6 Aug
2023
6 Aug
'23
6:43 p.m.
Dear Stefan,
I could not spot an error in the slurm or python script.
As Sandra already pointed out, it is advantageous to export some OMP
variable in your jobfile.
Besides OMP_NUM_THREADS, it is also good to set
* export OMP_PROC_BIND=TRUE -> pins the threads to certain cores,
increases NEST performance
* export OMP_DISPLAY_ENV=TRUE -> gives information on whether OMP was
set up correctly
* export OMP_DISPLAY_AFFINITY=TRUE -> gives information on whether OMP
was set up correctly
See also here
<https://nest-simulator.readthedocs.io/en/v3.5/hpc/parallel_computing.html>
for the part of the NEST documentation regarding parallel computing,
generally a good source of information.
Regarding your concrete problem, it is somewhat difficult to debug with
the information available
What would help is the standard error generated by slurm when exporting
the two OMP variables regarding the OMP configuration, i.e.
OMP_DISPLAY_ENV=TRUE and OMP_DISPLAY_AFFINITY=TRUE
Best
Anno
On 06.08.23 13:24, Stefan Dvoretskii wrote:
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
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