[gmx-users] problems with parallel mdrun

[Mark Abraham]

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