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
<[email protected]> 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 <[email protected]>
> 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
> <[email protected]> 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 <[email protected]>
> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]>
> 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,
>
>
>
>
>
>
>
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>
>
> --
> Jeff Squyres
> [email protected]
>
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