[gmx-users] Parallel instalation: gmx-users Digest, Vol 74, Issue 76

[Mark Abraham]

----- Original Message -----
From: abdul wadood <wadoodbiochemist at hotmail.com>
Date: Tuesday, June 15, 2010 18:12
Subject: [gmx-users] Parallel instalation:  gmx-users Digest, Vol 74,	Issue 76
To: gmx-users at gromacs.org, ckutzne at gwdg.de


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>  Dear Carsten Kutzner
> 
> First, I am very thankful to you and highly appreciate your help. According to your guideness I given the path for mdrun_mpi and the command run successfully. But now the problem is the simulation run for some time and the killed and give the error which is :
> 
> p10_522:  p4_error: Timeout in establishing connection to remote process: 0
> p8_468:  p4_error: Timeout in establishing connection to remote process: 0
> p9_495:  p4_error: Timeout in establishing connection to remote process: 0
> p0_32740:  p4_error: net_recv read:  probable EOF on socket: 1
> Killed by signal 2.
> Killed by signal 2.
> p4_359:  p4_error: net_recv read:  probable EOF on socket: 1
> p6_413:  p4_error: net_recv read:  probable EOF on socket: 1
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> 
> I dont know how to solve this problem. Any help in this respect will be by highly appreciated by our research group.




It looks to me like you need to troubleshoot your MPI installation. The above was not generated by GROMACS. Unless you have some evidence in (say) GROMACS .log files that it's reporting a problem, then you'll need to look elsewhere for clues. Does a simple MPI test program work?




Mark

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