Hi Simone,

For what it's worth, anaconda usually adds its activation commands in your ~/.bashrc file, should be something like:

# >>> conda initialize >>>
[... some commands here...]
# <<< conda initialize <<<

If you comment out those lines (and open a new shell), you should be able to install and run firedrake without conflicts. (To check that anaconda has indeed been disabled, the command 'conda' should return 'command not found' error).

If you copy those commands into another file, for example, 'activate_anaconda.sh', you can then activate anaconda by saying
. path/to/activate_anaconda.sh
whenever you need it.

Cheers,
Tuomas


On 6/20/19 4:52 PM, Matthew Knepley wrote:
On Thu, Jun 20, 2019 at 9:24 AM Simone Puel <spuel@utexas.edu> wrote:
Hi Matt,

Thank you so much for your email. Do you mean remove the entire Anaconda, or removing some directories in the firedrake folder?
Thanks in advance. Have a wonderful day.

I mean that you do not want Firedrake to _see_ Anaconda. I believe you can do this by taking any Anaconda directory
out of your environment. Something like

  env | grep conda

and taking it out of all those.

  Thanks,

    Matt
 
Best regards,
Simone

On Thu, Jun 20, 2019 at 2:40 AM Matthew Knepley <knepley@gmail.com> wrote:
On Wed, Jun 19, 2019 at 9:50 AM Simone Puel <spuel@utexas.edu> wrote:
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:

I think the easiest thing to do is not let Firedrake see the Anaconda libraries. I think
this should be easy by just removing those directories from the environment variables.
Does this make sense?

  Thanks,

    Matt
 
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
+1 (737)-230-6811


--
What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener



--
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


--
What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener


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