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

[Diego Nolasco]

Hi there,

Try giving the complete address of the command you want to run, just like
this:

/usr/bin/grompp -f *.mdp -c *.gro -p *.top -o *.tpr -np 4

mpirun -np 4 /usr/bin/mdrun_mpi.lam -s *.tpr -x *.xtc -c *.gro -g *.log -e
*.edr -v

The address depends on your installation. In my case is /usr/bin/.

I hope it helps,
Diego.


2007/8/6, Anupam Nath Jha <anupam at mbu.iisc.ernet.in>:
>
> 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
>
>
>
> --
> This message has been scanned for viruses and
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>
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