On 1/03/2012 12:31 AM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to use option -p of mdrun for particle decomposition.
I used:
mpiexec mdrun -pd -deffnm nvt
I obtain:
apps/intel/ict/mpi/3.1.038/bin/mpdlib.py:37: DeprecationWarning: the
md5 module is deprecated; use hashlib instead
from md5 import new as md5new
NODEID=0 argc=4
:-) G R O M A C S (-:
NODEID=2 argc=4
NODEID=6 argc=4
NODEID=1 argc=4
NODEID=5 argc=4
NODEID=11 argc=4
NODEID=3 argc=4
NODEID=7 argc=4
NODEID=8 argc=4
NODEID=9 argc=4
NODEID=10 argc=4
NODEID=4 argc=4
Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision)
starting mdrun 'Protein'
1000000 steps, 500.0 ps.
/apps/intel/ict/mpi/3.1.038/bin/mpdlib.py:27: DeprecationWarning: The
popen2 module is deprecated. Use the subprocess module.
import sys, os, signal, popen2, socket, select, inspect
/apps/intel/ict/mpi/3.1.038/bin/mpdlib.py:37: DeprecationWarning: the
md5 module is deprecated; use hashlib instead
from md5 import new as md5new
Then trajectory files are empty
Your MPI configuration is probably broken. You should observe similar
output from mdrun without using -pd. You should find out if a simple MPI
test program can run.
Mark
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