[gmx-users] mpich - mdrun problem and md using mpich
yhsong at ccb.wustl.edu
Wed Aug 10 22:08:03 CEST 2005
Thanks, David. I will try CVS code and change to LAM MPI to see how it goes.
Sorry for the mistake about the multiple messages, is there is a way that I
could delete the repeated message?
----- Original Message -----
From: "David" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, August 10, 2005 2:50 PM
Subject: Re: [gmx-users] mpich - mdrun problem and md using mpich
> On Wed, 2005-08-10 at 10:59 -0500, Yuhua Song wrote:
>> Dear Colleague:
>> When I try to run Gromacs 3.2.1 on supercomputer with multiprocessor,
>> After I launch the simulation using 6 processors or more it doesn't
>> work. The odd thing is that it doesn't exit with errors, but it waits
>> for data which never arrive. Finally report the error about Timeout
>> /opt/mpich/gnu/bin/mpirun -np 6 -nolocal -machinefile machines
>> /usr/local/bin/mdrun_mpi -np 6 -v
>> and the output is something like
>> starting mdrun 'Generated by genbox'
>> 100 steps, 0.2 ps.
>> and, after some time, it writes out
>> p4_1636: p4_error: Timeout in establishing connection to remote
>> I search the mailing list, the same issue that has been reported on
>> mailing list on 2004-10-18 by gianluca santarossa titled as: “md using
>> David van der Spoel ‘s reply indicate that “there is a problem in mpich
>> that makes that jobs never end, it has to do with interaction between MPI
>> and grid software.
>> There is a workaround in the CVS code that will shortly be released in
>> I am wondering whether current public version of 3.2.1 have solved this
>> problem, the error comes from the MPI installation. Or need to download
>> special patch for this.
>> I appreciate any input and suggestions.
> You'll have to use the CVS code to make this work, or change to LAM MPI
> Please don't send the same message multiple times to the list.
>> Thank you very much,
>> gmx-users mailing list
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> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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