Ryan, Can you
export OMPI_MCA_io=^ompio and try again after you made sure this environment variable is passed by srun to the MPI tasks ? We have identified and fixed several issues specific to the (default) ompio component, so that could be a valid workaround until the next release. Cheers, Gilles Ryan Novosielski <novos...@rutgers.edu> wrote: >Hi there, > >Honestly don’t know which piece of this puzzle to look at or how to get more >information for troubleshooting. I successfully built HDF5 1.10.4 with RHEL >system GCC 4.8.5 and OpenMPI 3.1.3. Running the “make check” in HDF5 is >failing at the below point; I am using a value of RUNPARALLEL='srun --mpi=pmi2 >-p main -t 1:00:00 -n6 -N1’ and have a SLURM that’s otherwise properly >configured. > >Thanks for any help you can provide. > >make[4]: Entering directory >`/scratch/novosirj/install-files/hdf5-1.10.4-build-gcc-4.8-openmpi-3.1.3/testpar' >============================ >Testing t_mpi >============================ >t_mpi Test Log >============================ >srun: job 84126610 queued and waiting for resources >srun: job 84126610 has been allocated resources >srun: error: slepner023: tasks 0-5: Alarm clock >0.01user 0.00system 20:03.95elapsed 0%CPU (0avgtext+0avgdata 5152maxresident)k >0inputs+0outputs (0major+1529minor)pagefaults 0swaps >make[4]: *** [t_mpi.chkexe_] Error 1 >make[4]: Leaving directory >`/scratch/novosirj/install-files/hdf5-1.10.4-build-gcc-4.8-openmpi-3.1.3/testpar' >make[3]: *** [build-check-p] Error 1 >make[3]: Leaving directory >`/scratch/novosirj/install-files/hdf5-1.10.4-build-gcc-4.8-openmpi-3.1.3/testpar' >make[2]: *** [test] Error 2 >make[2]: Leaving directory >`/scratch/novosirj/install-files/hdf5-1.10.4-build-gcc-4.8-openmpi-3.1.3/testpar' >make[1]: *** [check-am] Error 2 >make[1]: Leaving directory >`/scratch/novosirj/install-files/hdf5-1.10.4-build-gcc-4.8-openmpi-3.1.3/testpar' >make: *** [check-recursive] Error 1 > >-- >____ >|| \\UTGERS, |---------------------------*O*--------------------------- >||_// the State | Ryan Novosielski - novos...@rutgers.edu >|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus >|| \\ of NJ | Office of Advanced Research Computing - MSB C630, >Newark > `' _______________________________________________ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
