Ryan, What filesystem are you running on ?
Open MPI defaults to the ompio component, except on Lustre filesystem where ROMIO is used. (if the issue is related to ROMIO, that can explain why you did not see any difference, in that case, you might want to try an other filesystem (local filesystem or NFS for example)\ Cheers, Gilles On Sun, Feb 17, 2019 at 3:08 AM Ryan Novosielski <novos...@rutgers.edu> wrote: > > I verified that it makes it through to a bash prompt, but I’m a little less > confident that something make test does doesn’t clear it. Any recommendation > for a way to verify? > > In any case, no change, unfortunately. > > Sent from my iPhone > > > On Feb 16, 2019, at 08:13, Gabriel, Edgar <egabr...@central.uh.edu> wrote: > > > > What file system are you running on? > > > > I will look into this, but it might be later next week. I just wanted to > > emphasize that we are regularly running the parallel hdf5 tests with ompio, > > and I am not aware of any outstanding items that do not work (and are > > supposed to work). That being said, I run the tests manually, and not the > > 'make test' commands. Will have to check which tests are being run by that. > > > > Edgar > > > >> -----Original Message----- > >> From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Gilles > >> Gouaillardet > >> Sent: Saturday, February 16, 2019 1:49 AM > >> To: Open MPI Users <users@lists.open-mpi.org> > >> Subject: Re: [OMPI users] HDF5 1.10.4 "make check" problems w/OpenMPI > >> 3.1.3 > >> > >> 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 > > _______________________________________________ > > users mailing list > > users@lists.open-mpi.org > > https://lists.open-mpi.org/mailman/listinfo/users > _______________________________________________ > users mailing list > users@lists.open-mpi.org > https://lists.open-mpi.org/mailman/listinfo/users _______________________________________________ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
