Ok. Thank you both by the way. You guys have been incredibly helpful, and sorry I bothered you guys so much. I'll still attempt to troubleshoot this and potentially fix it. When I find out what the solution is, I will let you guys know. Thank you.
Sincerely, Sam On Wed, Oct 5, 2016 at 3:10 PM, Troels Emtekær Linnet <tlin...@nmr-relax.com > wrote: > 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> 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_process >>>> or_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
