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:[email protected]] On Behalf > Of Kóbori József > Sent: Tuesday, November 24, 2015 8:04 AM > To: [email protected] > 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 <[email protected]>): > > > 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 <[email protected]>): > >> > >>> 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:[email protected]] On > >>>> Behalf Of Kóbori József > >>>> Sent: Monday, November 16, 2015 5:30 AM > >>>> To: [email protected] > >>>> 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. > >>>> [email protected] > >>>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup > >>>> .org > >>>> Twitter: https://twitter.com/hdf5 > >>> > >>> _______________________________________________ > >>> Hdf-forum is for HDF software users discussion. > >>> [email protected] > >>> 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. > >> [email protected] > >> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.o > >> rg > >> Twitter: https://twitter.com/hdf5 > > > > > > _______________________________________________ > > Hdf-forum is for HDF software users discussion. > > [email protected] > > 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. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
