[gmx-users] tune_pme error with GROMACS 2018

[Kutzner, Carsten]

> On 12. Feb 2018, at 22:44, Daniel Kozuch <dan.kozuch at gmail.com> wrote:
> 
> Carsten,
> 
> I was hoping yo use tune_pme to optimize a REMD job across multiple nodes,
> so I think I need it compiled with MPI (please let me know if that logic is
> incorrect).
Strictly speaking, tune_pme is a serial program that calls MPI-enabled
mdruns, so only the mdrun needs to be compiled in parallel. However, often
it does not hurt if tune_pme is linked to an MPI lib (IBM poe does not
like that, though).

I use tune_pme manly to optimze the number of PNE ranks on CPU-only runs,
but you may see a benefit also with GPUs. But in combination with REMD
I would not bother too much, since each individual simulation is probably
not large enough to benefit from separate PME ranks.

Carsten


> I am indeed running on GPU nodes (I tested mdrun on the nodes and and there
> was no issue).
> 
> Best,
> Dan
> 
> On Mon, Feb 12, 2018 at 8:32 AM, Kutzner, Carsten <ckutzne at gwdg.de> wrote:
> 
>> Hi Dan,
>> 
>>> On 11. Feb 2018, at 20:13, Daniel Kozuch <dan.kozuch at gmail.com> wrote:
>>> 
>>> Hello,
>>> 
>>> I was recently trying to use the tune_pme tool with GROMACS 2018 with the
>>> following command:
>>> 
>>> gmx tune_pme -np 84 -s my_tpr.tpr -mdrun 'gmx mdrun’
>> Maybe you need to compile gmx without MPI (so that gmx tune_pme
>> is a serial executable), and a separate mdrun which naturally
>> needs to be MPI-enabled (the latter you pass via -mdrun argument).
>> 
>>> 
>>> but I'm getting the following error:
>>> 
>>> "Fatal error:
>>> Cannot execute mdrun. Please check benchtest.log for problems!"
>>> 
>>> Unfortunately benchtest.log is an empty file. I saw that there were some
>>> similar problems with GROMACS 5. Is this still an issue?
>> What output is there on the command line?
>> 
>> Are you running on GPU nodes? Are all shared libraries needed by
>> mdrun actually found?
>> 
>> Best,
>>  Carsten
>> 
>> 
>>> 
>>> Thanks,
>>> Dan
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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
>> 
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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