merge pull request #1307 from ESMCI/jgfouca/remove_useless_newlines_from_casestatus


Modified files: git diff --name-status [previous_tag]
M	README.unit_testing
M	config/acme/machines/config_machines.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_batch.xml
M	config/cesm/machines/config_compilers.xml
M	config/cesm/machines/config_machines.xml
M	config/cesm/machines/config_pio.xml
M	config/xml_schemas/config_machines.xsd
M	scripts/Tools/cime_bisect
M	scripts/Tools/xmlquery
M	scripts/create_clone
M	scripts/create_newcase
M	scripts/create_test
M	scripts/lib/CIME/SystemTests/erp.py
M	scripts/lib/CIME/SystemTests/homme.py
M	scripts/lib/CIME/SystemTests/system_tests_common.py
M	scripts/lib/CIME/SystemTests/system_tests_compare_two.py
M	scripts/lib/CIME/XML/compsets.py
M	scripts/lib/CIME/XML/entry_id.py
M	scripts/lib/CIME/XML/env_base.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/machines.py
M	scripts/lib/CIME/aprun.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/hist_utils.py
M	scripts/lib/CIME/preview_namelists.py
M	scripts/lib/CIME/provenance.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/CIME/wait_for_tests.py
M	scripts/tests/scripts_regression_tests.py
M	src/drivers/mct/cime_config/config_component.xml
M	src/externals/pio1/timing/COPYING
M	src/externals/pio2/src/gptl/COPYING
M	src/share/timing/COPYING
M	src/share/util/mct_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/INSTALL
M	tools/mapping/gen_mapping_files/runoff_to_ocn/README
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_r05_to_gx1v7_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_r05_to_gx3v7_nnsm_e1000r500.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_rx1_to_gx1v7_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_rx1_to_gx3v7_nnsm_e1000r500.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_wr50a_to_ar9v4_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/map_wr50a_to_gx3v7_nnsm_e1000r300.nml
A	tools/mapping/gen_mapping_files/runoff_to_ocn/maps/.gitignore
A	tools/mapping/gen_mapping_files/runoff_to_ocn/ncl/merge_mapping_files.ncl
A	tools/mapping/gen_mapping_files/runoff_to_ocn/run_merge_mapping_files.sh
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map.nml
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map_r05_gx3v7.nml
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map_rx1_gx1v6.nml
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map_tx01.nml
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map_wr50a_ar9v4.nml
D	tools/mapping/gen_mapping_files/runoff_to_ocn/runoff_map_wr50a_gx3v7.nml
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/Makefile
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/fixroff_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/kind_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/main.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/map_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/mapsort_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/shr_kind_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/shr_sys_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/shr_timer_mod.F90
M	tools/mapping/gen_mapping_files/runoff_to_ocn/src/smooth_mod.F90
M	tools/unit_testing/run_tests.py

======================================================================

Originator:Chris Fischer
Date: 4-4-2017
Tag: cime5.3.0-alpha.06
Answer Changes: None
Tests: code_checker, NODEFAIL
Dependencies:

Brief Summary:
    - Fix handling of spare nodes

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
95019a3 Merge pull request #1302 from ESMCI/jgfouca/fixes_to_recent_prs

Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/XML/env_mach_pes.py
M       scripts/lib/CIME/case.py
M       scripts/lib/CIME/case_run.py

======================================================================

Originator: Chris Fischer
Date: 4-4-2017
Tag: cime5.3.0-alpha.05
Answer Changes: None
Tests: scripts_regression_test, code checker
Dependencies:

Brief Summary:
    - First try to support titan restart.
    - Pull back ACME repo changes of CIME since last subtree split (late
      January?) up to March 29 back into CIME master.
    - Allow a custom input root through create_test.
    - Update pio stubs to include new derived field needed in pio_init.
    - Set a default value for esmf_logging so it does not have to appear in
      drv_in.
    - Add logging options to ESMF_Initialize
    - Fix pylint issues.
    - Fix manage_case --query-grids for cesm.
    - Adds support for namelist entries of the form foo(3) = 'a'
    - Add mpilib and compiler command line options to configure.
    - summarize_cprnc_diffs: Print unnormalized RMS diffs.
    - Make sure pio_typename is valid.
    - New hooks for runnning external scripts for pre-run and post-run.
    - Enable PIO rearranger options for PIO2.
    - code_checker needs to work outside of ESMCI/CIME.
    - Fix pylint error in buildnml.
    - Add flags to make create_newcase non-interactive.
    - Added mct/cime_config/namelist_definition_drv_flds.xml with updated
      schema.
    - Some driver code no longer needed to do this for cam.
    - Supress a future warning on the use of condition in expect subroutine.
    - Couple fixes to recent PR that added SUBMIT phase.

User interface changes:
    - Add --input-dir argument to create_test
    - esmf_logging (and therefore drv_in) are now optional
    - New run time XML variable: ESMF_LOGFILE_KIND
    - New --answer flag to create_newcase
    - Removes a distracting warning

PR summary: git log --oneline --first-parent [previous_tag]..master
eeb1e2c Merge pull request #1275 from ESMCI/jgfouca/titan_restart
fbf1b0c Merge pull request #1287 from ESMCI/agsalin/merge-from-acme-03292017
dda631e Merge pull request #1298 from ESMCI/jgfouca/allow_custom_input_root
2dc9a8a Merge pull request #1301 from jedwards4b/unit_test_stubs_update
3d76b10 Merge pull request #1300 from gold2718/esmfLog
0d320ec Merge pull request #1289 from gold2718/esmfLog
8890873 Merge pull request #1290 from ESMCI/jgfouca/grids_pylint_fixes
55a084b Merge pull request #1285 from ESMCI/mvertens/manage_case
9d8396a Merge pull request #1259 from jedwards4b/index_in_namelist
4e125ee Merge pull request #1268 from jedwards4b/configure_update
9759e15 Merge pull request #1279 from billsacks/summarize_rms
840ae3c Merge pull request #1273 from jedwards4b/pio_typename_fix
07e61ed Merge pull request #1256 from ESMCI/mvertens/phys_cycle
85f831d Merge pull request #1260 from ESMCI/jayeshkrishna/enable_rearr_opts_pio2
fbfa996 Merge pull request #1269 from ESMCI/jgfouca/code_checker_work_outside_esmci
300cbf3 Merge pull request #1253 from ESMCI/jgfouca/pylint_fix_to_buildnml
d44970c Merge pull request #1249 from ESMCI/jgfouca/create_newcase_non_interactive
8270602 Merge pull request #1231 from ESMCI/mvertens/drv_flds_in
5f3072c Merge pull request #1237 from jedwards4b/jpe_fix_atm_simple_settings
ffa61ea Merge pull request #1242 from jedwards4b/jpe/futurewarning
fecaaad Merge pull request #1240 from ESMCI/jgfouca/fixes_to_submit_phase_pr


Modified files: git diff --name-status [previous_tag]
M	config/acme/allactive/config_pes.xml
M	config/acme/allactive/config_pesall.xml
M	config/acme/config_archive.xml
M	config/acme/config_files.xml
M	config/acme/config_grids.xml
M	config/acme/machines/Makefile
M	config/acme/machines/config_batch.xml
M	config/acme/machines/config_compilers.xml
M	config/acme/machines/config_machines.xml
M	config/acme/machines/config_pio.xml
A	config/acme/machines/syslog.anvil
A	config/acme/testmods_dirs/allactive/cam/outfrq9s/xmlchange_cmnds
A	config/acme/testmods_dirs/allactive/force_netcdf_pio/shell_commands
A	config/acme/testmods_dirs/allactive/force_netcdf_pio/xmlchange_cmnds
M	config/cesm/config_files.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/config_pio.xml
M	config/config_tests.xml
M	scripts/Tools/check_input_data
M	scripts/create_newcase
M	scripts/create_test
M	scripts/lib/CIME/BuildTools/configure.py
M	scripts/lib/CIME/BuildTools/macrowriterbase.py
M	scripts/lib/CIME/SystemTests/dae.py
M	scripts/lib/CIME/SystemTests/homme.py
A	scripts/lib/CIME/SystemTests/nodefail.py
M	scripts/lib/CIME/XML/compilers.py
M	scripts/lib/CIME/XML/entry_id.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/XML/env_mach_pes.py
M	scripts/lib/CIME/XML/env_mach_specific.py
M	scripts/lib/CIME/XML/grids.py
M	scripts/lib/CIME/XML/namelist_definition.py
A	scripts/lib/CIME/aprun.py
M	scripts/lib/CIME/bless_test_results.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/buildnml.py
M	scripts/lib/CIME/case.py
M	scripts/lib/CIME/case_run.py
M	scripts/lib/CIME/case_setup.py
M	scripts/lib/CIME/case_st_archive.py
M	scripts/lib/CIME/case_submit.py
M	scripts/lib/CIME/code_checker.py
M	scripts/lib/CIME/get_timing.py
M	scripts/lib/CIME/namelist.py
M	scripts/lib/CIME/nmlgen.py
M	scripts/lib/CIME/preview_namelists.py
M	scripts/lib/CIME/test_scheduler.py
M	scripts/lib/CIME/utils.py
M	scripts/lib/update_acme_tests.py
M	scripts/manage_case
M	scripts/tests/scripts_regression_tests.py
M	src/build_scripts/buildlib.pio
M	src/components/data_comps/datm/cime_config/buildnml
M	src/components/data_comps/desp/cime_config/buildnml
M	src/components/data_comps/dice/cime_config/buildnml
M	src/components/data_comps/dlnd/cime_config/buildnml
M	src/components/data_comps/docn/cime_config/buildnml
M	src/components/data_comps/drof/cime_config/buildnml
M	src/components/data_comps/dwav/cime_config/buildnml
D	src/drivers/mct/bld/namelist_files/namelist_defaults_drv.xml
D	src/drivers/mct/bld/namelist_files/namelist_definition_drv.xml
D	src/drivers/mct/bld/namelist_files/namelist_definition_drv_flds.xml
D	src/drivers/mct/bld/namelist_files/namelist_definition_modio.xml
D	src/drivers/mct/bld/testdir/Buildconf/camconf/drv_flds_in
D	src/drivers/mct/bld/testdir/Buildconf/clmconf/drv_flds_in
D	src/drivers/mct/bld/testdir/env_build.xml
D	src/drivers/mct/bld/testdir/env_case.xml
D	src/drivers/mct/bld/testdir/env_mach_pes.xml
D	src/drivers/mct/bld/testdir/env_run.xml
D	src/drivers/mct/bld/testdir/runtest
D	src/drivers/mct/bld/testdir/user_nl_cpl
M	src/drivers/mct/cime_config/buildnml
M	src/drivers/mct/cime_config/config_component.xml
M	src/drivers/mct/cime_config/config_component_acme.xml
M	src/drivers/mct/cime_config/namelist_definition_drv.xml
A	src/drivers/mct/cime_config/namelist_definition_drv_flds.xml
M	src/drivers/mct/main/cesm_driver.F90
M	src/drivers/mct/shr/seq_comm_mct.F90
M	src/externals/pio1/pio/CMakeLists.txt
M	src/share/esmf_wrf_timemgr/ESMF_Stubs.F90
M	src/share/unit_test_stubs/pio/pio.F90.in
M	src/share/util/shr_pio_mod.F90
M	tools/Readme.configure
M	tools/configure
M	tools/cprnc/summarize_cprnc_diffs
M	tools/mapping/map_field/src/map_field.F90

======================================================================

Originator: Chris Fischer
Date: 3-14-2017
Tag: cime5.3.0-alpha.04
Answer Changes: Answer changes for gx3v7
Tests: scripts_regression_test, SMS.f09_g16.B1850
Dependencies:

Brief Summary:
  -Need to set RTM to NULL in both cases in order to have this work with fix
   needed for upcoming pythonization of rtm and mosart buildnml
  -Improve create_test output
  -Remove a misleading print statement from tests.
  -Better way to handle batch errors.
  -Change in location of $SRCROOT/config/allactive to $SRCROOT/cime_config.
  -Update so that all relevent grids contain a mask variable.

User interface changes: New SUBMIT phase!

PR summary: git log --oneline --first-parent [previous_tag]..master
34a244a Merge pull request #1239 from ESMCI/mvertens/fix_ssptest
867711d Merge pull request #1238 from ESMCI/jgfouca/create_test_better_output
d050c08 Merge pull request #1235 from jedwards4b/mask_updates
5058c33 Merge pull request #1234 from ESMCI/fischer/config_cesm_allactive_mv
64d6bd2 Merge pull request #1230 from ESMCI/jgfouca/add_submit_phase_2
dec7437 Merge pull request #1232 from jedwards4b/remove_incorrect_statement



Modified files: git diff --name-status [previous_tag]
M       config/cesm/config_files.xml
M       config/cesm/config_grids.xml
M       config/xml_schemas/config_grids_v2.xsd
M       scripts/lib/CIME/SystemTests/ssp.py
M       scripts/lib/CIME/SystemTests/system_tests_common.py
M       scripts/lib/CIME/XML/env_batch.py
M       scripts/lib/CIME/case_submit.py
M       scripts/lib/CIME/case_test.py
M       scripts/lib/CIME/test_scheduler.py
M       scripts/lib/CIME/test_status.py
M       scripts/tests/scripts_regression_tests.p

======================================================================
Originator: Chris Fischer
Date: 3-11-2017
Tag: cime5.3.0-alpha.03
Answer Changes: None
Tests: scripts_regression_tests, various CESM tests.
Dependencies:

Brief Summary:
   Added new aliases for resolutions supporting a gx1v7 mask.
   Move location of config/cesm/allactive.
   Get rid of hard coded comp_class settings and use get_values instead.
   Fix build model message.
   Ignore prereq if forced.
   Additional include path needed for cmake check_function_exists.
   PIO 2 import.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
   3627e16 Merge pull request #1228 from jtruesdal/add_gx1v7
   7b10920 Merge pull request #1227 from ESMCI/fischer/config_cesm_allactive_mv
   ab579b3 Merge pull request #1226 from jedwards4b/compclasses_cleanup
   dc0a87c Merge pull request #1225 from ESMCI/jgfouca/fix_build_msg
   5f4f989 Merge pull request #1218 from jedwards4b/ignore_prereq_if_forced
   ff3d97f Merge pull request #1219 from jedwards4b/cmake_module_fix
   37fe05b Merge pull request #1202 from jedwards4b/pio2_import

Modified files: git diff --name-status [previous_tag]
M	config/acme/machines/Makefile
M	config/cesm/config_files.xml
M	config/cesm/config_grids.xml
M	config/cesm/machines/Makefile
M	scripts/lib/CIME/SystemTests/pem.py
M	scripts/lib/CIME/SystemTests/pet.py
M	scripts/lib/CIME/XML/env_batch.py
M	scripts/lib/CIME/build.py
M	scripts/lib/CIME/get_timing.py
M	scripts/lib/CIME/test_scheduler.py
M	src/build_scripts/buildlib.pio
M	src/components/data_comps/docn/cime_config/config_component.xml
M	src/externals/pio2/CMakeLists.txt
M	src/externals/pio2/CTestConfig.cmake
M	src/externals/pio2/CTestScript.cmake
M	src/externals/pio2/cmake/FindNetCDF.cmake
M	src/externals/pio2/cmake/LibCheck.cmake
M	src/externals/pio2/cmake/LibMPI.cmake
A	src/externals/pio2/cmake/mpiexec.nwscla
A	src/externals/pio2/cmake/mpiexec.olcf
A	src/externals/pio2/ctest/CTestEnvironment-anlworkstation.cmake
M	src/externals/pio2/ctest/CTestEnvironment-nwsc.cmake
A	src/externals/pio2/ctest/CTestEnvironment-nwscla.cmake
M	src/externals/pio2/ctest/runcdash-alcf-ibm.sh
A	src/externals/pio2/ctest/runcdash-anlworkstation.sh
M	src/externals/pio2/ctest/runcdash-cgd-nag.sh
M	src/externals/pio2/ctest/runcdash-nersc-cray.sh
M	src/externals/pio2/ctest/runcdash-nersc-intel.sh
M	src/externals/pio2/ctest/runcdash-nwsc-gnu.sh
M	src/externals/pio2/ctest/runcdash-nwsc-intel-mpiserial.sh
M	src/externals/pio2/ctest/runcdash-nwsc-intel.sh
M	src/externals/pio2/ctest/runcdash-nwsc-pgi.sh
A	src/externals/pio2/ctest/runcdash-nwscla-intel.sh
A	src/externals/pio2/ctest/runctest-anlworkstation.sh
M	src/externals/pio2/ctest/runctest-cgd.sh
M	src/externals/pio2/ctest/runctest-nersc.sh
A	src/externals/pio2/ctest/runctest-nwscla.sh
M	src/externals/pio2/doc/CMakeLists.txt
M	src/externals/pio2/doc/Doxyfile.in
M	src/externals/pio2/doc/source/Error.txt
M	src/externals/pio2/doc/source/Examples.txt
M	src/externals/pio2/doc/source/Installing.txt
A	src/externals/pio2/doc/source/Testing.txt
M	src/externals/pio2/doc/source/base.txt
A	src/externals/pio2/doc/source/contributing_code.txt
M	src/externals/pio2/doc/source/mach_walkthrough.txt
M	src/externals/pio2/examples/CMakeLists.txt
M	src/externals/pio2/examples/c/CMakeLists.txt
M	src/externals/pio2/examples/c/example1.c
M	src/externals/pio2/examples/c/example2.c
M	src/externals/pio2/examples/c/examplePio.c
A	src/externals/pio2/examples/c/valsupp_example1.supp
M	src/externals/pio2/examples/f03/CMakeLists.txt
M	src/externals/pio2/examples/f03/examplePio.f90
M	src/externals/pio2/src/CMakeLists.txt
M	src/externals/pio2/src/clib/CMakeLists.txt
M	src/externals/pio2/src/clib/bget.c
M	src/externals/pio2/src/clib/bget.h
M	src/externals/pio2/src/clib/config.h.in
D	src/externals/pio2/src/clib/ncparser.pl
D	src/externals/pio2/src/clib/ncputgetparser.pl
M	src/externals/pio2/src/clib/pio.h
D	src/externals/pio2/src/clib/pio_c_get_template.c
D	src/externals/pio2/src/clib/pio_c_put_template.c
D	src/externals/pio2/src/clib/pio_c_template.c
M	src/externals/pio2/src/clib/pio_darray.c
A	src/externals/pio2/src/clib/pio_darray_int.c
M	src/externals/pio2/src/clib/pio_file.c
M	src/externals/pio2/src/clib/pio_get_nc.c
A	src/externals/pio2/src/clib/pio_getput_int.c
M	src/externals/pio2/src/clib/pio_internal.h
M	src/externals/pio2/src/clib/pio_lists.c
A	src/externals/pio2/src/clib/pio_msg.c
M	src/externals/pio2/src/clib/pio_nc.c
M	src/externals/pio2/src/clib/pio_nc4.c
M	src/externals/pio2/src/clib/pio_put_nc.c
M	src/externals/pio2/src/clib/pio_rearrange.c
M	src/externals/pio2/src/clib/pio_spmd.c
A	src/externals/pio2/src/clib/pio_varm.c
M	src/externals/pio2/src/clib/pioc.c
M	src/externals/pio2/src/clib/pioc_sc.c
M	src/externals/pio2/src/clib/pioc_support.c
M	src/externals/pio2/src/clib/topology.c
M	src/externals/pio2/src/flib/CMakeLists.txt
M	src/externals/pio2/src/flib/pio.F90
M	src/externals/pio2/src/flib/pio_nf.F90
M	src/externals/pio2/src/flib/pio_types.F90
M	src/externals/pio2/src/flib/piodarray.F90.in
M	src/externals/pio2/src/flib/piolib_mod.F90
M	src/externals/pio2/src/flib/pionfatt_mod.F90.in
M	src/externals/pio2/src/flib/pionfget_mod.F90.in
M	src/externals/pio2/src/flib/pionfput_mod.F90.in
M	src/externals/pio2/src/gptl/CMakeLists.txt
M	src/externals/pio2/src/gptl/gptl.c
M	src/externals/pio2/src/gptl/perf_mod.F90
M	src/externals/pio2/tests/CMakeLists.txt
A	src/externals/pio2/tests/cunit/CMakeLists.txt
A	src/externals/pio2/tests/cunit/pio_tests.h
A	src/externals/pio2/tests/cunit/test_async_2comp.c
A	src/externals/pio2/tests/cunit/test_async_3proc.c
A	src/externals/pio2/tests/cunit/test_async_4proc.c
A	src/externals/pio2/tests/cunit/test_async_simple.c
A	src/externals/pio2/tests/cunit/test_common.c
A	src/externals/pio2/tests/cunit/test_darray.c
A	src/externals/pio2/tests/cunit/test_darray_1d.c
A	src/externals/pio2/tests/cunit/test_darray_3d.c
A	src/externals/pio2/tests/cunit/test_darray_multivar.c
A	src/externals/pio2/tests/cunit/test_decomps.c
A	src/externals/pio2/tests/cunit/test_intercomm2.c
A	src/externals/pio2/tests/cunit/test_iosystem2.c
A	src/externals/pio2/tests/cunit/test_iosystem2_simple.c
A	src/externals/pio2/tests/cunit/test_iosystem2_simple2.c
A	src/externals/pio2/tests/cunit/test_iosystem3.c
A	src/externals/pio2/tests/cunit/test_iosystem3_simple.c
A	src/externals/pio2/tests/cunit/test_iosystem3_simple2.c
A	src/externals/pio2/tests/cunit/test_pioc.c
A	src/externals/pio2/tests/cunit/test_pioc_fill.c
A	src/externals/pio2/tests/cunit/test_pioc_putget.c
A	src/externals/pio2/tests/cunit/test_pioc_unlim.c
A	src/externals/pio2/tests/cunit/test_shared.c
A	src/externals/pio2/tests/cunit/test_spmd.c
M	src/externals/pio2/tests/general/CMakeLists.txt
A	src/externals/pio2/tests/general/README.md
M	src/externals/pio2/tests/general/ncdf_fail.F90.in
M	src/externals/pio2/tests/general/ncdf_get_put.F90.in
A	src/externals/pio2/tests/general/ncdf_inq.F90.in
D	src/externals/pio2/tests/general/pio_decomp_fillval2.F90
A	src/externals/pio2/tests/general/pio_decomp_frame_tests.F90.in
M	src/externals/pio2/tests/general/pio_decomp_tests.F90.in
A	src/externals/pio2/tests/general/pio_decomp_tests_1d.F90.in
A	src/externals/pio2/tests/general/pio_decomp_tests_2d.F90.in
A	src/externals/pio2/tests/general/pio_decomp_tests_3d.F90.in
M	src/externals/pio2/tests/general/pio_file_simple_tests.F90.in
A	src/externals/pio2/tests/general/pio_iosystem_tests.F90.in
A	src/externals/pio2/tests/general/pio_iosystem_tests2.F90.in
A	src/externals/pio2/tests/general/pio_iosystem_tests3.F90.in
A	src/externals/pio2/tests/general/pio_rearr.F90.in
A	src/externals/pio2/tests/general/pio_rearr_opts.F90.in
A	src/externals/pio2/tests/general/pio_rearr_opts2.F90.in
M	src/externals/pio2/tests/general/test_memleak.c
M	src/externals/pio2/tests/general/util/pio_tf_f90gen.pl
M	src/externals/pio2/tests/general/util/pio_tutil.F90
M	src/externals/pio2/tests/performance/CMakeLists.txt
M	src/externals/pio2/tests/unit/CMakeLists.txt
D	src/externals/pio2/tests/unit/README
M	src/externals/pio2/tests/unit/basic_tests.F90
M	src/externals/pio2/tests/unit/driver.F90
M	src/externals/pio2/tests/unit/global_vars.F90
M	src/externals/pio2/tests/unit/nc_set_log_level2.c
M	src/externals/pio2/tests/unit/ncdf_tests.F90
D	src/externals/pio2/tests/unit/test_names.c
D	src/externals/pio2/tests/unit/test_nc4.c

