Add PyAlbany

[kliegeois]

This PR includes a python interface for Albany: PyAlbany.

The original goal of this interface was to ease the usage of reduced Hessian-vector products by providing ways to read and write distributed multivectors.

PyAlbany is not enabled by default and none of the work included in this PR should impact existing tests or builds.

PyAlbany is built against PyTrilinos, the python interface of Trilinos.
Currently, it is required to list both the source directory and the build directory of Trilinos to compile PyAlbany correctly.
It will be possible to avoid this in the future if PyTrilinos installs some swig files.

A detailed explanation of the building process and the dependencies can be found in this ReadMe.

This PR includes tests and an example.
The code has been tested with Python 2 and 3 (note that Python 3 build needs a small modification of Trilinos which is not merged yet PR #8444); in debug and release (note that PyAlbany cannot be compiled warning-free; I did not achieve to build PyTrilinos warning-free).

I tried to be verbose on the comments and documentation.

@mperego @ikalash @bartgol @jewatkins

[bartgol]

What if we ignored python2 completely and require python3?

[kliegeois]

@bartgol it will mainly simplify the cmake files. Except that, I don't think that it will impact the other files.

[mperego]

It looks great! However, I get a seg fault when I try to run the tests

[mperego]

I had to add also
-D SWIG_EXECUTABLE:FILEPATH="${HOME}/Workspace/TPL/swig/swig-3.0.11/install/bin/swig"
both in the Trilinos and in the Albany cmake script.

[kliegeois]

Thanks for your inputs about the README.md, I updated it to include them.

[mperego]

Thanks, but -D SWIG_EXECUTABLE="/usr/bin/swig" \ needs to be added to the Albany config as well.

[mperego]

All the 4 PyAlbany tests fail in a similar way:
LastTest.log

[kliegeois]

All the 4 PyAlbany tests fail in a similar way:
LastTest.log

@mperego thanks a lot for having tested them.

There is definitely something wrong.

I wonder whether the issue could be related to the version of mpi used by mpi4py.

Could you test the following first?

1. Reconfigure and build Trilinos with:

   -D PyTrilinos_ENABLE_TESTS:BOOL=ON \
   

   (this should not require any extra compilation as the tests are basically written in python).

2. And run:

   ctest -R PyTrilinos
   

   In particular, does the test PyTrilinos_testTeuchos_Comm_MPI_4 passed?

   1. If PyTrilinos_testTeuchos_Comm_MPI_4 failed, the issue is not directly related to PyAlbany itself.
      It is probably related to mpi4py which might be using a different version of mpi than the one used by Trilinos.
      Can you verify if the mpi4py .so is linked to the version of mai used to compile Trilinos/Albany?
      To do so, start by locating the MPI.so file as follows:

      -bash-4.2$ python
      >>> import mpi4py as MPI
      >>> print(MPI.__file__)
      

      this will print something such as: /ascldap/users/knliege/local/python_blake/lib/python2.7/site-packages/mpi4py/__init__.pyc

      And, check the mpi lib as follows (based on the output of the previous script):

      ldd /ascldap/users/knliege/local/python_blake/lib/python2.7/site-packages/mpi4py/MPI.so | grep "libmpi"
      

      Do the same with a Trilinos library such as libteuchoscore.so:

      ldd /ascldap/users/knliege/local/trilinos_all/blake_Albany/lib/libteuchoscore.so | grep "libmpi"
      

      Finally, verify that mpirun is consistent with both of those libs.

   2. If PyTrilinos_testTeuchos_Comm_MPI_4 passed, can you test the following and check if it is failing when importing wpyalbany?

      -bash-4.2$ python
      >>> from PyTrilinos import Tpetra
      >>> from PyTrilinos import Teuchos
      >>> from PyAlbany import wpyalbany as wpa
      

[kliegeois]

Thanks @mperego for your review, I updated the files as suggested.

[mperego]

@kliegeois Only this PyTrilinos test fail:
PyTrilinos_testEpetraExt_HDF5_MPI_4

Here's the path of mpi4py

>>> import mpi4py as MPI
>>> print(MPI.__file__)
/ascldap/users/mperego/anaconda3/lib/python3.8/site-packages/mpi4py/__init__.py

It can import Tpetra and Teuchos but not wpyalbany

from PyAlbany import wpyalbany as wpa
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: cannot import name 'wpyalbany' from 'PyAlbany' (/ascldap/users/mperego/Workspace/albany/sources/albany-src/PyAlbany/PyAlbany/__init__.py)

[mperego]

It looks good!

[kliegeois]

Thanks @mperego ! I will update the README.md tomorrow and, at least to me, the PR will be good to be merged.

[kliegeois]

@mperego I have just updated the README.md (and squashed the related commits).
Could you let me know if the precision is fine for you?

[mperego]

@kliegeois Looks good to me. Thanks. Feel free to go ahead and merge the branch.

[kliegeois]

@mperego thanks!

Well, actually, it seems that the access that I have received is not sufficient to merge the PR:

@ikalash would you agree to give me the required write access?

[mperego]

@mperego thanks!

Well, actually, it seems that the access that I have received is not sufficient to merge the PR:

@ikalash would you agree to give me the required write access?

I'll merge this PR for you

[kliegeois]

Thanks @mperego !