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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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SLURM `srun` vs `sbatch` and their parameters

I am trying to understand what the difference is between SLURM's srun and sbatch commands. I will be happy with a general explanation, rather than specific answers to the following questions, but here are some specific points of confusion that can…
dkv
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How to submit a job to any [subset] of nodes from nodelist in SLURM?

I have a couple of thousand jobs to run on a SLURM cluster with 16 nodes. These jobs should run only on a subset of the available nodes of size 7. Some of the tasks are parallelized, hence use all the CPU power of a single node while others are…
Faber
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How to activate a specific Python environment as part of my submission to Slurm?

I want to run a script on cluster (SBATCH file). How can activate my virtual environment (path/to/env_name/bin/activate). Does I need only to add the following code to my_script.sh file? module load python/2.7.14 source…
bib
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Is it possible to run SLURM jobs in the background using SRUN instead of SBATCH?

I was trying to run slurm jobs with srun on the background. Unfortunately, right now due to the fact I have to run things through docker its a bit annoying to use sbatch so I am trying to find out if I can avoid it all together. From my…
Charlie Parker
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SLURM sbatch job array for the same script but with different input arguments run in parallel

I have a problem where I need to launch the same script but with different input arguments. Say I have a script myscript.py -p -i , where I need to consider N different par_values (between x0 and x1) and M trials for each value…
maurizio
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SLURM: Changing the maximum number of simultaneously running tasks for a running array job

I have set of an array job as follows: sbatch --array=1:100%5 ... which will limit the number of simultaneously running tasks to 5. The job is now running, and I would like to change this number to 10 (i.e. I wish I'd run sbatch --array=1:100%10…
James Owers
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How to get the ID of GPU allocated to a SLURM job on a multiple GPUs node?

When I submit a SLURM job with the option --gres=gpu:1 to a node with two GPUs, how can I get the ID of the GPU which is allocated for the job? Is there an environment variable for this purpose? The GPUs I'm using are all nvidia GPUs. Thanks.
Negelis
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SLURM sbatch output buffering

I created some slurm scripts and then tried to execute them with sbatch. But the output file is updated not frequently (once a minute maybe). Is there a way to change the output buffering latency in sbatch? I know stdbuf is used in such situations…
ahemya
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Is there a "one-liner" for submitting many jobs to SLURM (similar to LSF)?

Can I submit "one-liners" to SLURM? Using bsub from LSF and the standard Linux utility xargs, I can easily submit a separate job for uncompressing all of the files in a directory: ls *.gz | sed 's/.gz$//g' | xargs -I {} bsub 'gunzip -c {}.gz >…
Christopher Bottoms
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Using SBATCH Job Name as a Variable in File Output

With SBATCH you can use the job-id in automatically generated output files using the following syntax with %j: #!/bin/bash # omitting some other sbatch commands here ... #SBATCH -o slurm-%j.out-%N # name of the stdout, using the job number (%j)…
ctesta01
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SLURM / Sbatch creates many small output files

I am running a pipeline on a SLURM-cluster, and for some reason a lot of smaller files (between 500 and 2000 bytes in size) named along the lines of slurm-XXXXXX.out (where XXXXXX is a number). I've tried to find out what these files are on the…
erikfas
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SLURM Submit multiple tasks per node?

I found some very similar questions which helped me arrive at a script which seems to work however I'm still unsure if I fully understand why, hence this question.. My problem (example): On 3 nodes, I want to run 12 tasks on each node (so 36 tasks…
Shiwayari
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Why do I keep getting NonZeroExitCode when using sbatch SLURM?

I have a simple test.ksh that I am running with the command: sbatch test.ksh I keep getting "JobState=FAILED Reason=NonZeroExitCode" (using "scontrol show job") I have already made sure of the following: slurmd and slurmctld are up and running…
user3200387
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Batch job submission failed: I/O error writing script/environment to file

I installed slurm on a workstation and it seemed to work, i can use the slurm commands, srun is working too. But when i try to launch a job from a script using sbatch test.sh i get the following error : Batch job submission failed: I/O error writing…
Daoud El Kadiri
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Snakemake slurm ouput file redirect to new directory

I'm putting together a snakemake slurm workflow and am having trouble with my working directory becoming cluttered with slurm output files. I would like my workflow to, at a minimum, direct these files to a 'slurm' directory inside my working…
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