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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 make sbatch job run after a previous one has completed?

I was provided two sbatch scripts to submit and run. The input of the second one is based on the output of the first one. The assignment I need to do this for simply tells us to check on the first one every few hours or so and then to submit the…
user8578415
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SLURM error - sbatch HS8_main.sbatch sbatch: error: Unable to open file HS8_main.sbatch

I am trying to send an sbatch file to run a code in 200 cores in the system. My code is #!/bin/sh #SBATCH --job-name=sm #Job name #SBATCH --mail-type=ALL # Mail events (NONE, BEGIN, END, FAIL, ALL) #SBATCH --mail-user=sankalpmathur@ufl.edu # Where…
Sankalp Mathur
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sbatch: error: Batch job submission failed: Socket timed out on send/recv operation when running Snakemake

I am running a snakemake pipeline on a HPC that uses slurm. The pipeline is rather long, consisting of ~22 steps. Periodically, snakemake will encounted a problem when attempting to submit a job. This reults in the error sbatch: error: Batch job…
Manninm
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Slurm inline sbatch command submission

with PBS scheduler is possible launch a batch command without script in this way: qsub -l select=1:ncpus=12:mem=112GB -l walltime=00:30:00 -- /usr/bin/bash -c "mpirun -np 12 sleep 10" Is it possible do it in Slurm with sbatch?
epascolo
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How to run Tensorflow on SLURM cluster with properly configured parameter server?

I am in the fortunate position of having access to my university's SLURM powered GPU cluster. I have been trying to get Tensorflow to run a in a cluster node, but so far I have failed to find any documentation. (Everyone I have spoken to at the…
Skylion
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How to let SBATCH send stdout via email?

I would like to let the slurm system send myprogram output via email when the computing is done. So I wrote the SBATCH as following #!/bin/bash -l #SBATCH -J MyModel #SBATCH -n 1 # Number of cores #SBATCH -t 1-00:00 # Runtime in D-HH:MM #SBATCH -o…
Feng
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How could I run Open MPI under Slurm

I am unable to run Open MPI under Slurm through a Slurm-script. In general, I am able to obtain the hostname and run Open MPI on my machine. $ mpirun hostname myHost $ cd NPB3.3-SER/ && make ua CLASS=B && mpirun -n 1 bin/ua.B.x inputua.data #…
alper
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Insert system variables to SBATCH

I would like to ask you if is possible to pass global system variables to #SBATCH tags. I would like to do somethink like that SBATCH FILE #!/bin/bash -l ARG=64.dat NODES=4 TASK_PER_NODE=8 NP=$((NODES*TASK_PER_NODE)) #SBATCH -J…
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slurm: How to submit a job under another user and prevent to read other users' files?

Based on following thread, I am trying to send a job under another user. I am logged in as the main_user, and slurm jobs are submit via main_user that can do rm -rf /home/main_user that is pretty dangerous. In order to prevent this I want to run a…
alper
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SLURM: How can I run different executables on parallel on the same compute node or in different nodes?

Goal: learn how to run or co-schedule or execute executables/applications with a sbatch job submission using either srun or mpirun Research: Code snippet: #!/bin/bash #SBATCH --job-name LEBT #SBATCH --partition=angel #SBATCH…
itsmrbeltre
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Run a "monitor" task alongside mpi task in SLURM

I've got an mpi job I run in slurm using an sbatch script which looks something like: # request 384 processors across 16 nodes for exclusive use: #SBATCH --exclusive #SBATCH --ntasks-per-node=24 #SBATCH -n 384 #SBATCH -N 16 #SBATCH --time…
lost
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how do I get the slurm job id?

#!/bin/bash #SBATCH -N 1 # nodes requested #SBATCH -n 1 # tasks requested #SBATCH -c 4 # cores requested #SBATCH --mem=10 # memory in Mb #SBATCH -o outfile # send stdout to outfile #SBATCH -e errfile # send stderr to…
more on my thoughts
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changing slurm bash script after submission (I want to change the script for a queuing job to avoid resubmission)

I have submitted several bash scripts to slurm in a school cluster and there is a long queue. By some chance, I found I made a typo in one of my scripts in a dependence chain. If that is possible to modify the script without canceling the job and…
William Wong
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How to submit/run multiple parallel jobs with Slurm/Sbatch?

I am trying to submit a large number of jobs (several hundred) to a Slurm server and was hoping to avoid having to submit a new shell script for each job I wanted to run. The code submitted is a Python script that takes two input variables in the…
Marcus K.
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How do I find the queuing time for completed SLURM jobs?

I am trying to find a way to see the waiting time of completed jobs until they started on a cluster with SLURM as the Workload manager. I know the "sacct" command can print a lot of information about completed jobs but I don't find anything useful…
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