Hi Lawrence and Matt, Thank you so much for your email. Thanks Matt, what can I do? I was wondering that the problem might be related to have installed most of the packages with both anaconda and directly on my computer. This is the output: simone@simone:~$ ldd /home/simone/firedrake/src/h5py/h5py/ defs.cpython-36m-x86_64-linux-gnu.so linux-vdso.so.1 (0x00007fffd29f4000) libhdf5.so.103 => /home/simone/anaconda3/lib/libhdf5.so.103 (0x00007f7380c31000) libhdf5_hl.so.100 => /home/simone/anaconda3/lib/libhdf5_hl.so.100 (0x00007f738118c000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f7380a12000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f7380621000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f7380419000) libz.so.1 => /home/simone/anaconda3/lib/./libz.so.1 (0x00007f7380202000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f737fffe000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f737fc60000) /lib64/ld-linux-x86-64.so.2 (0x00007f7380fc7000) Thanks, have a wonderful day. Best regards, Simone On Wed, Jun 19, 2019 at 2:53 AM Lawrence Mitchell <wence@gmx.li> wrote:
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
-- *Simone Puel* Ph.D. student in Geological Sciences at the University of Texas at Austin Jackson School of Geosciences & Institute for Geophysics (UTIG) JGB 5.332 & ROC 2.116L spuel@utexas.edu +1 (737)-230-6811