Hi all, We're using EasyBuild 4.0.0 on a Centos 7 + Slurm 19.05 system. We're able to build and use 'foss-2019a' EasyBuild toolchain (which includes OpenMPI 3.1.3) using the libpmi2 provided by the Slurm folks (by uncommenting "configopts = '--with-slurm --with-pmi" in OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb). However, when trying to build R 3.6.0 and Rmpi with that toolchain we get:
... ** building package indices ** testing if installed package can be loaded from temporary location -------------------------------------------------------------------------- PMI2_Init failed to intialize. Return code: 14 -------------------------------------------------------------------------- -------------------------------------------------------------------------- The application appears to have been direct launched using "srun", but OMPI was not built with SLURM's PMI support and therefore cannot execute. There are several options for building PMI support under SLURM, depending upon the SLURM version you are using: version 16.05 or later: you can use SLURM's PMIx support. This requires that you configure and build SLURM --with-pmix. Versions earlier than 16.05: you must use either SLURM's PMI-1 or PMI-2 support. SLURM builds PMI-1 by default, or you can manually install PMI-2. You must then build Open MPI using --with-pmi pointing to the SLURM PMI library location. Please configure as appropriate and try again. -------------------------------------------------------------------------- *** An error occurred in MPI_Init *** on a NULL communicator *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, *** and potentially your MPI job) [bessemer-node019.shef.ac.uk:199102] 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! ERROR: loading failed ... We also see a similar error when trying to build GROMACS 19.3. We have 'MpiDefault=pmi2' in our Slurm config; interestingly if we override this with '--mpi=openmpi' (e.g. use "srun -A cstest --mpi=openmpi --cpus-per-task=4 --pty /bin/bash -i" to give me an interactive session then run eb from there) then EasyBuild's able to build Rmpi. However, I'm curious to know how/why we can't use pmi2 here. Anyone got any thoughts? Apologies if you think this query should have been posted to the Slurm users list instead; I thought I'd ask on here first in case anyone's encountered anything similar when using OpenMPI and R easyconfigs/easyblocks. Regards, Will -- Dr Will Furnass | Research Software Engineering team Computer Science | University of Sheffield +44 (0) 114 22 21903 | https://rse.shef.ac.uk @willfurnass | https://learningpatterns.me --- Book a code clinic session: https://rse.shef.ac.uk/support/code-clinic/
