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

[Anupam Nath Jha]

Now i am using this much only:

#This is a PBS script for Parallel Jobs
#!/bin/bash -f
#PBS -o /home/anupam/MD/lyd
#PBS -e /home/anupam/MD/lyd
#PBS -q default

cd /home/anupam/MD/lyd

mpirun -np 4 /usr/local/gromacs/bin/mdrun_mpi -v -deffnm em

but still it's giving this error:
totalnum=2  numhosts=1
there are not enough hosts on which to start all processes







> 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
>
> These latter two should probably be file names, not directory names...
>
>> #PBS -q default
>>
>> cd /home/anupam/MD/lyd
>
> ... since this seems to be a directory? Check out the #PBS -wd option too...
>
>> mpirun grompp -f em.mdp -p topol.top -c solvated.gro -np 4 -o em.tpr
>
> grompp is not an MPI code, run it without mpirun
>
>> mpirun mdrun_mpi -v -deffnm -np 4 em
>
> Unless you have a PBS-customized install of mpirun, you should use
> "mpirun -np 4 mdrun_mpi -v deffnm em" since mdrun_mpi will pick up the
> four processors from the environment, but mpirun won't.
>
>> 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
>
> First get grompp working interactively, then get grompp working in a
> script, (neither of which need MPI), and only then worry about mpirun
> -np 4 mdrun
>
> Mark
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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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