slurm

Below are three different sbatch scripts that produce roughly similar results. (I show only the parts where the scripts differ; the ## prefix indicates the output obtained by submitting the scripts to sbatch .) Script 0 #SBATCH -n 4 srun -l hostname -s ## ==> slurm-7613732.out <== ## 0: node-73 ## 1: node-73 ## 2: node-73 ## 3: node-73 Script 1 #SBATCH -n 1 #SBATCH -a 1-4 srun hostname -s ## ==> slurm-7613733_1.out <== ## node-72 ## ## ==> slurm-7613733_2.out <== ## node-73 ## ## ==> slurm-7613733_3.out <== ## node-72 ## ## ==> slurm-7613733_4.out <== ## node-73 Script 2 #SBATCH -N 4 srun -l

The server just switched from CONDOR to SLURM, so I am learning and trying to translate my submission script to SLURM. My question is the following, I have two job arrays. The second is dependent on the first one. For the time being, I something like the following events1=$(sbatch --job-name=events --array=1-3 --output=z-events-%a.stdout myfirst.sh) jobid_events1=`echo ${events1} | sed -n -e 's/^.*job //p' ` echo "The job ID of the events is "${jobid_events1} postevents1=$(sbatch --job-name=postevents --dependency=afterany:${jobid_events1} --array=1-3 mysecond.sh) jobid_postevents1=`echo $

I have a piece of Python code where I use joblib and multiprocessing to make parts of the code run in parallel. I have no trouble running this on my desktop where I can use Task Manager to see that it uses all four cores and runs the code in parallel. I recently learnt that I have access to a HPC cluster with 100+ 20 core nodes. The cluster uses SLURM as the workload manager. The first question is: Is it possible to run parallelized Python code on a cluster? If it is possible, Does the Python code I have need to be changed at all to run on the cluster, and What #SBATCH instructions need to be

My goal is to build a pipeline using slurm dependencies and handle a case where a slurm job crashes. Based on following answer and guide 29th section, it is recommended to use scontrol requeue $jobID , that will re-queue the already cancelled job. if job crashes can be detected from within the submission script, and crashes are random, you can simply requeue the job with scontrol requeue $SLURM_JOB_ID so that it runs again. After I have re-queued a cancelled job, its dependent job remain as DependencyNeverSatisfied and even dependent job completed nothing happens. Is there any way to update

I have an executable that takes multiple options and multiple file inputs in order to run. The executable can be called with a variable number of cores to run. E.g. executable -a -b -c -file fileA --file fileB ... --file fileZ --cores X I'm trying to create an sbatch file that will enable me to have multiple calls of this executable with different inputs. Each call should be allocated in a different node (in parallel with the rest), using X cores. The parallelization at core level is taken care of the executable, while at the node level by SLURM. I tried with ntasks and multiple sruns but the

I have the following script to submit job with slurm: #!/bin/sh #!/bin/bash #SBATCH -J $3 #job_name #SBATCH -n 1 #Number of processors #SBATCH -p CA nwchem $1 > $2 The first argument ($1) is my input, the second ($2) is my output and I would like the third ($3) to be my jobname. If I do like this, the job name is '$3'. How can I proceed to give the jobname as an argument of the script? Thanks The SBATCH directives are seen as comments by the shell and it does not perform variable substitution on $3 . There are several courses of action: Option 1: pass the -J argument on the command line: