[gmx-users] Various questions related to Gromacs performance tuning

[Tobias Klöffel]

Hi Carsten,


On 3/24/20 9:02 PM, Kutzner, Carsten wrote:
> Hi,
>
>> Am 24.03.2020 um 16:28 schrieb Tobias Klöffel <tobias.kloeffel at fau.de>:
>>
>> Dear all,
>> I am very new to Gromacs so maybe some of my problems are very easy to fix:)
>> Currently I am trying to compile and benchmark gromacs on AMD rome cpus, the benchmarks are taken from:
>> https://www.mpibpc.mpg.de/grubmueller/bench
>>
>> 1) OpenMP parallelization: Is it done via OpenMP tasks?
> Yes, all over the code loops are parallelized via OpenMP via #pragma omp parallel for
> and similar directives.
Ok but that's not OpenMP tasking:)
>
>> If the Intel toolchain is detected and  -DGMX_FFT_LIBRARY=mkl is set,-mkl=serial is used, even though -DGMX_OPENMP=on is set.
> GROMACS uses only the serial transposes - allowing mkl to open up its own OpenMP threads
> would lead to oversubscription of cores and performance degradation.
Ah I see. But then it should be noted somewhere in the docu that all 
FFTW/MKL calls are inside a parallel region. Is there a specific reason 
for this? Normally you can achieve much better performance if you call a 
threaded library outside of a parallel region and let the library use 
its own threads.
>> 2) I am trying to use gmx_mpi tune_pme but I never got it to run. I do not really understand what I have to specify for -mdrun. I
> Normally you need a serial (read: non-mpi enabled) 'gmx' so that you can call
> gmx tune_pme. Most queueing systems don't like it if one parallel program calls
> another parallel program.
>
>> tried -mdrun 'gmx_mpi mdrun' and export MPIRUN="mpirun -use-hwthread-cpus -np $tmpi -map-by ppr:$tnode:node:pe=$OMP_NUM_THREADS --report-bindings" But it just complains that mdrun is not working.
> There should be an output somewhere with the exact command line that
> tune_pme invoked to test whether mdrun works. That should shed some light
> on the issue.
>
> Side note: Tuning is normally only useful on CPU-nodes. If your nodes also
> have GPUs, you will probably not want to do this kind of PME tuning.
Yes it's CPU only... I will tune pp:ppme procs manually. However, most 
of the times it is failing with 'too large prime number' what is 
considered to be 'too large'?

Thanks,
Tobias
>> Normal  execution via $MPIRUN gmx_mpi mdrun -s ... works
>>
>>
>> 3) As far as I understood, most time of PME is spent in a 3d FFT and hence probably most time is spent in a mpi alltoall communication.
> Yes, but that also depends a lot on the number of nodes you are running on.
> Check for yourself: Do a 'normal' mdrun (without tune_pme) on the number of
> nodes that you are interested and check the detailed timings at the end of
> the log file. There you will find how much time is spent in various PME
> routines.
>
> Best,
>    Carsten
>
>> For that reason I would like to place all PME tasks on a separate node via -ddorder pp_pme. If I do so, the calculations just hangs. Specifying -ddorder interleave or cartesian works without problems. Is this a known issue?
>>
>> Kind regards,
>> Tobias Klöffel
>>
>> -- 
>> M.Sc. Tobias Klöffel
>> =======================================================
>> HPC (High Performance Computing) group
>> Erlangen Regional Computing Center(RRZE)
>> Friedrich-Alexander-Universität Erlangen-Nürnberg
>> Martensstr. 1
>> 91058 Erlangen
>>
>> Room: 1.133
>> Phone: +49 (0) 9131 / 85 - 20101
>>
>> =======================================================
>>
>> E-mail: tobias.kloeffel at fau.de
>>
>> -- 
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> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>

-- 
M.Sc. Tobias Klöffel
=======================================================
HPC (High Performance Computing) group
Erlangen Regional Computing Center(RRZE)
Friedrich-Alexander-Universität Erlangen-Nürnberg
Martensstr. 1
91058 Erlangen

Room: 1.133
Phone: +49 (0) 9131 / 85 - 20101

=======================================================

E-mail: tobias.kloeffel at fau.de