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Batch Jobs (batch job)

How to use the batch job​

When you run a small number of programs that use only one CPU core and run for a long time, run them as the batch job. (When you execute many jobs, use the array job described later.)

Example: to execute the following shell script(example.sh)

This shell script will generate a list of biotools Singularity containers installed on the NIG Supercomputer.

#!/bin/bash

ls /usr/local/biotools > $1

Prepare job_script.sh as follows and execute qsub job_script.sh. Then the batch job will be submitted to the queue of Grid Engine.

#!/bin/bash

#$ -cwd 
#$ -V 
#$ -l short
#$ -l d_rt=00:10:00
#$ -l s_rt=00:10:00
#$ -l s_vmem=4G 
#$ -l mem_req=4G
#$ -N an_example
#$ -S /bin/bash


example.sh biotools_list.txt

  • -cwd: The batch job will be executed in the same directory as the current. Without this option, the job will be executed in $HOME directory.

  • -V : All environment variables when you execute qsub are inherited to the compute node that executes the batch job.

  • l short : Specifies the type of queue that submits the batch job.

    • The general analysis division has queues such as epyc, intel, gpu, short, medium and etc. for each computer type. For details, see the Grid Engine Queue Type page.
    • On the personal genome analysis division, it depends on the configuration. When you specify nothing, only the all queue exists, so specify -l all.

  • -l d_rt, -l s_rt : the maximum execution time for the batch job. -The batch job will be forcibly terminated when the maximum execution time has passed from the start of the batch job.

    • Therefore, it is safer to specify the upper limit of the execution time a little longer, but when it is too long, the job may not be executed easily.
    • In this example, 00:10:00 specifies 10 minutes.
    • For example, when you specify a job execution frame of up to 8 days because the job is expected to be completed within 8 days, specify 192 hours (8 days x 24 hours) 192:00:00 for the option.
    • The maximum time is 2976 hours(= about 4 months). (However, the short queue is 1 hour.)
    • When this option is not specified, 72 hours = 3 days (default value) is specified.
    • The -l d_rt and -l s_rt options must have the same value.

  • -l s_vmem, -l mem_req: Specify the amount of memory to use. Normally, specify the same value for -l s_vmem and -l mem_req. You can use G, M, K, etc. as the unit.

  • -N: Specify the job name.

  • -S: Specify the interpreter used to execute the script (example.sh in this example).

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