HI Aziz, Oh I see you referenced the faq. That section of the faq is discussing how to make the Open MPI 4 series (and older) job launcher “know” about the batch scheduler you are using. The relevant section for launching with srun is covered by this faq - https://www-lb.open-mpi.org/faq/?category=slurm
Howard From: "Pritchard Jr., Howard" <howa...@lanl.gov> Date: Tuesday, July 25, 2023 at 8:26 AM To: Open MPI Users <users@lists.open-mpi.org> Cc: Aziz Ogutlu <aziz.ogu...@eduline.com.tr> Subject: Re: [EXTERNAL] Re: [OMPI users] MPI_Init_thread error HI Aziz, Did you include –with-pmi2 on your Open MPI configure line? Howard From: users <users-boun...@lists.open-mpi.org> on behalf of Aziz Ogutlu via users <users@lists.open-mpi.org> Organization: Eduline Bilisim Reply-To: Open MPI Users <users@lists.open-mpi.org> Date: Tuesday, July 25, 2023 at 8:18 AM To: Open MPI Users <users@lists.open-mpi.org> Cc: Aziz Ogutlu <aziz.ogu...@eduline.com.tr> Subject: [EXTERNAL] Re: [OMPI users] MPI_Init_thread error Hi Gilles, Thank you for your response. When I run srun --mpi=list, I get only pmi2. When I run command with --mpi=pmi2 parameter, I got same error. OpenMPI automatically support slurm after 4.x version. https://www.open-mpi.org/faq/?category=building#build-rte<https://urldefense.com/v3/__https:/www.open-mpi.org/faq/?category=building*build-rte__;Iw!!Bt8fGhp8LhKGRg!DNaoJu7zrmKRHUF76zzyFXi9n2Bq8K8Ud-yvTEIkUYtxz_1_2DFwrZAKofSbiBD1rhLyttDpQVrl12eaQ2CN$> On 7/25/23 12:55, Gilles Gouaillardet via users wrote: Aziz, When using direct run (e.g. srun), OpenMPI has to interact with SLURM. This is typically achieved via PMI2 or PMIx You can srun --mpi=list to list the available options on your system if PMIx is available, you can srun --mpi=pmix ... if only PMI2 is available, you need to make sure Open MPI was built with SLURM support (e.g. configure --with-slurm ...) and then srun --mpi=pmi2 ... Cheers, Gilles On Tue, Jul 25, 2023 at 5:07 PM Aziz Ogutlu via users <users@lists.open-mpi.org<mailto:users@lists.open-mpi.org>> wrote: Hi there all, We're using Slurm 21.08 on Redhat 7.9 HPC cluster with OpenMPI 4.0.3 + gcc 8.5.0. When we run command below for call SU2, we get an error message: $ srun -p defq --nodes=1 --ntasks-per-node=1 --time=01:00:00 --pty bash -i $ module load su2/7.5.1 $ SU2_CFD config.cfg *** An error occurred in MPI_Init_thread *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [cnode003.hpc:17534] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! -- Best regards, Aziz Öğütlü Eduline Bilişim Sanayi ve Ticaret Ltd. Şti. www.eduline.com.tr<https://urldefense.com/v3/__http:/www.eduline.com.tr__;!!Bt8fGhp8LhKGRg!DNaoJu7zrmKRHUF76zzyFXi9n2Bq8K8Ud-yvTEIkUYtxz_1_2DFwrZAKofSbiBD1rhLyttDpQVrl1wUXbUrh$> Merkez Mah. Ayazma Cad. No:37 Papirus Plaza Kat:6 Ofis No:118 Kağıthane - İstanbul - Türkiye 34406 Tel : +90 212 324 60 61 Cep: +90 541 350 40 72 -- İyi çalışmalar, Aziz Öğütlü Eduline Bilişim Sanayi ve Ticaret Ltd. Şti. www.eduline.com.tr<https://urldefense.com/v3/__http:/www.eduline.com.tr__;!!Bt8fGhp8LhKGRg!DNaoJu7zrmKRHUF76zzyFXi9n2Bq8K8Ud-yvTEIkUYtxz_1_2DFwrZAKofSbiBD1rhLyttDpQVrl1wUXbUrh$> Merkez Mah. Ayazma Cad. No:37 Papirus Plaza Kat:6 Ofis No:118 Kağıthane - İstanbul - Türkiye 34406 Tel : +90 212 324 60 61 Cep: +90 541 350 40 72
