[gmx-users] mpich - mdrun problem and md using mpich

[Yuhua Song]

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?

Thanks,

Yuhua


----- 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
>> ect.
>>
>>  /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
>> process:
>>
>> 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
>> mpich”.
>>
>> 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 
>> beta.”
>> 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
> (www.lam-mpi.org).
>
> Please don't send the same message multiple times to the list.
>
>
>> Thank you very much,
>> Yuhua
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> -- 
> David.
> ________________________________________________________________________
> 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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