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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.

231 questions
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starting slurm array job with a specified number of nodes

I’m trying to align 168 sequence files on our HPC using slurm version 14.03.0. I’m only allowed to use a maximum of 9 compute nodes at once to keep some nodes open for other people. I changed the file names so I could use the array function in…
Matt
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What happens if I am running more subjobs than the number of core allocated

So I have a sbatch (slurm job scheduler) script in which I am processing a lot of data through 3 scripts: foo1.sh, foo2.sh and foo3.sh. foo1.sh and foo2.sh are independent and I want to run them simultaneously. foo3.sh needs the outputs of foo1.sh…
Nicolas Najdovski
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Dollar sign to get the value not working in my shell script?

Our school uses SLURM as the queueing system, where one has to specify some "preambles" before other commands. Hence, a shell script in this case usually starts with #!/bin/bash #SBATCH -n 10 # Number of cores requested #SBATCH -N 1 …
Sibbs Gambling
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Srun only launching one process

I am trying to run a job using slurm, but the srun is only launching 1 process, the job script I am using is below #!/bin/bash #SBATCH -N 1 #SBATCH -p RM #SBATCH -t 00:01:00 #SBATCH --ntasks-per-node=128 #SBATCH --error=job.err #SBATCH…
Sap BH
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Run on-worker setup programs in SLURM sbatch script

How do I run setup code in a SLURM sbatch script? Can I just use two srun lines? Are these two srun lines guaranteed to run on the same node, without cleanup inbetween? #!/bin/bash # Parameters #SBATCH ... # setup srun cp /nfs/data $TMPDIR #…
Nils Werner
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Sbatch and srun SLURM sch

I've been pulling my hair for about a week to get the sbatch job script to submit to multiple nodes. I have two compute nodes with (2)sockets (12)cores/socket (2)threads/core. I have a simple c program which calculates the Fibonacci series (no…
Bhargav
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