AMBER Archive (2009)

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

From: Dechang Li (li.dc06_at_gmail.com)
Date: Mon Apr 06 2009 - 05:56:53 CDT

Dear Dr. Simmerling,

        Thank you for your reply!
        I check the .out file, it displayed "Running AMBER/MPI version on 4 nodes".
If there some things not actually doing work, however, when I killed either one
of them, the simulation down immediately.

        

>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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