Hello,
Here are some words of warning: MMPBSA.py.MPI is an advanced option, and you
should only try and use this if you really require the benefit of running on
multiple processors. Next, if the available MPI is mvapich, then I'm
guessing you're running this on a cluster with infiniband, correct? It's
tricky to run multiple MPIs on a cluster, and care has to be taken to keep
them separate and not to have one stepping on the toes of the other
(different MPI implementations are generally incompatible with each other).
There should not be any issues in building mpi4py with mvapich2 to my
knowledge. I installed it just fine with mvapich. You just have to make
sure that it has a working mpicc compiler. You can run "python setup.py
build" in the mpi4py source directory to build the binaries in the build/
directory inside mpi4py-1.2.1b/ . Then you have to add the corresponding
library path to PYTHONPATH. (python setup install will likely not work
without root privileges unless you're using a python that you've built)
This will all hopefully be streamlined in the future.
Finally, what error messages do you get when you try to run MMPBSA.py.MPI?
Can you run MMPBSA.py?
Good luck!
Jason
On Wed, Sep 29, 2010 at 11:45 AM, Senthil Natesan <sen.natesan.yahoo.com>wrote:
> Hi Amber Users,
>
> Greetings. I compiled Amber11 and Ambertools1.4 with MVAPICH2 and
> everything
> works fine.
> I am wondering if MMPBSA.py. MPI can be run using MVAPICH too ?
> I don't see any option for compiling mpi4py with MVAPICH, so I compiled
> with
> MPICH2.
> Now I am not able to run MMPBSA.py.MPI ?!!.
>
> Please suggest me how to go about ?
> thanks,
>
> Senthil Natesan
>
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Sep 29 2010 - 09:30:04 PDT
