- Introduction31621240
- Example of a Job Script
How to Convert a Task ID to a More Useful Set of Parameters
- How to Consolidate Small Jobs into Fewer Larger Jobs Using Job Arrays
- Rules for Submitting Job Arrays that use Parallel Environments (like MPI)
1. Introduction
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The syntax for the -t flag is -t n[-m[:s]], namely:
-t 1-20 | run 20 tasks, with task IDs ranging from1 to 20 |
-t 10-30 | run 21 tasks, with task IDs ranging from 10 to 30 |
-t 50-140:10 | run 10 tasks, with task IDs ranging from 50 to 140 by step of 10 (50, 60, ..., 140) |
-t 20 | run one task, with task ID 20 |
Each instantiation of the job will have access to the following four environment variables:
SGE_TASK_ID | unique ID for the specific task |
SGE_TASK_FIRST | ID of the first task, as specified with qsub |
SGE_TASK_LAST | ID of the last task, as specified with qsub |
SGE_TASK_STEPSIZE | task ID step size, as specified with qsub |
You can also limit the number of concurrent tasks with the -tc flag, for example:
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The following job script with embedded directives must be broken into two files:
| one job script with embedded directives | is replaced by two files, a qsub_XXX.sou and a XXX.sh |
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| Code Block |
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| language | bash |
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| title | demo.job |
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| #--------
#$ -q mThC.q
#$ -pe orte 20
#$ -l mres=4G,h_data=4G,h_vmem=4G
#$ -cwd -y j -N demo -o demo.$TASK_ID.log
#$ -t 1-100
#-------
module load some/thing
#-------
echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
echo + taskID=$SGE_TASK_ID
echo + NSLOTS=$NSLOTS distributed over:
cat $PE_HOSTFILE
#
mpirun -np $NSLOTS crunch -i input.$SGE_TASK_ID -o output.$SGE_TASK_ID
#
echo = `date` job $JOB_NAME done |
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| Code Block |
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| language | bash |
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| title | qsub_demo.sou |
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| qsub \
-q mThC.q \
-pe orte 20 \
-l mres=4G,h_data=4G,h_vmem=4G \
-cwd -y j -N demo -o 'demo.$TASK_ID.log' \
-t 1-100 \
-b y $PWD/demo.sh |
 no spaces after the '\'
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| Code Block |
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| #!/bin/sh
# any embedded directives here will be ignored
#-------
source /etc/profile.d/modules.sh
module load some/thing
#-------
echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
echo + taskID=$SGE_TASK_ID
echo + NSLOTS=$NSLOTS distributed over:
cat $PE_HOSTFILE
#
mpirun -np $NSLOTS crunch -i input.$SGE_TASK_ID -o output.$SGE_TASK_ID
#
echo = `date` job $JOB_NAME done |
 this can be any type of executable script, the line "source /etc/profile.d/modules.sh" is bash/sh specific tho.
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Before submitting the job array, make sure the script is executable:
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