======================================================================
Originator: Chris Fischer
Date: 3-7-2017
Tag: cime5.3.0-alpha.02
Answer Changes: None
Tests:
Dependencies:

Brief Summary:  Revert PR# 1210, remove hardcoded compclasses

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master
   4cc7e22 Merge pull request #1213 from ESMCI/revert-1210-compclasses_cleanup

Modified files: git diff --name-status [previous_tag]
M       scripts/lib/CIME/SystemTests/ncr.py
M       scripts/lib/CIME/SystemTests/pem.py
M       scripts/lib/CIME/SystemTests/pet.py
M       scripts/lib/CIME/get_timing.py

======================================================================

Originator: Chris Fischer
Date: 3-6-2017
Tag: cime5.3.0-alpha.01
Answer Changes: None
Tests: code_checker,hist_utils.py,scripts_regression_tests.py, on
       different PRs..
Dependencies:

Brief Summary:
   - Adjust pio layout if pe layout is changed.
   - Make baseline perms setting more robust.
   - Allows user to rm -rf their build area and rebuild without having
     to re-run case.setup.
   - Big refactor of CaseStatus management.
   - cdf64 only valid for serial netcdf, fix seq test
   - Fix bug in ERP namelist comparison.
   - Refactor env_batch
   - fix issue with compset not printing to timing file
   - copy rather than follow links in create_clone
   - update compare_xml to find more differences
   - remove hardcoded compclasses

User interface changes:
   - case.setup has a new option --no-adjust-pio
   - case.build behavior slightly different case.build behavior slightly
     different
   - CaseStatus will look slightly different
   - env_batch.xml now looks different

PR summary: git log --oneline --first-parent [previous_tag]..master
3fd75db Merge pull request #1210 from jedwards4b/compclasses_cleanup
78cab9a Merge pull request #1207 from jedwards4b/fix_compare_xml
bd0f19d Merge pull request #1209 from jedwards4b/symlinks_in_clone
d308873 Merge pull request #1208 from jedwards4b/fix_compset_not_in_timing
77dc910 Merge pull request #1204 from ESMCI/jgfouca/refactor_env_batch
c10fe46 Merge pull request #1203 from ESMCI/jgfouca/fix_erp_namelist_issue
30e8e79 Merge pull request #1200 from jedwards4b/seq_test_fix
5eee02a Merge pull request #1199 from ESMCI/jgfouca/refactor_case_status
4219bfd Merge pull request #1196 from ESMCI/jgfouca/build_needs_to_make_dirs
33ac01a Merge pull request #1197 from ESMCI/jgfouca/minor_hist_chg
7e7f805 Merge pull request #1195 from jedwards4b/pio_layout_adjust
0131a12 resolve merge conflicts
6c93fc3 Merge branch 'agsalin/mkdir_src'
215e459 Merge pull request #1182 from jedwards4b/config_archive_split


