Hi Jason,
Thanks for the reply.
yes, MMPBSA.py works fine. I will be running this calculation on large number
of complexes and it seems that for a single calculation, it takes more than an
hour or so,
(still my first calculation is not completed yet). This particular protein has ~
299 residues.
But I gave instruction to read every 1 ps frame of 1 ns trajectory. Probably I
should
increase this number to 10 ps.
By the way, I am working on Craycx1 machine which has 4 computing nodes (each
with 8 processors).
I haven't compiled mpi4py with MVAPICH yet. I did it with MPICH2 only as I
didn't see MVAPICH
given as one of the options.
I do have working mpicc compiler with MVAPICH2 and I will try now.
The error message was to install mpi4py, as if it was not able to find it.
Though it is installed.
are there any other tips to increase the speed of calculations without loosing
the quality of the output?
thanks,
Senthil Natesan
Jason wrote:
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
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 - 10:00:09 PDT
