Edgar, It seems this the consequence of an abstraction violation (fcoll/two_phases directly calls the io/ompio component) and that was fixed in master. Can you confirm that ?
Delphine, The problem should disappear if you use romio instead of ompio Cheers, Gilles On Wednesday, February 10, 2016, Edgar Gabriel <egabr...@central.uh.edu <javascript:_e(%7B%7D,'cvml','egabr...@central.uh.edu');>> wrote: > which version of Open MPI is this? > Thanks > Edgar > > On 2/10/2016 4:13 AM, Delphine Ramalingom wrote: > > Hello, > > I try to compile a parallel version of hdf5. > I have error messages when I check with openmpi. > > Support on HDF5 told me that the errors seem related to the new ompio > implementation inside > open MPI for MPI-I/O. He suggests that I talk to the OMPI mailing list to > resolve these errors. > > For information, my version of openmpi is : gcc (GCC) 4.8.2 > mpicc --showme > gcc -I/programs/Compilateurs2/usr/include -pthread -Wl,-rpath > -Wl,/programs/Compilateurs2/usr/lib -Wl,--enable-new-dtags > -L/programs/Compilateurs2/usr/lib -lmpi > > Errors are : > > .../hdf5-1.8.16_gnu/testpar/.libs/t_mpi: symbol lookup error:f > /programs/Compilateurs2/usr/lib/openmpi/mca_fcoll_two_phase.so: undefined > symbol: ompi_io_ompio_decode_datatype > .../hdf5-1.8.16_gnu/testpar/.libs/t_mpi: symbol lookup error: > /programs/Compilateurs2/usr/lib/openmpi/mca_fcoll_two_phase.so: undefined > symbol: ompi_io_ompio_decode_datatype > ------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code.. Per user-direction, the job has been aborted. > ------------------------------------------------------- > .../hdf5-1.8.16_gnu/testpar/.libs/t_mpi: symbol lookup error: > /programs/Compilateurs2/usr/lib/openmpi/mca_fcoll_two_phase.so: undefined > symbol: ompi_io_ompio_set_aggregator_props > .../hdf5-1.8.16_gnu/testpar/.libs/t_mpi: symbol lookup error: > /programs/Compilateurs2/usr/lib/openmpi/mca_fcoll_two_phase.so: undefined > symbol: ompi_io_ompio_set_aggregator_props > .../hdf5-1.8.16_gnu/testpar/.libs/t_mpi: symbol lookup error: > /programs/Compilateurs2/usr/lib/openmpi/mca_fcoll_two_phase.so: undefined > symbol: ompi_io_ompio_set_aggregator_props > > > Thanks in advance for your help. > > Regards > Delphine > > -- > <http://www.univ-reunion.fr> *Delphine Ramalingom Barbary | Ingénieure en > Calcul Scientifique * > Direction des Usages du Numérique (DUN) > Centre de Développement du Calcul Scientifique > TEL : 02 62 93 84 87- FAX : 02 62 93 81 06 > > > -- > Edgar Gabriel > Associate Professor > Parallel Software Technologies Lab http://pstl.cs.uh.edu > Department of Computer Science University of Houston > Philip G. Hoffman Hall, Room 524 Houston, TX-77204, USA > Tel: +1 (713) 743-3857 Fax: +1 (713) 743-3335 > -- > >
