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
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