[gmx-users] mdrun -pd

[Mark Abraham]

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