FYI, Just noticed this post from the hdf group:
https://forum.hdfgroup.org/t/hdf5-and-openmpi/5437
/Peter K
pgpmcS_mBlpzB.pgp
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> On Feb 20, 2019, at 7:14 PM, Gilles Gouaillardet wrote:
>
> Ryan,
>
> That being said, the "Alarm clock" message looks a bit suspicious.
>
> Does it always occur at 20+ minutes elapsed ?
>
> Is there some mechanism that automatically kills a job if it does not write
> anything to stdout
ailto:users-boun...@lists.open-mpi.org] On Behalf Of Ryan
>> Novosielski
>> Sent: Thursday, February 21, 2019 1:59 PM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] HDF5 1.10.4 "make check" problems w/OpenMPI
>> 3.1.3
>>
>>
>>
nt: Thursday, February 21, 2019 1:59 PM
> To: Open MPI Users
> Subject: Re: [OMPI users] HDF5 1.10.4 "make check" problems w/OpenMPI
> 3.1.3
>
>
> > On Feb 21, 2019, at 2:52 PM, Gabriel, Edgar
> wrote:
> >
> >> -Original Message-
> >
> On Feb 21, 2019, at 2:52 PM, Gabriel, Edgar wrote:
>
>> -Original Message-
>>> Does it always occur at 20+ minutes elapsed ?
>>
>> Aha! Yes, you are right: every time it fails, it’s at the 20 minute and a
>> couple
>> of seconds mark. For comparison, every time it runs, it runs for
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
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
lists.open-mpi.org] On Behalf Of
Gabriel, Edgar
Sent: Sunday, February 17, 2019 10:34 AM
To: Open MPI Users
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 s
gt;
> btl = tcp,self
>
>
>
> Thanks
> Edgar
>
>
>
>> -Original Message-
>> From: users [mailto:users-boun...@lists.open-mpi.org] On Behalf Of Ryan
>> Novosielski
>> Sent: Wednesday, February 20, 2019 12:02 PM
>> To: Open MPI Users
>>
s.open-mpi.org] On Behalf Of Ryan
> Novosielski
> Sent: Wednesday, February 20, 2019 12:02 PM
> To: Open MPI Users
> Subject: Re: [OMPI users] HDF5 1.10.4 "make check" problems w/OpenMPI
> 3.1.3
>
> Does it make any sense that it seems to work fine when OpenMPI and HDF5
gt;> 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
>>> Su
: Sunday, February 17, 2019 10:34 AM
To: Open MPI Users
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
; 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
>> Subject: Re: [OMPI users] HDF5 1.10.4 &qu
pi.org] On Behalf Of
> Gabriel, Edgar
> Sent: Sunday, February 17, 2019 10:34 AM
> To: Open MPI Users
> 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
>
f 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 XF
t'
>>> 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 Gouailla
k 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
> >
Gouaillardet
>> Sent: Saturday, February 16, 2019 1:49 AM
>> To: Open MPI Users
>> Subject: Re: [OMPI users] HDF5 1.10.4 "make check" problems w/OpenMPI
>> 3.1.3
>>
>> Ryan,
>>
>> Can you
>>
>> export OMPI_MCA_io=^omp
t; To: Open MPI Users
> 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 MP
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,
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
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