never mind, issue was resolved by simply updating petsc-dev. On Fri, Jul 24, 2015 at 2:17 PM, Justin Chang <jychang48@gmail.com> wrote:
Not sure if this is related, but I had to update my petsc4py to get this branch to work. But now I am getting this error, even in PyOP2
Traceback (most recent call last): File "/usr/local/bin/py.test", line 11, in <module> sys.exit(main()) File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 18, in main config = _prepareconfig(args, plugins) File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 62, in _prepareconfig pluginmanager=pluginmanager, args=args) File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 376, in __call__ return self._docall(methods, kwargs) File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 387, in _docall res = mc.execute() File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 288, in execute res = method(**kwargs) File "/usr/lib/python2.7/dist-packages/_pytest/helpconfig.py", line 25, in pytest_cmdline_parse config = __multicall__.execute() File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 288, in execute res = method(**kwargs) File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 617, in pytest_cmdline_parse self.parse(args) File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 710, in parse self._preparse(args) File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 690, in _preparse args=args, parser=self._parser) File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 376, in __call__ return self._docall(methods, kwargs) File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 387, in _docall res = mc.execute() File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 288, in execute res = method(**kwargs) File "/usr/lib/python2.7/dist-packages/_pytest/capture.py", line 42, in pytest_load_initial_conftests return __multicall__.execute() File "/usr/lib/python2.7/dist-packages/_pytest/core.py", line 288, in execute res = method(**kwargs) File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 673, in pytest_load_initial_conftests self._conftest.setinitial(args) File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 486, in setinitial self._try_load_conftest(anchor) File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 492, in _try_load_conftest self._path2confmods[None] = self.getconftestmodules(anchor) File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 511, in getconftestmodules clist.append(self.importconftest(conftestpath)) File "/usr/lib/python2.7/dist-packages/_pytest/config.py", line 537, in importconftest self._conftestpath2mod[conftestpath] = mod = conftestpath.pyimport() File "/usr/lib/python2.7/dist-packages/py/_path/local.py", line 620, in pyimport __import__(modname) File "/home/justin/Software/firedrake-deps/PyOP2/test/conftest.py", line 40, in <module> from pyop2 import op2 File "/home/justin/Software/firedrake-deps/PyOP2/pyop2/__init__.py", line 9, in <module> from op2 import * File "/home/justin/Software/firedrake-deps/PyOP2/pyop2/op2.py", line 39, in <module> import base File "/home/justin/Software/firedrake-deps/PyOP2/pyop2/base.py", line 56, in <module> from sparsity import build_sparsity File "PETSc.pxd", line 70, in init pyop2.sparsity (pyop2/sparsity.cpp:22252) File "/usr/local/lib/python2.7/dist-packages/petsc4py/PETSc.py", line 3, in <module> PETSc = ImportPETSc(ARCH) File "/usr/local/lib/python2.7/dist-packages/petsc4py/lib/__init__.py", line 29, in ImportPETSc return Import('petsc4py', 'PETSc', path, arch) File "/usr/local/lib/python2.7/dist-packages/petsc4py/lib/__init__.py", line 64, in Import module = imp.load_module(fullname, fo, fn, stuff) ImportError: /usr/local/lib/python2.7/dist-packages/petsc4py/lib/arch-linux2-c-opt/PETSc.so: undefined symbol: DMShellSetCreateSubDM make: *** [unit_sequential] Error 1
Is this more a petsc4py error? As in should it be reported to the petsc-users list?
Thanks, Justin
On Fri, Jul 24, 2015 at 7:36 AM, Lawrence Mitchell < lawrence.mitchell@imperial.ac.uk> wrote:
On 24 Jul 2015, at 12:50, Lawrence Mitchell < lawrence.mitchell@imperial.ac.uk> wrote: ... Oh, I think I failed to correctly implement this case. I'll try and put something together.
I think the firedrake branch indexed-fixes does this correctly.
To ensure one way we don't regress later, if this works for you can you provide some small test code (similar to the ones you've been sending) and we'll incorporate it into the test suite.
Cheers,
Lawrence
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