You are using a very old version of Open MPI. Open MPI: 1.4.5 Open MPI SVN revision: r25905 Open MPI release date: Feb 10, 2012
Please use latest. Thanks, Mohamad > -----Original Message----- > From: Hdf-forum [mailto:hdf-forum-boun...@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 <chaar...@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-boun...@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.h...@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 <chaar...@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-boun...@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 _______________________________________________ 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
