[firedrake] error installing PyOP2

[Justin Chang]

Coming back to this.

I believe I have puled the latest petsc, petsc4py, and PyOP2 repositories
onto my laptop. Following through with all the (re)installation, I come
across this error when I run 'make test' in PyOP2:

Error in atexit._run_exitfuncs:

Traceback (most recent call last):

  File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/atexit.py",
line 24, in _run_exitfuncs

    func(*targs, **kargs)

  File
"/Library/Python/2.7/site-packages/PyOP2-0.11.0_366_ga8923c7-py2.7-macosx-10.10-intel.egg/pyop2_utils/prefork.py",
line 148, in _quit

    self._remote_invoke("quit")

  File
"/Library/Python/2.7/site-packages/PyOP2-0.11.0_366_ga8923c7-py2.7-macosx-10.10-intel.egg/pyop2_utils/prefork.py",
line 138, in _remote_invoke

    _send_packet(self.socket, (name, args, kwargs))

  File
"/Library/Python/2.7/site-packages/PyOP2-0.11.0_366_ga8923c7-py2.7-macosx-10.10-intel.egg/pyop2_utils/prefork.py",
line 64, in _send_packet

    from six.moves.cPickle import dumps

ImportError: No module named cPickle

Error in sys.exitfunc:

Traceback (most recent call last):

  File
"/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/atexit.py",
line 24, in _run_exitfuncs

    func(*targs, **kargs)

  File
"/Library/Python/2.7/site-packages/PyOP2-0.11.0_366_ga8923c7-py2.7-macosx-10.10-intel.egg/pyop2_utils/prefork.py",
line 148, in _quit

    self._remote_invoke("quit")

  File
"/Library/Python/2.7/site-packages/PyOP2-0.11.0_366_ga8923c7-py2.7-macosx-10.10-intel.egg/pyop2_utils/prefork.py",
line 138, in _remote_invoke

    _send_packet(self.socket, (name, args, kwargs))

  File
"/Library/Python/2.7/site-packages/PyOP2-0.11.0_366_ga8923c7-py2.7-macosx-10.10-intel.egg/pyop2_utils/prefork.py",
line 64, in _send_packet

    from six.moves.cPickle import dumps

ImportError: No module named cPickle

make: *** [unit_sequential] Error 1

/Library/Python/2.7/site-packages/PyOP2-0.11.0_366_ga8923c7-py2.7-macosx-10.10-intel.egg/pyop2_utils/prefork.py:78:
UserWarning: Prefork server exiting upon apparent death of parent

  warn("%s exiting upon apparent death of %s" % (who, partner))

Traceback (most recent call last):

  File "/Library/Python/2.7/site-packages/_pytest/config.py", line 543, in
importconftest

    mod = conftestpath.pyimport()

  File "/Library/Python/2.7/site-packages/py/_path/local.py", line 650, in
pyimport

    __import__(modname)

RuntimeError: not holding the import lock

ERROR: could not load
/Users/justin/Software/firedrake-deps/PyOP2/test/conftest.py

These happened to be only the last few lines. The entire log is too big for
me to attach. I have tried reinstalling petsc, petsc4py, and PyOP2 to
reinstalling the dependencies, but nothing seems to work. Any idea what's
going on here?

Thanks,

Justin



On Wed, Jul 15, 2015 at 4:58 AM, Justin Chang <jychang48 at gmail.com> wrote:

> Alright, I got it working after uninstalling and reinstalling everything.
> I guess that works every time. Thanks again for all your help!
>
> On Tue, Jul 14, 2015 at 8:07 AM, Lawrence Mitchell <
> lawrence.mitchell at imperial.ac.uk> wrote:
>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> On 14/07/15 13:03, Justin Chang wrote:
>> > I had my PETSc use the globally installed MPI. Now it seems they
>> > all point to the same MPI library
>> >
>> > However, now I am getting this new error when running 'make test':
>>
>> ...
>>
>> > File "PETSc.pxd", line 61, in init pyop2.sparsity
>> > (pyop2/sparsity.cpp:22149) ValueError: petsc4py.PETSc.Comm has the
>> > wrong size, try recompiling make: *** [unit_sequential] Error 1
>>
>> You'll want to recompile petsc4py, and probably the extension modules
>> in PyOP2.  You can do the latter by typing "make ext" in the PyOP2
>> directory.  When you get to firedrake you'll also want to recompile
>> its extension modules: "make clean all" in the firedrake directory.
>>
>> Cheers,
>>
>> Lawrence
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>>
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>
>
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