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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 can I use Bash to pull a series of strings from one file and replace a separate series of strings in another file?

I have two files: file1.txt and file2.txt which both have a set of coordinates amongst other information. new_coords=$(sed -n '/Begin/,/End/{//b;p}' file1.txt) new_coords=$(echo "${new_coords//ATOMIC_POSITIONS (angstrom)}") old_coords=$(sed -n…
jekusz
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Requesting 2 GPUs using SLURM and running 1 python script

I am trying to allocate 2 GPUs and run 1 python script over these 2 GPUs. The python script requires the variables $AMBERHOME, which is obtained by sourcing the amber.sh script, and $CUDA_VISIBLE_DEVICES. The $CUDA_VISIBLE_DEVICES variable should…
Chemist not a Programmer
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How to get count of failed and completed jobs in an array job of SLURM

I am running multiple array jobs using slurm. For a given array job id, let's say 885881, I want to list the count of failed and completed number of jobs. Something like this: Input: -j 885881 Output: Let's say we have 200 jobs in…
Saqib
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sbatch error Memory specification can not be satisfied

I wan to submit a sequential job, but I got: sbatch: error: Memory specification can not be satisfied sbatch: error: Batch job submission failed: Requested node configuration is not available This is my .sh file: #SBATCH --nodes=1 #SBATCH…
user599086
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Slurm: Error when submitting to multiple nodes ("slurmstepd: error: execve(): python: No such file or directory")

I have have a bash script submit.sh for submitting training jobs to a Slurm server. It works as follows. Doing bash submit.sh p1 8 config_file will submit some task corresponding to config_file to 8 GPUs of partition p1. Each node of p1 has 4 GPUs,…
f10w
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How do I create a new directory for a Slurm job prior to setting the working directory?

I want to create a unique directory for each Slurm job I run. However, mkdir appears to interrupt SBATCH commands. E.g. when I try: #!/bin/bash #SBATCH blah blah other Slurm commands mkdir /path/to/my_dir_$SLURM_JOB_ID #SBATCH…
WesH
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is it possible to run sbatch in blocking mode?

Is it possible to run sbatch in input blocking mode? I have sbatch called via another controller script. Before going to the next step in the controller script I want to make sure the submitted job is completed and the results of the job are…
hamid attar
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How to generate different scripts to run on each directory in linux?

I have a directory main in which there are around 100 directories. For example it looks like below: main |__ test_1to50000 |__ test_50001to60000 |__ test_60001to70000 |__ test_70001to80000 |__ test1.sh I have a sbatch script test1.sh to run on…
beginner
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Is there a way to set certain nodes within a SLURM partition to be preferred over other nodes?

I have a cluster that consists of mostly CPU+GPU nodes with a couple of CPU only nodes. At the moment they are in two partitions, 'gpuNodes' and 'cpuNodes', respectively. Our needs are growing and our CPU only jobs are needing to use the CPU+GPU…
handfulofsharks
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Slurm - running multiple tasks at one node

Suppose I want to run a program with 100 different input arguments. This is what I would do on my laptop for example: for i in {1..32} do ./test.sh $i done where test.sh is just a dummy program #!/bin/bash name=$(hostname) touch…
Yoxcu
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Does SLURM sbatch Automatically Copy User Script Across Nodes?

Should SLURM (specifically sbatch) automatically copy the user script (not the job configuration script) to the cluster's compute nodes for execution? Upon executing the sbatch file from my login node, the output file is created on one of my compute…
littleK
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Several questions on running Rmpi and foreach on a HPC cluster

I am queueing and running an R script on a HPC cluster via sbatch and mpirun; the script is meant to use foreach in parallel. To do this I've used several useful questions & answers from StackOverflow: R Running foreach dopar loop on HPC MPIcluster,…
pglpm
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How to hide the job submission message of SLURM's sbatch

I am trying to hide "Submitted batch job xxxx" message after running sbatch -Q -N 16 -c 8 --time 10:00:00 job.sh. However, the message "Submitted batch job xxxx" still comes out. Is anyone familiar with the situation? According to SLURM…
Fangzhou Li
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how to run multiple .sbatch scripts sequentially

I have to run multiple sbatch slurm scripts for cluster. Say, I have 50 sbatch files and I am running them sequentially in terminal (am using Ubundu) as follows: sbatch file1.sbatch sbatch file2.sbatch . . . sbatch file50.sbatch I want to…
Sumathi Gokul
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Slurm Array Job: output file on same node possible?

I have a computing cluster with four nodes A, B, C and D and Slurm Version 17.11.7. I am struggling with Slurm array jobs. I have the following bash script: #!/bin/bash -l #SBATCH --job-name testjob #SBATCH --output output_%A_%a.txt #SBATCH --error…
ManuelAllh
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