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

Yuhua Song yhsong at ccb.wustl.edu
Wed Aug 10 17:37:07 CEST 2005

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 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.
Thank you very much,
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