In this case, some Open MPI plugins are missing some third party libraries, so you would have to ldd all the plugins (e.g. the .so files) located in <prefix>/lib/openmpi in order to evidence any issue.
Cheers, Gilles On Thu, Oct 4, 2018 at 4:34 PM 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
