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Questions tagged [sbatch]

sbatch submits a batch script to SLURM (Simple Linux Utility for Resource Management). The batch script may be given to sbatch through a file name on the command line, or if no file name is specified, sbatch will read in a script from standard input. The batch script may contain options preceded with "#SBATCH" before any executable commands in the script.

sbatch submits a batch script to SLURM (Simple Linux Utility for Resource Management). The batch script may be given to sbatch through a file name on the command line, or if no file name is specified, sbatch will read in a script from standard input. The batch script may contain options preceded with "#SBATCH" before any executable commands in the script.

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Calling sbatch on an executable that calls srun

If I have a bash script that contains the sbatch options that specify the resources that need to be available before running the script, and in that script, instead of a series of srun commands, I have an executable that calls srun multiple…
hra1234
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Binding more processes than cpus error in SLURM openmpi

I am trying to run a job that uses explicit message passing between nodes on SLURM (i.e. not just running parallel jobs) but am getting a recurring error that "a request was made to bind to that would result in binding more processes than cpus on a…
waser2
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Running multiples files jobs with one sbatch

I want to run N files (N jobs) that are inside N folders that are in my pwd such : Folder_1 contains file_1 Folder_2 contains file_2 | | | Folder_N contains file_N For one file_1 i just have to do : sbatch script.sh ./folder1/file_1. But…
haswellrefresh
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MPI bind ranks to specific nodes via Slurm

I use sbatch to allocate an MPI job with (let's say) 8 ranks. I use 4 nodes: node0[01-04]. I would like to bind rank 0 to the first node (node001) and the other ranks to the other nodes (node0[02-04]). How can it be done using sbatch? Thank you!
Yoni4949
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How to debug the job array for SLURM through two loops?

I need to submit many jobs for the cluster by slurm. Each job takes different input files from different folders. My problem is the output is incomplete, and outputs after the first 8 combinations keep overwriting the previous ones. I suspected the…
Yifangt
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several mpiruns in parallel on several nodes

I want to run two programs using mpi in parallel in the same job script. In SLURM I would usually just write a script for sbatch (shortened): #SBATCH --nodes=1 #SBATCH --ntasks-per-node=4 mpirun program1 & mpirun program2 This works fine. The two…
Martin
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Run multiple files consecutively via SLURM with individual timeout

I have a python script I run on HPC that takes a list of files in a text file and starts multiple SBATCH runs: ./launch_job.sh 0_folder_file_list.txt launch_job.sh goes through 0_folder_file_list.txt and starts an SBATCH for each…
Damian
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How to determine job array size for lots of jobs?

What is the best way to process lots of files in parallel via Slurm? I have a lot of files (let's say 10000) in a folder (Each files get 10 secs or so to process). I want to determine sbatch job array size as 1000, naturally. (#SBATCH…
Bra
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Iterative slurm job

I'm trying to optimize a study I'm doing. I currently have to job scripts I call them step1 and step2. In step1 #!/bin/bash #SBATCH --output=slurm-%j.out #SBATCH --nodes=16 #SBATCH --ntasks-per-node=28 #SBATCH --time=24:00:00 module load…
Linus
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conversion of xarray to numpy array - oom-kill event

I'm using xarray to read in and modify a data set for my analysis. That's the data repr.: To plot the data I have to convert it to numpy array: Z_diff.values() When doing so I get the error message: slurmstepd: error: Detected 1 oom-kill event(s)…
Martina
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Storing the output(cout) of a program in a text file using SLURM

sbatch -o ${WORKDIR}/logs/submit_${RUN}.out -e ${WORKDIR}/logs/submit_${RUN}.err -p normal --job-name Rivet_${RUN} --export WORKDIR,RUN,JO,DATASET run_rivet_onnode.sh How do I tell slurm that store the output(cout) of my c++ program in .txt file in…
Bill maher
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How can I setup Visdom on a remote server?

I'd like to use visdom for visualization of results in a deep learning algorithm which is trained in a remote cluster server. I found a link that tried to describe a correct way to setup everything in a slurm script. python -u Script.py…
Dalek
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running a python script with ptemcee (a package of Monte Carlo) in SBATCH / SLURM

I need to run a python script using sbatch / slurm The script works until the step which it must use the ptemcee (i.e. runs a monte carlo markov chain). In this step, nothing happens (as if the script fell in a infinite loop). I know that there is…
Liner Santos
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Prevent SLURM from running in /home folder

Is there a way for SLURM to prevent users from executing tasks via sbatch or srun that involve writing to the /home/username folder? Can SLURM actually monitor this? If not, what could be a good workaround?
ajthealchemist
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Duplicate Output Data by Sbatch script Command in Linux

I am using Srun command to submit a computational job onto the Linux but the output data was duplicated. Here is the shell script for job submission. #!/bin/bash #SBATCH --partition=short #SBATCH --job-name="vasp" #SBATCH --nodes=2 #SBATCH…
Kieran
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