>From a quick look at the documentation, the Maker tool use mpich2 http://gmod.org/wiki/MAKER_Tutorial#Prerequisites
Should you not install mpich on your cluster? . Are you trying to use MPI to run multiple copies of the Maker tool? You would probably be better using SLurm srun or an array job https://slurm.schedmd.com/job_array.html On Thu, 18 Feb 2021 at 13:06, Joseph Schuchart via users < users@lists.open-mpi.org> wrote: > Thomas, > > The post you are referencing suggests to run > > mpiexec -mca btl ^openib -n 40 maker -help > > but you are running > > mpiexec -mca btl ^openib -N 5 gcc --version > > which will run 5 instances of GCC. The out put you're seeing is totally > to be expected. > > I don't think anyone here can help you with getting maker to work > correctly with MPI. I suggest you first check whether make is actually > configured to use MPI. The test using maker (as suggested in the post) > does not necessarily mean that Open MPI isn't working, it might also > happen if maker is not correctly configured. > > One way to check whether Open MPI is working correctly on your system is > to use a simple MPI program that prints the world communicator size and > rank. Any MPI hello world program you find online should do. > > Cheers > Joseph > > On 2/18/21 1:39 PM, Thomas Eylenbosch via users 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 > > >
