Error with --exclusive option

USCbiostats / slurmR

slurmR: A Lightweight Wrapper for Slurm

https://uscbiostats.github.io/slurmR/

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Error with --exclusive option #44

Open MahmAbdelwahab opened 7 months ago

MahmAbdelwahab commented 7 months ago

Hello everyone,

When using sourceSlurm or slurmr via command line, and the R file contain the following sbatch directives

!/bin/sh

SBATCH --job-name=simRMD

SBATCH --mem-per-cpu=10G

SBATCH --nodes=1

SBATCH --ntasks=1

SBATCH --cpus-per-task=1

SBATCH --exclusive

it returns the following error: sbatch: error: Invalid --exclusive specification Return code (status): 255

looking at the generated .sh file I see that slurmr appends the following : #SBATCH --exclusive=--exclusive is that behaviour expected ?

Best,

Mahmoud

gvegayon commented 7 months ago

Interesting! Can you provide a little bit more of detail? Could you share the created batch file?

MahmAbdelwahab commented 7 months ago

Sure, hers's the header in the .R file

#!/bin/sh
#SBATCH --job-name=Exclusive_Test
#SBATCH --mem-per-cpu=5G
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --time=2-00:00:00
#SBATCH --exclusive

the outputed .sh file fails and the content:

#!/bin/sh
#SBATCH --job-name=Exclusive_Test
#SBATCH --mem-per-cpu=5G
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --time=2-00:00:00
#SBATCH --exclusive=--exclusive
.../Rscript --vanilla *.R