[gmx-users] Gromacs in Parallel

TJ Piggot t.piggot at bristol.ac.uk
Tue Aug 11 03:45:54 CEST 2009

I agree. Mpich 1 is very old, you should try mpich 2 or lam or openmpi.


--On Tuesday, August 11, 2009 09:16:54 +1000 Mark Abraham 
<Mark.Abraham at anu.edu.au> wrote:

> Andrew Paluch wrote:
>> To whom this may concern,
>> I am receiving the following errors when attempting to run Gromacs in
>> parallel:
>> Making 1D domain decomposition 4 x 1 x 1
>> p2_21562:  p4_error: Timeout in establishing connection to remote
>> process: 0 p2_21562: (302.964844) net_send: could not write to fd=5,
>> errno = 32
>> where I am using mpich 1.2.7 for 64 bit processors.  From what I can
>> find, it seems as if this is a mpich issue and not an issue of Gromacs.
>> Has anyone else encountered such a problem?  Also, does anyone have any
>> suggestions for a solution?
> Indeed, this is not a problem intrinsic to GROMACS. I'm not aware of
> problems with particular MPI libraries, but you might try compiling
> GROMACS with another such library. Whoever configured this machine should
> probably look into the problem.
> Mark
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TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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