In /global/homes/s/syao/src/jgi-bbtools/current:
syao@gpint110:~/src/jgi-bbtools/current$ ll
total 96
-rw-------  1 syao syao  176 Oct 20 09:47 ReadMe
drwx------  2 syao syao 4096 Oct 19 14:49 align2
drwx------  2 syao syao 4096 Oct 19 14:49 assemble
drwx------ 14 syao syao  512 Oct 20 09:46 bin
drwx------  2 syao syao 4096 Oct 19 14:49 bloom
drwx------  2 syao syao  512 Oct 19 14:49 cluster
drwx------  2 syao syao 4096 Oct 19 14:49 dna
drwx------  2 syao syao 4096 Oct 19 14:49 driver
drwx------  2 syao syao 4096 Oct 19 14:49 fileIO
drwx------  2 syao syao 4096 Oct 20 09:34 jgi
drwx------  2 syao syao 4096 Oct 19 14:49 kmer
drwx------  2 syao syao  512 Oct 20 09:44 lib
drwx------  2 syao syao 4096 Oct 19 14:49 pacbio
drwx------  3 syao syao 4096 Oct 19 14:49 stream
drwx------  2 syao syao  512 Oct 19 14:49 tax
drwx------  2 syao syao 4096 Oct 19 14:50 ukmer
drwx------  2 syao syao 4096 Oct 19 14:50 var

where:
lib/mpi.jar

=========================================================
To compile jgi/A_Sample_SY.java, run javac from this dir:


%javac -d bin -sourcepath ./ -cp lib/mpi.jar jgi/A_Sample_SY.java
(create class files that A_Sample_SY.java depends on into bin/)

-d : destination
-sourcepath : java file root dir
-cp : or -classpath: list all jar files the project requires

=========================================================
To run the byecode:
%cd bin
%java jgi.A_Sample_SY
Exception in thread "main" java.lang.RuntimeException: TODO
        at jgi.A_Sample_SY.printOptions(A_Sample_SY.java:322)
        at jgi.A_Sample_SY.<init>(A_Sample_SY.java:55)
        at jgi.A_Sample_SY.main(A_Sample_SY.java:43)


