Just a follow-up. RPATH was the trouble. All is well now in the land
of the climatologists again. Thanks again for the help.
Ray
On 6/12/2015 8:00 AM, Ray Sheppard wrote:
Thanks again Gilles,
You might be on to something. Dynamic libraries sound like
something a Python developer might love (no offense intended to the
stereotype). It would also explain why the build went smoothly but the
test run crashed. I am going to try putting an RPATH variable in the
environment and rebuilding.
Ray
On 6/12/2015 7:15 AM, Gilles Gouaillardet wrote:
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
<mailto: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
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--
Respectfully,
Ray Sheppard
rshep...@iu.edu
http://rt.uits.iu.edu/systems/SciAPT
317-274-0016
Principal Analyst
Senior Technical Lead
Scientific Applications and Performance Tuning
Research Technologies
University Information Technological Services
IUPUI campus
Indiana University
My "pithy" saying: Science is the art of translating the world
into language. Unfortunately, that language is mathematics.
Bumper sticker wisdom: Make it idiot-proof and they will make a
better idiot.
