yes and no :-) That particular functions was fixed, but there are a few
other especially in the shardefp framework that would cause similar
problems if compiled without RTLD_GLOBAL.
But more importantly, I can confirm that ompio in the 1.8 and 1.10
series does *not* pass the HDF5 tests and should not be used for that
(it passes on master and the 2.x series). ROMIO is the default in 1.7,
1.8 and 1.10 and should be used therefore.
Thganks
Edgar
On 2/10/2016 6:32 AM, Gilles Gouaillardet wrote:
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 Labhttp://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
--
--
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
--
