Carsten Kutzner wrote:
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.
Hi,
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.
Aha, that explains it. Gurpreet, don't bother with the testing procedure
I just outlined. Try one of Carsten's suggestions.
Mark
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