Modified files: git diff --name-status [previous_tag]
M	CMakeLists.txt
M	ChangeLog
D	cime_config/acme/allactive/config_compsets.xml
D	cime_config/acme/allactive/config_compsets.xml.cime2
D	cime_config/acme/allactive/config_pes.xml
D	cime_config/acme/allactive/config_pes.xml.cime2
D	cime_config/acme/allactive/config_pesall.xml
D	cime_config/acme/allactive/testlist_allactive.xml
D	cime_config/acme/allactive/testmods_dirs/cam/outfrq9s/shell_commands
D	cime_config/acme/allactive/testmods_dirs/force_netcdf_pio/shell_commands
D	cime_config/acme/allactive/usermods_dirs/b1850/shell_commands
D	cime_config/acme/allactive/usermods_dirs/b1850_cism/include_user_mods
D	cime_config/acme/allactive/usermods_dirs/b1850_cism/user_nl_cism
D	cime_config/acme/config_archive.xml
D	cime_config/acme/config_files.xml
D	cime_config/acme/config_grids.xml
D	cime_config/acme/machines/Depends.cetus
D	cime_config/acme/machines/Depends.corip1
D	cime_config/acme/machines/Depends.cray
D	cime_config/acme/machines/Depends.gnu
D	cime_config/acme/machines/Depends.intel
D	cime_config/acme/machines/Depends.intel14
D	cime_config/acme/machines/Depends.intelmic
D	cime_config/acme/machines/Depends.intelmic14
D	cime_config/acme/machines/Depends.mira
D	cime_config/acme/machines/Depends.nag
D	cime_config/acme/machines/Depends.titan.cray
D	cime_config/acme/machines/Depends.titan.intel
D	cime_config/acme/machines/Depends.titan.pgi
D	cime_config/acme/machines/Depends.titan.pgiacc
D	cime_config/acme/machines/Makefile
D	cime_config/acme/machines/README
D	cime_config/acme/machines/config_batch.xml
D	cime_config/acme/machines/config_batch.xsd
D	cime_config/acme/machines/config_compilers.xml
D	cime_config/acme/machines/config_lt_archive.xml
D	cime_config/acme/machines/config_machines.xml
D	cime_config/acme/machines/config_pio.xml
D	cime_config/acme/machines/mkDepends
D	cime_config/acme/machines/mkSrcfiles
D	cime_config/acme/machines/syslog.cetus
D	cime_config/acme/machines/syslog.cori-haswell
D	cime_config/acme/machines/syslog.cori-knl
D	cime_config/acme/machines/syslog.edison
D	cime_config/acme/machines/syslog.mira
D	cime_config/acme/machines/syslog.noop
D	cime_config/acme/machines/syslog.titan
D	cime_config/acme/machines/template.case.run
D	cime_config/acme/machines/template.case.test
D	cime_config/acme/machines/template.lt_archive
D	cime_config/acme/machines/template.ocn_diagnostics
D	cime_config/acme/machines/template.st_archive
D	cime_config/acme/machines/template.timeseries
D	cime_config/acme/machines/userdefined_laptop_template/README.md
D	cime_config/acme/machines/userdefined_laptop_template/config_compilers.xml
D	cime_config/acme/machines/userdefined_laptop_template/config_machines.xml
D	cime_config/acme/machines/userdefined_laptop_template/config_pes.xml
D	cime_config/acme/testmods_dirs/allactive/cam/outfrq9s/user_nl_cam
D	cime_config/acme/testmods_dirs/allactive/cam/outfrq9s/user_nl_clm
D	cime_config/buildlib.csm_share
D	cime_config/buildlib.gptl
D	cime_config/buildlib.mct
D	cime_config/buildlib.mpi-serial
D	cime_config/buildlib.pio
D	cime_config/cesm/config_archive.xml
D	cime_config/cesm/config_files.xml
D	cime_config/cesm/config_grids.xml
D	cime_config/cesm/machines/Depends.babbageKnc
D	cime_config/cesm/machines/Depends.bluewaters
D	cime_config/cesm/machines/Depends.corip1
D	cime_config/cesm/machines/Depends.cray
D	cime_config/cesm/machines/Depends.gnu
D	cime_config/cesm/machines/Depends.goldbach
D	cime_config/cesm/machines/Depends.intel
D	cime_config/cesm/machines/Depends.intel14
D	cime_config/cesm/machines/Depends.intelmic
D	cime_config/cesm/machines/Depends.intelmic14
D	cime_config/cesm/machines/Depends.mira
D	cime_config/cesm/machines/Depends.nag
D	cime_config/cesm/machines/Makefile
D	cime_config/cesm/machines/README
D	cime_config/cesm/machines/config_batch.xml
D	cime_config/cesm/machines/config_compilers.xml
D	cime_config/cesm/machines/config_lt_archive.xml
D	cime_config/cesm/machines/config_machines.xml
D	cime_config/cesm/machines/config_pio.xml
D	cime_config/cesm/machines/mkDepends
D	cime_config/cesm/machines/mkSrcfiles
D	cime_config/cesm/machines/nag_mpi_argument.txt
D	cime_config/cesm/machines/template.case.run
D	cime_config/cesm/machines/template.case.test
D	cime_config/cesm/machines/template.lt_archive
D	cime_config/cesm/machines/template.st_archive
D	cime_config/cesm/machines/userdefined_laptop_template/README.md
D	cime_config/cesm/machines/userdefined_laptop_template/config_compilers.xml
D	cime_config/cesm/machines/userdefined_laptop_template/config_machines.xml
D	cime_config/cesm/machines/userdefined_laptop_template/config_pes.xml
D	cime_config/config_headers.xml
D	cime_config/config_tests.xml
D	cime_config/xml_schemas/archive.xsd
D	cime_config/xml_schemas/cimeteststatus.xsd
D	cime_config/xml_schemas/config_batch.xsd
D	cime_config/xml_schemas/config_compilers_v2.xsd
D	cime_config/xml_schemas/config_compsets.xsd
D	cime_config/xml_schemas/config_grids_v2.xsd
D	cime_config/xml_schemas/config_machines.xsd
D	cime_config/xml_schemas/config_machines_template.xml
D	cime_config/xml_schemas/config_pes.xsd
D	cime_config/xml_schemas/entry_id.xsd
D	cime_config/xml_schemas/entry_id_base.xsd
D	cime_config/xml_schemas/entry_id_namelist.xsd
D	cime_config/xml_schemas/testlist.xsd
D	components/data_comps/datm/atm_comp_mct.F90
D	components/data_comps/datm/cime_config/buildlib
D	components/data_comps/datm/cime_config/buildnml
D	components/data_comps/datm/cime_config/config_component.xml
D	components/data_comps/datm/cime_config/namelist_definition_datm.xml
D	components/data_comps/datm/cime_config/user_nl_datm
D	components/data_comps/datm/datm_comp_mod.F90
D	components/data_comps/datm/datm_shr_mod.F90
D	components/data_comps/datm/doc/SOM.pdf
D	components/data_comps/datm/doc/bookinfo.xml
D	components/data_comps/datm/doc/datacomps.xml
D	components/data_comps/datm/doc/intro.xml
D	components/data_comps/datm/doc/rundocbook.csh
D	components/data_comps/datm/doc/streams.xml
D	components/data_comps/datm/doc/ug.xml
D	components/data_comps/desp/cime_config/buildlib
D	components/data_comps/desp/cime_config/buildnml
D	components/data_comps/desp/cime_config/config_component.xml
D	components/data_comps/desp/cime_config/namelist_definition_desp.xml
D	components/data_comps/desp/cime_config/user_nl_desp
D	components/data_comps/desp/desp_comp_mod.F90
D	components/data_comps/desp/esp_comp_mct.F90
D	components/data_comps/desp/esp_utils.F90
D	components/data_comps/dice/cime_config/buildlib
D	components/data_comps/dice/cime_config/buildnml
D	components/data_comps/dice/cime_config/config_component.xml
D	components/data_comps/dice/cime_config/namelist_definition_dice.xml
D	components/data_comps/dice/cime_config/user_nl_dice
D	components/data_comps/dice/dice_comp_mod.F90
D	components/data_comps/dice/ice_comp_mct.F90
D	components/data_comps/dlnd/cime_config/buildlib
D	components/data_comps/dlnd/cime_config/buildnml
D	components/data_comps/dlnd/cime_config/config_component.xml
D	components/data_comps/dlnd/cime_config/namelist_definition_dlnd.xml
D	components/data_comps/dlnd/cime_config/user_nl_dlnd
D	components/data_comps/dlnd/dlnd_comp_mod.F90
D	components/data_comps/dlnd/lnd_comp_mct.F90
D	components/data_comps/docn/cime_config/buildlib
D	components/data_comps/docn/cime_config/buildnml
D	components/data_comps/docn/cime_config/config_component.xml
D	components/data_comps/docn/cime_config/namelist_definition_docn.xml
D	components/data_comps/docn/cime_config/user_nl_docn
D	components/data_comps/docn/docn_comp_mod.F90
D	components/data_comps/docn/ocn_comp_mct.F90
D	components/data_comps/docn/tools/pop_som_frc/README
D	components/data_comps/docn/tools/pop_som_frc/SOM.doc
D	components/data_comps/docn/tools/pop_som_frc/SOM.pdf
D	components/data_comps/docn/tools/pop_som_frc/pop_frc.csh
D	components/data_comps/docn/tools/pop_som_frc/pop_frc_mlann.ncl
D	components/data_comps/docn/tools/pop_som_frc/pop_frc_mlt.ncl
D	components/data_comps/docn/tools/pop_som_frc/pop_interp.ncl
D	components/data_comps/docn/tools/pop_som_frc/read_from_mss.csh
D	components/data_comps/docn/tools/pop_som_frc/read_from_mss_month.csh
D	components/data_comps/drof/cime_config/buildlib
D	components/data_comps/drof/cime_config/buildnml
D	components/data_comps/drof/cime_config/config_component.xml
D	components/data_comps/drof/cime_config/namelist_definition_drof.xml
D	components/data_comps/drof/cime_config/user_nl_drof
D	components/data_comps/drof/drof_comp_mod.F90
D	components/data_comps/drof/rof_comp_mct.F90
D	components/data_comps/dwav/README
D	components/data_comps/dwav/bld/README
D	components/data_comps/dwav/cime_config/buildlib
D	components/data_comps/dwav/cime_config/buildnml
D	components/data_comps/dwav/cime_config/config_component.xml
D	components/data_comps/dwav/cime_config/namelist_definition_dwav.xml
D	components/data_comps/dwav/cime_config/user_nl_dwav
D	components/data_comps/dwav/dwav_comp_mod.F90
D	components/data_comps/dwav/wav_comp_mct.F90
D	components/stub_comps/satm/cime_config/buildlib
D	components/stub_comps/satm/cime_config/buildnml
D	components/stub_comps/satm/cime_config/config_component.xml
D	components/stub_comps/satm/cpl/atm_comp_mct.F90
D	components/stub_comps/sesp/cime_config/buildlib
D	components/stub_comps/sesp/cime_config/buildnml
D	components/stub_comps/sesp/cime_config/config_component.xml
D	components/stub_comps/sesp/cpl/esp_comp_mct.F90
D	components/stub_comps/sglc/cime_config/buildlib
D	components/stub_comps/sglc/cime_config/buildnml
D	components/stub_comps/sglc/cime_config/config_component.xml
D	components/stub_comps/sglc/cpl/glc_comp_mct.F90
D	components/stub_comps/sice/cime_config/buildlib
D	components/stub_comps/sice/cime_config/buildnml
D	components/stub_comps/sice/cime_config/config_component.xml
D	components/stub_comps/sice/cpl/ice_comp_mct.F90
D	components/stub_comps/slnd/cime_config/buildlib
D	components/stub_comps/slnd/cime_config/buildnml
D	components/stub_comps/slnd/cime_config/config_component.xml
D	components/stub_comps/slnd/cpl/lnd_comp_mct.F90
D	components/stub_comps/socn/cime_config/buildlib
D	components/stub_comps/socn/cime_config/buildnml
D	components/stub_comps/socn/cime_config/config_component.xml
D	components/stub_comps/socn/cpl/ocn_comp_mct.F90
D	components/stub_comps/srof/cime_config/buildlib
D	components/stub_comps/srof/cime_config/buildnml
D	components/stub_comps/srof/cime_config/config_component.xml
D	components/stub_comps/srof/cpl/rof_comp_mct.F90
D	components/stub_comps/swav/cime_config/buildlib
D	components/stub_comps/swav/cime_config/buildnml
D	components/stub_comps/swav/cime_config/config_component.xml
D	components/stub_comps/swav/cpl/wav_comp_mct.F90
D	components/xcpl_comps/xatm/cime_config/buildlib
D	components/xcpl_comps/xatm/cime_config/buildnml
D	components/xcpl_comps/xatm/cime_config/config_component.xml
D	components/xcpl_comps/xatm/cpl/atm_comp_mct.F90
D	components/xcpl_comps/xglc/cime_config/buildlib
D	components/xcpl_comps/xglc/cime_config/buildnml
D	components/xcpl_comps/xglc/cime_config/config_component.xml
D	components/xcpl_comps/xglc/cpl/glc_comp_mct.F90
D	components/xcpl_comps/xice/cime_config/buildlib
D	components/xcpl_comps/xice/cime_config/buildnml
D	components/xcpl_comps/xice/cime_config/config_component.xml
D	components/xcpl_comps/xice/cpl/ice_comp_mct.F90
D	components/xcpl_comps/xlnd/cime_config/buildlib
D	components/xcpl_comps/xlnd/cime_config/buildnml
D	components/xcpl_comps/xlnd/cime_config/config_component.xml
D	components/xcpl_comps/xlnd/cpl/lnd_comp_mct.F90
D	components/xcpl_comps/xocn/cime_config/buildlib
D	components/xcpl_comps/xocn/cime_config/buildnml
D	components/xcpl_comps/xocn/cime_config/config_component.xml
D	components/xcpl_comps/xocn/cpl/ocn_comp_mct.F90
D	components/xcpl_comps/xrof/cime_config/buildlib
D	components/xcpl_comps/xrof/cime_config/buildnml
D	components/xcpl_comps/xrof/cime_config/config_component.xml
D	components/xcpl_comps/xrof/cpl/rof_comp_mct.F90
D	components/xcpl_comps/xshare/dead_data_mod.F90
D	components/xcpl_comps/xshare/dead_mct_mod.F90
D	components/xcpl_comps/xshare/dead_mod.F90
D	components/xcpl_comps/xwav/cime_config/buildlib
D	components/xcpl_comps/xwav/cime_config/buildnml
D	components/xcpl_comps/xwav/cime_config/config_component.xml
D	components/xcpl_comps/xwav/cpl/wav_comp_mct.F90
A	config/acme/allactive/config_compsets.xml
A	config/acme/allactive/config_compsets.xml.cime2
A	config/acme/allactive/config_pes.xml
A	config/acme/allactive/config_pes.xml.cime2
A	config/acme/allactive/config_pesall.xml
A	config/acme/allactive/testlist_allactive.xml
A	config/acme/allactive/testmods_dirs/cam/outfrq9s/shell_commands
A	config/acme/allactive/testmods_dirs/force_netcdf_pio/shell_commands
A	config/acme/allactive/usermods_dirs/b1850/shell_commands
A	config/acme/allactive/usermods_dirs/b1850_cism/include_user_mods
A	config/acme/allactive/usermods_dirs/b1850_cism/user_nl_cism
A	config/acme/config_archive.xml
A	config/acme/config_files.xml
A	config/acme/config_grids.xml
A	config/acme/machines/Depends.cetus
A	config/acme/machines/Depends.corip1
A	config/acme/machines/Depends.cray
A	config/acme/machines/Depends.gnu
A	config/acme/machines/Depends.intel
A	config/acme/machines/Depends.intel14
A	config/acme/machines/Depends.intelmic
A	config/acme/machines/Depends.intelmic14
A	config/acme/machines/Depends.mira
A	config/acme/machines/Depends.nag
A	config/acme/machines/Depends.titan.cray
A	config/acme/machines/Depends.titan.intel
A	config/acme/machines/Depends.titan.pgi
A	config/acme/machines/Depends.titan.pgiacc
A	config/acme/machines/Makefile
A	config/acme/machines/README
A	config/acme/machines/config_batch.xml
A	config/acme/machines/config_batch.xsd
A	config/acme/machines/config_compilers.xml
A	config/acme/machines/config_lt_archive.xml
A	config/acme/machines/config_machines.xml
A	config/acme/machines/config_pio.xml
A	config/acme/machines/mkDepends
A	config/acme/machines/mkSrcfiles
A	config/acme/machines/syslog.cetus
A	config/acme/machines/syslog.cori-haswell
A	config/acme/machines/syslog.cori-knl
A	config/acme/machines/syslog.edison
A	config/acme/machines/syslog.mira
A	config/acme/machines/syslog.noop
A	config/acme/machines/syslog.titan
A	config/acme/machines/template.case.run
A	config/acme/machines/template.case.test
A	config/acme/machines/template.lt_archive
A	config/acme/machines/template.ocn_diagnostics
A	config/acme/machines/template.st_archive
A	config/acme/machines/template.timeseries
A	config/acme/machines/userdefined_laptop_template/README.md
A	config/acme/machines/userdefined_laptop_template/config_compilers.xml
A	config/acme/machines/userdefined_laptop_template/config_machines.xml
A	config/acme/machines/userdefined_laptop_template/config_pes.xml
A	config/acme/testmods_dirs/allactive/cam/outfrq9s/user_nl_cam
A	config/acme/testmods_dirs/allactive/cam/outfrq9s/user_nl_clm
A	config/cesm/config_archive.xml
A	config/cesm/config_files.xml
A	config/cesm/config_grids.xml
A	config/cesm/machines/Depends.babbageKnc
A	config/cesm/machines/Depends.bluewaters
A	config/cesm/machines/Depends.corip1
A	config/cesm/machines/Depends.cray
A	config/cesm/machines/Depends.gnu
A	config/cesm/machines/Depends.goldbach
A	config/cesm/machines/Depends.intel
A	config/cesm/machines/Depends.intel14
A	config/cesm/machines/Depends.intelmic
A	config/cesm/machines/Depends.intelmic14
A	config/cesm/machines/Depends.mira
A	config/cesm/machines/Depends.nag
A	config/cesm/machines/Makefile
A	config/cesm/machines/README
A	config/cesm/machines/config_batch.xml
A	config/cesm/machines/config_compilers.xml
A	config/cesm/machines/config_lt_archive.xml
A	config/cesm/machines/config_machines.xml
A	config/cesm/machines/config_pio.xml
A	config/cesm/machines/mkDepends
A	config/cesm/machines/mkSrcfiles
A	config/cesm/machines/nag_mpi_argument.txt
A	config/cesm/machines/template.case.run
A	config/cesm/machines/template.case.test
A	config/cesm/machines/template.lt_archive
A	config/cesm/machines/template.st_archive
A	config/cesm/machines/userdefined_laptop_template/README.md
A	config/cesm/machines/userdefined_laptop_template/config_compilers.xml
A	config/cesm/machines/userdefined_laptop_template/config_machines.xml
A	config/cesm/machines/userdefined_laptop_template/config_pes.xml
A	config/config_headers.xml
A	config/config_tests.xml
A	config/xml_schemas/cimeteststatus.xsd
A	config/xml_schemas/config_archive.xsd
A	config/xml_schemas/config_batch.xsd
A	config/xml_schemas/config_compilers_v2.xsd
A	config/xml_schemas/config_compsets.xsd
A	config/xml_schemas/config_grids_v2.xsd
A	config/xml_schemas/config_machines.xsd
A	config/xml_schemas/config_machines_template.xml
A	config/xml_schemas/config_pes.xsd
A	config/xml_schemas/entry_id.xsd
A	config/xml_schemas/entry_id_base.xsd
A	config/xml_schemas/entry_id_namelist.xsd
A	config/xml_schemas/env_archive.xsd
A	config/xml_schemas/env_entry_id.xsd
A	config/xml_schemas/testlist.xsd
D	driver_cpl/bld/namelist_files/namelist_defaults_drv.xml
D	driver_cpl/bld/namelist_files/namelist_definition_drv.xml
D	driver_cpl/bld/namelist_files/namelist_definition_drv_flds.xml
D	driver_cpl/bld/namelist_files/namelist_definition_modio.xml
D	driver_cpl/bld/testdir/Buildconf/camconf/drv_flds_in
D	driver_cpl/bld/testdir/Buildconf/clmconf/drv_flds_in
D	driver_cpl/bld/testdir/env_build.xml
D	driver_cpl/bld/testdir/env_case.xml
D	driver_cpl/bld/testdir/env_mach_pes.xml
D	driver_cpl/bld/testdir/env_run.xml
D	driver_cpl/bld/testdir/runtest
D	driver_cpl/bld/testdir/user_nl_cpl
D	driver_cpl/cime_config/buildexe
D	driver_cpl/cime_config/buildnml
D	driver_cpl/cime_config/config_component.xml
D	driver_cpl/cime_config/config_component_acme.xml
D	driver_cpl/cime_config/config_component_cesm.xml
D	driver_cpl/cime_config/config_compsets.xml
D	driver_cpl/cime_config/config_pes.xml
D	driver_cpl/cime_config/namelist_definition_drv.xml
D	driver_cpl/cime_config/namelist_definition_modelio.xml
D	driver_cpl/cime_config/testdefs/testlist_drv.xml
D	driver_cpl/cime_config/testdefs/testmods_dirs/drv/5steps/shell_commands
D	driver_cpl/cime_config/user_nl_cpl
D	driver_cpl/doc/bookinfo.xml
D	driver_cpl/doc/chap1.xml
D	driver_cpl/doc/chap2.xml
D	driver_cpl/doc/figx1.jpg
D	driver_cpl/doc/namelist.xml
D	driver_cpl/doc/rundocbook.csh
D	driver_cpl/doc/stylesheet.dsl
D	driver_cpl/doc/ug.xml
D	driver_cpl/driver/CMakeLists.txt
D	driver_cpl/driver/cesm_comp_mod.F90
D	driver_cpl/driver/cesm_driver.F90
D	driver_cpl/driver/component_mod.F90
D	driver_cpl/driver/component_type_mod.F90
D	driver_cpl/driver/cplcomp_exchange_mod.F90
D	driver_cpl/driver/map_glc2lnd_mod.F90
D	driver_cpl/driver/map_lnd2glc_mod.F90
D	driver_cpl/driver/map_lnd2rof_irrig_mod.F90
D	driver_cpl/driver/mrg_mod.F90
D	driver_cpl/driver/prep_aoflux_mod.F90
D	driver_cpl/driver/prep_atm_mod.F90
D	driver_cpl/driver/prep_glc_mod.F90
D	driver_cpl/driver/prep_ice_mod.F90
D	driver_cpl/driver/prep_lnd_mod.F90
D	driver_cpl/driver/prep_ocn_mod.F90
D	driver_cpl/driver/prep_rof_mod.F90
D	driver_cpl/driver/prep_wav_mod.F90
D	driver_cpl/driver/seq_diag_mct.F90
D	driver_cpl/driver/seq_domain_mct.F90
D	driver_cpl/driver/seq_flux_mct.F90
D	driver_cpl/driver/seq_frac_mct.F90
D	driver_cpl/driver/seq_hist_mod.F90
D	driver_cpl/driver/seq_io_mod.F90
D	driver_cpl/driver/seq_map_mod.F90
D	driver_cpl/driver/seq_map_type_mod.F90
D	driver_cpl/driver/seq_rest_mod.F90
D	driver_cpl/driver/t_driver_timers_mod.F90
D	driver_cpl/driver/vertical_gradient_calculator_2nd_order.F90
D	driver_cpl/driver/vertical_gradient_calculator_base.F90
D	driver_cpl/driver/vertical_gradient_calculator_factory.F90
D	driver_cpl/shr/CMakeLists.txt
D	driver_cpl/shr/glc_elevclass_mod.F90
D	driver_cpl/shr/seq_cdata_mod.F90
D	driver_cpl/shr/seq_comm_mct.F90
D	driver_cpl/shr/seq_drydep_mod.F90
D	driver_cpl/shr/seq_flds_mod.F90
D	driver_cpl/shr/seq_infodata_mod.F90
D	driver_cpl/shr/seq_io_read_mod.F90
D	driver_cpl/shr/seq_timemgr_mod.F90
D	driver_cpl/shr/shr_carma_mod.F90
D	driver_cpl/shr/shr_expr_parser_mod.F90
D	driver_cpl/shr/shr_fire_emis_mod.F90
D	driver_cpl/shr/shr_megan_mod.F90
D	driver_cpl/unit_test/CMakeLists.txt
D	driver_cpl/unit_test/avect_wrapper_test/CMakeLists.txt
D	driver_cpl/unit_test/avect_wrapper_test/test_avect_wrapper.pf
D	driver_cpl/unit_test/glc_elevclass_test/CMakeLists.txt
D	driver_cpl/unit_test/glc_elevclass_test/test_glc_elevclass.pf
D	driver_cpl/unit_test/map_glc2lnd_test/CMakeLists.txt
D	driver_cpl/unit_test/map_glc2lnd_test/test_map_glc2lnd.pf
D	driver_cpl/unit_test/map_lnd2glc_test/CMakeLists.txt
D	driver_cpl/unit_test/map_lnd2glc_test/test_map_lnd2glc.pf
D	driver_cpl/unit_test/map_lnd2rof_irrig_test/CMakeLists.txt
D	driver_cpl/unit_test/map_lnd2rof_irrig_test/test_map_lnd2rof_irrig.pf
D	driver_cpl/unit_test/seq_map_test/CMakeLists.txt
D	driver_cpl/unit_test/seq_map_test/test_seq_map.pf
D	driver_cpl/unit_test/stubs/CMakeLists.txt
D	driver_cpl/unit_test/stubs/vertical_gradient_calculator_constant.F90
D	driver_cpl/unit_test/utils/CMakeLists.txt
D	driver_cpl/unit_test/utils/avect_wrapper_mod.F90
D	driver_cpl/unit_test/utils/create_mapper_mod.F90
D	driver_cpl/unit_test/utils/mct_wrapper_mod.F90
D	driver_cpl/unit_test/utils/simple_map_mod.F90
D	driver_cpl/unit_test/vertical_gradient_calculator_test/CMakeLists.txt
D	driver_cpl/unit_test/vertical_gradient_calculator_test/README
D	driver_cpl/unit_test/vertical_gradient_calculator_test/gradient_example.txt
D	driver_cpl/unit_test/vertical_gradient_calculator_test/plot_gradient
D	driver_cpl/unit_test/vertical_gradient_calculator_test/test_vertical_gradient_calculator_2nd_order.pf
D	driver_cpl/unit_test/vertical_gradient_calculator_test/test_vertical_gradient_calculator_factory.pf
D	externals/CMake/.gitignore
D	externals/CMake/CESM_utils.cmake
D	externals/CMake/CIME_utils.cmake
D	externals/CMake/ChangeLog
D	externals/CMake/Compilers.cmake
D	externals/CMake/FindpFUnit.cmake
D	externals/CMake/LICENSE
D	externals/CMake/README.md
D	externals/CMake/Sourcelist_utils.cmake
D	externals/CMake/TryCSizeOf.f90
D	externals/CMake/TryMPIIO.f90
D	externals/CMake/TryMPIMod.f90
D	externals/CMake/TryMPISERIAL.f90
D	externals/CMake/TryPnetcdf_inc.f90
D	externals/CMake/TryPnetcdf_mod.f90
D	externals/CMake/genf90_utils.cmake
D	externals/CMake/mpiexec.cmake
D	externals/CMake/pFUnit_utils.cmake
D	externals/genf90/ChangeLog
D	externals/genf90/genf90.pl
D	externals/mct/.gitignore
D	externals/mct/COPYRIGHT
D	externals/mct/Makefile
D	externals/mct/Makefile.conf.in
D	externals/mct/README
D	externals/mct/aclocal.m4
D	externals/mct/benchmarks/.gitignore
D	externals/mct/benchmarks/Makefile
D	externals/mct/benchmarks/RouterTestDis.F90
D	externals/mct/benchmarks/RouterTestOvr.F90
D	externals/mct/benchmarks/T42.8pC
D	externals/mct/benchmarks/T42.8pR
D	externals/mct/benchmarks/gx1.8pC
D	externals/mct/benchmarks/gx1.8pR
D	externals/mct/benchmarks/importBench.F90
D	externals/mct/config.h.in
D	externals/mct/configure
D	externals/mct/configure.ac
D	externals/mct/doc/.gitignore
D	externals/mct/doc/Makefile
D	externals/mct/doc/README
D	externals/mct/doc/coupler.bib
D	externals/mct/doc/mct_APIs.tex
D	externals/mct/doc/texsrc/.gitignore
D	externals/mct/doc/texsrc/Makefile
D	externals/mct/doc/texsrc/SRCS_tex.mk
D	externals/mct/examples/Makefile
D	externals/mct/examples/README
D	externals/mct/examples/climate_concur1/.gitignore
D	externals/mct/examples/climate_concur1/Makefile
D	externals/mct/examples/climate_concur1/README
D	externals/mct/examples/climate_concur1/coupler.F90
D	externals/mct/examples/climate_concur1/master.F90
D	externals/mct/examples/climate_concur1/model.F90
D	externals/mct/examples/climate_sequen1/.gitignore
D	externals/mct/examples/climate_sequen1/Makefile
D	externals/mct/examples/climate_sequen1/README
D	externals/mct/examples/climate_sequen1/TS1.dat
D	externals/mct/examples/climate_sequen1/coupler.F90
D	externals/mct/examples/climate_sequen1/dst.rc
D	externals/mct/examples/climate_sequen1/dstmodel.F90
D	externals/mct/examples/climate_sequen1/master.F90
D	externals/mct/examples/climate_sequen1/mutils.F90
D	externals/mct/examples/climate_sequen1/src.rc
D	externals/mct/examples/climate_sequen1/srcmodel.F90
D	externals/mct/examples/simple/.gitignore
D	externals/mct/examples/simple/Makefile
D	externals/mct/examples/simple/README
D	externals/mct/examples/simple/script.babyblue
D	externals/mct/examples/simple/twocmp.con.F90
D	externals/mct/examples/simple/twocmp.seq.F90
D	externals/mct/examples/simple/twocmp.seqNB.F90
D	externals/mct/examples/simple/twocmp.seqUnvn.F90
D	externals/mct/install-sh
D	externals/mct/m4/README
D	externals/mct/m4/acx_mpi.m4
D	externals/mct/m4/ax_fc_version.m4
D	externals/mct/m4/fortran.m4
D	externals/mct/mct/Makefile
D	externals/mct/mct/README
D	externals/mct/mct/m_Accumulator.F90
D	externals/mct/mct/m_AccumulatorComms.F90
D	externals/mct/mct/m_AttrVect.F90
D	externals/mct/mct/m_AttrVectComms.F90
D	externals/mct/mct/m_AttrVectReduce.F90
D	externals/mct/mct/m_ConvertMaps.F90
D	externals/mct/mct/m_ExchangeMaps.F90
D	externals/mct/mct/m_GeneralGrid.F90
D	externals/mct/mct/m_GeneralGridComms.F90
D	externals/mct/mct/m_GlobalMap.F90
D	externals/mct/mct/m_GlobalSegMap.F90
D	externals/mct/mct/m_GlobalSegMapComms.F90
D	externals/mct/mct/m_GlobalToLocal.F90
D	externals/mct/mct/m_MCTWorld.F90
D	externals/mct/mct/m_MatAttrVectMul.F90
D	externals/mct/mct/m_Merge.F90
D	externals/mct/mct/m_Navigator.F90
D	externals/mct/mct/m_Rearranger.F90
D	externals/mct/mct/m_Router.F90
D	externals/mct/mct/m_SparseMatrix.F90
D	externals/mct/mct/m_SparseMatrixComms.F90
D	externals/mct/mct/m_SparseMatrixDecomp.F90
D	externals/mct/mct/m_SparseMatrixPlus.F90
D	externals/mct/mct/m_SparseMatrixToMaps.F90
D	externals/mct/mct/m_SpatialIntegral.F90
D	externals/mct/mct/m_SpatialIntegralV.F90
D	externals/mct/mct/m_Transfer.F90
D	externals/mct/mkinstalldirs
D	externals/mct/mpeu/Makefile
D	externals/mct/mpeu/README
D	externals/mct/mpeu/assertmpeu.H
D	externals/mct/mpeu/get_zeits.c
D	externals/mct/mpeu/m_FcComms.F90
D	externals/mct/mpeu/m_FileResolv.F90
D	externals/mct/mpeu/m_Filename.F90
D	externals/mct/mpeu/m_IndexBin_char.F90
D	externals/mct/mpeu/m_IndexBin_integer.F90
D	externals/mct/mpeu/m_IndexBin_logical.F90
D	externals/mct/mpeu/m_List.F90
D	externals/mct/mpeu/m_MergeSorts.F90
D	externals/mct/mpeu/m_Permuter.F90
D	externals/mct/mpeu/m_SortingTools.F90
D	externals/mct/mpeu/m_StrTemplate.F90
D	externals/mct/mpeu/m_String.F90
D	externals/mct/mpeu/m_StringLinkedList.F90
D	externals/mct/mpeu/m_TraceBack.F90
D	externals/mct/mpeu/m_chars.F90
D	externals/mct/mpeu/m_die.F90
D	externals/mct/mpeu/m_dropdead.F90
D	externals/mct/mpeu/m_flow.F90
D	externals/mct/mpeu/m_inpak90.F90
D	externals/mct/mpeu/m_ioutil.F90
D	externals/mct/mpeu/m_mall.F90
D	externals/mct/mpeu/m_mpif.F90
D	externals/mct/mpeu/m_mpif90.F90
D	externals/mct/mpeu/m_mpout.F90
D	externals/mct/mpeu/m_rankMerge.F90
D	externals/mct/mpeu/m_realkinds.F90
D	externals/mct/mpeu/m_stdio.F90
D	externals/mct/mpeu/m_zeit.F90
D	externals/mct/mpi-serial/.gitignore
D	externals/mct/mpi-serial/Makefile
D	externals/mct/mpi-serial/Makefile.conf.in
D	externals/mct/mpi-serial/NOTES
D	externals/mct/mpi-serial/README
D	externals/mct/mpi-serial/aclocal.m4
D	externals/mct/mpi-serial/cart.c
D	externals/mct/mpi-serial/collective.c
D	externals/mct/mpi-serial/comm.c
D	externals/mct/mpi-serial/config.h.in
D	externals/mct/mpi-serial/configure
D	externals/mct/mpi-serial/configure.in
D	externals/mct/mpi-serial/copy.c
D	externals/mct/mpi-serial/fort.F90
D	externals/mct/mpi-serial/getcount.c
D	externals/mct/mpi-serial/group.c
D	externals/mct/mpi-serial/handles.c
D	externals/mct/mpi-serial/info.c
D	externals/mct/mpi-serial/list.c
D	externals/mct/mpi-serial/list.h
D	externals/mct/mpi-serial/listP.h
D	externals/mct/mpi-serial/listops.h
D	externals/mct/mpi-serial/m4/README
