Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-11 Thread Jeff Squyres (jsquyres) via users
If you don't have ibv_devinfo installed on your compute nodes, then you likely don't have the verbs package installed at all on your compute nodes. That's why you're getting errors about not finding libibverbs.so. Specifically: - It sounds like Open MPI was able to find libibverbs.so when it

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-10 Thread Bennet Fauber
There is a linux utility program `locate` that may be installed on your system. You could try $ locate ibv_devinfo Thus, mine returns $ locate ibv_devinfo /usr/bin/ibv_devinfo /usr/share/man/man1/ibv_devinfo.1.gz That should find it if it is on local disk and not in a network filesystem, and

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-10 Thread Castellana Michele
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

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-09 Thread John Hearns via users
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 runibv_devinfo On Tue, 9 Oct 2018 at 16:03, Castellana Michele wrote: > > Dear John, > Thank you for your

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-09 Thread Castellana Michele
Dear John, Thank you for your reply. Here is the output of ldd $ ldd ./code.io linux-vdso.so.1 => (0x7ffcc759f000) liblapack.so.3 => /usr/lib64/liblapack.so.3 (0x7fbc1c613000) libgsl.so.0 => /usr/lib64/libgsl.so.0 (0x7fbc1c1ea000) libgslcblas.so.0 =>

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-04 Thread Jeff Squyres (jsquyres) via users
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

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-04 Thread John Hearns via users
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 wrote: > > Dear John, > Thank you for your reply. I have

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-04 Thread Castellana Michele
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

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-04 Thread Gilles Gouaillardet
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 /lib/openmpi in order to evidence any issue. Cheers, Gilles On Thu, Oct 4, 2018 at 4:34 PM John Hearns via users wrote: > > Michele one tip:

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-04 Thread John Hearns via users
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

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-03 Thread Castellana Michele
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 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

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-03 Thread Castellana Michele
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.

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-03 Thread Jeff Squyres (jsquyres) via users
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 > wrote: > > Dear Ralph, > Thank you for your reply. Do you know where I could find libcrypto.so.0.9.8 ?

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-03 Thread Castellana Michele
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 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

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-03 Thread Ralph H Castain
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 wrote: > > Did you configure OMPI —with-tm=? It looks like we didn’t > build PBS support and so we

Re: [OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-03 Thread Ralph H Castain
Did you configure OMPI —with-tm=? 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 > wrote: > > Dear all, > I am having trouble running an MPI code across multiple cores on a new >

[OMPI users] Cannot run MPI code on multiple cores with PBS

2018-10-03 Thread Castellana Michele
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