Dear Mark,
As you suggested, i ran the simulations with fourier spacing of
0.08,0.09,0.10 & 0.11 with mpirun -np 4 mdrun_d_mpi -np 4
following is the output
fourierspacing =0.08
-------------------------------------------------------
Program mdrun_d_mpi, VERSION 3.3.99_development_20070720
Source code file: gmx_parallel_3dfft.c, line: 90
Fatal error:
nx (63) and ny (63) must be divisible by the number of nodes (4).
-------------------------------------------------------
corresponding values from tpr files are
nkx = 63
nky = 63
nkz = 189
fourierspacing =0.09 ; no errors in simulations
corresponding values from tpr files are
nkx = 56
nky = 56
nkz = 168
fourierspacing =0.10 ;
-------------------------------------------------------
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).
-------------------------------------------------------
corresponding values from tpr files are
nkx = 50
nky = 50
nkz = 150
fourier spacing 0.11 ; no errors in simulations
corresponding values from tpr files are
nkx = 48
nky = 48
nkz = 140
As you mentioned, the error does not occur when nx is divisible by number of
nodes
I have updated and compiled the CVS version yesterday only.
With Regards,
Gurpreet Singh
-------------------------------------------------
University of Dortmund
Department of Chemistry
Physical Chemistry I - Biophysical Chemistry
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Office: C1-06 room 176
Phone: +49 231 755 3916
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-------------------------------------------------
-----Original Message-----
From: Mark Abraham [mailto:[EMAIL PROTECTED]
Sent: Thursday, August 09, 2007 10:01 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] problems with parallel mdrun
singh wrote:
> Dear Mark,
> Thanks for the reply.
> I am using the following options for the electrostatics in the mdp file
> coulombtype = pme
> fourierspacing = 0.1
> pmeorder = 4
> optimize_fft = yes
> ewald_rtol = 1.0e-5
> ewald_geometry = 3dc
>
> So if I understood you correctly, I have to change either fourier spacing
or
> my box size in order to get it running with -np 4
Hmm. If that's all the options relevant to electrostatics in your .mdp
file, then this looks weird enough to be a possible bug, given that
you're using a development version of mdrun.
First, update your CVS source, check this problem still happens. Then
try it for a small range of fourierspacing values around 0.1 and see
what behaviour you get. I suggest 0.08, 0.09, 0.1, 0.11, 0.12. If you
report what you find, please use gmxdump on the input .tpr to report on
nx/ny/nz.
On what I've seen so far, the automatic "choose nx/ny/nz suitable for
grid spacing and number of nodes" might be broken. With this test, we're
looking to see whether only choices of fourierspacing that produce
nx/ny/nz that are accidentally divisible by the number of nodes are the
only successful ones... The good news is the fix will be easy if this is
the problem.
Mark
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