ImportError: undefined symbol: H5Pget_fapl_mpio

[Brad Hollister]

Hi,

I've successfully build hdf5-1.8.13 (for parallel usage) and have build h5py-2.3.1 with the -mpi option. I've used the following guides:

http://docs.h5py.org/en/2.3/mpi.html#parallel

http://docs.h5py.org/en/latest/build.html

However, after installing h5py and trying to import the module, I get the following error:

ImportError: /home/behollis/.python-eggs/h5py-2.3.1-py2.7-linux-x86_64.egg-tmp/h5py/defs.so: undefined symbol: H5Pget_fapl_mpio

Any suggestions to fix this?

Regards,

Brad

[Andrew Collette]

Hi Brad,

Looks like you're not linking against Parallel HDF5 for some reason.
Double-check the value for --hdf5=/path/to/hdf5 in your build; it
should point to a directory including things like "include", "lib",
etc.

Also double-check Parallel HDF5 is built with both --enable-parallel
and --enable-shared.

Andrew

[florad...@gmail.com]

Hi,

I think you need a MPI version of libhdf5 :

$ldd /usr/local/lib/python2.7/dist-packages/h5py-2.5.0-py2.7-linux-x86_64.egg/h5py/defs.so
        linux-vdso.so.1 =>  (0x00007ffe05bfc000)
        libhdf5.so.7 => /usr/lib/libhdf5.so.7 (0x00007fbfa492d000)
        libhdf5_hl.so.7 => /usr/lib/libhdf5_hl.so.7


So try to install libhdf5-mpi-dev libhdf5-openmpi-7 libhdf5-openmpi-dev mpi-default-dev

Debian  :
#apt-get install libhdf5-mpi-dev

$dpkg -L   libhdf5-openmpi-7
/usr/lib/libhdf5.so.7
/usr/lib/libhdf5_fortran.so.7
/usr/lib/libhdf5_hl.so.7

Emmanuel