[gmx-users] mdrun -pd

[Steven Neumann]

On Wed, Feb 29, 2012 at 1:47 PM, Mark Abraham <Mark.Abraham at 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120229/2b999044/attachment.html>