D	externals/mct/mpi-serial/m4/ax_fc_version.m4
D	externals/mct/mpi-serial/mpi.c
D	externals/mct/mpi-serial/mpi.h
D	externals/mct/mpi-serial/mpiP.h
D	externals/mct/mpi-serial/mpif.F90
D	externals/mct/mpi-serial/mpif.h
D	externals/mct/mpi-serial/op.c
D	externals/mct/mpi-serial/pack.c
D	externals/mct/mpi-serial/probe.c
D	externals/mct/mpi-serial/protify.awk
D	externals/mct/mpi-serial/recv.c
D	externals/mct/mpi-serial/req.c
D	externals/mct/mpi-serial/send.c
D	externals/mct/mpi-serial/tests/.gitignore
D	externals/mct/mpi-serial/tests/Makefile
D	externals/mct/mpi-serial/tests/ctest.c
D	externals/mct/mpi-serial/tests/ctest_old.c
D	externals/mct/mpi-serial/tests/ftest.F90
D	externals/mct/mpi-serial/tests/ftest_internal.F90
D	externals/mct/mpi-serial/tests/ftest_old.F90
D	externals/mct/mpi-serial/time.c
D	externals/mct/mpi-serial/type.c
D	externals/mct/mpi-serial/type.h
D	externals/mct/mpi-serial/type_const.c
D	externals/mct/protex/protex
D	externals/mct/testsystem/Makefile
D	externals/mct/testsystem/testall/.gitignore
D	externals/mct/testsystem/testall/Makefile
D	externals/mct/testsystem/testall/ReadSparseMatrixAsc.F90
D	externals/mct/testsystem/testall/UNTESTED
D	externals/mct/testsystem/testall/ccm.F90
D	externals/mct/testsystem/testall/convertPOPT.F90
D	externals/mct/testsystem/testall/convertgauss.F90
D	externals/mct/testsystem/testall/cpl.F90
D	externals/mct/testsystem/testall/job.ut-all.jaguar
D	externals/mct/testsystem/testall/m_ACTEST.F90
D	externals/mct/testsystem/testall/m_AVTEST.F90
D	externals/mct/testsystem/testall/m_GGRIDTEST.F90
D	externals/mct/testsystem/testall/m_GMAPTEST.F90
D	externals/mct/testsystem/testall/m_GSMAPTEST.F90
D	externals/mct/testsystem/testall/m_MCTWORLDTEST.F90
D	externals/mct/testsystem/testall/m_ROUTERTEST.F90
D	externals/mct/testsystem/testall/m_SMATTEST.F90
D	externals/mct/testsystem/testall/master.F90
D	externals/mct/testsystem/testall/mph.F90
D	externals/mct/testsystem/testall/pop.F90
D	externals/mct/testsystem/testall/processors_map.in
D	externals/mct/testsystem/testall/script.jag
D	externals/mct/testsystem/testall/ut_SparseMatrix.rc
D	externals/mct/testunit/.gitignore
D	externals/mct/testunit/AttrVect_Test.F90
D	externals/mct/testunit/Makefile
D	externals/mct/testunit/master.F90
D	externals/pio1/CMakeLists.txt
D	externals/pio1/ChangeLog
D	externals/pio1/ChangeLog_template
D	externals/pio1/Doxyfile
D	externals/pio1/DoxygenLayout.xml
D	externals/pio1/SVN_EXTERNAL_DIRECTORIES
D	externals/pio1/customdoxygen.css
D	externals/pio1/doc/CAMexample.txt
D	externals/pio1/doc/Decomp.txt
D	externals/pio1/doc/DoxygenLayout.xml
D	externals/pio1/doc/Error.txt
D	externals/pio1/doc/Examples.txt
D	externals/pio1/doc/GettingStarted.txt
D	externals/pio1/doc/Installing.txt
D	externals/pio1/doc/api.txt
D	externals/pio1/doc/base.txt
D	externals/pio1/doc/example/errorhandle
D	externals/pio1/doc/example/simple-bc
D	externals/pio1/doc/example/simple-bc-rearr
D	externals/pio1/doc/example/simple-bc-rearr-pe1
D	externals/pio1/doc/example/simple-bc-rearr-pe2
D	externals/pio1/doc/example/simple-dof
D	externals/pio1/doc/example/simple-dof-rearr
D	externals/pio1/doc/faq.txt
D	externals/pio1/doc/footer.html
D	externals/pio1/doc/header.html
D	externals/pio1/doc/images/baseimage.graffle
D	externals/pio1/doc/images/block-cyclic-rearr.eps
D	externals/pio1/doc/images/block-cyclic-rearr.graffle
D	externals/pio1/doc/images/block-cyclic-rearr.png
D	externals/pio1/doc/images/block-cyclic.eps
D	externals/pio1/doc/images/block-cyclic.graffle
D	externals/pio1/doc/images/block-cyclic.png
D	externals/pio1/doc/images/dof-rearr.eps
D	externals/pio1/doc/images/dof-rearr.graffle
D	externals/pio1/doc/images/dof-rearr.png
D	externals/pio1/doc/images/dof.eps
D	externals/pio1/doc/images/dof.graffle
D	externals/pio1/doc/images/dof.png
D	externals/pio1/doc/testpio_example.txt
D	externals/pio1/doxygen.sty
D	externals/pio1/pio/CMakeLists.txt
D	externals/pio1/pio/C_interface_mod.F90
D	externals/pio1/pio/Makefile.conf.in
D	externals/pio1/pio/README.config
D	externals/pio1/pio/alloc_mod.F90.in
D	externals/pio1/pio/box_rearrange.F90.in
D	externals/pio1/pio/calcdecomp.F90
D	externals/pio1/pio/calcdisplace_mod.F90
D	externals/pio1/pio/config.h.in
D	externals/pio1/pio/dtypes.h
D	externals/pio1/pio/fdepends.awk
D	externals/pio1/pio/iompi_mod.F90.in
D	externals/pio1/pio/ionf_mod.F90
D	externals/pio1/pio/nf_mod.F90
D	externals/pio1/pio/pio.F90
D	externals/pio1/pio/pio_kinds.F90
D	externals/pio1/pio/pio_mpi_utils.F90
D	externals/pio1/pio/pio_msg_callbacks.F90
D	externals/pio1/pio/pio_msg_getput_callbacks.F90.in
D	externals/pio1/pio/pio_msg_mod.F90
D	externals/pio1/pio/pio_nf_utils.F90
D	externals/pio1/pio/pio_spmd_utils.F90.in
D	externals/pio1/pio/pio_support.F90
D	externals/pio1/pio/pio_types.F90
D	externals/pio1/pio/pio_utils.F90
D	externals/pio1/pio/piodarray.F90.in
D	externals/pio1/pio/piolib_mod.F90
D	externals/pio1/pio/pionfatt_mod.F90.in
D	externals/pio1/pio/pionfget_mod.F90.in
D	externals/pio1/pio/pionfput_mod.F90.in
D	externals/pio1/pio/pionfread_mod.F90.in
D	externals/pio1/pio/pionfwrite_mod.F90.in
D	externals/pio1/pio/piovdc.F90
D	externals/pio1/pio/rearr_options.h
D	externals/pio1/pio/rearrange.F90.in
D	externals/pio1/pio/topology.c
D	externals/pio1/scripts/Utils.pm
D	externals/pio1/scripts/config.pl
D	externals/pio1/scripts/testpio_yellowstone.pl
D	externals/pio1/tests/testpio/CAM05.csh
D	externals/pio1/tests/testpio/CMakeLists.txt
D	externals/pio1/tests/testpio/MPASA30km.csh
D	externals/pio1/tests/testpio/MPASA60km.csh
D	externals/pio1/tests/testpio/POPB.csh
D	externals/pio1/tests/testpio/POPC.csh
D	externals/pio1/tests/testpio/POPD.csh
D	externals/pio1/tests/testpio/POPDv0.csh
D	externals/pio1/tests/testpio/POPDv1.csh
D	externals/pio1/tests/testpio/POPDv2.csh
D	externals/pio1/tests/testpio/POPDv3.csh
D	externals/pio1/tests/testpio/POPDv4.csh
D	externals/pio1/tests/testpio/POPDv5.csh
D	externals/pio1/tests/testpio/README.testpio
D	externals/pio1/tests/testpio/WRFB.csh
D	externals/pio1/tests/testpio/build_defaults.xml
D	externals/pio1/tests/testpio/check_mod.F90
D	externals/pio1/tests/testpio/config_bench.xml
D	externals/pio1/tests/testpio/fdepends.awk
D	externals/pio1/tests/testpio/gdecomp_mod.F90
D	externals/pio1/tests/testpio/kinds_mod.F90
D	externals/pio1/tests/testpio/kraken.128.csh
D	externals/pio1/tests/testpio/kraken.1K.csh
D	externals/pio1/tests/testpio/kraken.256.csh
D	externals/pio1/tests/testpio/kraken.512.csh
D	externals/pio1/tests/testpio/kraken.64.csh
D	externals/pio1/tests/testpio/namelist_mod.F90
D	externals/pio1/tests/testpio/namelists/testpio_in.apb05
D	externals/pio1/tests/testpio/namelists/testpio_in.asb01
D	externals/pio1/tests/testpio/namelists/testpio_in.asb04
D	externals/pio1/tests/testpio/namelists/testpio_in.b01
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D	externals/pio1/tests/testpio/namelists/testpio_in.b04
D	externals/pio1/tests/testpio/namelists/testpio_in.b05
D	externals/pio1/tests/testpio/namelists/testpio_in.b06
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D	externals/pio1/tests/testpio/namelists/testpio_in.b09
D	externals/pio1/tests/testpio/namelists/testpio_in.b10
D	externals/pio1/tests/testpio/namelists/testpio_in.b11
D	externals/pio1/tests/testpio/namelists/testpio_in.b12
D	externals/pio1/tests/testpio/namelists/testpio_in.b13
D	externals/pio1/tests/testpio/namelists/testpio_in.bb01
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D	externals/pio1/tests/testpio/namelists/testpio_in.bb03
D	externals/pio1/tests/testpio/namelists/testpio_in.bb04
D	externals/pio1/tests/testpio/namelists/testpio_in.bb05
D	externals/pio1/tests/testpio/namelists/testpio_in.bb06
D	externals/pio1/tests/testpio/namelists/testpio_in.bb07
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D	externals/pio1/tests/testpio/namelists/testpio_in.wr01
D	externals/pio1/tests/testpio/namelists/testpio_in.wr02
D	externals/pio1/tests/testpio/perl5lib/ChangeLog
D	externals/pio1/tests/testpio/perl5lib/README
D	externals/pio1/tests/testpio/perl5lib/XML/Changes
D	externals/pio1/tests/testpio/perl5lib/XML/Lite.pm
D	externals/pio1/tests/testpio/perl5lib/XML/Lite/Element.pm
D	externals/pio1/tests/testpio/perl5lib/XML/README
D	externals/pio1/tests/testpio/perl5lib/XML/man3/XML::Lite.3
D	externals/pio1/tests/testpio/perl5lib/XML/man3/XML::Lite::Element.3
D	externals/pio1/tests/testpio/test.csh
D	externals/pio1/tests/testpio/test_lib.F90
D	externals/pio1/tests/testpio/testdecomp.F90
D	externals/pio1/tests/testpio/testdecomp.bluefire.run
D	externals/pio1/tests/testpio/testdecomp_in
D	externals/pio1/tests/testpio/testpio.F90
D	externals/pio1/tests/testpio/testpio_bench.pl
D	externals/pio1/tests/testpio/testpio_build.pl
D	externals/pio1/tests/testpio/testpio_run.pl
D	externals/pio1/tests/testpio/utils_mod.F90
D	externals/pio1/tests/testpio/ystest.sh
D	externals/pio1/tests/unittests/CMakeLists.txt
D	externals/pio1/tests/unittests/Levy_Notes
D	externals/pio1/tests/unittests/README
D	externals/pio1/tests/unittests/basic_tests.F90
D	externals/pio1/tests/unittests/driver.F90
D	externals/pio1/tests/unittests/global_vars.F90
D	externals/pio1/tests/unittests/input.nl
D	externals/pio1/tests/unittests/nc_set_log_level2.c
D	externals/pio1/tests/unittests/ncdf_tests.F90
D	externals/pio1/tests/unittests/not_netcdf.ieee
D	externals/pio1/timing/CMakeLists.txt
D	externals/pio1/timing/COPYING
D	externals/pio1/timing/ChangeLog
D	externals/pio1/timing/GPTLget_memusage.c
D	externals/pio1/timing/GPTLprint_memusage.c
D	externals/pio1/timing/GPTLutil.c
D	externals/pio1/timing/Makefile
D	externals/pio1/timing/README
D	externals/pio1/timing/XXXdotF/perf_mod.F
D	externals/pio1/timing/XXXdotF/perf_utils.F
D	externals/pio1/timing/f_wrappers.c
D	externals/pio1/timing/gptl.c
D	externals/pio1/timing/gptl.h
D	externals/pio1/timing/gptl.inc
D	externals/pio1/timing/gptl_papi.c
D	externals/pio1/timing/perf_mod.F90
D	externals/pio1/timing/perf_utils.F90
D	externals/pio1/timing/private.h
D	externals/pio1/timing/threadutil.c
D	externals/pio2/.gitignore
D	externals/pio2/CMakeLists.txt
D	externals/pio2/CTestConfig.cmake
D	externals/pio2/CTestScript.cmake
D	externals/pio2/README.md
D	externals/pio2/cmake/FindGPTL.cmake
D	externals/pio2/cmake/FindHDF5.cmake
D	externals/pio2/cmake/FindLIBRT.cmake
D	externals/pio2/cmake/FindLIBZ.cmake
D	externals/pio2/cmake/FindMPE.cmake
D	externals/pio2/cmake/FindMPISERIAL.cmake
D	externals/pio2/cmake/FindNetCDF.cmake
D	externals/pio2/cmake/FindPAPI.cmake
D	externals/pio2/cmake/FindPnetCDF.cmake
D	externals/pio2/cmake/FindSZIP.cmake
D	externals/pio2/cmake/LibCheck.cmake
D	externals/pio2/cmake/LibFind.cmake
D	externals/pio2/cmake/LibMPI.cmake
D	externals/pio2/cmake/TryHDF5_HAS_SZIP.c
D	externals/pio2/cmake/TryNetCDF_DAP.c
D	externals/pio2/cmake/TryNetCDF_PARALLEL.c
D	externals/pio2/cmake/TryNetCDF_PNETCDF.c
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D	externals/pio2/ctest/CTestEnvironment-alcf.cmake
D	externals/pio2/ctest/CTestEnvironment-cgd.cmake
D	externals/pio2/ctest/CTestEnvironment-ncsa.cmake
D	externals/pio2/ctest/CTestEnvironment-nersc.cmake
D	externals/pio2/ctest/CTestEnvironment-nwsc.cmake
D	externals/pio2/ctest/CTestEnvironment-unknown.cmake
D	externals/pio2/ctest/CTestScript-Test.cmake
D	externals/pio2/ctest/runcdash-alcf-ibm.sh
D	externals/pio2/ctest/runcdash-cgd-nag.sh
D	externals/pio2/ctest/runcdash-nersc-cray.sh
D	externals/pio2/ctest/runcdash-nersc-intel.sh
D	externals/pio2/ctest/runcdash-nwsc-gnu.sh
D	externals/pio2/ctest/runcdash-nwsc-intel-mpiserial.sh
D	externals/pio2/ctest/runcdash-nwsc-intel.sh
D	externals/pio2/ctest/runcdash-nwsc-pgi.sh
D	externals/pio2/ctest/runctest-alcf.sh
D	externals/pio2/ctest/runctest-cgd.sh
D	externals/pio2/ctest/runctest-ncsa.sh
D	externals/pio2/ctest/runctest-nersc.sh
D	externals/pio2/ctest/runctest-nwsc.sh
D	externals/pio2/ctest/runctest-unknown.sh
D	externals/pio2/doc/CMakeFiles/3.2.3/CMakeSystem.cmake
D	externals/pio2/doc/CMakeFiles/CMakeOutput.log
D	externals/pio2/doc/CMakeFiles/cmake.check_cache
D	externals/pio2/doc/CMakeLists.txt
D	externals/pio2/doc/Doxyfile.in
D	externals/pio2/doc/DoxygenLayout.xml
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D	externals/pio2/doc/doxygen.sty
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D	externals/pio2/doc/source/CAMexample.txt
D	externals/pio2/doc/source/Decomp.txt
D	externals/pio2/doc/source/Error.txt
D	externals/pio2/doc/source/Examples.txt
D	externals/pio2/doc/source/GettingStarted.txt
D	externals/pio2/doc/source/Installing.txt
D	externals/pio2/doc/source/api.txt
D	externals/pio2/doc/source/base.txt
D	externals/pio2/doc/source/example/errorhandle
D	externals/pio2/doc/source/example/simple-bc
D	externals/pio2/doc/source/example/simple-bc-rearr
D	externals/pio2/doc/source/example/simple-bc-rearr-pe1
D	externals/pio2/doc/source/example/simple-bc-rearr-pe2
D	externals/pio2/doc/source/example/simple-dof
D	externals/pio2/doc/source/example/simple-dof-rearr
D	externals/pio2/doc/source/faq.txt
D	externals/pio2/doc/source/mach_walkthrough.txt
D	externals/pio2/doc/source/testpio_example.txt
D	externals/pio2/examples/CMakeLists.txt
D	externals/pio2/examples/basic/CAM05.csh
D	externals/pio2/examples/basic/CMakeLists.txt
D	externals/pio2/examples/basic/MPASA30km.csh
D	externals/pio2/examples/basic/MPASA60km.csh
D	externals/pio2/examples/basic/POPB.csh
D	externals/pio2/examples/basic/POPC.csh
D	externals/pio2/examples/basic/POPD.csh
D	externals/pio2/examples/basic/POPDv0.csh
D	externals/pio2/examples/basic/POPDv1.csh
D	externals/pio2/examples/basic/POPDv2.csh
D	externals/pio2/examples/basic/POPDv3.csh
D	externals/pio2/examples/basic/POPDv4.csh
D	externals/pio2/examples/basic/POPDv5.csh
D	externals/pio2/examples/basic/README.testpio
D	externals/pio2/examples/basic/WRFB.csh
D	externals/pio2/examples/basic/alloc_mod.F90.in
D	externals/pio2/examples/basic/build_defaults.xml
D	externals/pio2/examples/basic/check_mod.F90
D	externals/pio2/examples/basic/config_bench.xml
D	externals/pio2/examples/basic/fdepends.awk
D	externals/pio2/examples/basic/gdecomp_mod.F90
D	externals/pio2/examples/basic/kinds_mod.F90
D	externals/pio2/examples/basic/kraken.128.csh
D	externals/pio2/examples/basic/kraken.1K.csh
D	externals/pio2/examples/basic/kraken.256.csh
D	externals/pio2/examples/basic/kraken.512.csh
D	externals/pio2/examples/basic/kraken.64.csh
D	externals/pio2/examples/basic/namelist_mod.F90
D	externals/pio2/examples/basic/namelists/testpio_in.apb05
D	externals/pio2/examples/basic/namelists/testpio_in.asb01
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D	externals/pio2/examples/basic/namelists/testpio_in.n4n01
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D	externals/pio2/examples/basic/namelists/testpio_in.pb08
D	externals/pio2/examples/basic/namelists/testpio_in.pn01
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D	externals/pio2/examples/basic/namelists/testpio_in.ps01
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D	externals/pio2/examples/basic/namelists/testpio_in.ps04
D	externals/pio2/examples/basic/namelists/testpio_in.ps05
D	externals/pio2/examples/basic/namelists/testpio_in.ps06
D	externals/pio2/examples/basic/namelists/testpio_in.ps07
D	externals/pio2/examples/basic/namelists/testpio_in.ps08
D	externals/pio2/examples/basic/namelists/testpio_in.sb01
D	externals/pio2/examples/basic/namelists/testpio_in.sb02
D	externals/pio2/examples/basic/namelists/testpio_in.sb03
D	externals/pio2/examples/basic/namelists/testpio_in.sb04
D	externals/pio2/examples/basic/namelists/testpio_in.sb05
D	externals/pio2/examples/basic/namelists/testpio_in.sb06
D	externals/pio2/examples/basic/namelists/testpio_in.sb07
D	externals/pio2/examples/basic/namelists/testpio_in.sb08
D	externals/pio2/examples/basic/namelists/testpio_in.sn01
D	externals/pio2/examples/basic/namelists/testpio_in.sn02
D	externals/pio2/examples/basic/namelists/testpio_in.sn03
D	externals/pio2/examples/basic/namelists/testpio_in.wr01
D	externals/pio2/examples/basic/namelists/testpio_in.wr02
D	externals/pio2/examples/basic/perl5lib/ChangeLog
D	externals/pio2/examples/basic/perl5lib/README
D	externals/pio2/examples/basic/perl5lib/XML/Changes
D	externals/pio2/examples/basic/perl5lib/XML/Lite.pm
D	externals/pio2/examples/basic/perl5lib/XML/Lite/Element.pm
D	externals/pio2/examples/basic/perl5lib/XML/README
D	externals/pio2/examples/basic/perl5lib/XML/man3/XML::Lite.3
D	externals/pio2/examples/basic/perl5lib/XML/man3/XML::Lite::Element.3
D	externals/pio2/examples/basic/test.csh
D	externals/pio2/examples/basic/testdecomp.F90
D	externals/pio2/examples/basic/testdecomp.bluefire.run
D	externals/pio2/examples/basic/testdecomp_in
D	externals/pio2/examples/basic/testpio.F90
D	externals/pio2/examples/basic/testpio_bench.pl
D	externals/pio2/examples/basic/testpio_build.pl
D	externals/pio2/examples/basic/testpio_run.pl
D	externals/pio2/examples/basic/utils_mod.F90
D	externals/pio2/examples/basic/wstest.c
D	externals/pio2/examples/basic/ystest.sh
D	externals/pio2/examples/c/CMakeLists.txt
D	externals/pio2/examples/c/example1.c
D	externals/pio2/examples/c/example2.c
D	externals/pio2/examples/c/examplePio.c
D	externals/pio2/examples/cxx/CMakeLists.txt
D	externals/pio2/examples/cxx/examplePio.cxx
D	externals/pio2/examples/f03/CMakeLists.txt
D	externals/pio2/examples/f03/examplePio.f90
D	externals/pio2/scripts/prune_decomps.pl
D	externals/pio2/src/CMakeLists.txt
D	externals/pio2/src/clib/CMakeLists.txt
D	externals/pio2/src/clib/bget.c
D	externals/pio2/src/clib/bget.h
D	externals/pio2/src/clib/config.h.in
D	externals/pio2/src/clib/dtypes.h
D	externals/pio2/src/clib/ncparser.pl
D	externals/pio2/src/clib/ncputgetparser.pl
D	externals/pio2/src/clib/pio.h
D	externals/pio2/src/clib/pio_c_get_template.c
D	externals/pio2/src/clib/pio_c_put_template.c
D	externals/pio2/src/clib/pio_c_template.c
D	externals/pio2/src/clib/pio_darray.c
D	externals/pio2/src/clib/pio_file.c
D	externals/pio2/src/clib/pio_get_nc.c
D	externals/pio2/src/clib/pio_internal.h
D	externals/pio2/src/clib/pio_lists.c
D	externals/pio2/src/clib/pio_nc.c
D	externals/pio2/src/clib/pio_nc4.c
D	externals/pio2/src/clib/pio_put_nc.c
D	externals/pio2/src/clib/pio_rearrange.c
D	externals/pio2/src/clib/pio_spmd.c
D	externals/pio2/src/clib/pioc.c
D	externals/pio2/src/clib/pioc_sc.c
D	externals/pio2/src/clib/pioc_support.c
D	externals/pio2/src/clib/topology.c
D	externals/pio2/src/flib/CMakeLists.txt
D	externals/pio2/src/flib/pio.F90
D	externals/pio2/src/flib/pio_kinds.F90
D	externals/pio2/src/flib/pio_nf.F90
D	externals/pio2/src/flib/pio_support.F90
D	externals/pio2/src/flib/pio_types.F90
D	externals/pio2/src/flib/piodarray.F90.in
D	externals/pio2/src/flib/piolib_mod.F90
D	externals/pio2/src/flib/pionfatt_mod.F90.in
D	externals/pio2/src/flib/pionfget_mod.F90.in
D	externals/pio2/src/flib/pionfput_mod.F90.in
D	externals/pio2/src/gptl/CMakeLists.txt
D	externals/pio2/src/gptl/COPYING
D	externals/pio2/src/gptl/ChangeLog
D	externals/pio2/src/gptl/GPTLget_memusage.c
D	externals/pio2/src/gptl/GPTLprint_memusage.c
D	externals/pio2/src/gptl/GPTLutil.c
D	externals/pio2/src/gptl/README
D	externals/pio2/src/gptl/f_wrappers.c
D	externals/pio2/src/gptl/gptl.c
D	externals/pio2/src/gptl/gptl.h
D	externals/pio2/src/gptl/gptl.inc
D	externals/pio2/src/gptl/gptl_papi.c
D	externals/pio2/src/gptl/perf_mod.F90
D	externals/pio2/src/gptl/perf_utils.F90
D	externals/pio2/src/gptl/private.h
D	externals/pio2/src/gptl/threadutil.c
D	externals/pio2/tests/CMakeLists.txt
D	externals/pio2/tests/general/CMakeLists.txt
D	externals/pio2/tests/general/ncdf_fail.F90.in
D	externals/pio2/tests/general/ncdf_get_put.F90.in
D	externals/pio2/tests/general/ncdf_simple_tests.F90.in
D	externals/pio2/tests/general/pio_decomp_fillval.F90.in
D	externals/pio2/tests/general/pio_decomp_fillval2.F90
D	externals/pio2/tests/general/pio_decomp_tests.F90.in
D	externals/pio2/tests/general/pio_fail.F90.in
D	externals/pio2/tests/general/pio_file_fail.F90.in
D	externals/pio2/tests/general/pio_file_simple_tests.F90.in
D	externals/pio2/tests/general/pio_init_finalize.F90.in
D	externals/pio2/tests/general/test_memleak.c
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D	scripts/Testing/Testcases/ICP_script
D	scripts/Testing/Testcases/LAR_script
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D	scripts/Testing/Testcases/README
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A	scripts/lib/CIME/wait_for_tests.py
A	scripts/lib/cs.status.template
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A	src/share/timing/gptl.inc
A	src/share/timing/gptl_papi.c
A	src/share/timing/perf_mod.F90
A	src/share/timing/perf_utils.F90
A	src/share/timing/private.h
A	src/share/unit_test_stubs/README
A	src/share/unit_test_stubs/pio/CMakeLists.txt
A	src/share/unit_test_stubs/pio/README
A	src/share/unit_test_stubs/pio/pio.F90.in
A	src/share/util/CMakeLists.txt
A	src/share/util/mct_mod.F90
A	src/share/util/shr_assert_mod.F90.in
A	src/share/util/shr_cal_mod.F90
A	src/share/util/shr_const_mod.F90
A	src/share/util/shr_dmodel_mod.F90
A	src/share/util/shr_file_mod.F90
A	src/share/util/shr_flux_mod.F90
A	src/share/util/shr_frz_mod.F90.in
A	src/share/util/shr_infnan_mod.F90.in
A	src/share/util/shr_kind_mod.F90
A	src/share/util/shr_log_mod.F90
A	src/share/util/shr_map_mod.F90
A	src/share/util/shr_mct_mod.F90
A	src/share/util/shr_mem_mod.F90
A	src/share/util/shr_mpi_mod.F90
A	src/share/util/shr_msg_mod.F90
A	src/share/util/shr_ncread_mod.F90
A	src/share/util/shr_nl_mod.F90
A	src/share/util/shr_orb_mod.F90
A	src/share/util/shr_pcdf_mod.F90
A	src/share/util/shr_pio_mod.F90
A	src/share/util/shr_precip_mod.F90
A	src/share/util/shr_reprosum_mod.F90
A	src/share/util/shr_reprosumx86.c
A	src/share/util/shr_scam_mod.F90
A	src/share/util/shr_spfn_mod.F90
A	src/share/util/shr_strconvert_mod.F90
A	src/share/util/shr_strdata_mod.F90
A	src/share/util/shr_stream_mod.F90
A	src/share/util/shr_string_mod.F90
A	src/share/util/shr_sys_mod.F90
A	src/share/util/shr_tInterp_mod.F90
A	src/share/util/shr_timer_mod.F90
A	src/share/util/shr_vmath_mod.F90
A	src/share/util/shr_wv_sat_mod.F90
A	src/share/util/water_isotopes.F90
A	src/share/util/water_types.F90
D	tests/unit/test_names.c
M	tools/configure
M	tools/cprnc/CMakeLists.txt
M	tools/cprnc/Makefile
M	tools/unit_testing/run_tests.py
D	utils/data_assimilation/da_no_data_mod.sh
M	utils/perl5lib/compilers_translation_tool.pl
D	utils/python/CIME/BuildTools/__init__.py
D	utils/python/CIME/BuildTools/cmakemacroswriter.py
D	utils/python/CIME/BuildTools/configure.py
D	utils/python/CIME/BuildTools/macroconditiontree.py
D	utils/python/CIME/BuildTools/macrowriterbase.py
D	utils/python/CIME/BuildTools/makemacroswriter.py
D	utils/python/CIME/BuildTools/possiblevalues.py
D	utils/python/CIME/BuildTools/valuesetting.py
D	utils/python/CIME/SystemTests/README
D	utils/python/CIME/SystemTests/__init__.py
D	utils/python/CIME/SystemTests/dae.py
D	utils/python/CIME/SystemTests/eri.py
D	utils/python/CIME/SystemTests/erio.py
D	utils/python/CIME/SystemTests/erp.py
D	utils/python/CIME/SystemTests/err.py
D	utils/python/CIME/SystemTests/ers.py
D	utils/python/CIME/SystemTests/ert.py
D	utils/python/CIME/SystemTests/homme.py
D	utils/python/CIME/SystemTests/icp.py
D	utils/python/CIME/SystemTests/lii.py
D	utils/python/CIME/SystemTests/nck.py
D	utils/python/CIME/SystemTests/ncr.py
D	utils/python/CIME/SystemTests/pea.py
D	utils/python/CIME/SystemTests/pem.py
D	utils/python/CIME/SystemTests/pet.py
D	utils/python/CIME/SystemTests/pfs.py
D	utils/python/CIME/SystemTests/pre.py
D	utils/python/CIME/SystemTests/rep.py
D	utils/python/CIME/SystemTests/seq.py
D	utils/python/CIME/SystemTests/sms.py
D	utils/python/CIME/SystemTests/ssp.py
D	utils/python/CIME/SystemTests/system_tests_common.py
D	utils/python/CIME/SystemTests/system_tests_compare_two.py
D	utils/python/CIME/SystemTests/test_utils/__init__.py
D	utils/python/CIME/SystemTests/test_utils/user_nl_utils.py
D	utils/python/CIME/XML/__init__.py
D	utils/python/CIME/XML/archive.py
D	utils/python/CIME/XML/batch.py
D	utils/python/CIME/XML/compilerblock.py
D	utils/python/CIME/XML/compilers.py
D	utils/python/CIME/XML/component.py
D	utils/python/CIME/XML/compsets.py
D	utils/python/CIME/XML/entry_id.py
D	utils/python/CIME/XML/env_archive.py
D	utils/python/CIME/XML/env_base.py
D	utils/python/CIME/XML/env_batch.py
D	utils/python/CIME/XML/env_build.py
D	utils/python/CIME/XML/env_case.py
D	utils/python/CIME/XML/env_mach_pes.py
D	utils/python/CIME/XML/env_mach_specific.py
D	utils/python/CIME/XML/env_run.py
D	utils/python/CIME/XML/env_test.py
D	utils/python/CIME/XML/files.py
D	utils/python/CIME/XML/generic_xml.py
D	utils/python/CIME/XML/grids.py
D	utils/python/CIME/XML/headers.py
D	utils/python/CIME/XML/lt_archive.py
D	utils/python/CIME/XML/machines.py
D	utils/python/CIME/XML/namelist_definition.py
D	utils/python/CIME/XML/pes.py
D	utils/python/CIME/XML/pio.py
D	utils/python/CIME/XML/standard_module_setup.py
D	utils/python/CIME/XML/testlist.py
D	utils/python/CIME/XML/tests.py
D	utils/python/CIME/XML/testspec.py
D	utils/python/CIME/__init__.py
D	utils/python/CIME/bless_test_results.py
D	utils/python/CIME/build.py
D	utils/python/CIME/buildlib.py
D	utils/python/CIME/buildnml.py
D	utils/python/CIME/case.py
D	utils/python/CIME/case_cmpgen_namelists.py
D	utils/python/CIME/case_lt_archive.py
D	utils/python/CIME/case_run.py
D	utils/python/CIME/case_setup.py
D	utils/python/CIME/case_st_archive.py
D	utils/python/CIME/case_submit.py
D	utils/python/CIME/case_test.py
D	utils/python/CIME/check_input_data.py
D	utils/python/CIME/check_lockedfiles.py
D	utils/python/CIME/code_checker.py
D	utils/python/CIME/compare_namelists.py
D	utils/python/CIME/compare_test_results.py
D	utils/python/CIME/get_timing.py
D	utils/python/CIME/hist_utils.py
D	utils/python/CIME/namelist.py
D	utils/python/CIME/nmlgen.py
D	utils/python/CIME/preview_namelists.py
D	utils/python/CIME/provenance.py
D	utils/python/CIME/simple_compare.py
D	utils/python/CIME/test_scheduler.py
D	utils/python/CIME/test_status.py
D	utils/python/CIME/test_utils.py
D	utils/python/CIME/tests/README
D	utils/python/CIME/tests/SystemTests/__init__.py
D	utils/python/CIME/tests/SystemTests/test_system_tests_compare_two.py
D	utils/python/CIME/tests/SystemTests/test_system_tests_compare_two_link_to_case2_output.py
D	utils/python/CIME/tests/SystemTests/test_utils/__init__.py
D	utils/python/CIME/tests/SystemTests/test_utils/test_user_nl_utils.py
D	utils/python/CIME/tests/__init__.py
D	utils/python/CIME/tests/case_fake.py
D	utils/python/CIME/tests/test_case_fake.py
D	utils/python/CIME/user_mod_support.py
D	utils/python/CIME/utils.py
D	utils/python/CIME/wait_for_tests.py
D	utils/python/cs.status.template
D	utils/python/cs.submit.template
D	utils/python/jenkins_generic_job.py
D	utils/python/tests/CMakeLists.txt
D	utils/python/tests/CTestConfig.cmake
D	utils/python/tests/cpl.hi1.nc.test
D	utils/python/tests/cpl.hi2.nc.test
D	utils/python/tests/cpl.log.failmemleak.gz
D	utils/python/tests/cpl.log.passmemleak.gz
D	utils/python/tests/list_tests
D	utils/python/tests/scripts_regression_tests.py
D	utils/python/tests/user_mods_test1/include_user_mods
D	utils/python/tests/user_mods_test1/user_nl_comp
D	utils/python/tests/user_mods_test1/user_nl_cpl
D	utils/python/tests/user_mods_test2/SourceMods/src.drv/somefile.F90
D	utils/python/tests/user_mods_test2/user_nl_cpl
D	utils/python/update_acme_tests.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 2-23-2017
Tag: cime5.2.0-alpha.26
Answer Changes: None
Tests: scripts_regression_tests on some for PRs #1159,#1172
       B1850 test for PR#1159
Dependencies:  For allactive configurations, https://github.com/CESM-Development/cime_config
               is needed.

