[gmx-users] problem extending simulation 64 proc

Rebeca García Fandiño regafan at hotmail.com
Thu Mar 5 16:21:08 CET 2009

I have a problem in extending a MD simulation in Gromacs.
When I use 32 processors for the calculation, everything goes OK. The simulation finishes well and I can extend it with tpbconv.
However, I would like to increase the number of processors used up to 64. 
Using the same options for mdrun as I have used for 32 proc except for the number of processors:
srun  -n 64 /gpfs/apps/GROMACS/4.0.2/bin/mdrun -v -deffnm equilibrado9 -dlb auto
I get this error:
Program mdrun, VERSION 4.0.2
Source code file: domdec_setup.c, line: 132
Fatal error:
Could not find an appropriate number of separate PME nodes. i.e. >= 0.474960*#nodes (58) and <= #nodes/2 (64) and reasonable performance wise (grid_x=384, grid_y=162).
Use the -npme option of mdrun or change the number of processors or the PME grid dimensions, see the manual for details.
When I changed to 
srun  -n 64 /gpfs/apps/GROMACS/4.0.2/bin/mdrun -v -deffnm equilibrado9 -dlb auto –npme 32
the calculation finished correctly. However, when I try to extend this simulation with tpbconv:
/gpfs/apps/GROMACS/4.0.4/bin/tpbconv -s equilibrado9.tpr -f equilibrado9.trr -e equilibrado9.edr -n index.ndx -o equilibrado10.tpr -extend 1600
The process dies, I don´t know why:
Opened equilibrado9.edr as single precision energy file
trn version: GMX_trn_file (single precision)
Read    trr frame    452: step 2652000 time 5304.000Killed
When I used gmxcheck I have not found anything strange. I have also tried with the version 4.0.4 of Gromacs to do tpbconv, but the error is the same. This occurred in several calculations, always using 64 processors and -npme 32, so it is not a punctual error, something must be happening in the calculation but I don´t know what.
Does anybody has any idea?
Thank you very much for your help in advance,
Rebeca Garcia
Parc Cientific of Barcelona
regafan at hotmail.com
Nuevo Windows Live, un mundo lleno de posibilidades. Descúbrelo.
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