How to recover files before a job times out

Possibly you would like to clean up the work directory or recover files for restart in case a job times out. This is perhaps most useful when using the $SCRATCH work directory (FIXME: link), so that is what we are going to use here.

In this example we ask Slurm to send a signal to our script 120 seconds before it times out to give us a chance to perform clean-up actions.

#!/bin/bash

# job name
#SBATCH --job-name=example

# replace this by your account
#SBATCH --account=YourAccount

#SBATCH --qos=devel
#SBATCH --ntasks=1
## Note: On Saga, you will also have to specify --mem-per-cpu

# we give this job 4 minutes
#SBATCH --time=0-00:04:00

# asks SLURM to send the USR1 signal 120 seconds before end of the time limit
#SBATCH --signal=B:USR1@120

# define the handler function
# note that this is not executed here, but rather
# when the associated signal is sent
your_cleanup_function()
{
    echo "function your_cleanup_function called at $(date)"
    # do whatever cleanup you want here
}

# call your_cleanup_function once we receive USR1 signal
trap 'your_cleanup_function' USR1

echo "starting calculation at $(date)"

# the calculation "computes" (in this case sleeps) for 1000 seconds
# but we asked slurm only for 240 seconds so it will not finish
# the "&" after the compute step and "wait" are important
sleep 1000 &
wait

Download the script: timeout_cleanup.sh (you might have to right-click and select Save Link As... or similar).

Also note that jobs which use $SCRATCH as the work directory can use the savefile and cleanup commands to copy files back to the submit directory before the work directory is deleted. See FIXME.

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