All
Thank you all your help and for the example. It seems openmpi is correctly installed like Gilles said $ mpiexec --mca btl ^openib -N 5 ./hello_c Hello, world, I am 0 of 5, (Open MPI v4.0.5, package: Open MPI easybu...@by0q5b.eu.seeds.basf.net Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 1 of 5, (Open MPI v4.0.5, package: Open MPI easybu...@by0q5b.eu.seeds.basf.net Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 3 of 5, (Open MPI v4.0.5, package: Open MPI easybu...@by0q5b.eu.seeds.basf.net Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 4 of 5, (Open MPI v4.0.5, package: Open MPI easybu...@by0q5b.eu.seeds.basf.net Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) Hello, world, I am 2 of 5, (Open MPI v4.0.5, package: Open MPI easybu...@by0q5b.eu.seeds.basf.net Distribution, ident: 4.0.5, repo rev: v4.0.5, Aug 26, 2020, 129) I will go back to the topic of maker where I will take a deeper look into the issue. Best regards / met vriendelijke groeten Thomas Eylenbosch DevOps Engineer (OnSite), Gluo N.V. Currently available at BASF Belgium Coordination Center CommV Email: thomas.eylenbo...@partners.basf.com Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium BASF Belgium Coordination Center CommV Scheldelaan 600, 2040 Antwerpen, België RPR Antwerpen (afd. Antwerpen) BTW BE0862.390.376 www.basf.be Deutsche Bank AG IBAN: BE43 8262 8044 4801 BIC: DEUTBEBE Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html From: devel <devel-boun...@lists.open-mpi.org> On Behalf Of Gilles Gouaillardet via devel Sent: Thursday, February 18, 2021 1:57 PM To: Open MPI Developers <devel@lists.open-mpi.org> Cc: Gilles Gouaillardet <gilles.gouaillar...@gmail.com> Subject: [EXT] Re: [OMPI devel] OpenMPI and maker - Multiple messages Thomas, in order to test Open MPI, you can download https://raw.githubusercontent.com/open-mpi/ompi/master/examples/hello_c.c and build it $ mpicc -o hello_c examples/hello_c.c and then run $ mpiexec --mca btl ^openib -N 5 ./hello_c It should display 5 different lines (rank 0 to 4 of 5). If you see the same line (I am 0 of 1) 5 times, this indicates an issue. Cheers, Gilles On Thu, Feb 11, 2021 at 12:36 AM Thomas Eylenbosch via devel <devel@lists.open-mpi.org<mailto:devel@lists.open-mpi.org>> wrote: Hello We are trying to run maker(http://www.yandell-lab.org/software/maker.html) in combination with OpenMPI But when we are trying to submit a job with the maker and openmpi, We see the following error in the log file: --Next Contig-- #--------------------------------------------------------------------- Another instance of maker is processing this contig!! SeqID: chrA10 Length: 17398227 #--------------------------------------------------------------------- According to http://gmod.827538.n3.nabble.com/Does-maker-support-muti-processing-for-a-single-long-fasta-sequence-using-openMPI-td4061342.html We have to run the following command mpiexec -mca btl ^openib -n 40 maker -help “If you get a single help message then everything is fine. If you get 40 help messages, then MPI is not communicating correctly.” We are using the following command to demonstrate what is going wrong: mpiexec -mca btl ^openib -N 5 gcc --version gcc (GCC) 10.2.0 Copyright (C) 2020 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. gcc (GCC) 10.2.0 Copyright (C) 2020 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. gcc (GCC) 10.2.0 Copyright (C) 2020 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. gcc (GCC) 10.2.0 Copyright (C) 2020 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. gcc (GCC) 10.2.0 Copyright (C) 2020 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. So we are getting the message 5 times, which means OpenMPI is not correctly installed on our cluster? We are using EasyBuild to build/install our OpenMPI module. ( with the default OpenMPI easyblock module) Best regards / met vriendelijke groeten Thomas Eylenbosch DevOps Engineer (OnSite), Gluo N.V. Currently available at BASF Belgium Coordination Center CommV Email: thomas.eylenbo...@partners.basf.com<mailto:thomas.eylenbo...@partners.basf.com> Postal Address: BASF Belgium Coordination Center CommV, Technologiepark 101, 9052 Gent Zwijnaarde, Belgium BASF Belgium Coordination Center CommV Scheldelaan 600, 2040 Antwerpen, België RPR Antwerpen (afd. Antwerpen) BTW BE0862.390.376 www.basf.be<http://www.basf.be> Deutsche Bank AG IBAN: BE43 8262 8044 4801 BIC: DEUTBEBE Information on data protection can be found here: https://www.basf.com/global/en/legal/data-protection-at-basf.html
