Re: [IMP-users] ReplicaExchange: Could not find MPI. Using Serial Replica Exchange

[Julian <>]

Thanks for the quick reply.

I was doing what you described but no luck.Â

I then compiled from source against openmpi, used the magic python import lines from the IMP.mpi docs and that turned out to be fairly straightforward. Everywhere along the way, things seemed to be working fine, no errors. But then when I ran it with

mpirun -np 10 ~/IMP/imp-2.6.2_release/setup_environment.sh python exosome.modeling.py --test

it doesn't appear to be any faster than a single process. I started it and then immediately started a single proc on the same 24-core box in a different dir

~/IMP/imp-2.6.2_release/setup_environment.sh python exosome.modeling.py --test

Looking at the number of frames it's outputting, it seems like the single proc is going faster. So it appears I'm getting all the downside from the MPI overhead without any of the benefits. Any ideas?

Thanks much

On Tue, Aug 30, 2016 at 1:27 PM, Ben Webb <" target="_blank">> wrote:

On 08/30/2016 09:00 AM, Julian wrote:

I'm trying to run the exosome example with MPI but can't seem to get it
to work. I installed binaries both on Fedora 19 and Ubuntu Trusty. I
have openmpi on both and mpich on Fedora as well. mpirun is in my path.

Do I need to build with MPI mysefl for this to work or is this supposed
to work with binaries out of the box?

You need the IMP.mpi module to use MPI (and you have to run IMP via mpirun). We don't include this in the regular binary package because we don't want to force everybody to install an MPI library just to use IMP, and there are multiple MPI libraries to choose from. But on Fedora you can simply install the IMP-mpich RPM which includes the IMP.mpi module built against MPICH, and then it should work. We don't currently include a similar package for Ubuntu, but it probably wouldn't be that hard to add one for future releases.

    Ben
--
" target="_blank">Â Â Â Â Â Â Â Â Â Â Â https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
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