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

David spoel at xray.bmc.uu.se
Wed Aug 10 21:50:57 CEST 2005

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

Please don't send the same message multiple times to the list.

> Thank you very much,
> Yuhua
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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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