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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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Why did crontab fail to show my rclone copied data in my desired destination directory

I have written a bash script to copy a complete directory between two remotes which worked perfectly (i.e. I can see the folder I copied to my desired destination) when I use sbatch command on it. However, when I set this to crontab, it doesn't show…
adeshina Ibrahim
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Cannot use Java in a SLURM job on an HPC

I am trying to run a simple script on a Linux HPC, where I am looping over a number of RNA-seq files and want to call fastQC, a Java based program, on each of the files. In the script I'm calling a wrapper script that runs the Java…
Ben Wendel
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Passing a parameter into a slurm script (matlab)

I am using slurm to submit jobs to the university supercomputer. My matlab function has one parameter: function test(variable_1) and my slurm file is (I am not sure if it is correct. I know how to define the value of the parameter in the slurm file,…
Jeremy
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multiple srun jobs within a single sbatch killed unexpectedly

I was trying to run multiple srun jobs within a single sbatch script on a cluster. The sbatch script is as follows: #!/bin/bash #SBATCH -N 1 #SBATCH -n 1 #SBATCH -c 64 #SBATCH --time=200:00:00 #SBATCH -p amd_256 for i in {0..6} ; do cd ${i} (…
andy90
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Running multiple similar job files (sbatch)

I am trying to run multiple (several hundred) very similar job-files with slurm using sbatch. My .job file look like: #SBATCH ... ... ... srun ./someProg -a A -b B -c C -d D Is there any convenient way to submit the job file using sbatch with…
iiiiiiiiiiiiiiiiiiii
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slurm sbatch --output and --error flags ignored

i'm currently using slurm in my project, and am trying to run an very simple hello world job. I want to redirect my stdout and errorout to an specific file in an specific location. Therefore I used the following command: sudo su -c 'sbatch…
Akira
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start a SBATCH array with big number?

Is it possible to start a SBATCH job array, i.e. #SBATCH ––array=1-5, with a big number, e.g. #SBATCH ––array=12-25 ?
fslack
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How would you check if SLURM or MOAB/Torque is available on an environment?

The title kind of says it all. I'm looking for a command line test to check if either SLURM, or MOAB/Torque is available for submitting jobs too. My thought is to check if the command qstat finishes with exit code, or if squeue finished with exit…
staggy
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How to run programs from a bash script on different GPUs?

I usually run two separate jobs (program1 and program2) on two different GPUs. I would like to be able to run these two jobs from a single bash script but still on two different GPUs with a slurm .out file for each programs. Is this…
Tim
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SLURM: how to run the same python script for different $arg from a catalogue in parallel

I have to run a series of python scripts for about 10'000 objects. Each object is characterised by arguments in a row of my catalogue. On my computer, to test the scripts, I was simply using a bash file like: totrow=`wc -l < catalogue.txt` for (( i…
LollaSap
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How to submit a SLURM job via sbatch that depends on a list of jobs

I have a shell script that submits multiple jobs to SLURM. These jobs are submitted within the following loop: nb_partitions=72 slurmids=() # storage of slurm job ids for k in $(seq 1 $nb_partitions); do cd results/partition$k/MainFolder …
Tim de Silva
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Use of sleep in bash within for loop launching sbatch

I want to submit an R script myjob.R that takes two arguments for which I have several scenarios (here only a few as an example). I want to pass these arguments by looping through scens and sets. In order to avoid overloading the squeue on the…
Sara
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How to configure slurm on ubuntu 20.04 with minimum requirements?

I am trying to set-up configuration file on Ubuntu 20.04. I have tried several thing and searched for errors on other websites (link1, link2, link3) and slurm-website as well. Another similar question on SO as well. Given the following information…
m.i.cosacak
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How to create a batch script, which submitts several jobs and allocates each of the this jobs on a separate node?

I am new to HPC and SLURM especially, and i ran into some troubles. I was provided with acces to a HPC cluster with 32 CPUs on each node. In order to do the needed calculations I made 12 Python multiprocessing Scripts, where each Script uses…
FuzzyData
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Modify output file of sbatch

I have a job that has a long job-name, and in the .out file, it doesn't show the full name. How can I make it to print the full job-name in the .out file?
Zeus
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