[gmx-users] problems with parallel mdrun

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 9 10:00:34 CEST 2007

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 

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.


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