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

Yuhua Song yhsong at ccb.wustl.edu
Wed Aug 10 17:56:40 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  ect.

 /opt/mpich/gnu/bin/mpirun -np 6 -nolocal -machinefile machines  /usr/local/bin/mdrun_mpi -np 6 -vand the output is something like starting mdrun 'Generated by genbox'100 steps,      0.2 ps.and, after some time, it writes outp4_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.Thank you very much,Yuhua 
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