6 Aug
2023
6 Aug
'23
1:24 p.m.
Dear Sandra,
I have done all of what you describe, and still only one OpenMP thread is
being used on each node. (I set all above listed variables to 16 threads)
For reproducibility: I attach my SLURM batch script and the simulation
script. I use NEST 3.4 compiled with openmp and mpi, and Intel(R) MPI
Library for Linux* OS, Version 2019 Update 12 Build 20210429 (id:
e380127cb).
Best regards,
On Sun, 6 Aug 2023 at 12:02, Sandra Diaz <s.diaz(a)fz-juelich.de> wrote:
Dear Stefan,
Have you tried setting the OMP variable in your batch script? Something
like:
export OMP_NUM_THREADS=<No. of threads>
You should do this before your srun call to the nest script and in
combination to setting the local_num_threads, as well as the right value
for -c (or --cpus-per-task).
All the best,
Sandra
On 05.08.23 13:05, Stefan Dvoretskii wrote:
Hello all,
I am trying to use as much parallelism as possible on my computing grid.
In this sense, I combine MPI+OpenMP. MPI processes are spawned fine, but
OpenMP threads always amount to 1, no matter that I set local_num_threads
correctly (
https://nest-simulator.readthedocs.io/en/latest/hpc/slurm_script.html#set-l…)
as well as all SLURM variables. I am sure I have compiled nest with OpenMP
too.
I use slightly modified izhikevich neurons with stdp synapses. Can the
model specifics be the cause of underutilizing available threads? Or is
there something else in the system that could be the reason for that?
Best regards,
--
Stefan Dvoretskii
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Dr. Sandra Diaz Pier
Simulation & Data Lab Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
Forschungszentrum Jülich
Office: +49 2461 61-8913
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Stefan Dvoretskii