Brief Summary:
   -Move cesm/allactive out of the cime tag.
   -Pop namelist changes,
   -Make sure pio1 finds netcdf4
   -add --mpilib option to create_test
   -Add S-case test to cime_developers

User interface changes: adds --mpilib optional argument to create_test

PR summary: git log --oneline --first-parent [previous_tag]..master
fd200f6 Merge pull request #1181 from ESMCI/agsalin/add_S_case_test
d33e6a2 Merge pull request #1180 from jedwards4b/create_test_mpilib_option
d210e0b Merge pull request #1159 from bertinia/master
ad5ff79 Merge pull request #1172 from ESMCI/mvertens/pop_python_namelist
4ab605f Merge pull request #1177 from jedwards4b/pio1_bld_fixes

Modified files: git diff --name-status [previous_tag]
D       cime_config/cesm/allactive/config_compsets.xml
D       cime_config/cesm/allactive/config_pes.xml
D       cime_config/cesm/allactive/testlist_allactive.xml
D       cime_config/cesm/allactive/testmods_dirs/allactive/cesm2dev01/include_user_mods
D       cime_config/cesm/allactive/testmods_dirs/allactive/cesm2dev01io/include_user_mods
D       cime_config/cesm/allactive/testmods_dirs/allactive/cism/oneway/README
D       cime_config/cesm/allactive/testmods_dirs/allactive/cism/oneway/shell_commands
D       cime_config/cesm/allactive/testmods_dirs/allactive/cism/trilinos/README
D       cime_config/cesm/allactive/testmods_dirs/allactive/cism/trilinos/include_user_mods
D       cime_config/cesm/allactive/testmods_dirs/allactive/cism/trilinos/shell_commands
D       cime_config/cesm/allactive/testmods_dirs/allactive/cism/trilinos/user_nl_cism
D       cime_config/cesm/allactive/testmods_dirs/allactive/default/user_nl_cam
D       cime_config/cesm/allactive/testmods_dirs/allactive/default/user_nl_cice
D       cime_config/cesm/allactive/testmods_dirs/allactive/default/user_nl_clm
D       cime_config/cesm/allactive/testmods_dirs/allactive/default/user_nl_mosart
D       cime_config/cesm/allactive/testmods_dirs/allactive/default/user_nl_pop
D       cime_config/cesm/allactive/testmods_dirs/allactive/default/user_nl_rtm
D       cime_config/cesm/allactive/testmods_dirs/allactive/defaultio/include_user_mods
D       cime_config/cesm/allactive/testmods_dirs/allactive/defaultio/user_nl_cam
D       cime_config/cesm/allactive/testmods_dirs/allactive/defaultio/user_nl_cice
D       cime_config/cesm/allactive/testmods_dirs/allactive/defaultio/user_nl_cism
D       cime_config/cesm/allactive/testmods_dirs/allactive/defaultio/user_nl_clm
D       cime_config/cesm/allactive/testmods_dirs/allactive/defaultio/user_nl_mosart
D       cime_config/cesm/allactive/testmods_dirs/allactive/defaultio/user_nl_pop
D       cime_config/cesm/allactive/testmods_dirs/allactive/defaultio/user_nl_rtm
D       cime_config/cesm/allactive/usermods_dirs/b1850/shell_commands
D       cime_config/cesm/allactive/usermods_dirs/b1850/user_nl_clm
D       cime_config/cesm/allactive/usermods_dirs/b1850/user_nl_cpl
D       cime_config/cesm/allactive/usermods_dirs/b1850_cism/include_user_mods
D       cime_config/cesm/allactive/usermods_dirs/b1850_cism/user_nl_cism
M       cime_config/cesm/machines/Makefile
M       externals/pio1/pio/CMakeLists.txt
M       scripts/create_newcase
M       scripts/create_test
M       utils/python/CIME/build.py
M       utils/python/CIME/namelist.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/update_acme_tests.py

======================================================================

======================================================================

Originator: Bill Sacks
Date: 02-21-2017
Tag: cime5.2.0-alpha.25
Answer Changes: Likely answer changes on yellowstone relative to
                alpha.24, but not relative to alpha.23
Tests: One CLM test that failed in alpha.24
Dependencies: none

Brief Summary: Back out the compiler update on yellowstone

User interface changes: none

PR summary: git log --oneline --first-parent [previous_tag]..master

bac0ce7 Merge pull request #1174 from jedwards4b/compiler_backout

Modified files: git diff --name-status [previous_tag]

M       cime_config/cesm/machines/config_machines.xml

======================================================================

======================================================================

Originator: Bill Sacks
Date: 02-17-2017
Tag: cime5.2.0-alpha.24
Answer Changes: None documented in merge log messages for 'Test status'
Tests: scripts_regression_tests.py run on some changes, but not this tag
Dependencies:

Brief Summary: Major changes include:
- Bring in ACME changes up to 5.1
- Fix Fortran unit tests

User interface changes: The following changes were documented:
- create_newcase --mach is now --machine to match create_test
- Removes PRE test from cime_developer
- Many changes in PR #1123 ("Merge the maint-cime5.1 branch along with ACME's
  changes to 5.1"), most (all?) of which just affect ACME
- -p flag to xmlquery
- -a option to case.submit

PR summary: git log --oneline --first-parent [previous_tag]..master

980a6b8 Merge pull request #1167 from fischer-ncar/drip_annual_changes_test_fix
e8929e2 Merge pull request #1165 from ESMCI/jayeshkrishna/cond_incl_make_undefine
9554cce Merge pull request #1160 from jedwards4b/get_timing_correction
642cc32 Merge pull request #1164 from billsacks/unit_tests_local
938e9b0 Merge pull request #1157 from billsacks/unit_test_parallel
3929369 Merge pull request #1149 from jedwards4b/correct_path_query_for_testlistxml
9b1630f Merge pull request #1152 from jedwards4b/pio_bld_fix
db95da1 Merge pull request #1151 from ESMCI/agsalin/gitignore
c80c65c Merge pull request #1145 from billsacks/unit_test_cleanup
e8d8c67 fix pylint issue
7ef40c0 Merge pull request #1140 from jedwards4b/cleanbld_refactor
bd3fc66 Merge pull request #1135 from jedwards4b/unit_test_refactor
534aade Merge branch 'jgfouca/allow_arbitrary_batch_args' (PR #1137)
d0a1616 Merge pull request #1136 from ESMCI/jgfouca/handle_batch_errors_better
26cd982 Merge pull request #1131 from bertinia/master
26dd1e2 Merge pull request #1126 from ESMCI/jgfouca/bless_test_update
98c0ff1 Merge pull request #1127 from ESMCI/jgfouca/namelist_allow_star
a51fb8c Merge pull request #1128 from ESMCI/jgfouca/xmlquery_partial_match
77cf83e Merge branch 'worleyph/timing/non-null-terminated_string_support_fix' into master (PR #895)
21ea438 Merge pull request #1122 from gold2718/DAEfix
7248aef Merge branch 'jgfouca/acme5.1_to_esmci_try2' (PR #1123)
69627c8 Hotfix for minor whitespace issue in exception text
2456b56 Merge pull request #1110 from ESMCI/jgfouca/fixes_to_recent_new_tests
18734f3 Merge pull request #1104 from jedwards4b/tested_msg
11e30d6 Merge pull request #1109 from gold2718/TimeMgrFix
e367fb4 Merge pull request #1098 from ESMCI/mfdeakin-sandia/map_field_build
ff4f207 Merge pull request #1095 from gold2718/DAdesp
a93184d Merge pull request #1097 from jedwards4b/tie_timers_to_xml
618f515 Merge pull request #1092 from mgduda/esmf_timemgr/i8_interval_division
654504c Merge pull request #1094 from ESMCI/jgfouca/err_resub_fix
f56a446 Merge pull request #1090 from jedwards4b/lt_archive_issues
ccd1e96 Merge pull request #1082 from jedwards4b/addback_mask_grid
81f08e1 Merge pull request #1081 from jedwards4b/fix_no_nesting_fail
1d083cc fix pylint issue
9e2764c Merge pull request #1080 from jedwards4b/config_compilers_conformity
ccb7c22 Revert "Change over acme env usage to correct syntax"

Modified files: git diff --name-status [previous_tag]

M	.gitignore
M	CMakeLists.txt
M	README.unit_testing
M	cime_config/acme/allactive/config_compsets.xml
M	cime_config/acme/allactive/config_compsets.xml.cime2
M	cime_config/acme/allactive/config_pes.xml
M	cime_config/acme/allactive/config_pes.xml.cime2
M	cime_config/acme/allactive/config_pesall.xml
D	cime_config/acme/allactive/testmods_dirs/cam/outfrq9s/user_nl_cam
D	cime_config/acme/allactive/testmods_dirs/cam/outfrq9s/user_nl_clm
M	cime_config/acme/config_files.xml
M	cime_config/acme/config_grids.xml
M	cime_config/acme/machines/Depends.cetus
M	cime_config/acme/machines/Depends.intel
M	cime_config/acme/machines/Depends.intel14
M	cime_config/acme/machines/Depends.intelmic
M	cime_config/acme/machines/Depends.intelmic14
M	cime_config/acme/machines/Depends.mira
D	cime_config/acme/machines/Depends.titan.pgi_acc
A	cime_config/acme/machines/Depends.titan.pgiacc
D	cime_config/acme/machines/Depends.titan.pgicuda
M	cime_config/acme/machines/Makefile
M	cime_config/acme/machines/config_batch.xml
M	cime_config/acme/machines/config_compilers.xml
M	cime_config/acme/machines/config_machines.xml
M	cime_config/acme/machines/config_pio.xml
D	cime_config/acme/machines/env_mach_specific.blues
D	cime_config/acme/machines/env_mach_specific.cascade
D	cime_config/acme/machines/env_mach_specific.cetus
D	cime_config/acme/machines/env_mach_specific.constance
D	cime_config/acme/machines/env_mach_specific.corip1
D	cime_config/acme/machines/env_mach_specific.edison
D	cime_config/acme/machines/env_mach_specific.eos
D	cime_config/acme/machines/env_mach_specific.juqueen
D	cime_config/acme/machines/env_mach_specific.lawrencium-lr2
D	cime_config/acme/machines/env_mach_specific.linux-generic
D	cime_config/acme/machines/env_mach_specific.mac
D	cime_config/acme/machines/env_mach_specific.mira
D	cime_config/acme/machines/env_mach_specific.mustang
D	cime_config/acme/machines/env_mach_specific.oic2
D	cime_config/acme/machines/env_mach_specific.oic5
D	cime_config/acme/machines/env_mach_specific.sierra
D	cime_config/acme/machines/env_mach_specific.sooty
D	cime_config/acme/machines/env_mach_specific.stampede
D	cime_config/acme/machines/env_mach_specific.titan
D	cime_config/acme/machines/env_mach_specific.userdefined
D	cime_config/acme/machines/env_mach_specific.wolf
M	cime_config/acme/machines/syslog.cetus
A	cime_config/acme/machines/syslog.cori-haswell
A	cime_config/acme/machines/syslog.cori-knl
D	cime_config/acme/machines/syslog.corip1
M	cime_config/acme/machines/syslog.edison
M	cime_config/acme/machines/syslog.mira
M	cime_config/acme/machines/syslog.titan
A	cime_config/acme/testmods_dirs/allactive/cam/outfrq9s/user_nl_cam
A	cime_config/acme/testmods_dirs/allactive/cam/outfrq9s/user_nl_clm
M	cime_config/buildlib.pio
M	cime_config/cesm/allactive/testlist_allactive.xml
M	cime_config/cesm/allactive/testmods_dirs/allactive/defaultio/user_nl_clm
M	cime_config/cesm/config_archive.xml
M	cime_config/cesm/config_files.xml
M	cime_config/cesm/machines/Makefile
M	cime_config/cesm/machines/config_compilers.xml
M	cime_config/cesm/machines/config_lt_archive.xml
M	cime_config/cesm/machines/config_machines.xml
M	cime_config/config_tests.xml
M	cime_config/xml_schemas/config_machines.xsd
M	components/data_comps/datm/cime_config/config_component.xml
A	components/data_comps/desp/cime_config/buildlib
A	components/data_comps/desp/cime_config/buildnml
A	components/data_comps/desp/cime_config/config_component.xml
A	components/data_comps/desp/cime_config/namelist_definition_desp.xml
A	components/data_comps/desp/cime_config/user_nl_desp
A	components/data_comps/desp/desp_comp_mod.F90
A	components/data_comps/desp/esp_comp_mct.F90
A	components/data_comps/desp/esp_utils.F90
M	components/data_comps/dlnd/cime_config/config_component.xml
M	components/data_comps/docn/cime_config/config_component.xml
M	driver_cpl/cime_config/buildnml
M	driver_cpl/cime_config/config_component.xml
M	driver_cpl/cime_config/config_component_acme.xml
M	driver_cpl/cime_config/config_component_cesm.xml
M	driver_cpl/cime_config/config_compsets.xml
M	driver_cpl/cime_config/namelist_definition_drv.xml
M	driver_cpl/cime_config/user_nl_cpl
M	driver_cpl/driver/cesm_comp_mod.F90
M	driver_cpl/driver/component_mod.F90
M	driver_cpl/driver/seq_flux_mct.F90
M	driver_cpl/driver/seq_io_mod.F90
M	driver_cpl/shr/seq_infodata_mod.F90
M	driver_cpl/shr/seq_timemgr_mod.F90
M	driver_cpl/unit_test/vertical_gradient_calculator_test/plot_gradient
M	externals/CMake/CESM_utils.cmake
A	externals/CMake/CIME_utils.cmake
M	externals/CMake/Compilers.cmake
D	externals/CMake/FindNETCDF.cmake
D	externals/CMake/FindNETCDF_C.cmake
D	externals/CMake/FindNETCDF_Fortran.cmake
D	externals/CMake/FindPnetcdf.cmake
M	externals/CMake/FindpFUnit.cmake
D	externals/CMake/LibFindMacros.cmake
M	externals/CMake/README.md
M	externals/pio1/pio/CMakeLists.txt
M	externals/pio2/src/flib/piolib_mod.F90
M	scripts/Tools/bless_test_results
M	scripts/Tools/case.build
M	scripts/Tools/case.submit
A	scripts/Tools/cron_script
M	scripts/Tools/xmlquery
M	scripts/create_newcase
M	scripts/create_test
M	share/csm_share/shr/shr_flux_mod.F90
M	share/csm_share/test/unit/dynamic_vector/CMakeLists.txt
M	share/esmf_wrf_timemgr/ESMF_TimeIntervalMod.F90
M	share/esmf_wrf_timemgr/ESMF_TimeMod.F90
M	share/timing/ChangeLog
M	share/timing/f_wrappers.c
M	share/timing/gptl.c
M	tools/configure
M	tools/mapping/map_field/INSTALL
M	tools/unit_testing/Examples/circle_area/tests/CMakeLists.txt
M	tools/unit_testing/Examples/circle_area/tests/pFUnit/CMakeLists.txt
M	tools/unit_testing/Examples/interpolate_1d/tests/CMakeLists.txt
M	tools/unit_testing/Examples/interpolate_1d/tests/pFUnit/CMakeLists.txt
M	tools/unit_testing/README
M	tools/unit_testing/run_tests.py
M	utils/data_assimilation/da_no_data_mod.sh
M	utils/python/CIME/BuildTools/cmakemacroswriter.py
M	utils/python/CIME/SystemTests/dae.py
M	utils/python/CIME/SystemTests/err.py
M	utils/python/CIME/SystemTests/homme.py
A	utils/python/CIME/SystemTests/pre.py
M	utils/python/CIME/SystemTests/system_tests_common.py
M	utils/python/CIME/XML/compilerblock.py
M	utils/python/CIME/XML/compilers.py
M	utils/python/CIME/XML/entry_id.py
M	utils/python/CIME/XML/env_batch.py
M	utils/python/CIME/XML/grids.py
M	utils/python/CIME/XML/namelist_definition.py
M	utils/python/CIME/XML/pes.py
M	utils/python/CIME/bless_test_results.py
M	utils/python/CIME/build.py
M	utils/python/CIME/case.py
M	utils/python/CIME/case_cmpgen_namelists.py
M	utils/python/CIME/case_lt_archive.py
M	utils/python/CIME/case_run.py
M	utils/python/CIME/case_st_archive.py
M	utils/python/CIME/case_submit.py
M	utils/python/CIME/check_input_data.py
M	utils/python/CIME/code_checker.py
M	utils/python/CIME/compare_namelists.py
M	utils/python/CIME/compare_test_results.py
M	utils/python/CIME/get_timing.py
M	utils/python/CIME/provenance.py
M	utils/python/CIME/test_scheduler.py
M	utils/python/CIME/test_status.py
M	utils/python/CIME/utils.py
M	utils/python/tests/scripts_regression_tests.py
M	utils/python/update_acme_tests.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 01-30-2017
Tag: cime5.2.0-alpha.23
Answer Changes: None
Tests: cesm_tests, scripts_regression_tests.py
Dependencies:

Brief Summary: new tfreeze_option setting for cesm, some system test refactoring for
	improved reuse of tests, single test no longer has external SHAREDLIBROOT setting
	New pop default settings.  Fix for clm test mapping file.

User interface changes:

PR summary: git log --oneline --first-parent [previous_tag]..master

feb28f3 Merge pull request #1076 from ESMCI/mvertens/fix_clm_usrdat
853da02 Merge pull request #1069 from jtruesdal/cime_plus_defs
38cc009 Merge pull request #1068 from jedwards4b/test_fixes
3d0965a Merge pull request #1062 from ESMCI/mvertens/tfreeze_option
19a104d Change over acme env usage to correct syntax
8d92fa0 Merge pull request #1048 from jedwards4b/depends_file_precidence
1e3008f Merge pull request #1054 from ESMCI/jgfouca/fix_eri_resub
5de3b4d Merge pull request #1055 from ESMCI/jgfouca/add_support_for_shell_in_XML
18479ce Merge pull request #1039 from ESMCI/jgfouca/lock_env_batch
3a84a6e Merge pull request #1046 from jedwards4b/some_log_issues
0489798 Fix Z_FullSystemTests on batch machines
742c8dc Merge pull request #1036 from ESMCI/jgfouca/fix_resubmission_of_some_testcases
49a7de6 fix pylint issue
289e39e Merge pull request #1034 from ESMCI/jgfouca/better_support_for_custom_input_files
869f904 Merge pull request #1025 from ESMCI/jgfouca/more_create_test_force_pecount_chgs
25de83b update ChangeLog
33d74c3 Merge pull request #1030 from jedwards4b/fix_drive_namelist_issue


Modified files: git diff --name-status
M       cime_config/acme/machines/config_batch.xml
M       cime_config/acme/machines/config_compilers.xml
M       cime_config/acme/machines/config_machines.xml
M       cime_config/cesm/config_grids.xml
M       cime_config/cesm/machines/Makefile
M       cime_config/cesm/machines/config_machines.xml
M       cime_config/config_tests.xml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/cime_config/config_component_acme.xml
M       driver_cpl/cime_config/config_component_cesm.xml
M       driver_cpl/cime_config/namelist_definition_drv.xml
M       scripts/create_newcase
M       utils/python/CIME/BuildTools/configure.py
M       utils/python/CIME/SystemTests/eri.py
M       utils/python/CIME/SystemTests/erp.py
M       utils/python/CIME/SystemTests/ers.py
M       utils/python/CIME/SystemTests/ncr.py
M       utils/python/CIME/SystemTests/seq.py
M       utils/python/CIME/SystemTests/system_tests_common.py
M       utils/python/CIME/XML/generic_xml.py
M       utils/python/CIME/XML/namelist_definition.py
M       utils/python/CIME/build.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_run.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/check_input_data.py
M       utils/python/CIME/check_lockedfiles.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/utils.py
M       utils/python/tests/scripts_regression_tests.py
M       utils/python/update_acme_tests.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 01-20-2017
Tag: cime5.2.0-alpha.22
Answer Changes: None
Tests: cesm tests, scripts_regression_tests
Dependencies:

Brief Summary: Fix issue in drv buildnml reading xml file.

User interface changes: Added error if buildnml file not found.

Modified files: git diff --name-status
M       driver_cpl/cime_config/buildnml
M       utils/python/CIME/XML/namelist_definition.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 01-19-2017
Tag: cime5.2.0-alpha.21
Answer Changes: None
Tests: scripts_regression_tests, cesm testing
Dependencies:

Brief Summary: Add science_support field for CESM.  Add schema files
	for config_batch, config_compsets xml files.
	Add a config_machines_template.xml for documentation and porting.
	Add model dependent config_component_$model.xml files for driver.

User interface changes: New flag in create_newcase --run-unsupported (cesm only)
	New flag in create_clone --cime-output-root to support cloning across user.

