On Sun, Dec 16, 2012 at 2:21 AM, Fabian Glaser <fglaser.technion.ac.il>wrote:
> Hi,
>
> I am using the following PBS file to run sander
>
> #PBS -l select=1:ncpus=12:mpiprocs=12
> ...
> mpirun -hostfile $PBS_NODEFILE pmemd.MPI -O -i prod.in -p
> 3SO6_clean.prmtop -c 3SO6_clean_prod_1.rst -o 3SO6_clean_prod_2.out -x
> 3SO6_clean_prod_2.mdcrd -r 3SO6_clean_prod_2.rst
>
> Which runs perfectly, at a rate of about ns/day = 3.67
>
> But if I try to use more than one node, for example:
> #PBS -l select=2:ncpus=12:mpiprocs=12
>
> The job does not seem to start or at least output files are not writte...
>
> Is there a way to use more than one node? Or any way to accelerate the
> process?
>
I have never had problems running on multiple nodes. Given the
communication required on each step, though, unless your nodes have a fast
interconnect (e.g., some type of infiniband) you will be better off just
using 1 node if each node has 12 cores available, IMO.
If you're really having a problem running on multiple nodes, the issue is
probably somewhere in your system configuration or your MPI installation.
Some systems may require you to set up password-less login between nodes
using an ssh-key, since multi-node jobs need to send information between
nodes. Since we just use the MPI API, the problem is highly unlikely to be
Amber.
I would suggest contacting your system administrator for this cluster with
the problems you're having. If you want to test inter-node MPI with a very
simple program, try running something like this:
mpiexec -hostfile $PBS_NODEFILE $AMBERHOME/test/numprocs
Which should just output the total number of processors you asked for to
the PBS output file (#PBS -o <pbs_output>)
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 16 2012 - 07:00:02 PST
