[gmx-users] problems with parallel mdrun

singh singh at biophysik.chemie.uni-dortmund.de
Thu Aug 9 09:47:47 CEST 2007

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

With Regards,

-----Original Message-----
From: Mark Abraham [mailto:Mark.Abraham at anu.edu.au] 
Sent: Wednesday, August 08, 2007 10:17 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] problems with parallel mdrun

Gurpreet Singh wrote:
> Dear gmx users,
> I am using a current CVS version of Gromacs and using the newly introduced
> options for simulations with walls. I am facing the following two
> problems.

You should send separate emails for each problem, with different subject 
headings, so that people with relevant expertise have the maximum chance 
of seeing your problem. The second problem here has nothing to do with 
your email subject line...

> 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.

> second question is regarding wall_denstiy option.
> As i understood from the manual the wall density is a number density in
> units of number/nm2 in case of 10-4 potential
> and is number/nm3 in case of 9-3 potential.
> please correct me if i am wrong.

I don't know.


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