Ray, one possibility is one of the loaded library was built with -rpath and this causes the mess
an other option is you have to link _error.so with libmpi.so Cheers, Gilles On Friday, June 12, 2015, Ray Sheppard <rshep...@iu.edu> wrote: > Hi Gilles, > Thanks for the reply. I completely forgot that lived in the main > library. ldd doesn't show that it read my LD_LIBRARY_PATH (I also push out > an LPATH variable just for fun). I force modules to echoed when users > initialize them. You can see OpenMPI was visible to H5py. Now I wonder > why it didn't pick it up... Thanks again. > Ray > GMP arithmetic library version 5.1.1 loaded. > MPFR version 3.1.1 loaded. > Mpc version 1.0.1 loaded. > gcc version 4.9.2 loaded. > Moab Workload Manager scheduling and management system version 7.1.1 > loaded. > Python programming language version 2.7.3 loaded. > Perl programming language version 5.16.2 loaded. > Intel compiler suite version 15.0.1 loaded. > OpenMPI libraries (Intel) version 1.8.4 loaded. > TotalView version 8.15.0-15 loaded. > FFTW (Intel, Double precision) version 3.3.3 loaded. > hdf4 version 4.2.10 loaded. > Curl version 7.28.1 loaded. > HDF5 (MPI) version 1.8.14 loaded. > netcdf-c version 4.3.3 loaded. > netcdf-fortran version 4.4.1 loaded. > Gnuplot graphing utility version 4.6.1 loaded. > [rsheppar@h2 ~]$ ldd > /N/dc2/projects/ray/quarry/h5py/h5py-2.5.0/build/lib.linux-x86_64-2.7/h5py/_errors.so > linux-vdso.so.1 => (0x00007fff39db7000) > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007facfe887000) > libc.so.6 => /lib64/libc.so.6 (0x00007facfe4f3000) > /lib64/ld-linux-x86-64.so.2 (0x00007facff049000) > > > On 6/11/2015 8:09 PM, Gilles Gouaillardet wrote: > > Ray, > > this symbol is defined in libmpi.so. > > can you run > ldd > */N/dc2/projects/ray/quarry/h5py/h5py-2.5.0/build/lib.linux-x86_64-2.7/h5py/* > _errors.so > and make sure this is linked with openmpi 1.8.4 ? > > Cheers, > > Gilles > > On 6/12/2015 1:29 AM, Ray Sheppard wrote: > > Hi List, > I know I saw this issue years ago but have forgotten the details. I > looked through old posts but only found about half a dozen pertaining to > WinDoze. I am trying to build a Python (2.7.3) extension (h5py) that calls > HDF5 (1.8.14). I built both the OpenMPI (1.8.4) and the HDF5 modules so I > know they are consistent. All goes well until I try to run the tests. Then > I get: > > ImportError: > /N/dc2/projects/ray/quarry/h5py/h5py-2.5.0/build/lib.linux-x86_64-2.7/h5py/_errors.so: > undefined symbol: ompi_mpi_info_null > > I am not sure I completely trust the h5py package but I don't have a real > good reason for believing that way. I would appreciate it if someone could > explain where ompi_mpi_info_null is defined and possibly a way to tell > Python about it. Thanks! > Ray > > > > > _______________________________________________ > users mailing listus...@open-mpi.org > <javascript:_e(%7B%7D,'cvml','us...@open-mpi.org');> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2015/06/27117.php > > >
