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.

Best regards,

Simone

ERROR:
simone@simone:~$ source firedrake/bin/activate
(firedrake) simone@simone:~$ cd firedrake/src/firedrake/
(firedrake) simone@simone:~/firedrake/src/firedrake$ make alltest
    Building extension modules
    Linting firedrake codebase
    Linting firedrake test suite
    Linting firedrake scripts
    Running all regression tests
============================================================ test session starts =============================================================
platform linux -- Python 3.6.6, pytest-4.4.0, py-1.8.0, pluggy-0.9.0
rootdir: /home/simone/firedrake/src/firedrake, inifile: setup.cfg
plugins: xdist-1.27.0, forked-1.0.2
collected 0 items / 1 errors                                                                                                                

=================================================================== ERRORS ===================================================================
_______________________________________________________ ERROR collecting test session ________________________________________________________
../../lib/python3.6/site-packages/_pytest/config/__init__.py:435: in _importconftest
    return self._conftestpath2mod[conftestpath]
E   KeyError: local('/home/simone/firedrake/src/firedrake/tests/extrusion/conftest.py')

During handling of the above exception, another exception occurred:
../h5py/h5py/__init__.py:26: in <module>
    from . import _errors
E   ImportError: libhdf5.so.101: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:
../../lib/python3.6/site-packages/_pytest/config/__init__.py:441: in _importconftest
    mod = conftestpath.pyimport()
../../lib/python3.6/site-packages/py/_path/local.py:701: in pyimport
    __import__(modname)
../../lib/python3.6/site-packages/_pytest/assertion/rewrite.py:299: in load_module
    six.exec_(co, mod.__dict__)
tests/extrusion/conftest.py:2: in <module>
    from firedrake import ExtrudedMesh, UnitSquareMesh, UnitIntervalMesh
firedrake/__init__.py:48: in <module>
    from firedrake.checkpointing import *
firedrake/checkpointing.py:3: in <module>
    from firedrake import hdf5interface as h5i
firedrake/hdf5interface.pyx:1: in init firedrake.hdf5interface
    import h5py
../h5py/h5py/__init__.py:30: in <module>
    raise ImportError("You cannot import h5py from inside the install directory.\nChange to another directory first.")
E   ImportError: You cannot import h5py from inside the install directory.
E   Change to another directory first.

During handling of the above exception, another exception occurred:
../../lib/python3.6/site-packages/py/_path/common.py:377: in visit
    for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
../../lib/python3.6/site-packages/py/_path/common.py:418: in gen
    dirs = self.optsort([p for p in entries
../../lib/python3.6/site-packages/py/_path/common.py:419: in <listcomp>
    if p.check(dir=1) and (rec is None or rec(p))])
../../lib/python3.6/site-packages/_pytest/main.py:660: in _recurse
    ihook = self.gethookproxy(dirpath)
../../lib/python3.6/site-packages/_pytest/main.py:481: in gethookproxy
    my_conftestmodules = pm._getconftestmodules(fspath)
../../lib/python3.6/site-packages/_pytest/config/__init__.py:419: in _getconftestmodules
    mod = self._importconftest(conftestpath.realpath())
../../lib/python3.6/site-packages/_pytest/config/__init__.py:458: in _importconftest
    raise ConftestImportFailure(conftestpath, sys.exc_info())
E   _pytest.config.ConftestImportFailure: (local('/home/simone/firedrake/src/firedrake/tests/extrusion/conftest.py'), (<class 'ImportError'>, ImportError('You cannot import h5py from inside the install directory.\nChange to another directory first.',), <traceback object at 0x7fe2527a1848>))
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================================== 1 error in 4.85 seconds ===========================================================
Makefile:64: recipe for target 'test' failed
make: *** [test] Error 2