Hi, I tried as you suggested: export nvml_enable=no, then reconfigured and ran make all install again, but mpicc is still producing the same error. What should I try next?
Many thanks, Tim On 21 September 2017 at 16:12, Gilles Gouaillardet <gil...@rist.or.jp> wrote: > Tim, > > > do that in your shell, right before invoking configure. > > export nvml_enable=no > > ./configure ... > > make && make install > > > you can keep the --without-cuda flag (i think this is unrelated though) > > > Cheers, > > Gilles > > On 9/21/2017 3:54 PM, Tim Jim wrote: > >> Dear Gilles, >> >> Thanks for the mail - where should I set export nvml_enable=no? Should I >> reconfigure with default cuda support or keep the --without-cuda flag? >> >> Kind regards, >> Tim >> >> On 21 September 2017 at 15:22, Gilles Gouaillardet <gil...@rist.or.jp >> <mailto:gil...@rist.or.jp>> wrote: >> >> Tim, >> >> >> i am not familiar with CUDA, but that might help >> >> can you please >> >> export nvml_enable=no >> >> and then re-configure and rebuild Open MPI ? >> >> >> i hope this will help you >> >> >> Cheers, >> >> >> Gilles >> >> >> >> On 9/21/2017 3:04 PM, Tim Jim wrote: >> >> Hello, >> >> Apologies to bring up this old thread - I finally had a chance >> to try again with openmpi but I am still have trouble getting >> it to run. I downloaded version 3.0.0 hoping it would solve >> some of the problems but on running mpicc for the previous >> test case, I am still getting an undefined reference error. I >> did as you suggested and also configured it to install without >> cuda using >> >> ./configure --without-cuda --prefix=/opt/openmpi/openmpi-3.0.0 >> >> and at the end of the summary, CUDA support shows 'no'. >> Unfortunately, the error is still the same, and for some >> reason, mpicc still seems to have referenced my cuda targets. >> >> tjim@DESKTOP-TA3P0PS:~/Documents$ mpicc >> /opt/mpi4py/mpi4py_src/demo/helloworld.c -o hello.bin >> mpicc: >> /usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1: >> no version information available (required by >> /opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40) >> /opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40: undefined >> reference to `clGetPlatformInfo@OPENCL_1.0' >> /opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40: undefined >> reference to `clGetPlatformIDs@OPENCL_1.0' >> /opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40: undefined >> reference to `clGetDeviceInfo@OPENCL_1.0' >> /opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40: undefined >> reference to `clGetDeviceIDs@OPENCL_1.0' >> collect2: error: ld returned 1 exit status >> >> I also attempted to test mpirun, as suggested in the readme, >> however I get the following problem: >> >> tjim@DESKTOP-TA3P0PS:~/Documents$ mpirun >> /opt/openmpi/openmpi-3.0.0_src/examples/hello_c.c >> mpirun: >> /usr/local/cuda-8.0/targets/x86_64-linux/lib/libOpenCL.so.1: >> no version information available (required by >> /opt/openmpi/openmpi-3.0.0/lib/libopen-pal.so.40) >> ------------------------------------------------------------ >> -------------- >> Open MPI tried to fork a new process via the "execve" system >> call but >> failed. Open MPI checks many things before attempting to launch a >> child process, but nothing is perfect. This error may be >> indicative >> of another problem on the target host, or even something as >> silly as >> having specified a directory for your application. Your job >> will now >> abort. >> >> Local host: DESKTOP-TA3P0PS >> Working dir: /home/tjim/Documents >> Application name: >> /opt/openmpi/openmpi-3.0.0_src/examples/hello_c.c >> Error: Exec format error >> ------------------------------------------------------------ >> -------------- >> ------------------------------------------------------------ >> -------------- >> mpirun was unable to start the specified application as it >> encountered an >> error: >> >> Error code: 1 >> Error name: (null) >> Node: DESKTOP-TA3P0PS >> >> when attempting to start process rank 0. >> ------------------------------------------------------------ >> -------------- >> 4 total processes failed to start >> [DESKTOP-TA3P0PS:15231] 3 more processes have sent help >> message help-orte-odls-default.txt / execve error >> [DESKTOP-TA3P0PS:15231] Set MCA parameter >> "orte_base_help_aggregate" to 0 to see all help / error messages >> >> >> Do you have any suggestions to what might have gone wrong on >> this install? I'm not sure if this thread is still alive, so >> if you need a refresh on the situation/any more info, please >> let me know. >> Kind regards, >> Tim >> >> On 24 May 2017 at 09:12, Tim Jim <timothy.m....@gmail.com >> <mailto:timothy.m....@gmail.com> >> <mailto:timothy.m....@gmail.com >> <mailto:timothy.m....@gmail.com>>> wrote: >> >> 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 >> <mailto:re...@staff.uni-marburg.de> >> <mailto:re...@staff.uni-marburg.de >> <mailto: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 <mailto:re...@staff.uni-marburg.de> >> <mailto:re...@staff.uni-marburg.de >> <mailto:re...@staff.uni-marburg.de>>> wrote: >> > Hi, >> > >> > > Am 22.05.2017 um 07:22 schrieb Tim Jim >> <timothy.m....@gmail.com >> <mailto:timothy.m....@gmail.com> >> <mailto:timothy.m....@gmail.com >> >> <mailto: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 <mailto:re...@staff.uni-marburg.de> >> <mailto:re...@staff.uni-marburg.de >> >> <mailto: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- >> <https://bitbucket.org/mpi4py/mpi4py/issues/69/building-> >> >> <https://bitbucket.org/mpi4py/mpi4py/issues/69/building- >> <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/ >> <http://www.linkedin.com/in/timjim/> >> <http://www.linkedin.com/in/timjim/ >> <http://www.linkedin.com/in/timjim/>> >> > >>> _______________________________________________ >> > >>> users mailing list >> > >>> users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org> >> <mailto:users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org>> >> > >>> >> https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users> >> >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <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 >> <mailto:users@lists.open-mpi.org> >> <mailto:users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org>> >> > >> >> https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users> >> >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <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/ >> <http://www.linkedin.com/in/timjim/> >> <http://www.linkedin.com/in/timjim/ >> <http://www.linkedin.com/in/timjim/>> >> > > _______________________________________________ >> > > users mailing list >> > > users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org> >> <mailto:users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org>> >> > > >> https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users> >> >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users>> >> > >> > _______________________________________________ >> > users mailing list >> > users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org> >> <mailto:users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org>> >> > >> https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users> >> >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <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/ >> <http://www.linkedin.com/in/timjim/> >> <http://www.linkedin.com/in/timjim/ >> <http://www.linkedin.com/in/timjim/>> >> > _______________________________________________ >> > users mailing list >> > users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org> >> <mailto:users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org>> >> > >> https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users> >> >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users>> >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> <mailto:users@lists.open-mpi.org >> <mailto:users@lists.open-mpi.org>> >> https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users> >> >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users >> <https://rfd.newmexicoconsortium.org/mailman/listinfo/users>> >> >> >> >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users> >> >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org <mailto:users@lists.open-mpi.org> >> https://lists.open-mpi.org/mailman/listinfo/users >> <https://lists.open-mpi.org/mailman/listinfo/users> >> >> >> >> >> _______________________________________________ >> users mailing list >> users@lists.open-mpi.org >> https://lists.open-mpi.org/mailman/listinfo/users >> > > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.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/
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