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@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@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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1
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