-----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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBAgAGBQJVpNL7AAoJECOc1kQ8PEYvoC4H/iqMGswugo73P8MoJQiHGZ9j IsmvwD2TxXqf52eBWkZ+GEbYjp4p6HTRWARe5/ib9WD+Et6qD3aUeeu5aXNwnEFF PGPeJ4tWD0usYwqzgtY/Rh1g7JfoQxR5fSq9vTpjTFheUHZLUOHEbUz8ZAPE+MQ+ Oke+GbQZvg5fm4ddBwrQP8ramPIBnrszs4hG8Jelc+/Dp3950Iyeqd7PhBHGjLtK 0rHzVDWgTodlj6jdCT942BdOQpsEzbDayRXgbt/ivaGDOxPszbWIxHB8k1BvJT2g Y8z6zqB0pQNb05Wi0fcnagHSk/9nOdBREv3wqgqlfO9SYvd7T5uBV9oJwLEfOSw= =hXpq -----END PGP SIGNATURE-----