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
