[gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

[Carsten Kutzner]

Hi,

is this the only output?

Don’t you get a perf.out file that lists which settings are optimal?

What exactly was the command line you used?

Carsten


On 29 Sep 2014, at 15:01, Ebert Maximilian <m.ebert at umontreal.ca> wrote:

> Hi,
> 
> I just tried that and I got the following error message (bench.log). Any idea what could be wrong?
> 
> Thank you very much,
> 
> Max
> 
> Initializing Domain Decomposition on 48 ranks
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>    two-body bonded interactions: 0.422 nm, LJ-14, atoms 1444 1452
>  multi-body bonded interactions: 0.422 nm, Proper Dih., atoms 1444 1452
> Minimum cell size due to bonded interactions: 0.464 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm
> Estimated maximum distance required for P-LINCS: 0.218 nm
> 
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 5.0.1
> Source code file: /RQusagers/rqchpbib/stubbsda/gromacs-5.0.1/src/gromacs/mdlib/domdec_setup.c, line: 728
> 
> Fatal error:
> The number of ranks you selected (37) contains a large prime factor 37. In most cases this will lead to bad performance. Choose a number with smaller prime factors or set the decomposition (option -dd) manually.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Carsten Kutzner
> Sent: Donnerstag, 25. September 2014 19:29
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi
> 
> Hi,
> 
> don't invoke g_tune_pme with 'mpirun', because it is a serial executable that itself invokes parallel MD runs for testing.
> 
> use
> export MDRUN=mdrun_mpi
> 
> g_tune_pme -np 24 -s 1ZG4_nvt.tpr -launch
> 
> see also
> 
> g_tune_pme -h
> 
> You may need to recompile g_tune_pme without MPI enabled (depends on your queueing system)
> 
> Best,
> Carsten
> 
> 
> On 25 Sep 2014, at 15:10, Ebert Maximilian <m.ebert at umontreal.ca> wrote:
> 
>> Dear list,
>> 
>> I tried using g_tune_pme_mpi with the command:
>> 
>> mpirun -np 24 g_tune_pme_mpi -np 24 -s 1ZG4_nvt.tpr -launch
>> 
>> on GROMACS 5.0.1 but I get the following error message:
>> ----------------------------------------------------------------------
>> ---- mpirun was unable to launch the specified application as it could 
>> not find an executable:
>> 
>> Executable: mdrun
>> Node: xxxx
>> 
>> while attempting to start process rank 0.
>> ----------------------------------------------------------------------
>> ----
>> 24 total processes failed to start
>> 
>> 
>> Any idea why this is? Shouldn't g_tune_pme_mpi call mdrun_mpi instead?
>> 
>> Thank you very much,
>> 
>> Max
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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
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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