Thanks for the thoughts, I'll give it a go. For reference, I have installed it in the opt directory, as that is where I have kept my installs currently. Will this be a problem when calling mpi from other packages?
Thanks, Tim On 24 May 2017 06:30, "Reuti" <re...@staff.uni-marburg.de> wrote: > Hi, > > Am 23.05.2017 um 05:03 schrieb Tim Jim: > > > Dear Reuti, > > > > Thanks for the reply. What options do I have to test whether it has > successfully built? > > LIke before: can you compile and run mpihello.c this time – all as > ordinary user in case you installed the Open MPI into something like > $HOME/local/openmpi-2.1.1 and set paths accordingly. There is no need to be > root to install a personal Open MPI version in your home directory. > > -- Reuti > > > > > > Thanks and kind regards. > > Tim > > > > On 22 May 2017 at 19:39, Reuti <re...@staff.uni-marburg.de> wrote: > > Hi, > > > > > Am 22.05.2017 um 07:22 schrieb Tim Jim <timothy.m....@gmail.com>: > > > > > > Hello, > > > > > > Thanks for your message. I'm trying to get this to work on a single > > > machine. > > > > Ok. > > > > > > > How might you suggest getting OpenMPIworking without python and > > > CUDA? > > > > It looks like it's detected automatically. It should be possible to > disable it with the command line option: > > > > $ ./configure --without-cuda … > > > > At the end of the configure step out should liste some lines like: > > > > Miscellaneous > > ----------------------- > > CUDA support: no > > > > The mpi4py seems unrelated to the compilation of Open MPI itself AFAICS. > > > > > > > I don't recall setting anything for either, as the only command I had > > > run was "./configure --prefix=/opt/openmpi/openmpi-2.1.0" - did it > possibly > > > pick up the paths by accident? > > > > > > Regarding the lib directory, I checked that the path physically exists. > > > Regarding the final part of the email, is it a problem that 'undefined > > > reference' is appearing? > > > > Yes, it tries to resolve missing symbols and didn't succeed. > > > > -- Reuti > > > > > > > > > > Thanks and regards, > > > Tim > > > > > > On 22 May 2017 at 06:54, Reuti <re...@staff.uni-marburg.de> wrote: > > > > > >> -----BEGIN PGP SIGNED MESSAGE----- > > >> Hash: SHA1 > > >> > > >> Hi, > > >> > > >> Am 18.05.2017 um 07:44 schrieb Tim Jim: > > >> > > >>> Hello, > > >>> > > >>> I have been having some issues with trying to get OpenMPI working > with > > >> mpi4py. I've tried to break down my troubleshooting into a few chunks > > >> below, and I believe that there are a few, distinct issues that need > > >> solving. > > >> > > >> Are you speaking here of a single machine or a cluster? > > >> > > >> > > >>> Following some troubleshooting in the following link: > > >>> https://bitbucket.org/mpi4py/mpi4py/issues/69/building- > > >> mpi4py-with-openmpi-gives-error > > >>> -the mpi4py folks have suggested it an issue that might be better > > >> answered here. > > >> > > >> First approach would be to get Open MPI working, without CUDA and > Python > > >> being involved. > > >> > > >> > > >>> In summary, I have attempted to install OpenMPI on Ubuntu 16.04 to > the > > >> following prefix: /opt/openmpi-openmpi-2.1.0. I have also manually > added > > >> the following to my .bashrc: > > >>> export PATH="/opt/openmpi/openmpi-2.1.0/bin:$PATH" > > >>> MPI_DIR=/opt/openmpi/openmpi-2.1.0 > > >>> export LD_LIBRARY_PATH=$MPI_DIR/lib:$LD_LIBRARY_PATH > > >> > > >> This looks fine, although I don't recall setting MPI_DIR for Open MPI > > >> itself. It might be a necessity for mpi4py though. > > >> > > >> One pitfall might be that "lib" is sometimes being created as "lib64" > by > > >> `libtool`. I forgot the details when this is happening, but it > depends on > > >> the version of `libtool` being used. > > >> > > >> > > >>> I later became aware that Ubuntu may handle the LD_LIBRARY_PATH > > >> differently > > >> > > >> I don't think that Ubuntu will do anything different than any other > Linux. > > >> > > >> Did you compile Open MPI on your own, or did you install any > repository? > > >> > > >> Are the CUDA application