Modified files: git diff --name-status
M	cime_config/acme/config_files.xml
M	cime_config/acme/machines/config_batch.xml
M	cime_config/cesm/allactive/config_compsets.xml
M	cime_config/cesm/config_files.xml
M	cime_config/cesm/machines/config_batch.xml
D	cime_config/cesm/machines/config_batch.xsd
M	cime_config/cesm/machines/config_compilers.xml
A	cime_config/xml_schemas/config_batch.xsd
A	cime_config/xml_schemas/config_compsets.xsd
A	cime_config/xml_schemas/config_machines_template.xml
M	cime_config/xml_schemas/config_pes.xsd
M	cime_config/xml_schemas/entry_id_base.xsd
M	cime_config/xml_schemas/testlist.xsd
M	components/data_comps/datm/cime_config/buildnml
M	components/data_comps/dice/cime_config/buildnml
M	components/data_comps/dlnd/cime_config/buildnml
M	components/data_comps/docn/cime_config/buildnml
M	components/data_comps/drof/cime_config/buildnml
M	components/data_comps/dwav/cime_config/buildnml
M	driver_cpl/cime_config/buildnml
M	driver_cpl/cime_config/config_component.xml
A	driver_cpl/cime_config/config_component_acme.xml
A	driver_cpl/cime_config/config_component_cesm.xml
M	driver_cpl/cime_config/config_compsets.xml
M	scripts/create_clone
M	scripts/create_newcase
M	scripts/create_test
M	tools/cprnc/compare_vars_mod.F90.in
M	tools/cprnc/cprnc.F90
M	tools/cprnc/filestruct.F90
M	utils/python/CIME/XML/batch.py
M	utils/python/CIME/XML/compilers.py
M	utils/python/CIME/XML/compsets.py
M	utils/python/CIME/XML/env_mach_pes.py
M	utils/python/CIME/XML/files.py
M	utils/python/CIME/XML/generic_xml.py
M	utils/python/CIME/XML/grids.py
M	utils/python/CIME/XML/machines.py
M	utils/python/CIME/XML/namelist_definition.py
M	utils/python/CIME/XML/pes.py
M	utils/python/CIME/XML/testlist.py
M	utils/python/CIME/case.py
M	utils/python/CIME/nmlgen.py
M	utils/python/CIME/preview_namelists.py
M	utils/python/CIME/test_scheduler.py
M	utils/python/CIME/utils.py
M	utils/python/tests/scripts_regression_tests.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 01-15-2017
Tag: cime5.2.0-alpha.20
Answer Changes: None
Tests: scripts_regression_tests, cesm2_0_beta05 testing
Dependencies:

Brief Summary: Adds schema for config_pes and overrides section to that file
               Adds support for new machine cheyenne
User interface changes:

Modified files: git diff --name-status
M       cime_config/acme/allactive/config_pes.xml
	M       cime_config/acme/config_files.xml
	M       cime_config/cesm/allactive/config_pes.xml
	M       cime_config/cesm/allactive/testlist_allactive.xml
	M       cime_config/cesm/config_files.xml
	M       cime_config/cesm/machines/config_batch.xml
	M       cime_config/cesm/machines/config_compilers.xml
	M       cime_config/cesm/machines/config_machines.xml
	A       cime_config/xml_schemas/config_pes.xsd
	M       driver_cpl/cime_config/testdefs/testlist_drv.xml
	M       utils/python/CIME/XML/machines.py
	M       utils/python/CIME/XML/pes.py
	M       utils/python/CIME/case.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 01-12-2017
Tag: cime5.2.0-alpha.19
Answer Changes: None
Tests: scripts_regression_tests.py (on cheyenne)
Dependencies:

Brief Summary:  Add support for new NCAR HPC system Cheyenne

User interface changes: none

Modified files: git diff --name-status

======================================================================

======================================================================

Originator: Jim Edwards
Date: 01-11-2017
Tag: cime5.2.0-alpha.18
Answer Changes: Climate Changing
Tests: scripts_regression_tests cesm2_0_alpha05d
Dependencies: (cesm requires pop version 20161219 or older

Brief Summary:  Needed to back out changes that require a new pop version
                           Add schema definition for config_machines.xml

User interface changes:

Modified files: git diff --name-status
M       cime_config/acme/machines/config_machines.xml
M       cime_config/acme/machines/config_pio.xml
M       cime_config/buildlib.pio
M       cime_config/cesm/config_files.xml
M       cime_config/cesm/config_grids.xml
M       cime_config/cesm/machines/config_machines.xml
A       cime_config/xml_schemas/config_machines.xsd
M       driver_cpl/bld/testdir/env_run.xml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/cime_config/namelist_definition_drv.xml
M       driver_cpl/shr/seq_infodata_mod.F90
M       utils/python/CIME/XML/generic_xml.py
M       utils/python/CIME/XML/machines.py


======================================================================

======================================================================

Originator: Jim Edwards
Date: 01-10-2017
Tag: cime5.2.0-alpha.17
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:

Brief Summary: Fix issue with netcdf flags in Makefile, update nersc systems
	add runtime env to provenance output

User interface changes:

Modified files: git diff --name-status
M       cime_config/acme/machines/Makefile
M       cime_config/acme/machines/config_compilers.xml
M       cime_config/cesm/allactive/config_compsets.xml
M       cime_config/cesm/allactive/testlist_allactive.xml
M       cime_config/cesm/config_grids.xml
M       cime_config/cesm/machines/Makefile
M       cime_config/cesm/machines/config_compilers.xml
M       cime_config/cesm/machines/config_machines.xml
M       cime_config/xml_schemas/config_compilers_v2.xsd
M       driver_cpl/bld/testdir/env_run.xml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/cime_config/namelist_definition_drv.xml
M       driver_cpl/shr/seq_infodata_mod.F90
M       scripts/Tools/case_diff
M       scripts/Tools/code_checker
M       utils/python/CIME/SystemTests/system_tests_common.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/XML/machines.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_cmpgen_namelists.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/case_test.py
A       utils/python/CIME/code_checker.py
M       utils/python/CIME/compare_namelists.py
M       utils/python/CIME/provenance.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/utils.py
M       utils/python/tests/scripts_regression_tests.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 01-04-2017
Tag: cime5.2.0-alpha.15
Answer Changes: None
Tests: scripts_regression_tests, cesm development
Dependencies:

Brief Summary: fix issues with clm 1pt configurations, issues with pio namelist settings, data assimilation script arguments, sharedarea context manager,

User interface changes:

Modified files: git diff --name-status
M       cime_config/cesm/allactive/config_compsets.xml
M       cime_config/cesm/allactive/testlist_allactive.xml
M       cime_config/cesm/config_grids.xml
M       cime_config/cesm/machines/config_compilers.xml
M       cime_config/cesm/machines/config_machines.xml
M       scripts/Tools/pelayout
M       share/csm_share/shr/shr_pio_mod.F90
M       utils/python/CIME/case.py
M       utils/python/CIME/case_run.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/check_input_data.py
M       utils/python/CIME/preview_namelists.py
M       utils/python/CIME/provenance.py
M       utils/python/CIME/utils.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 01-03-2017
Tag: cime5.2.0-alpha.14
Answer Changes: None
Tests: scripts_regression_tests, cesm component testing

Dependencies:

Brief Summary: Changes several variables of the form XXX_COMP to variables of the
	form XXX with values for each COMP.   Remove clm40 from all active
	compsets.  Build gptl prior to MCT.   Performance improvements in buildnml

User interface changes: Perl scripts in component models can no longer read these
	COMP variables directely  - they must now use xmlquery.

Modified files: git diff --name-status
M       cime_config/acme/config_files.xml
M       cime_config/acme/machines/Makefile
M       cime_config/buildlib.mct
A       cime_config/buildlib.mpi-serial
M       cime_config/cesm/allactive/config_compsets.xml
M       cime_config/cesm/allactive/testlist_allactive.xml
M       cime_config/cesm/config_files.xml
M       cime_config/cesm/config_grids.xml
M       cime_config/cesm/machines/Makefile
M       cime_config/cesm/machines/config_machines.xml
M       cime_config/config_headers.xml
M       cime_config/xml_schemas/entry_id_base.xsd
M       cime_config/xml_schemas/entry_id_namelist.xsd
M       components/data_comps/datm/cime_config/buildnml
M       components/data_comps/datm/cime_config/namelist_definition_datm.xml
M       components/data_comps/dice/cime_config/buildnml
M       components/data_comps/dice/cime_config/namelist_definition_dice.xml
M       components/data_comps/dlnd/cime_config/buildnml
M       components/data_comps/dlnd/cime_config/namelist_definition_dlnd.xml
M       components/data_comps/docn/cime_config/buildnml
M       components/data_comps/docn/cime_config/namelist_definition_docn.xml
M       components/data_comps/drof/cime_config/buildnml
M       components/data_comps/drof/cime_config/namelist_definition_drof.xml
M       components/data_comps/dwav/cime_config/buildnml
M       driver_cpl/cime_config/buildnml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/cime_config/namelist_definition_drv.xml
M       driver_cpl/cime_config/namelist_definition_modelio.xml
M       scripts/Tools/case.build
M       scripts/Tools/case.setup
A       scripts/Tools/pelayout
M       scripts/Tools/xmlchange
M       scripts/Tools/xmlquery
M       scripts/create_test
M       scripts/manage_case
M       scripts/manage_pes
M       tools/mapping/map_field/README
M       utils/python/CIME/SystemTests/erp.py
M       utils/python/CIME/SystemTests/nck.py
M       utils/python/CIME/SystemTests/pea.py
M       utils/python/CIME/SystemTests/seq.py
M       utils/python/CIME/XML/component.py
M       utils/python/CIME/XML/entry_id.py
M       utils/python/CIME/XML/env_archive.py
M       utils/python/CIME/XML/env_base.py
M       utils/python/CIME/XML/env_batch.py
M       utils/python/CIME/XML/env_build.py
M       utils/python/CIME/XML/env_case.py
M       utils/python/CIME/XML/env_mach_pes.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/XML/env_run.py
M       utils/python/CIME/XML/env_test.py
M       utils/python/CIME/XML/generic_xml.py
M       utils/python/CIME/XML/namelist_definition.py
M       utils/python/CIME/XML/pes.py
M       utils/python/CIME/build.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_run.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/case_submit.py
M       utils/python/CIME/get_timing.py
M       utils/python/CIME/namelist.py
M       utils/python/CIME/nmlgen.py
M       utils/python/CIME/preview_namelists.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/test_status.py
M       utils/python/CIME/utils.py
M       utils/python/tests/scripts_regression_tests.py

======================================================================

======================================================================

Originator: Chris Fischer
Date: 12-23-2016
Tag: cime5.2.0-alpha.13.bhist
Answer Changes: None
Tests: prealpha pgi tests on hobart, BHIST restart on yellowstone

Dependencies:

Brief Summary: Fix pnetcdf module on hobart for pgi.  Update BHIST compset
names

User interface changes:

Modified files: git diff --name-status

        M       cime_config/cesm/allactive/config_compsets.xml
        M       cime_config/cesm/allactive/testlist_allactive.xml
        M       cime_config/cesm/machines/config_machines.xml

======================================================================

======================================================================

Originator: Jim Edwards
Date: 12-20-2016
Tag: cime5.2.0-alpha.13
Answer Changes: None
Tests: scripts_regression_tests, cesm2_0_alpha05b
Dependencies:

Brief Summary: fix nag and pgi compiler issues, refactor xmlquery tool,
	fix issues with dlnd buildnml

User interface changes: xmlquery options were changed

Modified files:
	M       cime_config/cesm/machines/config_compilers.xml
	M       components/data_comps/dlnd/cime_config/namelist_definition_dlnd.xml
	M       driver_cpl/cime_config/config_component.xml
	M       scripts/Tools/xmlquery
	M       utils/python/CIME/XML/entry_id.py
	M       utils/python/CIME/XML/env_batch.py
	M       utils/python/CIME/XML/env_mach_specific.py
	M       utils/python/CIME/XML/generic_xml.py
	M       utils/python/CIME/buildnml.py
	M       utils/python/CIME/case.py
	M       utils/python/CIME/case_submit.py
	M       utils/python/CIME/preview_namelists.py
	M       utils/python/tests/CMakeLists.txt
	M       utils/python/tests/list_tests
	M       utils/python/tests/scripts_regression_tests.py


======================================================================

======================================================================

Originator: Jim Edwards
Date: 12-16-2016
Tag: cime5.2.0-alpha.12
Answer Changes: None
Tests: scripts_regression_tests, aux_clm40, aux_clm50
Dependencies:

Brief Summary: Fix for cori-haswell, critical namelist bug fix for datm

User interface changes:
	M       cime_config/cesm/machines/config_compilers.xml
	M       cime_config/cesm/machines/config_machines.xml
	M       components/data_comps/datm/cime_config/namelist_definition_datm.xml
	M       utils/python/CIME/check_input_data.py
	M       utils/python/tests/scripts_regression_tests.py


Modified files: git diff --name-status

======================================================================

======================================================================

Originator: Jim Edwards
Date: 12-15-2016
Tag: cime5.2.0-alpha.11
Answer Changes: None
Tests: scripts_regression_tests + various cesm system tests
Dependencies:

Brief Summary: fix debug flag attribute, clone issues, buildnml direct in python
	prevent a div by 0 in xmlchange, fix bless_test_results, move config_build to
	config_compilers, fix starchive issue, remove doc directory, redo buildnml in python
	datm updates, clm bld fix

User interface changes:

Modified files: git diff --name-status
	M       cime_config/acme/config_files.xml
M       cime_config/acme/machines/Makefile
D       cime_config/acme/machines/config_build.xml
M       cime_config/acme/machines/config_compilers.xml
M       cime_config/acme/machines/config_machines.xml
M       cime_config/buildlib.gptl
M       cime_config/cesm/allactive/config_compsets.xml
M       cime_config/cesm/allactive/config_pes.xml
M       cime_config/cesm/allactive/testlist_allactive.xml
M       cime_config/cesm/config_files.xml
M       cime_config/cesm/config_grids.xml
M       cime_config/cesm/machines/Makefile
M       cime_config/cesm/machines/config_batch.xml
D       cime_config/cesm/machines/config_build.xml
M       cime_config/cesm/machines/config_compilers.xml
M       cime_config/cesm/machines/config_machines.xml
D       cime_config/xml_schemas/config_build.xsd
A       cime_config/xml_schemas/config_compilers_v2.xsd
M       components/data_comps/datm/cime_config/buildnml
M       components/data_comps/datm/cime_config/config_component.xml
M       components/data_comps/datm/cime_config/namelist_definition_datm.xml
M       components/data_comps/dice/cime_config/buildnml
M       components/data_comps/dice/cime_config/namelist_definition_dice.xml
M       components/data_comps/dlnd/cime_config/buildnml
M       components/data_comps/dlnd/cime_config/namelist_definition_dlnd.xml
M       components/data_comps/docn/cime_config/buildnml
M       components/data_comps/drof/cime_config/buildnml
M       components/data_comps/drof/cime_config/config_component.xml
M       components/data_comps/drof/cime_config/namelist_definition_drof.xml
M       components/data_comps/dwav/cime_config/buildnml
M       components/xcpl_comps/xatm/cime_config/buildnml
M       components/xcpl_comps/xglc/cime_config/buildnml
M       components/xcpl_comps/xice/cime_config/buildnml
M       components/xcpl_comps/xlnd/cime_config/buildnml
M       components/xcpl_comps/xocn/cime_config/buildnml
M       components/xcpl_comps/xrof/cime_config/buildnml
M       components/xcpl_comps/xwav/cime_config/buildnml
D       doc/
M       driver_cpl/cime_config/buildnml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/cime_config/namelist_definition_drv.xml
M       driver_cpl/driver/cesm_comp_mod.F90
M       driver_cpl/driver/seq_hist_mod.F90
M       driver_cpl/driver/seq_io_mod.F90
M       driver_cpl/shr/seq_flds_mod.F90
M       driver_cpl/shr/seq_infodata_mod.F90
M       externals/pio1/pio/pionfput_mod.F90.in
M       scripts/Tools/code_checker
M       scripts/Tools/compare_test_results
M       scripts/Tools/preview_namelists
M       scripts/query_testlists
M       share/csm_share/shr/shr_file_mod.F90
M       share/csm_share/shr/shr_strdata_mod.F90
M       share/timing/ChangeLog
M       share/timing/Makefile
M       share/timing/perf_mod.F90
M       tools/configure
M       tools/mapping/gen_mapping_files/runoff_to_ocn/src/map_mod.F90
M       tools/utils/find_circular_dependency.py
A       utils/python/CIME/BuildTools/__init__.py
A       utils/python/CIME/BuildTools/cmakemacroswriter.py
A       utils/python/CIME/BuildTools/configure.py
A       utils/python/CIME/BuildTools/macroconditiontree.py
A       utils/python/CIME/BuildTools/macrowriterbase.py
A       utils/python/CIME/BuildTools/makemacroswriter.py
A       utils/python/CIME/BuildTools/possiblevalues.py
A       utils/python/CIME/BuildTools/valuesetting.py
D       utils/python/CIME/XML/build.py
A       utils/python/CIME/XML/compilerblock.py
M       utils/python/CIME/XML/compilers.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/XML/generic_xml.py
M       utils/python/CIME/XML/grids.py
M       utils/python/CIME/XML/machines.py
M       utils/python/CIME/bless_test_results.py
M       utils/python/CIME/build.py
M       utils/python/CIME/buildnml.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_cmpgen_namelists.py
M       utils/python/CIME/case_run.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/case_st_archive.py
M       utils/python/CIME/case_submit.py
M       utils/python/CIME/compare_namelists.py
M       utils/python/CIME/compare_test_results.py
M       utils/python/CIME/get_timing.py
D       utils/python/CIME/macros_writers.py
M       utils/python/CIME/namelist.py
M       utils/python/CIME/nmlgen.py
M       utils/python/CIME/preview_namelists.py
M       utils/python/CIME/provenance.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/user_mod_support.py
M       utils/python/CIME/utils.py
M       utils/python/tests/scripts_regression_tests.py
M       utils/python/update_acme_tests.py


======================================================================

======================================================================

Originator: Jim Edwards
Date: 11-28-2016
Tag: cime5.2.0-alpha.10
Answer Changes: Namelist compare changes expected
Tests: scripts_regression_tests + various cesm system tests
Dependencies:

Brief Summary: config_grids.xml refactor, add machines cori-haswell and cori-knl,
	remove CCSM_BASELINE variable - replaced with BASELINE_ROOT
	add error checks in xmlquery and xmlchange

User interface changes:

Modified files: git diff --name-status
M       cime_config/acme/allactive/config_pes.xml
M       cime_config/acme/allactive/config_pesall.xml
M       cime_config/acme/machines/config_batch.xml
M       cime_config/acme/machines/config_build.xml
M       cime_config/acme/machines/config_compilers.xml
M       cime_config/acme/machines/config_machines.xml
M       cime_config/acme/machines/userdefined_laptop_template/config_machines.xml
M       cime_config/cesm/allactive/testlist_allactive.xml
M       cime_config/cesm/config_archive.xml
M       cime_config/cesm/config_files.xml
M       cime_config/cesm/config_grids.xml
M       cime_config/cesm/machines/Makefile
M       cime_config/cesm/machines/config_batch.xml
M       cime_config/cesm/machines/config_machines.xml
M       cime_config/cesm/machines/userdefined_laptop_template/config_machines.xml
M       cime_config/config_tests.xml
A       cime_config/xml_schemas/config_grids_v2.xsd
M       components/data_comps/dlnd/cime_config/config_component.xml
M       driver_cpl/cime_config/config_component.xml
D       scripts/Testing/Testcases/NOC_script
M       scripts/Tools/bless_test_results
M       scripts/Tools/compare_test_results
M       scripts/Tools/xmlchange
M       scripts/Tools/xmlconvertors/config_pes_converter.py
M       scripts/Tools/xmlconvertors/grid_xml_converter.py
M       scripts/Tools/xmlquery
A       tools/utils/find_circular_dependency.py
M       utils/python/CIME/SystemTests/erio.py
M       utils/python/CIME/SystemTests/homme.py
D       utils/python/CIME/SystemTests/noc.py
M       utils/python/CIME/XML/component.py
M       utils/python/CIME/XML/entry_id.py
M       utils/python/CIME/XML/generic_xml.py
M       utils/python/CIME/XML/grids.py
M       utils/python/CIME/bless_test_results.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_st_archive.py
M       utils/python/CIME/preview_namelists.py
M       utils/python/CIME/provenance.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/utils.py
M       utils/python/tests/scripts_regression_tests.py
======================================================================

======================================================================

Originator: Jim Edwards
Date: 11-10-2016
Tag: cime5.2.0-alpha.9
Answer Changes: None
Tests: script_regression_tests
Dependencies:

Brief Summary:port to updated cori and new laramie systems, erio test and gmake fix.

User interface changes:

Modified files: git diff --name-status
A       cime_config/acme/allactive/testmods_dirs/cam/outfrq9s/shell_commands
D       cime_config/acme/allactive/testmods_dirs/cam/outfrq9s/xmlchange_cmnds
A       cime_config/acme/allactive/testmods_dirs/force_netcdf_pio/shell_commands
D       cime_config/acme/allactive/testmods_dirs/force_netcdf_pio/xmlchange_cmnds
M       cime_config/acme/config_archive.xml
M       cime_config/acme/machines/config_batch.xml
M       cime_config/acme/machines/config_compilers.xml
M       cime_config/acme/machines/config_machines.xml
M       cime_config/buildlib.pio
M       cime_config/cesm/allactive/config_compsets.xml
M       cime_config/cesm/allactive/testlist_allactive.xml
A       cime_config/cesm/allactive/testmods_dirs/allactive/cism/oneway/shell_commands
D       cime_config/cesm/allactive/testmods_dirs/allactive/cism/oneway/xmlchange_cmnds
M       cime_config/cesm/config_archive.xml
M       cime_config/cesm/machines/config_batch.xml
M       cime_config/cesm/machines/config_compilers.xml
M       cime_config/cesm/machines/config_machines.xml
M       cime_config/cesm/machines/config_pio.xml
M       driver_cpl/cime_config/buildexe
M       driver_cpl/cime_config/config_component.xml
M       scripts/Tools/compare_test_results
M       share/csm_share/shr/shr_strdata_mod.F90
M       tools/cprnc/summarize_cprnc_diffs
M       utils/python/CIME/SystemTests/erio.py
M       utils/python/CIME/SystemTests/homme.py
M       utils/python/CIME/XML/env_batch.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/build.py
M       utils/python/CIME/buildlib.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_st_archive.py
M       utils/python/CIME/case_test.py
M       utils/python/CIME/compare_test_results.py
M       utils/python/CIME/hist_utils.py
M       utils/python/CIME/nmlgen.py
M       utils/python/CIME/preview_namelists.py
M       utils/python/CIME/user_mod_support.py
M       utils/python/CIME/utils.py
M       utils/python/tests/scripts_regression_tests.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 11-02-2016
Tag: cime5.2.0-alpha.8
Answer Changes: None
Tests: scripts_regression_tests problem specific tests
Dependencies:

Brief Summary: improved build logging, --output-root option, fix issues with user_mods,
	fix pea test, update laramie, testreporter fixes

User interface changes:
M       cime_config/acme/machines/Makefile
M       cime_config/acme/machines/config_batch.xml
M       cime_config/acme/machines/config_compilers.xml
M       cime_config/acme/machines/config_machines.xml
M       cime_config/acme/machines/userdefined_laptop_template/config_machines.xml
M       cime_config/cesm/allactive/testlist_allactive.xml
M       cime_config/cesm/machines/Makefile
M       cime_config/cesm/machines/config_batch.xml
M       cime_config/cesm/machines/config_machines.xml
M       cime_config/cesm/machines/userdefined_laptop_template/config_machines.xml
M       cime_config/config_tests.xml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/driver/cesm_comp_mod.F90
M       scripts/Testing/testreporter.pl
M       scripts/Tools/bless_test_results
M       scripts/Tools/case.cmpgen_namelists
M       scripts/Tools/cime_bisect
M       scripts/Tools/compare_test_results
M       scripts/Tools/jenkins_generic_job
M       scripts/create_newcase
M       scripts/create_test
M       utils/perl5lib/Config/SetupTools.pm
A       utils/python/CIME/SystemTests/erio.py
M       utils/python/CIME/SystemTests/system_tests_common.py
M       utils/python/CIME/XML/entry_id.py
M       utils/python/CIME/XML/env_batch.py
M       utils/python/CIME/build.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_cmpgen_namelists.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/preview_namelists.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/user_mod_support.py
M       utils/python/CIME/utils.py
M       utils/python/tests/scripts_regression_tests.py
M       utils/python/update_acme_tests.py


Modified files: git diff --name-status

======================================================================

======================================================================

Originator: Jim Edwards
Date: 10-27-2016
Tag: cime5.2.0-alpha.7
Answer Changes: None
Tests: scripts_regression_tests problem specific tests
Dependencies:

Brief Summary: backout change to xmlchange command , fix ERP and ERI and DAE tests

User interface changes:

Modified files: git diff --name-status
M       cime_config/acme/machines/config_machines.xml
M       cime_config/cesm/machines/config_batch.xml
M       cime_config/config_tests.xml
M       scripts/Tools/code_checker
M       scripts/Tools/xmlchange
M       utils/python/CIME/SystemTests/erp.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/tests/scripts_regression_tests.py
======================================================================

