[gmx-users] problems with parallel mdrun

Carsten Kutzner ckutzne at gwdg.de
Thu Aug 9 09:54:08 CEST 2007

Mark Abraham wrote:
> Gurpreet Singh wrote:
>> I get the following errors while using paralled version of mdrun compiled
>> with openmpi.
>> mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1
>> *****
>> Program mdrun_d_mpi, VERSION 3.3.99_development_20070720
>> Source code file: gmx_parallel_3dfft.c, line: 90
>> Fatal error:
>> nx (50) and ny (50) must be divisible by the number of nodes (4).
>> *******
>> I am using a cubic box of 5nm and grid spacing is 0.1. The simulations
>> runs fine if i use 5 nodes
>> I am using a machines with 2 dual xeon processors so -np 4 is more
>> appropriate for my sytems.
>>  Is there any way to use -np 4  without changing the gridspacing or
>> box size?
> No. I'm guessing your .mdp file is trying to specify nx/ny/nz, rather
> than the grid spacing. If you specify the latter, grompp will take care
> of this issue so that you get the largest allowable spacing smaller than
>  (or equal to) the requested grid spacing.

in the current CVS version of grompp you cannot use the -np switch
anymore. You will have to comment out the 'fourierspacing = 0.1' line
and set

fourier_nx               = 52
fourier_ny               = 52
fourier_nz               = 52

in order to get a tpr file that you can run on 4 processors.
Alternatively, stick to the original mpd settings but use the 3.3.1
version of grompp with -np 4. These tpr files are read by CVS gromacs.

Hope that helps,

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