On Wed, 19 Jun 2019 at 08:44, Matthew Knepley <knepley@gmail.com> wrote:
On Tue, Jun 18, 2019 at 1:25 PM Simone Puel <spuel@utexas.edu> wrote:
Dear Lawrence,
Thank you for your email. Yes, of course. Attached there is the "firedrake-install.log" while the output:
(firedrake) simone@simone:~$ python -c "import h5py" Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/simone/firedrake/src/h5py/h5py/__init__.py", line 36, in <module> from ._conv import register_converters as _register_converters File "h5py/h5r.pxd", line 21, in init h5py._conv File "h5py/_objects.pxd", line 12, in init h5py.h5r File "h5py/_objects.pyx", line 1, in init h5py._objects ImportError: /home/simone/firedrake/src/h5py/h5py/ defs.cpython-36m-x86_64-linux-gnu.so: undefined symbol: H5Pget_dxpl_mpio
Hi Simone,
I think this can happen if you have 2 copies of HDF5 floating around, where one is compiled with MPI turned on and one isn't.
Ah. I wonder if you have a system install. We ask petsc to build hdf5 for us and then try and link against that. Can you provide the output of ldd /home/simone/firedrake/src/h5py/h5py/ defs.cpython-36m-x86_64-linux-gnu.so Thanks, Lawrence