On Wed, Feb 29, 2012 at 1:47 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> 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. > > Well, without -pd everything works fine. > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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