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

[Anupam Nath Jha]

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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-- 
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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