I think there is nothing more to do here. Call the nearest computer wizard, and give a round of beer.
Best Troels Den onsdag den 5. oktober 2016 skrev Mahdi, Sam <sam.mahdi....@my.csun.edu>: > 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 > <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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 >>> <javascript:_e(%7B%7D,'cvml','edw...@nmr-relax.com');>> wrote: >>> >>>> On 5 October 2016 at 22:01, Mahdi, Sam <sam.mahdi....@my.csun.edu >>>> <javascript:_e(%7B%7D,'cvml','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
