'--force perf_threads' and CPU core oversubscription detected!

[Nanzhen]

Dear all,

I have checked a similar question brought on Oct 19, 2020. But still, I have a few questions. I would be very grateful if you could offer some help.

- When I runed 

#!/bin/bash

#SBATCH -J raxml-ng-mpi

#SBATCH -N 1

#SBATCH -c 70

#SBATCH -p normal

#SBATCH --output=%x-%j.out

raxml-ng-mpi -all --msa Lac_core_alignment_2.fasta --model LG+I+G+F --bs-trees 500 --threads 70

, I received a CPU core oversubscription error (see the attached raxml-ng-mpi-327098.out). My questions are: 1) How can I know if it's a false alarm? 2) Since the result of RAxML recommended 68 threads to be used (see the attached T1.raxml.log), why I can't follow the recommendation and run the analysis?

- So I added '--force perf_threads' as:

#!/bin/bash

#SBATCH -J raxml-ng-mpi

#SBATCH -N 1

#SBATCH -c 70

#SBATCH -p normal

#SBATCH --output=%x-%j.out

raxml-ng-mpi -all --msa Lac_core_alignment_2.fasta --model LG+I+G+F --bs-trees 500 --threads 70 --force perf_threads

. Please see the attached output file raxml-ng-mpi-327100.out. My questions are: 1) Do you think it's appropriate to simply add `--force perf_threads` to run it? 2) Will you suggest I to `play around with thread pinning` as the last similar question? 

Looking forward to any suggestions.

Best,

Nanzhen

[Alexey Kozlov]

Dear Nanzhen,

according to the raxml-ng log file, you compute nodes have 36 physical CPU cores:

System: Intel(R) Xeon(R) Gold 6139 CPU @ 2.30GHz, 36 cores, 125 GB RAM

which means that you should use at most 36 threads per node with raxml-ng.

So you can either decrease the number of threads, or use two cluster nodes with 36 threads each.

Please read this wiki page for more details on raxml-ng parallelization best practices:

https://github.com/amkozlov/raxml-ng/wiki/Parallelization

Best,
Alexey

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