Dear John, I see, thank you for your reply. Unfortunately the cluster support is of poor quality, and it would take a while to get this information from them. Is there any way in which I can check this by myself? Also, it looks like ibv_devinfo does not exist on the cluster
$ ibv_devinfo -bash: ibv_devinfo: command not found Best, Michele On Oct 9, 2018, at 5:53 PM, John Hearns <hear...@googlemail.com<mailto:hear...@googlemail.com>> wrote: Michele, as other have said libibverbs.so.1 is not in your library path. Can you ask the person who manages yoru cluster where libibverbs is located on the compute nodes? Also try to run ibv_devinfo On Tue, 9 Oct 2018 at 16:03, Castellana Michele <michele.castell...@curie.fr<mailto:michele.castell...@curie.fr>> wrote: Dear John, Thank you for your reply. Here is the output of ldd $ ldd ./code.io<http://code.io> linux-vdso.so.1 => (0x00007ffcc759f000) liblapack.so.3 => /usr/lib64/liblapack.so.3 (0x00007fbc1c613000) libgsl.so.0 => /usr/lib64/libgsl.so.0 (0x00007fbc1c1ea000) libgslcblas.so.0 => /usr/lib64/libgslcblas.so.0 (0x00007fbc1bfad000) libmpi.so.40 => /data/users/xx/openmpi/lib/libmpi.so.40 (0x00007fbc1bcad000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fbc1b9a6000) libm.so.6 => /usr/lib64/libm.so.6 (0x00007fbc1b6a4000) libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x00007fbc1b48e000) libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00007fbc1b272000) libc.so.6 => /usr/lib64/libc.so.6 (0x00007fbc1aea5000) libblas.so.3 => /usr/lib64/libblas.so.3 (0x00007fbc1ac4c000) libgfortran.so.3 => /usr/lib64/libgfortran.so.3 (0x00007fbc1a92a000) libsatlas.so.3 => /usr/lib64/atlas/libsatlas.so.3 (0x00007fbc19cdd000) libopen-rte.so.40 => /data/users/xx/openmpi/lib/libopen-rte.so.40 (0x00007fbc19a2d000) libopen-pal.so.40 => /data/users/xx/openmpi/lib/libopen-pal.so.40 (0x00007fbc19733000) libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007fbc1952f000) librt.so.1 => /usr/lib64/librt.so.1 (0x00007fbc19327000) libutil.so.1 => /usr/lib64/libutil.so.1 (0x00007fbc19124000) libz.so.1 => /usr/lib64/libz.so.1 (0x00007fbc18f0e000) /lib64/ld-linux-x86-64.so.2 (0x00007fbc1cd70000) libquadmath.so.0 => /usr/lib64/libquadmath.so.0 (0x00007fbc18cd2000) and the one for the PBS version $ qstat --version Version: 6.1.2 Commit: 661e092552de43a785c15d39a3634a541d86898e After I created the symbolic links libcrypto.so.0.9.8 libssl.so.0.9.8, I still have one error message left from MPI: mca_base_component_repository_open: unable to open mca_btl_openib: libibverbs.so.1: cannot open shared object file: No such file or directory (ignored) Please let me know if you have any suggestions. Best, On Oct 4, 2018, at 3:12 PM, John Hearns via users <users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>> wrote: Michele, the command is ldd ./code.io<http://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<mailto: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<mailto: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<http://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<http://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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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
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