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. Thanks, Matt
Thank you so much, have a wonderful day.
Best regards, Simone
On Tue, Jun 18, 2019 at 11:14 AM Lawrence Mitchell <wencel@gmail.com> wrote:
Dear Simone,
On 17 Jun 2019, at 17:46, Simone Puel <spuel@utexas.edu> wrote:
Hi,
My name is Simone Puel, a graduate student at the University of Texas at Austin. I would like to use Firedrake for my research, but once installed I run the test suggested to check that the Firedrake installation is fully functional, but I got the following error. I am using Ubuntu-Mate distribution with ubuntu bionic 18.04.2 LTS with Python 3.6.8 in Anaconda environment. Could you help me in the installation, please? Thank you so much in advance. Have a wonderful day.
This error suggests that somehow there were some problems in the installation. Can you send the contents of firedrake-install.log?
We can also check if importing h5py, which is the issue here, on its own works.
After activating the virtual environment, can you send the output of
python -c "import h5py"
?
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 _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
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