python -c "import pyop2; pyop2.init(); print pyop2.__version__" gives the following: [pacotaco-xps:26247] *** Process received signal *** [pacotaco-xps:26247] Signal: Segmentation fault (11) [pacotaco-xps:26247] Signal code: Address not mapped (1) [pacotaco-xps:26247] Failing at address: 0x44000098 [pacotaco-xps:26247] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x10340) [0x7f83c768b340] [pacotaco-xps:26247] [ 1] /usr/lib/libmpi.so.1(MPI_Comm_set_errhandler+0x4d) [0x7f83c5be3a1d] [pacotaco-xps:26247] [ 2] /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libpetsc.so.3.06(PetscInitialize+0x2a7) [0x7f83a83c66b6] [pacotaco-xps:26247] [ 3] /usr/local/lib/python2.7/dist-packages/petsc4py/lib/arch-linux2-c-opt/PETSc.so(+0x11d3e8) [0x7f83a60c33e8] [pacotaco-xps:26247] [ 4] python(PyEval_EvalFrameEx+0x40d) [0x49968d] [pacotaco-xps:26247] [ 5] python(PyEval_EvalCodeEx+0x2ac) [0x4a090c] [pacotaco-xps:26247] [ 6] python(PyEval_EvalCode+0x32) [0x588d42] [pacotaco-xps:26247] [ 7] python(PyImport_ExecCodeModuleEx+0xaa) [0x588dfa] [pacotaco-xps:26247] [ 8] python() [0x5b1f0f] [pacotaco-xps:26247] [ 9] python() [0x540948] [pacotaco-xps:26247] [10] python() [0x540d08] [pacotaco-xps:26247] [11] python() [0x541510] [pacotaco-xps:26247] [12] python() [0x51dd20] [pacotaco-xps:26247] [13] python(PyObject_Call+0x36) [0x505f96] [pacotaco-xps:26247] [14] python() [0x536095] [pacotaco-xps:26247] [15] python(PyObject_CallFunction+0xa5) [0x4ca095] [pacotaco-xps:26247] [16] python(PyImport_Import+0xdd) [0x525e8d] [pacotaco-xps:26247] [17] pyop2/sparsity.so(+0x770a) [0x7f83a936570a] [pacotaco-xps:26247] [18] pyop2/sparsity.so(initsparsity+0x1244) [0x7f83a93801a4] [pacotaco-xps:26247] [19] python(_PyImport_LoadDynamicModule+0x9b) [0x42266c] [pacotaco-xps:26247] [20] python() [0x540948] [pacotaco-xps:26247] [21] python() [0x540d08] [pacotaco-xps:26247] [22] python() [0x54111b] [pacotaco-xps:26247] [23] python() [0x51dd20] [pacotaco-xps:26247] [24] python(PyEval_CallObjectWithKeywords+0x6b) [0x4dc9cb] [pacotaco-xps:26247] [25] python(PyEval_EvalFrameEx+0x25fe) [0x49b87e] [pacotaco-xps:26247] [26] python(PyEval_EvalCodeEx+0x2ac) [0x4a090c] [pacotaco-xps:26247] [27] python(PyEval_EvalCode+0x32) [0x588d42] [pacotaco-xps:26247] [28] python(PyImport_ExecCodeModuleEx+0xaa) [0x588dfa] [pacotaco-xps:26247] [29] python() [0x5b1f0f] [pacotaco-xps:26247] *** End of error message *** Segmentation fault (core dumped) So I guess it's not working? ==================== Here are the other commands you have requested: justin@pacotaco-xps:~/Software/firedrake-deps/PyOP2$ ldd pyop2/sparsity.so linux-vdso.so.1 => (0x00007ffdd3190000) libpetsc.so.3.06 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libpetsc.so.3.06 (0x00007fe25cccd000) libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fe25c9c9000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fe25c7b3000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fe25c3ee000) libparmetis.so => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libparmetis.so (0x00007fe25c1b2000) libmetis.so => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libmetis.so (0x00007fe25bf43000) libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007fe25bc0e000) libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00007fe25b9af000) libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00007fe25b5d4000) libhdf5.so.8 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libhdf5.so.8 (0x00007fe25b100000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fe25aee2000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fe25abdc000) libmpifort.so.12 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libmpifort.so.12 (0x00007fe25a9a7000) libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007fe25a68d000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fe25a489000) libmpi.so.12 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libmpi.so.12 (0x00007fe25a067000) /lib64/ld-linux-x86-64.so.2 (0x00007fe25dfde000) libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007fe259e48000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fe259c2f000) libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007fe2599f3000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fe2597eb000) libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007fe2595e7000) libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007fe2593e1000) ================ justin@pacotaco-xps:~/Software/firedrake-deps/PyOP2$ ldd /usr/local/lib/python2.7/dist-packages/petsc4py/lib/arch-linux2-c-opt/PETSc.so linux-vdso.so.1 => (0x00007ffed0146000) libpetsc.so.3.06 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libpetsc.so.3.06 (0x00007f780089e000) libmpi.so.12 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libmpi.so.12 (0x00007f780047c000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f780025e000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f77ffe99000) libparmetis.so => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libparmetis.so (0x00007f77ffc5d000) libmetis.so => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libmetis.so (0x00007f77ff9ee000) libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f77ff6b9000) libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00007f77ff45a000) libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00007f77ff07f000) libhdf5.so.8 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libhdf5.so.8 (0x00007f77febab000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f77fe8a5000) libmpifort.so.12 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libmpifort.so.12 (0x00007f77fe670000) libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007f77fe356000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f77fe152000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f77fdf3c000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f77fdd34000) /lib64/ld-linux-x86-64.so.2 (0x00007f7801dbf000) libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f77fdb15000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f77fd8fc000) libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007f77fd6c0000) libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f77fd4bc000) libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f77fd2b6000) ================== justin@pacotaco-xps:~/Software/firedrake-deps/PyOP2$ ldd /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libpetsc.so linux-vdso.so.1 => (0x00007fff7c1f2000) libparmetis.so => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libparmetis.so (0x00007efc5b664000) libmetis.so => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libmetis.so (0x00007efc5b3f5000) libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007efc5b0c0000) libssl.so.1.0.0 => /lib/x86_64-linux-gnu/libssl.so.1.0.0 (0x00007efc5ae61000) libcrypto.so.1.0.0 => /lib/x86_64-linux-gnu/libcrypto.so.1.0.0 (0x00007efc5aa86000) libhdf5.so.8 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libhdf5.so.8 (0x00007efc5a5b2000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007efc5a394000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007efc5a08e000) libmpifort.so.12 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libmpifort.so.12 (0x00007efc59e59000) libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007efc59b3f000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007efc5993b000) libmpi.so.12 => /home/justin/Software/petsc-dev/arch-linux2-c-opt/lib/libmpi.so.12 (0x00007efc59519000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007efc59303000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007efc58f3e000) /lib64/ld-linux-x86-64.so.2 (0x00007efc5c975000) libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007efc58d1f000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007efc58b06000) libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007efc588ca000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007efc586c2000) libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007efc584be000) libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007efc582b8000) On Tue, Jul 14, 2015 at 5:12 AM, Lawrence Mitchell < lawrence.mitchell@imperial.ac.uk> wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
On 14/07/15 11:08, Justin Chang wrote:
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?
No, this is correct.
Let's check at point this is failing (I think it's failing early).
Does
python -c "import pyop2; pyop2.init(); print pyop2.__version__"
work?
Can you show also the output of the following:
ldd pyop2/sparsity.so ldd /path/to/petsc4py/PETSc.so ldd /path/to/petsc/libpetsc.so
?
Cheers,
Lawrence -----BEGIN PGP SIGNATURE----- Version: GnuPG v1
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