I'm starting the SLURM job with script and script must work depending on it's location which is obtained inside of script itself with SCRIPT_LOCATION=$(realpath $0)
. But SLURM copies script to slurmd
folder and starts job from there and it screws up further actions.
Are there any option to get location of script used for slurm job before it has been moved/copied?
Script is located in network shared folder /storage/software_folder/software_name/scripts/this_script.sh
and it must to:
software_name
foldersoftware_name
folder to a local folder /node_folder
on node/node_folder/software_name/scripts/launch.sh
My script is
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=my_partition_name
# getting location of software_name
SHARED_PATH=$(dirname $(dirname $(realpath $0)))
# separating the software_name from path
SOFTWARE_NAME=$(basename $SHARED_PATH)
# target location to copy project
LOCAL_SOFTWARE_FOLDER='/node_folder'
# corrected path for target
LOCAL_PATH=$LOCAL_SOFTWARE_FOLDER/$SOFTWARE_NAME
# Copying software folder from network storage to local
cp -r $SHARED_PATH $LOCAL_SOFTWARE_FOLDER
# running the script
sh $LOCAL_PATH/scripts/launch.sh
It runs perfectly, when I run it on the node itself (without using SLURM) via: sh /storage/software/scripts/this_script.sh
.
In case of running it with SLURM as
sbatch /storage/software/scripts/this_script.sh
it is assigned to one of nodes, but:
/var/spool/slurmd/job_number/slurm_script
and it screws everything up since $(dirname $(dirname $(realpath $0)))
returns /var/spool/slurmd
Is it possible to get original location (/storage/software_folder/software_name/
) inside of script when it is started with SLURM?
P.S. All machines are running Fedora 30 (x64)
UPDATE 1
There was a suggestion to run as sbatch -D /storage/software_folder/software_name ./scripts/this_script.sh
and use the SHARED_PATH="${SLURM_SUBMIT_DIR}"
inside of script itself.
But it raise the error sbatch: error: Unable to open file ./scripts/this_script.sh
.
Also, I tried to use absolute paths:
sbatch -D /storage/software_folder/software_name /storage/software_folder/software_name/scripts/this_script.sh
. It tries to run, but:
echo "${SLURM_SUBMIT_DIR}"
inside of script prints /home/username_who_started_script
instead of /storage/software_folder/software_name
Any other suggestions?
UPDATE 2:
Also tried to use #SBATCH --chdir=/storage/software_folder/software_name
inside of script, but in such case echo "${SLURM_SUBMIT_DIR}"
returns /home/username_who_started_script
or /
(if run as root)
UPDATE 3
Approach with ${SLURM_SUBMIT_DIR}
worked only if task is ran as:
cd /storage/software_folder/software_name
sbatch ./scripts/this_script.sh
But it doesn't seem to be a proper solution. Are there any other ways?
SOLUTION
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=my_partition_name
# check if script is started via SLURM or bash
# if with SLURM: there variable '$SLURM_JOB_ID' will exist
# `if [ -n $SLURM_JOB_ID ]` checks if $SLURM_JOB_ID is not an empty string
if [ -n $SLURM_JOB_ID ]; then
# check the original location through scontrol and $SLURM_JOB_ID
SCRIPT_PATH=$(scontrol show job $SLURM_JOBID | awk -F= '/Command=/{print $2}')
else
# otherwise: started with bash. Get the real location.
SCRIPT_PATH=$(realpath $0)
fi
# getting location of software_name
SHARED_PATH=$(dirname $(dirname $(SCRIPT_PATH)))
# separating the software_name from path
SOFTWARE_NAME=$(basename $SHARED_PATH)
# target location to copy project
LOCAL_SOFTWARE_FOLDER='/node_folder'
# corrected path for target
LOCAL_PATH=$LOCAL_SOFTWARE_FOLDER/$SOFTWARE_NAME
# Copying software folder from network storage to local
cp -r $SHARED_PATH $LOCAL_SOFTWARE_FOLDER
# running the script
sh $LOCAL_PATH/scripts/launch.sh
These scripts are also located at: /data/training/SLURM/, and can be copied from there. If you choose to copy one of these sample scripts, please make sure you understand what each #SBATCH directive before before using the script to submit your jobs.
Job information Information on all running and pending batch jobs managed by SLURM can be obtained from the SLURM command squeue . Note that information on completed jobs is only retained for a limited period. Information on jobs that ran in the past is via. sacct An example of the output squeue is shown below.
There are two ways of submitting a job to SLURM: Submit via a SLURM job script - create a bash script that includes directives to the SLURM scheduler. Submit via command-line options - provide directives to SLURM via command-line arguments.
As for finding the name of the node running your job, this can be found in the environment variable SLURMD_NODENAME. The variable SLURM_NODELIST will give you a list of nodes allocated to a job (unless you run a job across multiple nodes, this will only contain one name).
You can get the initial (i.e. at submit time) location of the submission script from scontrol
like this:
scontrol show job $SLURM_JOBID | awk -F= '/Command=/{print $2}'
So you can replace the realpath $0
part with the above. This will only work within a Slurm allocation of course. So if you want the script to work in any situation, you will need some logic like:
if [ -n $SLURM_JOB_ID ] ; then
THEPATH=$(scontrol show job $SLURM_JOBID | awk -F= '/Command=/{print $2}')
else
THEPATH=$(realpath $0)
fi
and then proceed with
SHARED_PATH=$(dirname $(dirname "${THEPATH}"))
I had to do the same in an array job, the accepted answer from @damienfrancois works well for all jobs except the jobid which is same as ArrayJobId. Just piping awk command to head command would do the trick
scontrol show job $SLURM_JOBID | awk -F= '/Command=/{print $2}' | head -n 1
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