[firedrake] error installing PyOP2

[Lawrence Mitchell]

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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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