It didn’t work any better with XFS, as it happens. Must be something else. I’m going to test some more and see if I can narrow it down any, as it seems to me that it did work with a different compiler.
--
____
|| \\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
`'
> On Feb 18, 2019, at 12:23 PM, Gabriel, Edgar <egabr...@central.uh.edu> wrote:
>
> While I was working on something else, I let the tests run with Open MPI
> master (which is for parallel I/O equivalent to the upcoming v4.0.1
> release), and here is what I found for the HDF5 1.10.4 tests on my local
> desktop:
>
> In the testpar directory, there is in fact one test that fails for both ompio
> and romio321 in exactly the same manner.
> I used 6 processes as you did (although I used mpirun directly instead of
> srun...) From the 13 tests in the testpar directory, 12 pass correctly
> (t_bigio, t_cache, t_cache_image, testphdf5, t_filters_parallel, t_init_term,
> t_mpi, t_pflush2, t_pread, t_prestart, t_pshutdown, t_shapesame).
>
> The one tests that officially fails ( t_pflush1) actually reports that it
> passed, but then throws message that indicates that MPI_Abort has been
> called, for both ompio and romio. I will try to investigate this test to see
> what is going on.
>
> That being said, your report shows an issue in t_mpi, which passes without
> problems for me. This is however not GPFS, this was an XFS local file system.
> Running the tests on GPFS are on my todo list as well.
>
> Thanks
> Edgar
>
>
>
>> -----Original Message-----
>> From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of
>> Gabriel, Edgar
>> Sent: Sunday, February 17, 2019 10:34 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
>>
>> 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 `'
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>>>
>>> - --
>>> ____
>>> || \\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
>>> `'
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