[gmx-users] how to run parallel jobs in gromacs

[Erik Lindahl]

Consult the documentation for your MPI library and queue system. This  
is not a Gromacs error message - mpirun is complaining that there  
aren't enough processors to start 4 jobs.

Cheers,

Erik


On Aug 6, 2007, at 1:14 PM, Anupam Nath Jha wrote:

>
> i have tried that also but still same error is coming.
>
> what else should i do now?
>
> anupam
>
>
>> The -np flag should be specified to the mpirun command (gromacs
>> determines it automatically).
>>
>> It could also be a problem with your MPI library or queue system - I
>> have no idea why it is trying to start 3 processes...
>>
>> Cheers,
>>
>> Erik
>>
>> On Aug 6, 2007, at 12:46 PM, Anupam Nath Jha wrote:
>>
>>> Dear all
>>>
>>> i am new in gromacs. i have installed gromacs-3.3.3 in our cluster
>>> (mpi is
>>> already there) with parallel version (using the following command):
>>>
>>>
>>> make clean
>>> ./configure --enable-mpi --disable-nice --program-suffix="_mpi"
>>> make mdrun
>>> make install-mdrun
>>>
>>> it went fine.
>>>
>>> but when i ran the command -
>>> qsub pbs_submit
>>>
>>> it's the pbs_submit file:
>>>
>>> #This is a PBS script for Parallel Jobs
>>> #!/bin/bash -f
>>> #PBS -l nodes=2:ppn=2
>>> #PBS -o /home/anupam/MD/lyd
>>> #PBS -e /home/anupam/MD/lyd
>>> #PBS -q default
>>>
>>> cd /home/anupam/MD/lyd
>>> mpirun grompp -f em.mdp -p topol.top -c solvated.gro -np 4 -o em.tpr
>>> mpirun mdrun_mpi -v -deffnm -np 4 em
>>>
>>> but it's not doing anything,except writing this:
>>>
>>> totalnum=3  numhosts=2
>>> there are not enough hosts on which to start all processes
>>> totalnum=3  numhosts=2
>>> there are not enough hosts on which to start all processes
>>>
>>>
>>>
>>> can you help me out?
>>>
>>> thanks in adavnce
>>> anupam
>>>
>>>
>>>
>>> --
>>> Science is facts; just as houses are made of stone, so is science
>>> is made of
>>> facts; but a pile of stones is not a house, and  a collection of
>>> facts is not
>>> necessarily sciece.
>>>
>>> Anupam Nath Jha
>>> Ph. D. Student
>>> Saraswathi Vishveshwara Lab
>>> Molecular Biophysics Unit
>>> IISc,Bangalore-560012
>>> Karnataka
>>> Ph. no.-22932611
>>>
>>>
>>>
>>> --
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>>>
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>>
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>>
>
>
> -- 
> Science is facts; just as houses are made of stone, so is science  
> is made of
> facts; but a pile of stones is not a house, and  a collection of  
> facts is not
> necessarily sciece.
>
> Anupam Nath Jha
> Ph. D. Student
> Saraswathi Vishveshwara Lab
> Molecular Biophysics Unit
> IISc,Bangalore-560012
> Karnataka
> Ph. no.-22932611
>
>
>
> -- 
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php