Thomas, I think OpenMP is installed correctly. This
$ mpiexec -mca btl ^openib -N 5 gcc --version asks OpenMPI to run `gcc --version` once for each processor assigned to the job, so if you did NOT get 5 sets of output, it would be incorrect. >From your error error message, it looks to me as though you have multiple makers running fine, but they are all trying to do that same work, so one of them came to a bit of work that one of the others was either working on or had finished. This is typically the case when the program uses the same temporary directory for every running instance, in which case they are overwriting each other's files, or the way the job got specified, all the maker instances got the same input parameter, so they all have identical work lists. You need to have some way to tell each instance of maker which parts to work on and/or to specify a different temporary directory for each one to use. I hope that is of some help, -- bennet On Thu, Feb 18, 2021 at 7:41 AM Thomas Eylenbosch via users < users@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 > 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 > > > > > > > > >
