Actually, after running git pull in the PyOP2 directory, I ran this: python setup.py build_ext --inplace and got this after running 'make test' again: cd test; py.test unit --backend=sequential Segmentation fault (core dumped) make: *** [unit_sequential] Error 139 should I have run something else? Thanks, Justin On Tue, Jul 14, 2015 at 5:04 AM, Justin Chang <jychang48@gmail.com> wrote:
Lawrence,
python -c "import petsc4py; petsc4py.init()" gives me no output, so I assume it's working?
btw I installed petsc4py using:
git clone .... && git checkout firedrake && sudo -E python setup.py install.
So when I now run:
pip show petsc4py
gives me the following:
--- Name: petsc4py Version: 3.5.1 Location: /usr/local/lib/python2.7/dist-packages Requires:
Doing the latest pull of PyOP2, I ran:
make test
And got these errors:
cd test; py.test unit --backend=sequential 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 ImportError: No module named sparsity make: *** [unit_sequential] Error 1
This is a different error now. Do you know what the problem is now?
Thanks, Justin
On Tue, Jul 14, 2015 at 4:14 AM, Lawrence Mitchell < lawrence.mitchell@imperial.ac.uk> wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
On 14/07/15 09:57, Justin Chang wrote:
Hi everyone,
I am trying to installing firedrake on my Ubuntu machine. Following the instructions for PyOP2, I get this error when I run "make test"
cd test; py.test unit --backend=sequential Segmentation fault (core dumped) make: *** [unit_sequential] Error 139
I have installed everything via sudo pip install ... with the exception of petsc4py which was installed via pip install --user -U --no-deps ...
python -c 'from pprint import pprint; import sys; pprint(sys.path)' gives the following:
['', '/usr/lib/python2.7/dist-packages', '/home/justin/.local/lib/python2.7/site-packages', '/home/justin/Software/firedrake-deps/PyOP2', '/home/justin/Software/firedrake-deps/firedrake', '/home/justin/.local/lib/python2.7/dist-packages', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/usr/lib/python2.7/lib-old', '/usr/lib/python2.7/lib-dynload', '/usr/local/lib/python2.7/dist-packages', '/usr/lib/python2.7/dist-packages/PILcompat', '/usr/lib/python2.7/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.7', '/usr/lib/python2.7/dist-packages/ubuntu-sso-client']
and py.test test/unit -vsx --tb=short --backend=sequential gives the following:
[pacotaco-xps:29386] *** Process received signal *** [pacotaco-xps:29386] Signal: Segmentation fault (11) [pacotaco-xps:29386] Signal code: Address not mapped (1) [pacotaco-xps:29386] Failing at address: 0x44000098 [pacotaco-xps:29386] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f7eafdd8340] [pacotaco-xps:29386] [ 1] /usr/lib/libmpi.so.1(MPI_Comm_set_errhandler+0x4d) [0x7f7ead7fca1d] [pacotaco-xps:29386] [ 2]
/home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libpetsc.so.3.06(PetscInitialize+0x2a7)
[0x7f7e9063f6b6] [pacotaco-xps:29386] [ 3]
/home/justin/.local/lib/python2.7/site-packages/petsc4py/lib/arch-linux2-c-opt/PETSc.so(+0x11d3e8)
[0x7f7e8e33c3e8] [pacotaco-xps:29386] [ 4] /usr/bin/python(PyEval_EvalFrameEx+0x40d) [0x49968d] [pacotaco-xps:29386] [ 5] /usr/bin/python(PyEval_EvalCodeEx+0x2ac) [0x4a090c] [pacotaco-xps:29386] [ 6] /usr/bin/python(PyEval_EvalCode+0x32) [0x588d42] [pacotaco-xps:29386] [ 7] /usr/bin/python(PyImport_ExecCodeModuleEx+0xaa) [0x588dfa] [pacotaco-xps:29386] [ 8] /usr/bin/python() [0x5b1f0f] [pacotaco-xps:29386] [ 9] /usr/bin/python() [0x540948] [pacotaco-xps:29386] [10] /usr/bin/python() [0x540d08] [pacotaco-xps:29386] [11] /usr/bin/python() [0x541510] [pacotaco-xps:29386] [12] /usr/bin/python() [0x51dd20] [pacotaco-xps:29386] [13] /usr/bin/python(PyObject_Call+0x36) [0x505f96] [pacotaco-xps:29386] [14] /usr/bin/python() [0x536095] [pacotaco-xps:29386] [15] /usr/bin/python(PyObject_CallFunction+0xa5) [0x4ca095] [pacotaco-xps:29386] [16] /usr/bin/python(PyImport_Import+0xdd) [0x525e8d] [pacotaco-xps:29386] [17] /home/justin/Software/firedrake-deps/PyOP2/pyop2/sparsity.so(+0x770a) [0x7f7e915de70a] [pacotaco-xps:29386] [18]
/home/justin/Software/firedrake-deps/PyOP2/pyop2/sparsity.so(initsparsity+0x1244)
[0x7f7e915f91a4] [pacotaco-xps:29386] [19] /usr/bin/python(_PyImport_LoadDynamicModule+0x9b) [0x42266c] [pacotaco-xps:29386] [20] /usr/bin/python() [0x540948] [pacotaco-xps:29386] [21] /usr/bin/python() [0x540d08] [pacotaco-xps:29386] [22] /usr/bin/python() [0x54111b] [pacotaco-xps:29386] [23] /usr/bin/python() [0x51dd20] [pacotaco-xps:29386] [24] /usr/bin/python(PyEval_CallObjectWithKeywords+0x6b) [0x4dc9cb] [pacotaco-xps:29386] [25] /usr/bin/python(PyEval_EvalFrameEx+0x25fe) [0x49b87e] [pacotaco-xps:29386] [26] /usr/bin/python(PyEval_EvalCodeEx+0x2ac) [0x4a090c] [pacotaco-xps:29386] [27] /usr/bin/python(PyEval_EvalCode+0x32) [0x588d42] [pacotaco-xps:29386] [28] /usr/bin/python(PyImport_ExecCodeModuleEx+0xaa) [0x588dfa] [pacotaco-xps:29386] [29] /usr/bin/python() [0x5b1f0f] [pacotaco-xps:29386] *** End of error message *** Segmentation fault (core dumped)
Any idea what's going on?
This doesn't immediately look like a PyOP2 related problem. Rather some mismatch between MPI pieces.
Does the following work?
python -c "import petsc4py; petsc4py.init()"
If not, can you compile and run C-based PETSc programs (using the same PETSC_DIR/PETSC_ARCH combo) ?
Cheers,
Lawrence
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