Note that what Gilles said is correct: it's not just the dependent libraries of libmpi.so (and friends) that matter -- it's also the dependent libraries of all of Open MPI's plugins that matter.
You can run "ldd *.so" in the lib directory where you installed Open MPI, but you'll also need to "ldd *.so" in the lib/openmpi directory -- that's where Open MPI installs its plugins. I suspect that if you run "ldd lib/openmpi/mca_plm_tm.so" on the head node, you'll see all the dependent libraries listed. But if you run the same command on your back-end compute nodes, it might say "not found" for some of the libraries. > On Oct 4, 2018, at 9:12 AM, John Hearns via users <users@lists.open-mpi.org> > wrote: > > Michele, the command is ldd ./code.io > I just Googled - ldd means List dynamic Dependencies > > To find out the PBS batch system type - that is a good question! > Try this: qstat --version > > > > On Thu, 4 Oct 2018 at 10:12, Castellana Michele > <michele.castell...@curie.fr> wrote: >> >> Dear John, >> Thank you for your reply. I have tried >> >> ldd mpirun ./code.o >> >> but I get an error message, I do not know what is the proper syntax to use >> ldd command. Here is the information about the Linux version >> >> $ cat /etc/os-release >> NAME="CentOS Linux" >> VERSION="7 (Core)" >> ID="centos" >> ID_LIKE="rhel fedora" >> VERSION_ID="7" >> PRETTY_NAME="CentOS Linux 7 (Core)" >> ANSI_COLOR="0;31" >> CPE_NAME="cpe:/o:centos:centos:7" >> HOME_URL="https://www.centos.org/"; >> BUG_REPORT_URL="https://bugs.centos.org/"; >> >> CENTOS_MANTISBT_PROJECT="CentOS-7" >> CENTOS_MANTISBT_PROJECT_VERSION="7" >> REDHAT_SUPPORT_PRODUCT="centos" >> REDHAT_SUPPORT_PRODUCT_VERSION=“7" >> >> May you please tell me how to check whether the batch system is PBSPro or >> OpenPBS? >> >> Best, >> >> >> >> >> On Oct 4, 2018, at 10:30 AM, John Hearns via users >> <users@lists.open-mpi.org> wrote: >> >> Michele one tip: log into a compute node using ssh and as your own >> username. >> If you use the Modules envirnonment then load the modules you use in >> the job script >> then use the ldd utility to check if you can load all the libraries >> in the code.io executable >> >> Actually you are better to submit a short batch job which does not use >> mpirun but uses ldd >> A proper batch job will duplicate the environment you wish to run in. >> >> ldd ./code.io >> >> By the way, is the batch system PBSPro or OpenPBS? Version 6 seems a bit >> old. >> Can you say what version of Redhat or CentOS this cluster is installed with? >> >> >> >> On Thu, 4 Oct 2018 at 00:02, Castellana Michele >> <michele.castell...@curie.fr> wrote: >> >> I fixed it, the correct file was in /lib64, not in /lib. >> >> Thank you for your help. >> >> On Oct 3, 2018, at 11:30 PM, Castellana Michele >> <michele.castell...@curie.fr> wrote: >> >> Thank you, I found some libcrypto files in /usr/lib indeed: >> >> $ ls libcry* >> libcrypt-2.17.so libcrypto.so.10 libcrypto.so.1.0.2k libcrypt.so.1 >> >> but I could not find libcrypto.so.0.9.8. Here they suggest to create a >> hyperlink, but if I do I still get an error from MPI. Is there another way >> around this? >> >> Best, >> >> On Oct 3, 2018, at 11:00 PM, Jeff Squyres (jsquyres) via users >> <users@lists.open-mpi.org> wrote: >> >> It's probably in your Linux distro somewhere -- I'd guess you're missing a >> package (e.g., an RPM or a deb) out on your compute nodes...? >> >> >> On Oct 3, 2018, at 4:24 PM, Castellana Michele <michele.castell...@curie.fr> >> wrote: >> >> Dear Ralph, >> Thank you for your reply. Do you know where I could find libcrypto.so.0.9.8 ? >> >> Best, >> >> On Oct 3, 2018, at 9:41 PM, Ralph H Castain <r...@open-mpi.org> wrote: >> >> Actually, I see that you do have the tm components built, but they cannot be >> loaded because you are missing libcrypto from your LD_LIBRARY_PATH >> >> >> On Oct 3, 2018, at 12:33 PM, Ralph H Castain <r...@open-mpi.org> wrote: >> >> Did you configure OMPI —with-tm=<path-to-PBS-libs>? It looks like we didn’t >> build PBS support and so we only see one node with a single slot allocated >> to it. >> >> >> On Oct 3, 2018, at 12:02 PM, Castellana Michele >> <michele.castell...@curie.fr> wrote: >> >> Dear all, >> I am having trouble running an MPI code across multiple cores on a new >> computer cluster, which uses PBS. Here is a minimal example, where I want to >> run two MPI processes, each on a different node. The PBS script is >> >> #!/bin/bash >> #PBS -l walltime=00:01:00 >> #PBS -l mem=1gb >> #PBS -l nodes=2:ppn=1 >> #PBS -q batch >> #PBS -N test >> mpirun -np 2 ./code.o >> >> and when I submit it with >> >> $qsub script.sh >> >> I get the following message in the PBS error file >> >> $ cat test.e1234 >> [shbli040:08879] mca_base_component_repository_open: unable to open >> mca_plm_tm: libcrypto.so.0.9.8: cannot open shared object file: No such file >> or directory (ignored) >> [shbli040:08879] mca_base_component_repository_open: unable to open >> mca_oob_ud: libibverbs.so.1: cannot open shared object file: No such file or >> directory (ignored) >> [shbli040:08879] mca_base_component_repository_open: unable to open >> mca_ras_tm: libcrypto.so.0.9.8: cannot open shared object file: No such file >> or directory (ignored) >> -------------------------------------------------------------------------- >> There are not enough slots available in the system to satisfy the 2 slots >> that were requested by the application: >> ./code.o >> >> Either request fewer slots for your application, or make more slots available >> for use. >> ————————————————————————————————————— >> >> The PBS version is >> >> $ qstat --version >> Version: 6.1.2 >> >> and here is some additional information on the MPI version >> >> $ mpicc -v >> Using built-in specs. >> COLLECT_GCC=/bin/gcc >> COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper >> Target: x86_64-redhat-linux >> […] >> Thread model: posix >> gcc version 4.8.5 20150623 (Red Hat 4.8.5-28) (GCC) >> >> Do you guys know what may be the issue here? >> >> Thank you >> Best, >> >> >> >> >> >> >> >> _______________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 >> >> >> >> -- >> Jeff Squyres >> jsquy...@cisco.com >> >> _______________________________________________ >> 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 >> >> >> _______________________________________________ >> 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 >> >> _______________________________________________ >> 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 -- Jeff Squyres jsquy...@cisco.com _______________________________________________ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
