But i already have mpi4py installed from the package list. On Wed, Oct 5, 2016 at 2:43 PM, Troels Emtekær Linnet <tlin...@nmr-relax.com > wrote:
> Hi Sam. > > Akk you PI to run this: > > sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip > install mpi4py' > or > sudo -i > setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc > pip install mpi4py > > > Where '/usr/lib64/openmpi-1.10/bin/mpicc' should be the path to mpicc. > > Find the path with: > which mpicc > > Look here: > https://mpi4py.scipy.org/docs/usrman/install.html > > Under: > "Using pip or easy_install" > > You need to tell where the mpicc is with the environment, so mpi4py can be > compiled correctly. > > Note: Setting the environment in BASH and TCSH is different! > > BASH: > sudo -- sh -c 'env MPICC=/usr/lib64/openmpi-1.10/bin/mpicc; pip install > mpi4py' > > TCSH: > sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip > install mpi4py' > > > > > > 2016-10-05 23:31 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: > >> Hi Edward, >> >> I installed mpi4py and OpenMPI both from the fedora packages. I had a >> mpi4py that I downloaded via the site itself, and compiled it, but I wasn't >> able to install it so I deleted it. The command >> mpirun --np 5 python -c "import mpi4py; from mpi4py import MPI; >> print('Mpi4py %s process %d of %d on %s.'%(mpi4py._version_,MPI>COM >> M_WORLD.Get_rank(),MPI>COMM_WORLD.Get_size(),MPI.Get_processor_name()))" >> >> gave no output. These are the mpi packages I have installed >> Openmpi: >> openmpi-1.7.3-1.fc.20(64-bit) >> openmpi-devel-1.7.3-1.fc20(64bit) >> pypar-openmpi-2.1.5_108_3.fc.20(64bit) >> python3-mpi4py-1.3.1-1.fc20(64bit) >> >> Mpi4py >> mpi4py-common-1.3.1-1.fc20 >> mpi4py-mpich-1.3.1-1.fc20 >> mpi4py-openmpi-1.3.1-1.fc20 >> python3-mpi4py-mpich-1.3.1-1.fc20 >> python3-mpi4py-openmpi-1.3.1-1.fc20 >> >> Could you reccomend which packages specifically I should install? I could >> just tell my PI to remove all the openmpi and mpi4py programs, and download >> the specific 2 that do work (if there is a problem with having different >> mpi's and mpi4py's) >> >> All of these were installed from the fedora packages themselves. Also the >> locate mpi list gave me a massive output (I assume this is because I have 5 >> programs that use mpi) >> Sincerely, >> Sam >> >> On Wed, Oct 5, 2016 at 2:09 PM, Edward d'Auvergne <edw...@nmr-relax.com> >> wrote: >> >>> On 5 October 2016 at 22:01, Mahdi, Sam <sam.mahdi....@my.csun.edu> >>> wrote: >>> > Hi Troels, >>> > >>> > The mpirun --np 2 gave no output, so I had to abort the command, but >>> here is >>> > the output. >>> > crowlab: [~]> python -c "import mpi4py; print mpi4py.__version__" >>> > 1.3.1 >>> > crowlab: [~]> mpirun --np 2 python -c "from mpi4py import MPI; print >>> > MPI.COMM_WORLD.Get_rank()" >>> > ^Ccrowlab: [~]> >>> >>> Hi Sam, >>> >>> This result I'm pretty sure shows that mpi4py is not functioning >>> correctly - i.e. there is an installation problem. This is what you >>> should see: >>> >>> [edward@localhost ~]$ mpirun --np 2 python -c "from mpi4py import MPI; >>> print MPI.COMM_WORLD.Get_rank()" >>> 0 >>> 1 >>> [edward@localhost ~]$ >>> >>> Note the printout of 0 and 1. Maybe try the following: >>> >>> [edward@localhost ~]$ mpirun --np 5 python -c "import mpi4py; from >>> mpi4py import MPI; print('Mpi4py %s process %d of %d on %s.' >>> %(mpi4py.__version__, >>> MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(), >>> MPI.Get_processor_name()))" >>> Mpi4py 1.3.1 process 0 of 5 on localhost.localdomain. >>> Mpi4py 1.3.1 process 1 of 5 on localhost.localdomain. >>> Mpi4py 1.3.1 process 4 of 5 on localhost.localdomain. >>> Mpi4py 1.3.1 process 2 of 5 on localhost.localdomain. >>> Mpi4py 1.3.1 process 3 of 5 on localhost.localdomain. >>> [edward@localhost ~]$ >>> >>> If you don't see a printout here, then clearly mpi4py and OpenMPI are >>> not working together correctly. Without a printout, your mpi4py is >>> FUBAR. Are you using the default OpenMPI and mpi4py packages form >>> fedora, and you don't have any backports or other non-standard sources >>> set up for your RPMs? Do you have any user installed MPI or mpi4py >>> software around? If you type: >>> >>> $ locate mpi >>> >>> What do you see? For me this is pretty clearly an installation problem. >>> >>> Regards, >>> >>> Edward >>> >> >> > _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
