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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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Adding a column to multiple files (900+) using #SBATCH

I am trying to add a column to a file: 1 12098 12258 0.00 1 12553 12721 1.37 1 13331 13701 34.69 1 30334 30503 0.00 1 35045 35544 0.00 1 35618 35778 0.00 1 69077 70017 0.24 1 …
hdjc90
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A Slurm job can't request GPUs resources for more than one node

all. In my Slurm cluster, when a srun or sbatch job requests resources more than one node, it will not be submitted correctly. This Slurm cluster has 4 nodes, each node has 4 GPUs. I can execute multiple jobs with 4 GPUs at the same time. But I…
gaiaismus
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Do I need a single bash file for each task in SLURM?

I am trying to launch several task in a SLURM-managed cluster, and would like to avoid dealing with dozens of files. Right now, I have 50 tasks (subscripted i, and for simplicity, i is also the input parameter of my program), and for each one a…
Clej
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Mpirun error with SLURM: "An ORTE daemon has unexpectedly failed", but only when passing parameters with sbatch

I get the following error when trying to submit a job with sbatch: An ORTE daemon has unexpectedly failed after launch and before communicating back to mpirun. This could be caused by a number of factors, including an inability to create a…
Chris Kervick
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Slurm only using all CPUs on some software when using srun?

I have a script defined like this: #!/bin/sh #SBATCH --nodes=1 #SBATCH --cpus-per-task=16 #SBATCH --mem 180000 ./program1 --threads 16 ./program2 --threads 16 I then submit my job with sbatch job.sh The thing is that program1 uses all 16…
Ivan
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Enter singularity container running in slurm job

I'm running following job_script.sh: #!/bin/bash singularity --debug run --app ${APP} \ --bind "vol/on/host":"vol/on/container" \ ${IMG_DIR}/${IMG_NAME} with sbatch command (it is long…
Taz
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slurm job executing python script parallelizing on different folders

The script detect.py performs some analysis: #!/usr/bin/python [...] for i in range(X, Y): [...] The idea is to run this python script inside some folders. This variable X and Y changes according to the folder we are in. This execution is…
DavidC.
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Can you help me run tasks in parallel in Slurm?

I am new to Slurm and I trying to launch several executables to run in parallel (in the example below it is just the date command). I would like them to start at different times, separated by a short time delay. I have made a few attemps, trying to…
Vincent
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SLURM - How can I determine what specific CPUs a job is using?

I'm working on a tool for monitoring the jobs currently running on a cluster (19 nodes, 40 cores). Is there any way to determine which specific cpus each job in the slurm queue is using? I'm getting data using 'pidstat', 'mpstat', and 'ps -eFj',…
O Ganter
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sbatch sends compute node to 'drained' status

On newly installed and configured compute nodes in our small cluster I am unable to submit slurm jobs using a batch script and the 'sbatch' command. After submitting, the requested node changes to the 'drained' status. However, I can run the same…
Iomsn
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Missing iterations in loop under SLURM

I have a simple code that iterates through a file and do some simple calculus. The code that follows is an excerpt of a biggest one: don't ask for any utility in this code, it is just a minimal example of the problem. #!/bin/bash #SBATCH…
Poshi
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How to submit parallel job steps with SLURM?

I have the following SLURM job script named gzip2zipslurm.sh: #!/bin/bash #SBATCH --mem 70G #SBATCH --ntasks 4 echo "Task 1" srun -n1 java -Xmx10g -jar tar2zip-1.0.0-jar-with-dependencies.jar articles.A-B.xml.tar.gz & echo "Task 2" srun -n1 java…
khituras
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sbatch slurm jobs which release CPU resources individually

I have a cluster of many nodes with many cores and I simply want to run thousands of jobs that just require a single CPU each on them. Preferably with sbatch. After going through the documentation for several hours I still run into problems. My…
David Schumann
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Snakemake deletes the temp files prematurely, while running with --immediate-submit option

While I submit jobs with --immediate-submit and --dependency=afterok:{dependencies}, the temp files are getting deleted even before the rules that depend on temp files are started. It's working perfectly when running in normal way. Does any other…
Veera
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How do I open .bov files that are on my university's cluster using python commands? The program runs on the cluster and creates .bov files

The program is separate. Once it runs, I get the .bov files in another directory I call output. Then I type, module load allpy then, python and then any bit of python code I want. But I don't know how to open these .bov files.
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