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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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"Batch job submission failed: Access/permission denied" when submitting a slurm job inside a slurm script

I have three slurm scripts: 1.slurm: #!/bin/bash #SBATCH --job-name=first #SBATCH --partition=cuda.q sbatch 2.slurm 2.slurm: #!/bin/bash #SBATCH --job-name=second #SBATCH --partition=cuda.q sbatch 3.slurm 3.slurm #!/bin/bash #SBATCH…
Noah Jornet Calomarde
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didn't get any gpu using sbatch when submitting a job script through slurm

Here is my slurm job script. I requested 4 gpu and 1 computing node. My script is as follows: #!/bin/bash #SBATCH --partition=gpu #SBATCH --gres=gpu:4 #SBATCH --ntasks-per-gpu=12 #SBATCH --mem-per-gpu=40G #SBATCH --time=0:15:00 module use…
rene smith
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SLURM job failing with sbatch, successful with srun

A researcher is submitting a job to our cluster that is failing when run with sbatch, but succeeding when run with srun. Any ideas on why this could be? I’ve included the error messages and the slurm script below: Error message: Unable to init…
hduece
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NCBI RemoteDisconnected error when trying to download genomes

I'm triying to download some bacteria genomes using the ncbi-genome-download command. But after a while the following error apear: ERROR: Download from NCBI failed: ConnectionError(ProtocolError('Connection aborted.', RemoteDisconnected('Remote end…
Alonso Cid
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SLURM not interpreting array for infile names

I'm trying to submit my first array job to SLURM and I don't understand its behaviour. I have 240 files like this: $pwd /nobackup/mdzm87/Diet_Pipeline/Sentinel/05_Ghana_BLAST/fwh2 $ls G* G1000_fwh2_unique.fasta…
Andreanna
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Multiple srun on a node (non-exclusive) and wait for completion

I have an sbatch script that looks like this (each node has 128 cores): #!/bin/tcsh #SBATCH --nodes=5 srun -n 1 -c 1 ./exec opt1 srun -n 1 -c 1 ./exec opt2 srun -n 1 -c 1 ./exec opt3 srun -n 1 -c 1 ./exec opt4 srun -n 1 -c 1 ./exec opt5 srun -n 1…
byrdman1982
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Pass IntelMPI flag to SLURM environment

How is it possible to pass the IntelMPI flag -print-rank-map as input to the srun command or as an environment variable into the batch script which is submitted in a SLURM system via the sbatch command?
intergallactic
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How to use for loop when I use sbatch command in Linux

Like title said. I want to submit multiple tasks at the same time so I use sbatch commond. first I use for loop + sbatch to multiple run, and then in each for loop I need to use another for loop. But error happened in the second for loop. Here is…
Ze Chen
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Sourcing an R script within another script executed through SLURM

I am executing an R script on a cluster, using the following sbatch file: #!/bin/bash #SBATCH --job-name=ReconstructScans #SBATCH --mem=4g #SBATCH --account=XXXXXX #SBATCH --array=1-1013%5 module load StdEnv/2020 module load gcc/9.3.0 module load…
Mrinmayi
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SLRUM Script question for batch processing

I am trying to reproduce a bioinformatics workflow hosted at https://bioinformaticsworkbook.org/dataAnalysis/VariantCalling/freebayes-dnaseq-workflow.html#gsc.tab=0 In step 1 of the workflow, I have made the commands and saved them to a file,…
GSA
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Error submitting jobscript (exit code 127) when invoking snakemake through cron job on SLURM cluster

I'm trying to run a snakemake pipeline through crontab on a SLURM cluster. Here is the bash script that I used to send to the slurm. #!/bin/bash #SBATCH --job-name=nextstrain snakemake --configfile config.yaml --jobs 100 --keep-going…
Giang Le
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Slurm job array fails to run Rscript with shapefiles

I would like to run a job array via Slurm on an HPC cluster, intersecting individual circle shapefiles with a large shapefile of Census blocks, then saving the resulting intersection shapefile. I will then combine these individual shapefiles into…
mhankinson
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Slurm: srun inside sbatch is ignored / skipped Can anyone explain why?

I'm still exploring how to work with the Slurm scheduler and this time I really got stuck. The following batch script somehow doesn't work: #!/usr/bin/env bash #SBATCH --job-name=parallel-plink #SBATCH --mem=400GB #SBATCH --ntasks=4 cd ~/RS1 for n…
mve
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Can I call sbatch recursively?

I want to run a program that runs and creates a checkpoint file. Then I want to run several variant configurations that all start from that checkpoint. For example, if I run: sbatch -n 1 -t 12:00:00 --mem=16g program.sh And program.sh looks like…
Sam Thomas
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How to loop through a text file using sbatch jobs

I have a text file containing some lines of text and I want to pass each line of the file as an argument in my python script. The issue I'm having is reading the file. If I can read the file, I should be able to pass each line of the file as…
Thomas Okonkwo
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