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

spuel@utexas.edu

+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

https://www.cse.buffalo.edu/~knepley/