[gmx-users] How to properly use tune_pme?

[Marcin Mielniczuk]

Hi!

I've just realized that my reply stayed in drafts.

This worked for me, thanks a lot!

Btw. if anyone else encounters such a problem: tune_pme works out of the
box only if a shared filesystem is present. Otherwise, the modified tpr
files need to be copied manually between the nodes.

Regards,
Marcin

On 22.11.2019 13:00, Kutzner, Carsten wrote:
> Hi,
>
>> Am 21.11.2019 um 17:15 schrieb Marcin Mielniczuk <marcin at golem.network>:
>>
>> Hi,
>>
>> I'm trying to make use of tune_pme to find out the optimal number of PME
>> ranks. My command line is:
>> UCX_LOG_LEVEL=info MPIRUN="mpirun" ./gmx_mpi tune_pme -v -s
>> ../tip4p_min2 -mdrun "./gmx_mpi mdrun" -np 4
>> When started in such a way, Gromacs exits with a fatal error, as shown
>> in the attached log file, `tune_pme.txt`. OTOH, benchtest.log is empty.
>> While these logs were created using Gromacs 2019.3, the same issue
>> persists with 2019.4.
>>
>> Manually executing the command `mpirun -np 4 ./gmx_mpi mdrun -version
>> -maxh 0.001` succeeds, as in the attached log file `mpirun.txt`.
>>
>> What's the correct way to use tune_pme then?
> Try compiling tune_pme without MPI, but then call the MPI-enabled mdrun:
>
> gmx tune_pme -s ../tip4p_min2 -mdrun "./gmx_mpi mdrun" -np 4
>
> Regards,
>   Carsten
>
>
>> It looks to me that what I'm doing is exactly what the documentation
>> says to.
>>
>> Thanks,
>> Marcin
>> <tune_pme.txt><mpirun.txt>-- 
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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
>