======================================================================

Originator: Jim Edwards
Date: 10-26-2016
Tag: cime5.2.0-alpha.6
Answer Changes: None
Tests: scripts_regression_tests, problem specific tests
Dependencies:

Brief Summary: Fix for ERP tests, Fix for shr_scam_mod, indentation in cs.status
			   Fix for testmods recurrsion, pylint testing extended
User interface changes: none

Modified files: git diff --name-status
M       cime_config/acme/machines/config_machines.xml
M       cime_config/buildlib.pio
M       scripts/Tools/bless_test_results
M       scripts/Tools/case.build
M       scripts/Tools/case.cmpgen_namelists
M       scripts/Tools/check_case
M       scripts/Tools/check_input_data
M       scripts/Tools/cime_bisect
M       scripts/Tools/cimeteststatus
M       scripts/Tools/code_checker
M       scripts/Tools/compare_test_results
D       scripts/Tools/config_pes_converter.py
M       scripts/Tools/cs_status
D       scripts/Tools/grid_xml_converter.py
M       scripts/Tools/jenkins_generic_job
M       scripts/Tools/standard_script_setup.py
M       scripts/Tools/update_acme_tests
M       scripts/Tools/xmlchange
A       scripts/Tools/xmlconvertors/config_pes_converter.py
A       scripts/Tools/xmlconvertors/grid_xml_converter.py
M       scripts/Tools/xmlquery
M       share/csm_share/shr/shr_scam_mod.F90
M       tools/cprnc/summarize_cprnc_diffs
M       utils/python/CIME/SystemTests/erp.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/XML/generic_xml.py
M       utils/python/CIME/build.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/test_status.py
M       utils/python/CIME/user_mod_support.py
M       utils/python/tests/scripts_regression_tests.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 10-24-2016
Tag: cime5.2.0-alpha.5
Answer Changes: None
Tests: scripts_regression_tests, aux_clm45, others
Dependencies:

Brief Summary:

User interface changes: changes when preview_namelists is run, first in case.build and less frequently overall
Changes where sharedlib builds are installed to avoid conflicts in builds

Modified files: git diff --name-status
M       cime_config/acme/machines/Makefile
D       cime_config/acme/machines/buildlib.csm_share
D       cime_config/acme/machines/buildlib.gptl
D       cime_config/acme/machines/buildlib.mct
D       cime_config/acme/machines/buildlib.pio
A       cime_config/buildlib.csm_share
A       cime_config/buildlib.gptl
A       cime_config/buildlib.mct
A       cime_config/buildlib.pio
M       cime_config/cesm/allactive/config_compsets.xml
M       cime_config/cesm/machines/Makefile
D       cime_config/cesm/machines/buildlib.csm_share
D       cime_config/cesm/machines/buildlib.gptl
D       cime_config/cesm/machines/buildlib.mct
D       cime_config/cesm/machines/buildlib.pio
M       cime_config/cesm/machines/config_machines.xml
M       components/data_comps/datm/cime_config/config_component.xml
M       components/data_comps/datm/cime_config/namelist_definition_datm.xml
M       components/data_comps/datm/datm_comp_mod.F90
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/driver/CMakeLists.txt
A       driver_cpl/driver/map_lnd2rof_irrig_mod.F90
M       driver_cpl/driver/prep_lnd_mod.F90
M       driver_cpl/driver/prep_ocn_mod.F90
M       driver_cpl/driver/prep_rof_mod.F90
M       driver_cpl/driver/seq_diag_mct.F90
M       driver_cpl/shr/seq_flds_mod.F90
M       driver_cpl/unit_test/CMakeLists.txt
A       driver_cpl/unit_test/map_lnd2rof_irrig_test/CMakeLists.txt
A       driver_cpl/unit_test/map_lnd2rof_irrig_test/test_map_lnd2rof_irrig.pf
A       scripts/Tools/case.cmpgen_namelists
M       scripts/Tools/code_checker
M       scripts/Tools/compare_namelists
M       scripts/Tools/preview_namelists
M       scripts/Tools/simple_compare
M       share/csm_share/shr/shr_pio_mod.F90
M       share/csm_share/test/unit/shr_string_test/test_shr_string.pf
M       share/csm_share/unit_test_stubs/pio/CMakeLists.txt
D       share/csm_share/unit_test_stubs/pio/do_genf90
D       share/csm_share/unit_test_stubs/pio/pio.F90
M       share/csm_share/unit_test_stubs/pio/pio.F90.in
M       utils/python/CIME/XML/entry_id.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/build.py
M       utils/python/CIME/case.py
A       utils/python/CIME/case_cmpgen_namelists.py
M       utils/python/CIME/case_run.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/case_submit.py
M       utils/python/CIME/compare_namelists.py
M       utils/python/CIME/preview_namelists.py
M       utils/python/CIME/simple_compare.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/test_status.py
M       utils/python/CIME/utils.py
M       utils/python/tests/list_tests
M       utils/python/tests/scripts_regression_tests.py
M       utils/python/update_acme_tests.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 10-14-2016
Tag: cime5.2.0-alpha.4
Answer Changes: None
Tests: scripts_regression_tests, aux_clm4, cesm prealpha
Dependencies:

Brief Summary: Bring the driver and data model build namelists into python,
	add xml schema checks for config_component and namelist_definition files

User interface changes: data model build namelists now in python

Modified files: git diff --name-status
M       cime_config/acme/config_grids.xml
D       cime_config/acme/machines/ccsm_getenv
M       cime_config/acme/machines/config_batch.xml
M       cime_config/acme/machines/config_machines.xml
D       cime_config/acme/machines/configure
D       cime_config/acme/machines/template.tseries_generate.pl
M       cime_config/cesm/allactive/testlist_allactive.xml
M       cime_config/cesm/config_files.xml
M       cime_config/cesm/config_grids.xml
M       cime_config/cesm/machines/config_batch.xml
M       cime_config/cesm/machines/config_machines.xml
M       cime_config/cesm/machines/template.case.run
M       cime_config/cesm/machines/template.lt_archive
M       cime_config/cesm/machines/template.st_archive
M       cime_config/config_tests.xml
A       cime_config/xml_schemas/entry_id.xsd
A       cime_config/xml_schemas/entry_id_base.xsd
A       cime_config/xml_schemas/entry_id_namelist.xsd
D       components/data_comps/datm/atm_comp_esmf.F90
D       components/data_comps/datm/bld/build-namelist
D       components/data_comps/datm/bld/namelist_files/namelist_defaults.xsl
D       components/data_comps/datm/bld/namelist_files/namelist_defaults_datm.xml
D       components/data_comps/datm/bld/namelist_files/namelist_definition.xsl
D       components/data_comps/datm/bld/namelist_files/namelist_definition_datm.xml
D       components/data_comps/datm/bld/unit_testers/build-namelist_test.pl
D       components/data_comps/datm/bld/unit_testers/env_run.xml
D       components/data_comps/datm/bld/unit_testers/user_xml_dir/namelist_defaults_datm.xml
D       components/data_comps/datm/bld/unit_testers/user_xml_dir/namelist_definition_datm.xml
M       components/data_comps/datm/cime_config/buildlib
M       components/data_comps/datm/cime_config/buildnml
M       components/data_comps/datm/cime_config/config_component.xml
A       components/data_comps/datm/cime_config/namelist_definition_datm.xml
M       components/data_comps/datm/datm_comp_mod.F90
D       components/data_comps/dice/bld/build-namelist
D       components/data_comps/dice/bld/namelist_files/namelist_defaults_dice.xml
D       components/data_comps/dice/bld/namelist_files/namelist_definition_dice.xml
M       components/data_comps/dice/cime_config/buildlib
M       components/data_comps/dice/cime_config/buildnml
M       components/data_comps/dice/cime_config/config_component.xml
A       components/data_comps/dice/cime_config/namelist_definition_dice.xml
M       components/data_comps/dice/dice_comp_mod.F90
D       components/data_comps/dice/ice_comp_esmf.F90
D       components/data_comps/dlnd/bld/build-namelist
D       components/data_comps/dlnd/bld/namelist_files/namelist_defaults_dlnd.xml
D       components/data_comps/dlnd/bld/namelist_files/namelist_definition_dlnd.xml
M       components/data_comps/dlnd/cime_config/buildlib
M       components/data_comps/dlnd/cime_config/buildnml
M       components/data_comps/dlnd/cime_config/config_component.xml
A       components/data_comps/dlnd/cime_config/namelist_definition_dlnd.xml
M       components/data_comps/dlnd/dlnd_comp_mod.F90
D       components/data_comps/dlnd/lnd_comp_esmf.F90
D       components/data_comps/docn/bld/build-namelist
D       components/data_comps/docn/bld/namelist_files/namelist_defaults_docn.xml
D       components/data_comps/docn/bld/namelist_files/namelist_definition_docn.xml
M       components/data_comps/docn/cime_config/buildlib
M       components/data_comps/docn/cime_config/buildnml
M       components/data_comps/docn/cime_config/config_component.xml
A       components/data_comps/docn/cime_config/namelist_definition_docn.xml
M       components/data_comps/docn/docn_comp_mod.F90
D       components/data_comps/docn/ocn_comp_esmf.F90
D       components/data_comps/drof/bld/build-namelist
D       components/data_comps/drof/bld/namelist_files/namelist_defaults_drof.xml
D       components/data_comps/drof/bld/namelist_files/namelist_definition_drof.xml
M       components/data_comps/drof/cime_config/buildlib
M       components/data_comps/drof/cime_config/buildnml
M       components/data_comps/drof/cime_config/config_component.xml
A       components/data_comps/drof/cime_config/namelist_definition_drof.xml
M       components/data_comps/drof/drof_comp_mod.F90
D       components/data_comps/drof/rof_comp_esmf.F90
D       components/data_comps/dwav/bld/build-namelist
D       components/data_comps/dwav/bld/namelist_files/namelist_defaults_dwav.xml
D       components/data_comps/dwav/bld/namelist_files/namelist_definition_dwav.xml
M       components/data_comps/dwav/cime_config/buildlib
M       components/data_comps/dwav/cime_config/buildnml
M       components/data_comps/dwav/cime_config/config_component.xml
A       components/data_comps/dwav/cime_config/namelist_definition_dwav.xml
M       components/data_comps/dwav/dwav_comp_mod.F90
M       components/stub_comps/satm/cime_config/buildlib
M       components/stub_comps/satm/cime_config/config_component.xml
M       components/stub_comps/sesp/cime_config/buildlib
M       components/stub_comps/sesp/cime_config/config_component.xml
M       components/stub_comps/sglc/cime_config/buildlib
M       components/stub_comps/sglc/cime_config/config_component.xml
M       components/stub_comps/sice/cime_config/buildlib
M       components/stub_comps/sice/cime_config/config_component.xml
M       components/stub_comps/slnd/cime_config/buildlib
M       components/stub_comps/slnd/cime_config/config_component.xml
M       components/stub_comps/socn/cime_config/buildlib
M       components/stub_comps/socn/cime_config/config_component.xml
M       components/stub_comps/srof/cime_config/buildlib
M       components/stub_comps/srof/cime_config/config_component.xml
M       components/stub_comps/swav/cime_config/buildlib
M       components/stub_comps/swav/cime_config/config_component.xml
M       components/xcpl_comps/xatm/cime_config/buildlib
M       components/xcpl_comps/xatm/cime_config/buildnml
M       components/xcpl_comps/xatm/cime_config/config_component.xml
M       components/xcpl_comps/xglc/cime_config/buildlib
M       components/xcpl_comps/xglc/cime_config/buildnml
M       components/xcpl_comps/xglc/cime_config/config_component.xml
M       components/xcpl_comps/xice/cime_config/buildlib
M       components/xcpl_comps/xice/cime_config/buildnml
M       components/xcpl_comps/xice/cime_config/config_component.xml
M       components/xcpl_comps/xlnd/cime_config/buildlib
M       components/xcpl_comps/xlnd/cime_config/buildnml
M       components/xcpl_comps/xlnd/cime_config/config_component.xml
M       components/xcpl_comps/xocn/cime_config/buildlib
M       components/xcpl_comps/xocn/cime_config/buildnml
M       components/xcpl_comps/xocn/cime_config/config_component.xml
M       components/xcpl_comps/xrof/cime_config/buildlib
M       components/xcpl_comps/xrof/cime_config/buildnml
M       components/xcpl_comps/xrof/cime_config/config_component.xml
M       components/xcpl_comps/xwav/cime_config/buildlib
M       components/xcpl_comps/xwav/cime_config/buildnml
M       components/xcpl_comps/xwav/cime_config/config_component.xml
D       driver_cpl/bld/build-namelist
M       driver_cpl/bld/namelist_files/namelist_defaults_drv.xml
M       driver_cpl/bld/namelist_files/namelist_definition_drv.xml
M       driver_cpl/bld/namelist_files/namelist_definition_drv_flds.xml
M       driver_cpl/cime_config/buildexe
M       driver_cpl/cime_config/buildnml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/cime_config/config_compsets.xml
A       driver_cpl/cime_config/namelist_definition_drv.xml
A       driver_cpl/cime_config/namelist_definition_modelio.xml
M       driver_cpl/driver/prep_ocn_mod.F90
M       driver_cpl/shr/seq_drydep_mod.F90
M       externals/pio2/src/flib/pio.F90
M       externals/pio2/src/flib/pio_types.F90
M       scripts/Testing/testreporter.pl
M       scripts/Tools/code_checker
M       scripts/Tools/standard_script_setup.py
M       scripts/Tools/xmlquery
M       scripts/create_clone
M       scripts/create_newcase
M       scripts/create_test
M       scripts/manage_case
M       scripts/manage_pes
M       scripts/query_testlists
M       share/csm_share/shr/shr_pio_mod.F90
M       share/csm_share/shr/shr_strdata_mod.F90
M       share/csm_share/shr/shr_stream_mod.F90
M       tools/configure
D       tools/system_tests/configure.test/configtest.pl
D       utils/perl5lib/Streams/TemplateGeneric.pm
M       utils/python/CIME/SystemTests/nck.py
M       utils/python/CIME/SystemTests/pea.py
M       utils/python/CIME/SystemTests/pem.py
M       utils/python/CIME/SystemTests/seq.py
M       utils/python/CIME/SystemTests/system_tests_common.py
M       utils/python/CIME/XML/component.py
M       utils/python/CIME/XML/entry_id.py
M       utils/python/CIME/XML/env_batch.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/XML/files.py
M       utils/python/CIME/XML/generic_xml.py
M       utils/python/CIME/XML/grids.py
A       utils/python/CIME/XML/namelist_definition.py
M       utils/python/CIME/XML/testlist.py
M       utils/python/CIME/XML/testspec.py
M       utils/python/CIME/build.py
M       utils/python/CIME/buildnml.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_run.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/case_submit.py
M       utils/python/CIME/compare_namelists.py
M       utils/python/CIME/get_timing.py
M       utils/python/CIME/hist_utils.py
A       utils/python/CIME/namelist.py
A       utils/python/CIME/nmlgen.py
M       utils/python/CIME/provenance.py
M       utils/python/CIME/simple_compare.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/test_status.py
M       utils/python/CIME/test_utils.py
M       utils/python/CIME/tests/SystemTests/test_system_tests_compare_two.py
M       utils/python/CIME/utils.py
M       utils/python/CIME/wait_for_tests.py
M       utils/python/tests/CTestConfig.cmake
M       utils/python/tests/scripts_regression_tests.py
M       utils/python/update_acme_tests.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 10-04-2016
Tag: cime5.2.0-alpha.3
Answer Changes: None
Tests:  scripts_regression_tests
Dependencies:

Brief Summary: updates based on cesm2_0_beta02 testing, add memleak_tolerance check, better TestStatus for incomplete tests. new query_testlist feature.

User interface changes:

Modified files: git diff --name-status
M       cime_config/acme/allactive/config_pesall.xml
M       cime_config/acme/config_archive.xml
M       cime_config/acme/config_files.xml
M       cime_config/acme/machines/config_batch.xml
M       cime_config/acme/machines/config_build.xml
M       cime_config/acme/machines/config_compilers.xml
M       cime_config/acme/machines/config_machines.xml
D       cime_config/acme/machines/env_mach_specific.penn
M       cime_config/cesm/allactive/testlist_allactive.xml
M       cime_config/cesm/config_archive.xml
M       cime_config/cesm/config_files.xml
M       cime_config/cesm/machines/config_batch.xml
M       cime_config/config_tests.xml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/cime_config/testdefs/testlist_drv.xml
M       externals/pio2/src/clib/pioc.c
M       scripts/create_test
A       scripts/query_testlists
D       tools/cprnc/CMake/FindNetcdf.cmake
M       tools/cprnc/CMakeLists.txt
M       tools/cprnc/README
M       utils/python/CIME/SystemTests/erp.py
M       utils/python/CIME/SystemTests/system_tests_common.py
M       utils/python/CIME/XML/env_batch.py
M       utils/python/CIME/XML/generic_xml.py
M       utils/python/CIME/XML/lt_archive.py
M       utils/python/CIME/XML/testlist.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/hist_utils.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/test_status.py
M       utils/python/CIME/test_utils.py
M       utils/python/CIME/utils.py
M       utils/python/tests/scripts_regression_tests.py

======================================================================

Originator: Jim Edwards
Date: 09-27-2016
Tag: cime5.2.0-alpha01
Answer Changes: None
Tests: scripts_regression_tests
Dependencies: None

Brief Summary: Bug fixes related to cesm2_0_beta02 testing, EBM liquid and ice mapping files seperated, RASM bug fix

User interface changes: none

Modified files: git diff --name-status
M       cime_config/acme/config_archive.xml
M       cime_config/acme/machines/buildlib.csm_share
M       cime_config/acme/machines/config_batch.xml
M       cime_config/acme/machines/config_compilers.xml
M       cime_config/acme/machines/config_machines.xml
M       cime_config/acme/machines/config_pio.xml
M       cime_config/cesm/machines/config_batch.xml
M       cime_config/cesm/machines/config_machines.xml
M       cime_config/config_tests.xml
M       driver_cpl/bld/build-namelist
M       driver_cpl/bld/namelist_files/namelist_definition_drv.xml
M       driver_cpl/cime_config/buildnml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/driver/cesm_comp_mod.F90
M       driver_cpl/driver/seq_diag_mct.F90
M       driver_cpl/shr/seq_flds_mod.F90
M       driver_cpl/shr/seq_infodata_mod.F90
M       scripts/Tools/cs_status
D       scripts/Tools/taskmaker
M       scripts/Tools/xmlquery
M       scripts/create_test
A       utils/data_assimilation/da_no_data_mod.sh
A       utils/python/CIME/SystemTests/dae.py
M       utils/python/CIME/SystemTests/eri.py
M       utils/python/CIME/SystemTests/pet.py
M       utils/python/CIME/SystemTests/pfs.py
M       utils/python/CIME/XML/entry_id.py
M       utils/python/CIME/XML/env_batch.py
M       utils/python/CIME/XML/env_mach_pes.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/XML/generic_xml.py
M       utils/python/CIME/XML/machines.py
M       utils/python/CIME/build.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_run.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/check_input_data.py
D       utils/python/CIME/task_maker.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/test_status.py
M       utils/python/tests/scripts_regression_tests.py
M       utils/python/update_acme_tests.py



======================================================================

======================================================================

Originator: Jim Edwards
Date: 09-08-2016
Tag: cime5.0.11
Answer Changes: None
Tests: scripts_regression_tests, problem related testing
Dependencies: none

Brief Summary: Fixes issues found in cime5.0.10
	Change DOUT_S default for cesm
	Fix cost_estimate for timing tables
	Fix issue with task count for archive tools
	Restore MASK_GRID xml variable
	Fix issues with user_mods path
	add provenance save capabilities for acme


User interface changes:

Modified files: git diff --name-status
M       cime_config/acme/allactive/config_pes.xml.cime2
M       cime_config/acme/allactive/config_pesall.xml
M       cime_config/acme/machines/config_compilers.xml
M       cime_config/acme/machines/config_machines.xml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/cime_config/config_compsets.xml
M       scripts/Tools/code_checker
M       scripts/Tools/getTiming
A       scripts/Tools/save_provenance
M       utils/python/CIME/SystemTests/ssp.py
M       utils/python/CIME/SystemTests/system_tests_common.py
M       utils/python/CIME/XML/env_batch.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/XML/grids.py
M       utils/python/CIME/build.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_run.py
M       utils/python/CIME/case_setup.py
A       utils/python/CIME/get_timing.py
M       utils/python/CIME/hist_utils.py
A       utils/python/CIME/provenance.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/user_mod_support.py
M       utils/python/CIME/utils.py
M       utils/python/tests/scripts_regression_tests.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: 08-31-2016
Tag: cime5.0.9
Answer Changes: None
Tests: scripts_regression_tests, several multiinstance and component tests
Dependencies:

Brief Summary: Fix a host of issues related to testing, remove remaining
	esmf code, update pio externals,

