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Error (or misunderstanding on my part) in the documentation, in the SLURM example

Open max-l opened this issue 2 years ago • 1 comments

In the following example:

https://github.com/bbuchfink/diamond/wiki/6.-Distributed-computing

There seems to be a contradicting slurm configuration between --ntasks-per-node=1 and --ntasks-per-core=2

#!/bin/bash -l
#SBATCH -D ./
#SBATCH -J DIAMOND
#SBATCH --mem=185000
#SBATCH --nodes=520
#SBATCH --ntasks-per-node=1
#SBATCH --ntasks-per-core=2
#SBATCH --cpus-per-task=80
#SBATCH --mail-type=none
#SBATCH --time=24:00:00

module purge
module load gcc impi
export SLURM_HINT=multithread

srun diamond FLAGS

From my understanding, there will be a single task per node, unless I'm mistaken, a node is a "machine", with potentialy multiple CPUs which may have multiple cores.

How can there be 2 tasks per core, if there is only one task for the whole node ?

max-l avatar Feb 28 '23 15:02 max-l

--ntasks-per-core=2 is to activate hyperthreading, maybe the SLURM syntax is a bit confusing here.

bbuchfink avatar Mar 02 '23 13:03 bbuchfink