Job Arrays

$ vi jobarray_isbyeon.sh

#!/bin/bash

## Usage : qsub jobarray_isbyeon.sh

#$ -S /bin/bash  ### [Shell path] 쉘 지정

#$ -V ### 작업 제출 노드의 쉘 환경변수를 컴퓨팅 노드에도 적용(default)

#$ -cwd ### 현재 디렉토리를 작업 디렉토리로 사용, .e, .o 파일 생성

#$ -q all.q  ### (default)

#$ -M iksubyeon@gmail.com ## 작업 관련 메일을 받을 사용자 메일 주소

#$ -t 1-10

#$ -m e  ### 작업 종료시 메일발송 -m b | e | a | s | n

         ### b : 작업 시작 시 메일 전송

         ### e : 작업 종료 시 메일 전송

         ### a : 작업 중단 또는 다시 예약 시 메일 전송

         ### s : 작업 일시 중단 시 메일 전송

         ### n : 메일 전송 하지 않음

##$ -j y ### Merge the standard out and standard error to one file("작업이름".o"작업번호")

##$ -wd /home/isbyeon/test  ### 작업 디렉토리를 설정

##$ -N isbyeon_job1  ### 작업 이름, 명시하지 않으면 script 이름으로 대체

##$ -pe pe_slots 32  ### Parallel Environment

##$ -R yes   ### Resource reservation

##$ -l h_rt=01:00:00  ### 작업 경과 시간(hh:mm:ss)(wall clock time), 누락 시 작업 강제 종료

##$ -l mem_10G  ### sets the memory limit

### sets the limit of virtual memory required (for parallel jobs per processor).

##$ -l h_vmem=60G  

### queue에 job실행 시 다른 queue보다 높은 priority를얻기 위해 반드시 명시, 누락 시 작업 강제 종료

##$ -l all.q 

### Export some environment varaibles:

#$ -v MY_TEST=isbyeon,MY_PREFIX=jobarray_isbyeon.out

MY_HOST=`hostname`

MY_DATE=`date`

echo "================================================================"

echo JOB_NAME=$JOB_NAME

echo JOB_ID=$JOB_ID

echo NSLOTS=$NSLOTS

echo QUEUE=$QUEUE

echo SGE_TASK_ID=$SGE_TASK_ID

echo SGE_TASK_FIRST=$SGE_TASK_FIRST

echo SGE_TASK_LAST=$SGE_TASK_LAST

echo SGE_CWD_PATH=$SGE_CWD_PATH

echo PATH=$PATH

echo SGE_STDIN_PATH=$SGE_STDIN_PATH

echo SGE_STDOUT_PATH=$SGE_STDOUT_PATH

echo SGE_STDERR_PATH=$SGE_STDERR_PATH

echo SGE_O_HOST=$SGE_O_HOST

echo SGE_O_PATH=$SGE_O_PATH

echo MY_TEST=$MY_TEST

echo "Got $NSLOTS slots."

cat $TMPDIR/machines

echo "================================================================"

echo "Running job JOB_NAME=$JOB_NAME task SGE_TASK_ID=$SGE_TASK_ID on $MY_HOST at $MY_DATE" 

echo "Running job JOB_NAME=$JOB_NAME task SGE_TASK_ID=$SGE_TASK_ID on $MY_HOST at $MY_DATE" > $MY_PREFIX.$SGE_TASK_ID

$ qsub jobarray_isbyeon.sh 

Your job-array 138.1-10:1 ("jobarray_isbyeon.sh") has been submitted

$ qstat

job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 

-------------------------------------------------------------------------------------------------------------

    138 0.31086 jobarray_i isbyeon      r     01/30/2013 18:01:49 all.q@pgp-0-1.local                1 1

    138 0.31086 jobarray_i isbyeon      r     01/30/2013 18:01:49 all.q@pgp-0-2.local                1 2

    138 0.31086 jobarray_i isbyeon      r     01/30/2013 18:01:49 all.q@pgp-0-9.local                1 3

    138 0.31086 jobarray_i isbyeon      r     01/30/2013 18:01:49 all.q@pgp-0-0.local                1 4

    138 0.31086 jobarray_i isbyeon      r     01/30/2013 18:01:49 all.q@pgp-0-6.local                1 5

    138 0.31086 jobarray_i isbyeon      r     01/30/2013 18:01:49 all.q@pgp-0-8.local                1 6

    138 0.31086 jobarray_i isbyeon      r     01/30/2013 18:01:49 all.q@pgp-0-7.local                1 7

    138 0.31086 jobarray_i isbyeon      r     01/30/2013 18:01:49 all.q@pgp-0-4.local                1 8

    138 0.31086 jobarray_i isbyeon      r     01/30/2013 18:01:49 all.q@pgp-0-5.local                1 9

    138 0.31086 jobarray_i isbyeon      r     01/30/2013 18:01:49 all.q@pgp-0-11.local               1 10

$ cat jobarray_isbyeon.sh.o138.9

JOB_NAME=jobarray_isbyeon.sh

JOB_ID=138

NSLOTS=1

QUEUE=all.q

SGE_TASK_ID=9

SGE_TASK_FIRST=1

SGE_TASK_LAST=10

SGE_CWD_PATH=/home/isbyeon/sge_scripts

PATH=/tmp/138.9.all.q:/share/apps/openmpi/bin:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java/latest/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin/linux-x64:/home/isbyeon/bin

SGE_STDIN_PATH=/dev/null

SGE_STDOUT_PATH=/home/isbyeon/sge_scripts/jobarray_isbyeon.sh.o138.9

SGE_STDERR_PATH=/home/isbyeon/sge_scripts/jobarray_isbyeon.sh.e138.9

SGE_O_HOST=pgplogin2

SGE_O_PATH=/share/apps/openmpi/bin:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java/latest/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin/linux-x64:/home/isbyeon/bin

MY_TEST=isbyeon

Got 1 slots.

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

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=9 on pgp-0-5.local at Wed Jan 30 10:01:39 KST 2013

$ cat jobarray_isbyeon.out.1

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=1 on pgp-0-1.local at Wed Jan 30 10:01:49 KST 2013

$ cat jobarray_isbyeon.out.2

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=2 on pgp-0-2.local at Wed Jan 30 10:01:40 KST 2013

$ cat jobarray_isbyeon.out.3

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=3 on pgp-0-9.local at Wed Jan 30 10:01:39 KST 2013

$ cat jobarray_isbyeon.out.4

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=4 on pgp-0-0.local at Wed Jan 30 10:01:34 KST 2013

$ cat jobarray_isbyeon.out.5

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=5 on pgp-0-6.local at Wed Jan 30 10:01:40 KST 2013

$ cat jobarray_isbyeon.out.6

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=6 on pgp-0-8.local at Wed Jan 30 10:01:38 KST 2013

$ cat jobarray_isbyeon.out.7

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=7 on pgp-0-7.local at Wed Jan 30 10:01:47 KST 2013

$ cat jobarray_isbyeon.out.8

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=8 on pgp-0-4.local at Wed Jan 30 10:01:40 KST 2013

$ cat jobarray_isbyeon.out.9

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=9 on pgp-0-5.local at Wed Jan 30 10:01:39 KST 2013

$ cat jobarray_isbyeon.out.10

Running job JOB_NAME=jobarray_isbyeon.sh task SGE_TASK_ID=10 on pgp-0-11.local at Wed Jan 30 18:01:36 KST 2013