-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf
Of Kóbori József
Sent: Wednesday, November 25, 2015 3:46 AM
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] unsupported data type
Hi Mohamad,
please found attached the output of "ompi_info" and the log of the faulty
hdf5 test.
Thanks!
Regards,
Joseph
Idézet (Mohamad Chaarawi <chaarawi@hdfgroup.org>):
> Hi Joseph,
>
> What is the test that fails in make check? When you run make check, it
> should tell you which test is running. Please provide that.
> I also would like to know the Open-MPI version you are using.
>
> Thanks,
> Mohamad
>
>> -----Original Message-----
>> From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On
>> Behalf Of Kóbori József
>> Sent: Tuesday, November 24, 2015 8:04 AM
>> To: hdf-forum@lists.hdfgroup.org
>> Subject: Re: [Hdf-forum] unsupported data type
>>
>> Hi Richard,
>>
>> I used "configure" with the following options:
>> --prefix=/some/dir --enable-parallel
>>
>> Platform:
>> Linux atlasz 3.2.0-4-amd64 #1 SMP Debian 3.2.68-1+deb7u1 x86_64
>> GNU/Linux
>>
>> The libhdf5.settings file is attached.
>>
>> Thanks!
>>
>> Regards,
>> Joseph
>>
>> Idézet (Richard van Hees <r.m.van.hees@sron.nl>):
>>
>> > Hi Joseph ,
>> >
>> > It would be helpful if you would indicate which way you configured
>> > HDF5. Using cmake? Using configure? Which options did you use? On
>> > which platform?
>> >
>> > Helpful also be the content of the file
>> > <HDF5_DIR>/lib/libhdf5.settings, where <HDF5_DIR> is the
>> > installation directory for HDF5, default "/usr/local" or specified
>> > by you using PREFIX or --prefix
>> >
>> > Greetings, Richard
>> >
>> > On 11/24/2015 12:40 PM, Kóbori József wrote:
>> >> Hi Mohamad,
>> >>
>> >> I compiled the latest version of HDF5: hdf5-1.8.16 After compiling
>> >> (make) I simply typed the "make check" command, and I got the
>> >> error below, so I don't have a particular test case.
>> >> If You need more info please let me know!
>> >> Thank You!
>> >>
>> >> Regards,
>> >> Joseph
>> >>
>> >> Idézet (Mohamad Chaarawi <chaarawi@hdfgroup.org>):
>> >>
>> >>> Hi Joseph,
>> >>>
>> >>> Could you please indicate the version of the HDF5 library and
>> >>> Open-MPI that you are using?
>> >>> Furthermore, could you provide a test case that replicates the
>> >>> failure below?
>> >>>
>> >>> You are correct that it seems that we are constructing a derived
>> >>> datatype that the ADIO driver in ROMIO doesn't seem to be able to
>> >>> parse properly. We don't test however much with Open-MPI, at
>> >>> lease to the extent that we do with MPICH. I'd be curious if you
>> >>> can try the same program with MPICH and see if it gives the same
error.
>> >>>
>> >>> Thanks,
>> >>> Mohamad
>> >>>
>> >>>> -----Original Message-----
>> >>>> From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org]
On
>> >>>> Behalf Of Kóbori József
>> >>>> Sent: Monday, November 16, 2015 5:30 AM
>> >>>> To: hdf-forum@lists.hdfgroup.org
>> >>>> Subject: [Hdf-forum] unsupported data type
>> >>>>
>> >>>> Dear All,
>> >>>>
>> >>>> when trying to test the previously compiled (with mpicc) HDF5
>> >>>> source I encountered the following error message:
>> >>>>
>> >>>> "MPI_ABORT was invoked on rank 3 in communicator
>> MPI_COMM_WORLD
>> >>>> with errorcode 1.
>> >>>>
>> >>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
processes.
>> >>>> You may or may not see output from other processes, depending
on
>> >>>> exactly when Open MPI kills them.
>> >>>> ----------------------------------------------------------------
>> >>>> ---
>> >>>> ------- Error: Unsupported datatype passed to
>> >>>> ADIOI_Count_contiguous_blocks, combiner = 17
>> >>>> Error: Unsupported datatype passed to
>> >>>> ADIOI_Count_contiguous_blocks, combiner = 17
>> >>>> Error: Unsupported datatype passed to
>> >>>> ADIOI_Count_contiguous_blocks, combiner = 17
>> >>>> Error: Unsupported datatype passed to
>> >>>> ADIOI_Count_contiguous_blocks, combiner = 17
>> >>>> Error: Unsupported datatype passed to
>> >>>> ADIOI_Count_contiguous_blocks, combiner = 17
>> >>>> Error: Unsupported datatype passed to
>> >>>> ADIOI_Count_contiguous_blocks, combiner = 17
>> >>>> ----------------------------------------------------------------
>> >>>> ---
>> >>>> ------- mpiexec has exited due to process rank 1 with PID 17756
>> >>>> on node XXXX exiting without calling "finalize". This may have
>> >>>> caused other processes in the application to be terminated by
>> >>>> signals sent by mpiexec (as reported here)."
>> >>>>
>> >>>> As I learnt it has to do something with a particular data type
>> >>>> (as the error message indicates it), but I'm stuck, I don't know
>> >>>> how to proceed.
>> >>>>
>> >>>> Could You give some help?
>> >>>>
>> >>>> Best regards,
>> >>>> Joseph
>> >>>>
>> >>>>
>> >>>> _______________________________________________
>> >>>> Hdf-forum is for HDF software users discussion.
>> >>>> Hdf-forum@lists.hdfgroup.org
>> >>>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgr
>> >>>> oup
>> >>>> .org
>> >>>> Twitter: https://twitter.com/hdf5
>> >>>
>> >>> _______________________________________________
>> >>> Hdf-forum is for HDF software users discussion.
>> >>> Hdf-forum@lists.hdfgroup.org
>> >>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.
>> >>> org
>> >>> Twitter: https://twitter.com/hdf5
>> >>>
>> >>
>> >>
>> >>
>> >> -------------------------------------------
>> >>
>> >> József Kóbori
>> >> PhD Student - Particle Physics and Astronomy Program
>> >> Room: Building North, Number 5.91, Phone: +36 30-266-5673 Eötvös
>> >> Loránd University
>> >> 1117 Budapest, Pázmány P. stny. 1/A
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> Hdf-forum is for HDF software users discussion.
>> >> Hdf-forum@lists.hdfgroup.org
>> >> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgrou
>> >> p.o
>> >> rg
>> >> Twitter: https://twitter.com/hdf5
>> >
>> >
>> > _______________________________________________
>> > Hdf-forum is for HDF software users discussion.
>> > Hdf-forum@lists.hdfgroup.org
>> > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup
>> > .or
>> > g
>> > Twitter: https://twitter.com/hdf5
>> >
>>
>>
>>
>> -------------------------------------------
>>
>> József Kóbori
>> PhD Student - Particle Physics and Astronomy Program
>> Room: Building North, Number 5.91, Phone: +36 30-266-5673 Eötvös
>> Loránd University
>> 1117 Budapest, Pázmány P. stny. 1/A
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@lists.hdfgroup.org
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.or
> g
> Twitter: https://twitter.com/hdf5
>
-------------------------------------------
József Kóbori
PhD Student - Particle Physics and Astronomy Program
Room: Building North, Number 5.91, Phone: +36 30-266-5673 Eötvös Loránd
University
1117 Budapest, Pázmány P. stny. 1/A
