Hello,
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:
READING COORDS, VELS AND BOX FROM TRAJECTORY equilibrado9.trr...
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
[email protected]
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