Votca - Parallel execution

[Christoph Junghans]

2010/2/17 Senthilkumar Muthiah <sen...@cyrus.andrew.cmu.edu>:
> But when I try to use your tip on running parallel processes, I am having a
> problem.  I try to run the following script:
>
>
> #PBS -l nodes=1:ppn=6
> #PBS -q default
> #PBS -m ae
>
> date
>
> source /export/home/senthil/gromacs/bin/bin/GMXRC.bash
> cd $PBS_O_WORKDIR
> mpirun -np 6 ./run.sh
>
>
> date
>
> after including
>
> <mpi>
> <tasks>6</tasks>
> <cmd>/usr/lib64/mpi/gcc/openmpi/bin/mpirun -np 6</cmd>
> </mpi>
>
> in the last inverse block.
>
> Is there something that I am missing here?
>
> Thanks,
> Senthil
Well, can you provide me an error message?
Last 40 lines of inverse.log or so.

The block has to be in <cg>. <inverse> block (not in an interaction block).
See my example.

[Christoph Junghans]

Forget what I was saying before, just remove "mpirun -np 6" in front
of ./run.sh, the mpi stuff is handled by csg_inverse (called by
run.sh) internally.

[Christoph Junghans]

2010/2/22 Senthilkumar Muthiah <smut...@andrew.cmu.edu>:

>>> Forget what I was saying before, just remove "mpirun -np 6" in front
>>> of ./run.sh, the mpi stuff is handled by csg_inverse (called by
>>> run.sh) internally.
>>>

>> Was your mpi issue solved by this?
>>
> Yes! My MPI issue was solved by that.  Thanks!
Super.

By now the MPI stuff is more a hack, that is why one has to remove the
mpirun in front of run.sh.
We add a check soon, which warns of this double calling or even pulls
the parameter to the inside of csg_inverse.