I will also run our testsuite and the HDF5 testsuite on GPFS, I have access to a GPFS file system since recently, and will report back on that, but it will take a few days.
Thanks Edgar > -----Original Message----- > From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Ryan > Novosielski > Sent: Sunday, February 17, 2019 2:37 AM > To: users@lists.open-mpi.org > Subject: Re: [OMPI users] HDF5 1.10.4 "make check" problems w/OpenMPI > 3.1.3 > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > This is on GPFS. I'll try it on XFS to see if it makes any difference. > > On 2/16/19 11:57 PM, Gilles Gouaillardet wrote: > > 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 > > > > - -- > ____ > || \\UTGERS, |----------------------*O*------------------------ > ||_// the State | Ryan Novosielski - novos...@rutgers.edu > || \\ University | Sr. Technologist - 973/972.0922 ~*~ RBHS Campus > || \\ of NJ | Office of Advanced Res. Comp. - MSB C630, Newark > `' > -----BEGIN PGP SIGNATURE----- > > iF0EARECAB0WIQST3OUUqPn4dxGCSm6Zv6Bp0RyxvgUCXGkdJQAKCRCZv6Bp > 0Ryx > vvO3AKChC0/SZ74xeY95WjYEgFhVz+bXlACfYZWEKe4ZDbbbafGAcCuMF04yIgs > = > =6QM1 > -----END PGP SIGNATURE----- > _______________________________________________ > 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
