Sun Grid Engine : SGE : Basic Commands

http://www.ats.ucla.edu/clusters/common/computing/batch/sge.htm

http://web.njit.edu/topics/HPC/basement/sge/SGE.html

http://star.mit.edu/cluster/docs/0.92rc2/guides/sge.html




0. First see available q : qstat -g c

1. ALWAYS USE -q queuename

2. To use any particular node use -l hostname (  -l hostname=himem03 )



qsub   -q  normal.q   -e pythonTeswt.err -o pythonTeswt.out   -cwd -S /bin/bash   -l hostname=himem03  testSingledataprep.sh


## using specific node

qsub   -q  normal.q   -e pythonTeswt.err -o pythonTeswt.out   -cwd -l hostname=himem03  -S /bin/bash   -l hostname=himem03  testSingledataprep.sh


python mafParser.py $mafRoot  $dataRoot  $fNameSpecies $fNameSubEXONLncrna  $fnmStatCount $fnmStatPrcnt $fnmStatSub $fnmSUBEXONStatDETECT  $fnapslncBed

/// check my submitted jobs

qstat
// alluser

qstat -u "*"

///// all details of user and nodes

userstat

/// details of queues

qstat -g c

// delete jobs

qdel jobID

// node informations
qhost

--------  RUN any binary installed in path -----------------------

qsub -q  normal.q -cwd -b y -o 1.out -e 1.err -q normal.q -N job1 binary
------------------  JAVA  -------------------------
#!/bin/sh
qsub -q  normal.q -e myErr.err -o myOut.out -S  /usr/bin/java Test.class

-------------------- PYTHON ----------------
#!/bin/sh
qsub -q  normal.q   -e myErr.err -o myOut.out  -s /usr/bin/python  test.py

--------------------  To run in cluster using several nodes ------------
-pe smp 32
// it will try to assign 32 nodes for this job