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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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How to write hostfile in Slurm script

Currently I am doing following #!/bin/bash -l #SBATCH --nodes=2 #SBATCH --ntasks-per-node=4 scontrol show hostname $SLURM_JOB_NODELIST | perl -ne 'chomb; print "$_" x4' > myhostfile This generates the following myhostfile compute-0 …
ATK
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How do I call a Perl script in an SBATCH script for SLURM submissions?

I received a Perl script that apparently is called from an SBATCH script to be submitted as a job to a computer cluster managed by SLURM. The script is old and I am yet to become more familiar with Perl. Additionally, the Perl script is being used…
dareToDiffer07
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How to use bc from head node to client node

I am running some computational calculations using my DFT software. To do so I need a job script that assigns the client node to my job. My job file is here #!/bin/sh #SBATCH -J test #SBATCH -p 52core #SBATCH -N 1 #SBATCH -n 16 #SBATCH -o…
astha
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slurmd.service is Failed & there is no PID file /var/run/slurmd.pid

I am trying to start slurmd.service using below commands but it is not successful permanently. I will be grateful if you could help me to resolve this issue! systemctl start slurmd scontrol update nodename=fwb-lab-tesla1 state=idle This is the…
Charlt
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sbatch: error: Batch job submission failed: Requested node configuration is not available

The problem is not related to the number of the CPU assigned to the job. Before this problem, I had an error with the Nvidia driver configuration in a way that I couldn't detect the GPUs by 'nvidia-smi', after solving that error by running…
Charlt
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srun used in a loop: srun: Job step aborted: Waiting up to 32 seconds for job step to finish

I got a .sh file to run by srun because I want to see the dynamic print-out of the scripts. But by running srun job_spinup.sh southfr_exp 1 & I always got error (time-out due to time limited error) after 2 main loops...here is the main codes in the…
Xu Shan
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How can I execute a SLURM script from within multiple directories simultaneously?

I want to execute a SLURM script from within multiple directories simultaneously. More specifically, I have ten array folders numbered array_1 through array_10 from which I want to execute the script. Within each of these directories, the script…
willford97
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Does the file get changed in squeue if I modify after being sent into queue?

I have a question: a have neural net file model.py with some parameters set. I have sent it to the slurm queue. When doing squeue I can see that it is still waiting because there are other jobs running. Now, I want to send another variation of…
alienflow
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Has anyone successfully used shopt -s extglob (extended globbing) in bash with SBATCH settings on a HPC?

To summarise: I am using bash shell, version: 4.2.46(2)-release I want to submit a batch job script to slurm job scheduler where, in the script I use extended globbing which is turned on using shopt -s extglob on a separate line to the extended…
DarrenMoore95
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Submit Slurm Jobs using Python

I have foo.sh as below #!/bin/bash #SBATCH -A research #SBATCH -p long #SBATCH --mem-per-cpu=1024 #SBATCH -N 1 #SBATCH -n 24 #SBATCH -t 2-00:00:00 #SBATCH --mail-type=END #SBATCH --exclude=node37 module load Gaussian/09revC export…
WhySoSerious
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How to have variable number of nodes for different mpi executions in a script file in SLURM?

I would like to have 4 different mpi executions of same program, with different number of nodes. The outputs should be n_out.txt depends on the nodes. I have tried the following .sh file, #!/bin/bash #SBATCH --partition=halley #SBATCH…
Deniz Ünal
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SLURM sbatch script not running all srun commands in while loop

I'm trying to submit multiple jobs in parallel as a preprocessing step in sbatch using srun. The loop reads a file containing 40 file names and uses "srun command" on each file. However, not all files are being sent off with srun and the rest of the…
jaegger
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Run simultaneous tasks followed by single task in one slurm script

I need a Slurm script to do the following: Create a directory in scratch space for temporary storage (requested using sbatch --gres disk:1024) Run samtools sort on hundreds of bam files and store sorted copies in scratch space (as many at once as…
jaegger
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the jobs option does not define the number of submited jobs

The command that I use to trigger snakemake is: snakemake --snakefile Snakefile --configfile config.json --latency-wait 60 --rerun-incomplete --keep-going --notemp --reason --use-singularity --singularity-args "--bind /somepath/folder" --jobs 400…
nicoluca
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Run many sbatch .sh files on a computing cluster

I have many folders that contain .sh files(as shown below). I need to run each one of them on the cluster. I need help on how to put the following sbatch command into a loop. cd file1 sbatch run_min.sh sbatch run_eqbr.sh sbatch run_prod.sh cd…
shome
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