[gmx-users] g_tune_pme_mpi is not compatible to mdrun_mpi

[Ebert Maximilian]

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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