AMBER Archive (2009)

Subject: Re: [AMBER] sander.MPI parallel run problem

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Apr 06 2009 - 05:09:11 CDT

how many nodes does sander say it is using (it really means mpi threads, not
nodes)? also, are all 7 collecting cpu time? some may be things not actually
doing work, such as one that starts up the other mpi jobs.

2009/4/6 Dechang Li <li.dc06_at_gmail.com>

> Dear all,
>
> I run the parallel simulation using sander.MPI in a cluster.
> The command I used was:
>
> mpirun -np 4 -machinefile myhosts ...
>
> I required 4 cpus to do the parallel simulation, but finally
> there were 7 programes run at the node:
>
> 9279 user1 25 0 37928 6088 1592 R 101 0.1 11:03.15
> /hpexport2/home/user1/amber9/exe/sander.MPI cn27 56237 -p4amslave
> -p4yourname cn27
> 9281 user1 25 0 38864 6128 1592 R 101 0.1 11:03.07
> /hpexport2/home/user1/amber9/exe/sander.MPI cn27 56237 -p4amslave
> -p4yourname cn27
> 9253 user1 16 0 37928 6088 1592 R 99 0.1 10:45.95
> /hpexport2/home/user1/amber9/exe/sander.MPI cn27 56237 -p4amslave
> -p4yourname cn27
> 9280 user1 25 0 37928 6068 1592 R 99 0.1 11:03.23
> /hpexport2/home/user1/amber9/exe/sander.MPI cn27 56237 -p4amslave
> -p4yourname cn27
> 9207 user1 16 0 38864 6128 1592 R 97 0.1 10:44.25
> /hpexport2/home/user1/amber9/exe/sander.MPI cn27 56237 -p4amslave
> -p4yourname cn27
> 9230 user1 16 0 37928 6068 1592 R 97 0.1 10:41.93
> /hpexport2/home/user1/amber9/exe/sander.MPI cn27 56237 -p4amslave
> -p4yourname cn27
> 9202 user1 16 0 35872 4848 2184 R 91 0.1 10:09.37
> /hpexport2/home/user1/amber9/exe/sander.MPI -O -i
> /hpexport2/home/user1/abc/water/
>
>
> What is the problem?
>
> Best regards,
> 2009-4-6
>
>
>
> =========================================
> Dechang Li, Ph.D Candidate
> Department of Engineering Mechanics
> Tsinghua University
> Beijing 100084
> P.R. China
>
> Tel: +86-10-62773574(O)
> Email: lidc02 at mails.tsinghua.edu.cn
> =========================================
>
>
>
>
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