[firedrake] error installing PyOP2
Justin Chang
jychang48 at gmail.com
Tue Jul 14 11:23:06 BST 2015
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 at 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 at 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 at 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 at 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
>
> iQEcBAEBAgAGBQJVpOCSAAoJECOc1kQ8PEYvmzEH/1L+/xClpLIwQIyLpcHMGgaL
> Ol9p/5xOEbLdCotx8kWgDmTtxfoyZEnU50GIEjvB0nQYCEfpD/kILpf6FmjVpl1W
> vh3dlPV3Mro7P79k4nY2On+HL4mgwCNjkddS1/v44uHVgZTki6YXU7BpNaDImDL1
> iCHNyrlZeAcGQhPb/suGR9Ad/ivH+cL332qzMgx411Lt236F/fOpTUlrdMOLS39C
> IXjwNKxYOAQ3LmRLtmF9E8B8mw/cDa5gJReEPOCKkZW2mEuAQLtyA6tW8qJdOgrs
> 20ZVTAJkgEyty6D3tvl5ToBy8JySAW1VB+G5t30pNnD8p6slD7EOPpGBvlXqzkE=
> =glNH
> -----END PGP SIGNATURE-----
>
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