how to generate batch files in a loop in Python (not a loop in a batch file) with slightly changed p-CodePudding

I am a researcher that needs to run files for a set of years on a SLURM system (high performance computing center). The available nodes for long compute times have a long queue. I have 42 years to run, and the only way to run them that gets my files processed quickly (due to the wait times, and that this is many GB of data, it takes time), is to submit them individually, one batch file per year, as jobs. I cannot include multiple years in a single batch file, or I have to wait a week in the queue to run my data due to the time I have to reserve per batch file. This is the fastest way my university's system lets me run my data.

To do this, I have 2 lines in my batch script that I have to change every time: the name of the job, and the last line which is the python script name plus a parameter being passed to it (the year) like so: pythonscript.py 2020.

I would like to generate batch files with a python or other script I can run, where it loops over a list of years and just changes the job name to jobNameYEAR and changes the last line to pythonscript.py YEAR, writes that to a file jobNameYEAR.sl, then continues in a loop to output the next batch file. ...Even better if it can write the batch file and submit the job (sjob jobNameYEAR) before continuing in the loop, but I realize maybe this is asking too much. But separately...

Is there a way to submit jobs in a loop once these files are created? E.g. loop through the year list and submit sjob jobName2000.sl, sjob jobName2001.sl, sjob jobName2002.sl

I do not want a loop in the batch file changing the variable, this would mean reserving too many hours on the SLURM system for a single job. I want a loop outside of the batch file that generates multiple batch files I can submit as jobs.

Thank you for your help!

This is what one of my .sl files looks like, it works fine, I just want to generate these files in a loop so I can stop editing them by hand:

#!/bin/bash -l
# The -l above is required to get the full environment with modules
# Set the allocation to be charged for this job
# not required if you have set a default allocation
#SBATCH -A MYFOLDER
# The name of the job
#SBATCH -J jobNameYEAR
# 24 hour wall-clock time will be given to this job
#SBATCH -t 3:00:00
# Job partition
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=6
#SBATCH --mem=30GB
#SBATCH -p main
# load the anaconda module
ml PDC/21.11
ml Anaconda3/2021.05
conda activate myEnv
python pythonfilename.py YEAR

CodePudding user response：

Create a script with the following content (let's call it chainsubmit.sh):

#!/bin/bash

SCRIPT=${1?Usage: $0 script.slum arg1 arg2 ...}
shift
ARG=$1
ID=$(sbatch --job-name=jobName$ARG --parsable $SCRIPT $ARG)
shift
for ARG in "$@"; do
  ID=$(sbatch --job-name=jobName$ARG --parsable --dependency=afterok:${ID%%;*} $SCRIPT $ARG)
done

Then, adapt your script so that the last line

python pythonfilename.py YEAR

is replaced with

python pythonfilename.py $1

Finally submit all the jobs with

./chainsubmit.sh jobName.sl {2000..2004}

for instance for YEAR ranging from 2000 to 2004

CodePudding user response：

… script I can run, where it loops over a list of years and just changes the job name to jobNameYEAR and changes the last line to pythonscript.py YEAR, writes that to a file jobNameYEAR.sl… submit the job (sjob jobNameYEAR) before continuing in the loop…

It can easily be done with a few shell commands and sed. Assume you have a template file jobNameYEAR.sl as shown, which literally contains jobNameYEAR and YEAR as the parameters. Then we can substitute YEAR with each given year in the loop, e. g.

seq 2000 2002|while read year
do  <jobNameYEAR.sl sed s/YEAR$/$year/ >jobName$year.sl
    sjob jobName$year.sl
done

If your years aren't in sequence, we can use e. g. echo 1962 1965 1970 instead of seq ….

Other variants are on Linux also possible, like for year in {2000..2002} instead of seq 2000 2002|while read year, and using envsubst instead of sed.