User interface changes: add --allow-baseline-overwrite flag

Modified files: git diff --name-status
M       cime_config/acme/config_files.xml
M       cime_config/acme/machines/config_batch.xml
M       cime_config/acme/machines/config_machines.xml
M       cime_config/cesm/config_archive.xml
M       cime_config/cesm/config_files.xml
M       cime_config/cesm/machines/config_batch.xml
M       cime_config/cesm/machines/config_build.xml
M       cime_config/cesm/machines/config_compilers.xml
M       cime_config/cesm/machines/config_machines.xml
M       cime_config/cesm/machines/config_pio.xml
A       cime_config/config_tests.xml
M       cime_config/xml_schemas/archive.xsd
M       components/data_comps/dice/bld/build-namelist
D       components/stub_comps/satm/cpl/atm_comp_esmf.F90
D       components/stub_comps/sesp/cpl/esp_comp_esmf.F90
D       components/stub_comps/sglc/cpl/glc_comp_esmf.F90
D       components/stub_comps/sice/cpl/ice_comp_esmf.F90
D       components/stub_comps/slnd/cpl/lnd_comp_esmf.F90
D       components/stub_comps/socn/cpl/ocn_comp_esmf.F90
D       components/stub_comps/srof/cpl/rof_comp_esmf.F90
D       components/stub_comps/swav/cpl/wav_comp_esmf.F90
D       components/xcpl_comps/xatm/cpl/atm_comp_esmf.F90
D       components/xcpl_comps/xglc/cpl/glc_comp_esmf.F90
D       components/xcpl_comps/xice/cpl/ice_comp_esmf.F90
D       components/xcpl_comps/xlnd/cpl/lnd_comp_esmf.F90
D       components/xcpl_comps/xocn/cpl/ocn_comp_esmf.F90
D       components/xcpl_comps/xrof/cpl/rof_comp_esmf.F90
D       components/xcpl_comps/xwav/cpl/wav_comp_esmf.F90
M       driver_cpl/bld/build-namelist
M       driver_cpl/bld/namelist_files/namelist_defaults_drv.xml
M       driver_cpl/bld/namelist_files/namelist_definition_drv.xml
M       driver_cpl/cime_config/config_component.xml
M       externals/pio1/pio/box_rearrange.F90.in
M       externals/pio1/pio/pio_types.F90
M       externals/pio1/pio/piolib_mod.F90
M       externals/pio2/CMakeLists.txt
M       externals/pio2/ctest/CTestEnvironment-nwsc.cmake
M       externals/pio2/ctest/runcdash-cgd-nag.sh
M       externals/pio2/ctest/runctest-cgd.sh
M       externals/pio2/doc/CMakeLists.txt
M       externals/pio2/doc/Doxyfile.in
M       externals/pio2/doc/source/Error.txt
M       externals/pio2/doc/source/Examples.txt
M       externals/pio2/doc/source/Installing.txt
A       externals/pio2/doc/source/Testing.txt
M       externals/pio2/doc/source/base.txt
M       externals/pio2/doc/source/mach_walkthrough.txt
M       externals/pio2/examples/c/example2.c
A       externals/pio2/examples/c/valsupp_example1.supp
M       externals/pio2/examples/f03/examplePio.f90
M       externals/pio2/src/clib/CMakeLists.txt
M       externals/pio2/src/clib/bget.c
M       externals/pio2/src/clib/config.h.in
M       externals/pio2/src/clib/pio.h
M       externals/pio2/src/clib/pio_darray.c
A       externals/pio2/src/clib/pio_darray_async.c
M       externals/pio2/src/clib/pio_file.c
A       externals/pio2/src/clib/pio_get_nc_async.c
M       externals/pio2/src/clib/pio_internal.h
M       externals/pio2/src/clib/pio_lists.c
A       externals/pio2/src/clib/pio_msg.c
M       externals/pio2/src/clib/pio_nc.c
M       externals/pio2/src/clib/pio_nc4.c
A       externals/pio2/src/clib/pio_nc_async.c
A       externals/pio2/src/clib/pio_put_nc_async.c
A       externals/pio2/src/clib/pio_varm.c
M       externals/pio2/src/clib/pioc.c
M       externals/pio2/src/clib/pioc_support.c
M       externals/pio2/src/flib/pio.F90
M       externals/pio2/src/flib/pio_nf.F90
M       externals/pio2/src/gptl/perf_mod.F90
A       externals/pio2/tests/performance/kt.PIO1.perfmakefile
M       externals/pio2/tests/performance/pioperformance.F90
M       externals/pio2/tests/unit/CMakeLists.txt
M       externals/pio2/tests/unit/basic_tests.F90
M       externals/pio2/tests/unit/driver.F90
A       externals/pio2/tests/unit/test_darray.c
A       externals/pio2/tests/unit/test_darray_async.c
A       externals/pio2/tests/unit/test_intercomm.c
A       externals/pio2/tests/unit/test_names.c
M       externals/pio2/tests/unit/test_nc4.c
M       scripts/Testing/Testcases/NOC_script
D       scripts/Testing/Testcases/config_tests.xml
M       scripts/Testing/testreporter.pl
D       scripts/Tools/baseline_gen_comp
M       scripts/Tools/bless_test_results
M       scripts/Tools/case.build
A       scripts/Tools/compare_test_results
D       scripts/Tools/component_compare.sh
A       scripts/Tools/component_compare_baseline
A       scripts/Tools/component_compare_move
D       scripts/Tools/component_compare_move.sh
A       scripts/Tools/component_compare_test
D       scripts/Tools/component_compare_test.sh
D       scripts/Tools/component_compgen_baseline.sh
D       scripts/Tools/component_generate.sh
A       scripts/Tools/component_generate_baseline
M       scripts/Tools/xmlchange
M       scripts/create_newcase
M       scripts/create_test
M       scripts/manage_case
M       share/csm_share/shr/shr_pio_mod.F90
M       tools/configure
M       tools/cprnc/README
M       tools/cprnc/compare_vars_mod.F90.in
M       utils/perl5lib/Streams/TemplateGeneric.pm
M       utils/python/CIME/SystemTests/README
M       utils/python/CIME/SystemTests/eri.py
M       utils/python/CIME/SystemTests/err.py
M       utils/python/CIME/SystemTests/lii.py
M       utils/python/CIME/SystemTests/nck.py
M       utils/python/CIME/SystemTests/pea.py
M       utils/python/CIME/SystemTests/pet.py
A       utils/python/CIME/SystemTests/rep.py
M       utils/python/CIME/SystemTests/ssp.py
M       utils/python/CIME/SystemTests/system_tests_common.py
A       utils/python/CIME/SystemTests/system_tests_compare_two.py
A       utils/python/CIME/SystemTests/test_utils/__init__.py
A       utils/python/CIME/SystemTests/test_utils/user_nl_utils.py
M       utils/python/CIME/XML/batch.py
A       utils/python/CIME/XML/build.py
M       utils/python/CIME/XML/compilers.py
M       utils/python/CIME/XML/env_batch.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/XML/machines.py
M       utils/python/CIME/XML/pes.py
M       utils/python/CIME/bless_test_results.py
M       utils/python/CIME/buildnml.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_run.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/case_test.py
M       utils/python/CIME/check_lockedfiles.py
M       utils/python/CIME/compare_namelists.py
A       utils/python/CIME/compare_test_results.py
A       utils/python/CIME/hist_utils.py
D       utils/python/CIME/macros.py
M       utils/python/CIME/preview_namelists.py
M       utils/python/CIME/test_scheduler.py
M       utils/python/CIME/test_status.py
A       utils/python/CIME/tests/README
A       utils/python/CIME/tests/SystemTests/__init__.py
A       utils/python/CIME/tests/SystemTests/test_system_tests_compare_two.py
A       utils/python/CIME/tests/SystemTests/test_system_tests_compare_two_link_to_case2_output.py
A       utils/python/CIME/tests/SystemTests/test_utils/__init__.py
A       utils/python/CIME/tests/SystemTests/test_utils/test_user_nl_utils.py
A       utils/python/CIME/tests/__init__.py
A       utils/python/CIME/tests/case_fake.py
A       utils/python/CIME/tests/test_case_fake.py
M       utils/python/CIME/utils.py
M       utils/python/jenkins_generic_job.py
M       utils/python/tests/scripts_regression_tests.py
M       utils/python/update_acme_tests.py

======================================================================


======================================================================

Originator: Jim Edwards
Date: Aug 11, 2012
Tag: cime5.0.8
Answer Changes: None
Tests: scripts_regression_tests,
Dependencies:

Brief Summary: fix error in taskmaker task counter,
	add error code for component_compare_test,
	fix unit test for run_cmd
	improve cime_bisect tool
	add back software_environement.txt


User interface changes:

Modified files: git diff --name-status
M       cime_config/acme/config_files.xml
D       scripts/Testing/Testcases/HOMME_script
M       scripts/Tools/cime_bisect
M       scripts/Tools/component_compare_test.sh
A       utils/python/CIME/SystemTests/homme.py
M       utils/python/CIME/SystemTests/system_tests_common.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/build.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/task_maker.py
M       utils/python/CIME/utils.py
M       utils/python/update_acme_tests.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: Aug 10, 2016
Tag: cime5.0.7
Answer Changes: None
Tests: None
Dependencies:

Brief Summary: Comment out code added in PR 337 until it works for tcsh and csh users

User interface changes:

Modified files: git diff --name-status
	utils/python/CIME/case_setup.py

======================================================================

======================================================================

Originator: Jim Edwards
Date: Aug 10, 2016
Tag: cime5.0.6
Answer Changes: None
Tests: scripts_regression_tests - others run for specific updates
Dependencies: None

Brief Summary:
d083933 (mydev/user_mod_0len_fix, user_mod_0len_fix) user_nl_ file was being removed if a user_nl file in any mods directory was missing
39de940 Fix comment
0773aac Increase default walltime for blues
c4dce0f Remove last uses of taskmaker.pl
76eb1bc Remove -A directive from edison
c9b8910 Seperate out modelio namelist definition since it uses the same names, but defines them differently
805ad7f Add -mismatch_all when compiling cism with nag
fff9a9b (origin/jgfouca/minor_timing_chg) Set CHECK_TIMING to true in addition to SAVE_TIMING if --save-timing given to create_test
f25a518 (origin/jgfouca/wait_for_test_refactor) wait_for_tests will now always specifically wait for the RUN phase
e19e72c Update drv buildnamelist test to work with cime5
893c6c6 Add support for LANL's mustang and wolf to cime
c103e08 (origin/rljacob/machines/fix-acme) Add SAVE_TIMING_DIR for edison
84000ee Fixing the runjob command for ACME on Mira
1a55232 Adding config for ERS_Ld3.ne30_g16_rx1.A test
d1df346 Error handling; check for correct length of key-value pair array after split
fa1cb49 listofsettings allways an array, test for length of array
a6a3d33 Changed number of expected positional arguments to 0 or 1 , warnings and debug statements
74d2100 checking for missing values in settings string from command line
cd350da (origin/santos/fix-env-leakage) Remove `GenericXML` check for env variables.
43807a5 Add white space after batch directives in script templates
edc1671 Autosave environment information in case_setup.
c3f8f84 (origin/jgfouca/fix_create_test_not_catching_missing_project) create_test was not failing the create_newcase phase when project info was missing
731f8a0 (origin/jgfouca/add_queue_option_to_create_test) Add ability to select queue to create_test and create_newcase
11877a2 (origin/jgfouca/even_more_sky_env_fixes) Fix mismatch between MPI_PATH and the mpi module being loaded
0268cb7 Only report present files in debug mode
47b4216 Fix spelling mistake
07aeb52 Get cime_developer building again on skybridge.
d8f331c moved batchdirectives to top of the template
dbbd3a1 Users should get a nice error when their python is too old
ca3e004 Fix skybridge environment problems, port to new SEMS modules
e266dd9 Remove sentinel concept from jenkins_generic_job


User interface changes: None

Modified files: git diff --name-status
M       cime_config/acme/allactive/config_pesall.xml
M       cime_config/acme/machines/config_batch.xml
M       cime_config/acme/machines/config_compilers.xml
M       cime_config/acme/machines/config_machines.xml
D       cime_config/acme/machines/env_mach_specific.melvin
D       cime_config/acme/machines/env_mach_specific.redsky
D       cime_config/acme/machines/env_mach_specific.skybridge
D       cime_config/acme/machines/taskmaker.pl
M       cime_config/acme/machines/template.case.run
M       cime_config/acme/machines/template.case.test
M       cime_config/acme/machines/template.lt_archive
M       cime_config/acme/machines/template.ocn_diagnostics
M       cime_config/acme/machines/template.st_archive
M       cime_config/acme/machines/template.timeseries
M       cime_config/acme/machines/template.tseries_generate.pl
D       cime_config/acme/machines/userdefined_laptop_template/mkbatch.no_batch_system
M       cime_config/cesm/machines/config_compilers.xml
M       cime_config/cesm/machines/config_machines.xml
D       cime_config/cesm/machines/taskmaker.pl
D       cime_config/cesm/machines/userdefined_laptop_template/mkbatch.no_batch_system
M       driver_cpl/bld/build-namelist
M       driver_cpl/bld/testdir/env_build.xml
M       driver_cpl/bld/testdir/env_case.xml
M       driver_cpl/bld/testdir/env_mach_pes.xml
M       driver_cpl/bld/testdir/env_run.xml
M       driver_cpl/cime_config/buildnml
M       scripts/Testing/Testcases/config_tests.xml
M       scripts/Tools/bless_test_results
M       scripts/Tools/case.build
M       scripts/Tools/case.submit
M       scripts/Tools/code_checker
M       scripts/Tools/compare_namelists
M       scripts/Tools/component_compgen_baseline.sh
M       scripts/Tools/cs_status
M       scripts/Tools/jenkins_generic_job
M       scripts/Tools/simple_compare
M       scripts/Tools/standard_script_setup.py
A       scripts/Tools/taskmaker
M       scripts/Tools/wait_for_tests
M       scripts/create_newcase
M       scripts/create_test
M       utils/python/CIME/SystemTests/eri.py
M       utils/python/CIME/SystemTests/erp.py
M       utils/python/CIME/SystemTests/err.py
M       utils/python/CIME/SystemTests/ers.py
M       utils/python/CIME/SystemTests/ert.py
M       utils/python/CIME/SystemTests/icp.py
M       utils/python/CIME/SystemTests/lii.py
M       utils/python/CIME/SystemTests/nck.py
M       utils/python/CIME/SystemTests/ncr.py
M       utils/python/CIME/SystemTests/pea.py
M       utils/python/CIME/SystemTests/pem.py
M       utils/python/CIME/SystemTests/pet.py
M       utils/python/CIME/SystemTests/pfs.py
M       utils/python/CIME/SystemTests/seq.py
M       utils/python/CIME/SystemTests/sms.py
M       utils/python/CIME/SystemTests/ssp.py
M       utils/python/CIME/SystemTests/system_tests_common.py
M       utils/python/CIME/XML/env_batch.py
M       utils/python/CIME/XML/env_mach_specific.py
M       utils/python/CIME/XML/generic_xml.py
A       utils/python/CIME/bless_test_results.py
M       utils/python/CIME/build.py
M       utils/python/CIME/case.py
M       utils/python/CIME/case_setup.py
M       utils/python/CIME/case_st_archive.py
M       utils/python/CIME/case_test.py
M       utils/python/CIME/check_input_data.py
A       utils/python/CIME/compare_namelists.py
A       utils/python/CIME/simple_compare.py
M       utils/python/CIME/task_maker.py
M       utils/python/CIME/test_scheduler.py
A       utils/python/CIME/test_status.py
M       utils/python/CIME/user_mod_support.py
M       utils/python/CIME/utils.py
A       utils/python/CIME/wait_for_tests.py
D       utils/python/compare_namelists.py
A       utils/python/jenkins_generic_job.py
D       utils/python/simple_compare.py
M       utils/python/tests/scripts_regression_tests.py
D       utils/python/wait_for_tests.py

======================================================================

======================================================================

Originator: Bill Sacks
Date: Aug 02, 2016
Tag: cime5.0.5
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:  None (removes dependency of cime5.0.4 on clm branch)

Description:
- move LII test from CLM back to CIME (until new API is solidified)

Modified files:
utils/python/CIME/SystemTests/lii.py

======================================================================

Originator: Jim Edwards
Date: Aug 01, 2016
Tag: cime5.0.4
Answer Changes: None
Tests: scripts_regression_tests
Dependencies: Needs clm branch containing LII test

Description:

- Updates of hobart machine
- Put provenance back in README -
- Update TestStatus to run tests multiple times in a case - Fix for
- Add README files back to test directories
- Dynamically search for system tests, move LII test to CLM cime_config
- Add python profiling tool
- Minor bug fixes in prep_ocn_mod and prep_wav_mod  pointed out by CRAY compiler

Modified files:

cime_config/acme/config_files.xml
cime_config/cesm/config_files.xml
cime_config/cesm/machines/config_batch.xml
cime_config/cesm/machines/config_compilers.xml
cime_config/cesm/machines/config_machines.xml
driver_cpl/driver/prep_ocn_mod.F90
driver_cpl/driver/prep_wav_mod.F90
scripts/Testing/Testcases/README
scripts/Tools/advanced-py-prof
scripts/Tools/bless_test_results
scripts/Tools/case.build
scripts/Tools/simple-py-prof
scripts/create_test
utils/python/CIME/SystemTests/README
utils/python/CIME/SystemTests/lii.py
utils/python/CIME/SystemTests/system_tests_common.py
utils/python/CIME/XML/env_test.py
utils/python/CIME/case.py
utils/python/CIME/case_test.py
utils/python/CIME/check_input_data.py
utils/python/CIME/system_test.py
utils/python/CIME/test_scheduler.py
utils/python/CIME/test_utils.py
utils/python/CIME/user_mod_support.py
utils/python/CIME/utils.py
utils/python/cs.submit.template
utils/python/tests/scripts_regression_tests.py



====================================================================

Originator: Jim Edwards
Date: July 26, 2016
Tag: cime5.0.3
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:

Brief Summary:
- fixes as a result of cesm2_alpha01b testing
- print output from buildnml
- improve mismatch argument to NAG compiler
- fix memleak error if baseline not found
- add support to create_test for ascii testfile
- move pecount support from create_test to create_newcase
- fix LII test, fix ERP test
- reintroduce --verbose option

User interface changes: none

Modified files: git diff --name-status
M       ChangeLog
M       cime_config/acme/config_files.xml
M       cime_config/cesm/machines/Makefile
M       cime_config/cesm/machines/config_compilers.xml
A       cime_config/cesm/machines/nag_mpi_argument.txt
M       driver_cpl/cime_config/buildexe
M       scripts/Tools/case.build
M       scripts/Tools/code_checker
M       scripts/Tools/component_compare_test.sh
M       scripts/Tools/preview_namelists
M       scripts/create_newcase
M       scripts/create_test
M       utils/python/CIME/SystemTests/erp.py
M       utils/python/CIME/SystemTests/lii.py
M       utils/python/CIME/SystemTests/system_tests_common.py
M       utils/python/CIME/XML/env_batch.py
M       utils/python/CIME/build.py
M       utils/python/CIME/case.py
M       utils/python/CIME/preview_namelists.py
M       utils/python/CIME/system_test.py
M       utils/python/CIME/utils.py
M       utils/python/tests/scripts_regression_tests.py
M       utils/python/update_acme_tests.py

======================================================================

Originator: Jim Edwards
Date: July 22, 2016
Tag: cime5.0.2
Answer Changes: None
Tests:
Dependencies:

Brief Summary: further fixes as a result of cesm2_alpha01 testing

User interface changes:

Modified files: git diff --name-status
	d518834 minor change for hobart only
	605e942 Merge pull request #283 from ESMCI/mira_walltime_fix
	5ef8068 Merge pull request #284 from mvertens/newtests
	462810e replaced ww3 with stub wave in several tests that are known to fail
	a8b9e7c need to return default walltime

======================================================================

======================================================================

Originator: Jim Edwards
Date: July 22, 2016
Tag: cime5.0.1
Answer Changes: None
Tests: cesm prealpha, prebeta, aux_*
Dependencies:

Brief Summary: fixes as a result of cesm2_alpha01 testing

User interface changes:

Modified files: git diff --name-status
49e3c29 (HEAD, tag: cime5.0.1) Minor fix
	11d61ce Merge pull request #279 from ESMCI/jgfouca/cime_bisect
	b15cf46 Upgrade cime_bisect
	873856a Merge pull request #278 from jedwards4b/minor_fixes_for_cesm_port
	b990f48 add code to cp testreporter script for cesm
	6ad54e9 Merge pull request #277 from fischer-ncar/testreporter_fix
	be6d1b3 both compare and generate baseline_action_codes are allowed
	e76ddc1 Fix for testreporter on hobart.
	49fb888 fix issue with _caseroot when cloning
	6d29a93 Update testreporter to work with updated ESMCI CIME
	b7ed88f Updating to current ESMCI cime master
	dbf9a47 Merge pull request #276 from ESMCI/jayeshkrishna/get_mira_working_for_ac
	me
	b5a2ce0 Get Mira working with acme
	7adda2e updates for cesm allactive tests and compsets
======================================================================

======================================================================

Originator: Jim Edwards
Date: July 20th 2016
Tag: cime5.0.0
Answer Changes: None
Tests: scripts_regression_tests
Dependencies:

Brief Summary: Scripts reimplemented in python

User interface changes: Lots of new options, options that are
	no longer there.

Modified files: too numerous to mention, please see the git log
======================================================================

Originator: mvertens
Date: July 9, 2016
Tag: cime4.5.23
Answer Changes: None
Tests: Ran prealph intel tests and compared to cesm1_5_alpha07e
Dependencies: None

Brief Summary:  Removed all code related to using the ESMF interfaces

Modified files: git diff --name-status

M       cime_config/cesm/config_grids.xml
M       driver_cpl/cime_config/config_component.xml
M       driver_cpl/driver/cesm_comp_mod.F90
M       driver_cpl/driver/cesm_driver.F90
M       driver_cpl/driver/component_mod.F90
M       driver_cpl/driver/component_type_mod.F90
M       driver_cpl/driver/seq_diag_mct.F90
M       driver_cpl/driver/seq_map_mod.F90
M       driver_cpl/driver/seq_map_type_mod.F90
M       driver_cpl/shr/seq_comm_mct.F90

Deleted files:

D       driver_cpl/driver/cpl_comp_esmf.F90
D       driver_cpl/driver/seq_map_esmf.F90
D       driver_cpl/shr_esmf/esmf2mct_mod.F90
D       driver_cpl/shr_esmf/esmfshr_attribute_mod.F90
D       driver_cpl/shr_esmf/esmfshr_infodata_mod.F90
D       driver_cpl/shr_esmf/esmfshr_mod.F90
D       driver_cpl/shr_esmf/esmfshr_util_mod.F90
D       driver_cpl/shr_esmf/mct2esmf_mod.F90
======================================================================

Originator: fischer-ncar
Date: July 7, 2016
Tag: cime4.5.22
Answer Changes: None
Tests:
Dependencies:

Brief Summary:  Fix broken compset names

User interface changes:

Modified files: git diff --name-status

M       cime_config/cesm/allactive/config_compsets.xml
M       cime_config/cesm/allactive/testlist_allactive.xml

======================================================================

Originator: cacraigucar, fischer-ncar
Date: July 7, 2016
Tag: cime4.5.21
Answer Changes: Possible answer changes only on corip1
Tests: Ran with CAM tag geotrace3_cac_n59_cam5_4_57
Dependencies: None

Brief Summary:
   Incorporating water isotopes
   Update modules for corip1

User interface changes: none

Modified files: git diff --name-status
M       ChangeLog
M       cime_config/cesm/allactive/config_compsets.xml
M       cime_config/cesm/allactive/config_pes.xml
M       cime_config/cesm/allactive/testlist_allactive.xml
M       cime_config/cesm/machines/config_machines.xml
M       driver_cpl/bld/build-namelist
M       driver_cpl/bld/namelist_files/namelist_definition_drv.xml
M       driver_cpl/cime_config/config_component.xml
A       driver_cpl/driver/mrg_mod.F90
M       driver_cpl/driver/prep_ice_mod.F90
M       driver_cpl/driver/prep_ocn_mod.F90
M       driver_cpl/driver/prep_rof_mod.F90
M       driver_cpl/driver/seq_diag_mct.F90
M       driver_cpl/driver/seq_flux_mct.F90
M       driver_cpl/shr/seq_flds_mod.F90
M       share/csm_share/shr/shr_const_mod.F90
M       share/csm_share/shr/shr_flux_mod.F90
A       share/csm_share/shr/water_isotopes.F90
A       share/csm_share/shr/water_types.F90

======================================================================

Originator: fischer-ncar, Brain Kauffman
Date: 6 July 2016
Tag: cime4.5.20
Answer Changes: None
Tests:
Dependencies:

Brief Summary: Updates to config_files.xml and config_grids.xml to support mpas-o

User interface changes:

Modified files: git diff --name-status
M       cime_config/cesm/config_files.xml
M       cime_config/cesm/config_grids.xml

======================================================================

Originator: apcraig
Date: 6 July 2016
Tag: cime4.5.19
Answer Changes: None
Tests:
Dependencies:

Brief Summary: Addition of ice to ocean coupling fields Fioi_bcphi,
	       Fioi_bcpho, Fioi_flxdst

User interface changes:

Modified files: git diff --name-status
M       driver_cpl/shr/seq_flds_mod.F90

======================================================================

Originator: fischer-ncar, jtruesdal
Date: 6 July 2016
Tag: cime4.5.18
Answer Changes: Answer changes for compset with WaveWatch turned on.
		All others are bit-for-bit.
Tests: Namelist test ran on yellowstone, WAV_GRID manually looked at.
Dependencies:

Brief Summary: Add support to run WaveWatch.  Allactive
	       compset not being tested were removed.

User interface changes:

Modified files: git diff --name-status
M       cime_config/cesm/allactive/config_compsets.xml
M       cime_config/cesm/allactive/config_pes.xml
M       cime_config/cesm/allactive/testlist_allactive.xml
M       cime_config/cesm/config_grids.xml

======================================================================

Originator: fischer-ncar
Date: 21 June 2016
Tag: cime4.5.17
Answer Changes: None
Tests:
Dependencies: None

Brief Summary:
   PR # 457: Remove ESMF tests and create ChangeLog and ChangeLog_template

User interface changes: none

Modified files: git diff --name-status
A       ChangeLog
A       ChangeLog_template
M       cime_config/cesm/allactive/testlist_allactive.xml
M       driver_cpl/cime_config/testdefs/testlist_drv.xml

======================================================================

Originator:
Date:
Tag: cimeX.Y.Z
Answer Changes: [None, Round Off, Climate Changing]
Tests:
Dependencies:

Brief Summary:

User interface changes:

Modified files: git diff --name-status

======================================================================
