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

[David]

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
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++