written by yourself or any freely available > > >> applications? > > >> > > >> - -- Reuti > > >> > > >> > > >>> and instead added a new file containing the library path > > >> /opt/openmpi/openmpi-2.1.0/lib to /etc/ld.so.conf.d/openmpi-2-1- > 0.conf, > > >> in the style of everything else in that directory. > > >>> > > >>> I tried to run "mpicc helloworld.c -o hello.bin" as a test on a demo > > >> file (as instructed in the link) to check the installation but I had > > >> permission issues, since it was installed win opt. However, when I > > >> attempted to run the previous with sudo, or sudo -E, in both cases, > mpicc > > >> could not be found. (Perhaps this is a separate issue with my sudo > env) > > >>> > > >>> To check that mpicc actually works, I have copied helloworld.c to a > > >> directory where I could execute mpicc without sudo. On running the > above > > >> command, I receive the following error: > > >>> > > >>> mpicc: /usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1: > no > > >> version information available (required by /opt/openmpi/openmpi-2.1.0/ > > >> lib/libopen-pal.so.20) > > >>> /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20: undefined > reference > > >> to `clGetPlatformInfo@OPENCL_1.0' > > >>> /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20: undefined > reference > > >> to `clGetPlatformIDs@OPENCL_1.0' > > >>> /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20: undefined > reference > > >> to `clGetDeviceInfo@OPENCL_1.0' > > >>> /opt/openmpi/openmpi-2.1.0/lib/libopen-pal.so.20: undefined > reference > > >> to `clGetDeviceIDs@OPENCL_1.0' > > >>> collect2: error: ld returned 1 exit status > > >>> > > >>> I am unsure if I have an installation or permission issues, and I'd > be > > >> grateful if anyone can shed some light based on the trials I've done > so > > >> far. (I should add I also have a CUDA installation, which I'd like to > > >> leverage too, if possible). I'm still fairly new to the ins and outs > of > > >> this, so I may have missed something obvious. Please let me know if > any > > >> other info is required. > > >>> > > >>> Many thanks and kind regards, > > >>> Tim > > >>> > > >>> -- > > >>> > > >>> Timothy Jim > > >>> PhD Researcher in Aerospace > > >>> Creative Flow Research Division, > > >>> Institute of Fluid Science, Tohoku University > > >>> www.linkedin.com/in/timjim/ > > >>> _______________________________________________ > > >>> users mailing list > > >>> users@lists.open-mpi.org > > >>> https://rfd.newmexicoconsortium.org/mailman/listinfo/users > > >> > > >> -----BEGIN PGP SIGNATURE----- > > >> Comment: GPGTools - https://gpgtools.org > > >> > > >> iEYEARECAAYFAlkiDKIACgkQo/GbGkBRnRou3wCeNztodNKHRxXBAp5ylz041OMP > > >> RIwAoLWkjzK1Qr8eWle/PdZGVUsvdN1M > > >> =R6up > > >> -----END PGP SIGNATURE----- > > >> _______________________________________________ > > >> users mailing list > > >> users@lists.open-mpi.org > > >> https://rfd.newmexicoconsortium.org/mailman/listinfo/users > > >> > > > > > > > > > > > > -- > > > > > > > > > *Timothy Jim**PhD Researcher in Aerospace* > > > > > > Creative Flow Research Division, > > > Institute of Fluid Science, Tohoku University > > > > > > www.linkedin.com/in/timjim/ > > > _______________________________________________ > > > users mailing list > > > users@lists.open-mpi.org > > > https://rfd.newmexicoconsortium.org/mailman/listinfo/users > > > > _______________________________________________ > > users mailing list > > users@lists.open-mpi.org > > https://rfd.newmexicoconsortium.org/mailman/listinfo/users > > > > > > > > -- > > > > Timothy Jim > > PhD Researcher in Aerospace > > Creative Flow Research Division, > > Institute of Fluid Science, Tohoku University > > www.linkedin.com/in/timjim/ > > _______________________________________________ > > users mailing list > > users@lists.open-mpi.org > > https://rfd.newmexicoconsortium.org/mailman/listinfo/users > > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://rfd.newmexicoconsortium.org/mailman/listinfo/users >
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