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
