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
+1 (737)-230-6811
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