-----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----- iF0EARECAB0WIQST3OUUqPn4dxGCSm6Zv6Bp0RyxvgUCXGkdJQAKCRCZv6Bp0Ryx vvO3AKChC0/SZ74xeY95WjYEgFhVz+bXlACfYZWEKe4ZDbbbafGAcCuMF04yIgs= =6QM1 -----END PGP SIGNATURE----- _______________________________________________ users mailing list users@lists.open-mpi.org https://lists.open-mpi.org/mailman/listinfo/users
