Johannes, Thanks for the indications. However, i have unistalled my likely-broken install and cannot try your suggestions. I have thus installed fenics as a vagrant box, which works flawlessy. I plan retrying the native install in the near future and I will report here any problems similar to this one.
Cheers, Davide On 10 July 2014 10:51, Johannes Ring <[email protected]> wrote: > On Tue, Jul 8, 2014 at 1:22 PM, Davide Lasagna <[email protected]> > wrote: > > I have installed dolfin from source and I get a segfault when running the > > demo-navier-stokes.py in the demo directory. > > > > Apparently the culprit is loading the xml mesh, i.e. at the line where > > > > mesh = Mesh("../lshape.xml.gz") > > > > is called. > > > > The full error message is > > > > [arcturus:32758] *** Process received signal *** > > [arcturus:32758] Signal: Segmentation fault (11) > > [arcturus:32758] Signal code: Address not mapped (1) > > [arcturus:32758] Failing at address: 0xa > > [arcturus:32758] [ 0] /usr/lib/libc.so.6(+0x33df0)[0x7f6ae8448df0] > > [arcturus:32758] [ 1] > > /usr/lib/libc.so.6(_IO_vfprintf+0x2279)[0x7f6ae845c499] > > [arcturus:32758] [ 2] > > /usr/lib/libc.so.6(__vasprintf_chk+0xb5)[0x7f6ae850e875] > > [arcturus:32758] [ 3] > > /usr/lib/libc.so.6(__asprintf_chk+0x82)[0x7f6ae850e7b2] > > [arcturus:32758] [ 4] > > /usr/lib64/openmpi/libmpi.so.1(ompi_mpi_init+0x2e2)[0x7f6acfa09b82] > > [arcturus:32758] [ 5] > > /usr/lib64/openmpi/libmpi.so.1(MPI_Init_thread+0xe0)[0x7f6acfa2fc80] > > [arcturus:32758] [ 6] > > > /usr/local/lib/libdolfin.so.1.4(_ZN6dolfin17SubSystemsManager8init_mpiEiPPci+0x88)[0x7f6adfdcbf28] > > [arcturus:32758] [ 7] > > > /usr/local/lib/libdolfin.so.1.4(_ZN6dolfin17SubSystemsManager8init_mpiEv+0x31)[0x7f6adfdcc181] > > [arcturus:32758] [ 8] > > > /usr/local/lib/libdolfin.so.1.4(_ZN6dolfin3MPI4sizeEP19ompi_communicator_t+0xd)[0x7f6adfdcb62d] > > [arcturus:32758] [ 9] > > > /usr/local/lib/libdolfin.so.1.4(_ZN6dolfin7XMLFilersERNS_4MeshE+0x34)[0x7f6adffad854] > > [arcturus:32758] [10] > > > /usr/local/lib/libdolfin.so.1.4(_ZN6dolfin4MeshC1ESs+0x23f)[0x7f6adfe051cf] > > [arcturus:32758] [11] > > > /usr/lib/python2.7/site-packages/dolfin/cpp/_mesh.so(+0xf5c5a)[0x7f6abc9c1c5a] > > [arcturus:32758] [12] > > /usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5d0b)[0x7f6ae8abf72b] > > [arcturus:32758] [13] > > /usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x830)[0x7f6ae8ac03c0] > > [arcturus:32758] [14] > /usr/lib/libpython2.7.so.1.0(+0x6e06d)[0x7f6ae8a4f06d] > > [arcturus:32758] [15] > > /usr/lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f6ae8a2b4c3] > > [arcturus:32758] [16] > /usr/lib/libpython2.7.so.1.0(+0x58a9d)[0x7f6ae8a39a9d] > > [arcturus:32758] [17] > > /usr/lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f6ae8a2b4c3] > > [arcturus:32758] [18] > > /usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x2efd)[0x7f6ae8abc91d] > > [arcturus:32758] [19] > > /usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x830)[0x7f6ae8ac03c0] > > [arcturus:32758] [20] > /usr/lib/libpython2.7.so.1.0(+0x6df9c)[0x7f6ae8a4ef9c] > > [arcturus:32758] [21] > > /usr/lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f6ae8a2b4c3] > > [arcturus:32758] [22] > /usr/lib/libpython2.7.so.1.0(+0x58a9d)[0x7f6ae8a39a9d] > > [arcturus:32758] [23] > > /usr/lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f6ae8a2b4c3] > > [arcturus:32758] [24] > /usr/lib/libpython2.7.so.1.0(+0x9e2d7)[0x7f6ae8a7f2d7] > > [arcturus:32758] [25] > /usr/lib/libpython2.7.so.1.0(+0x9d05f)[0x7f6ae8a7e05f] > > [arcturus:32758] [26] > > /usr/lib/libpython2.7.so.1.0(PyObject_Call+0x43)[0x7f6ae8a2b4c3] > > [arcturus:32758] [27] > > /usr/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3a5d)[0x7f6ae8abd47d] > > [arcturus:32758] [28] > > /usr/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x830)[0x7f6ae8ac03c0] > > [arcturus:32758] [29] > > /usr/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x19)[0x7f6ae8ac04b9] > > [arcturus:32758] *** End of error message *** > > Does it work if you run it with mpirun? Try: > > mpirun python demo_navier-stokes.py > > Also try to run the demo in a debugger. Run: > > gdb python > > Then, inside the debugger, run > > run demo_navier-stokes.py > > Then type "where" when you get the segfault and post the output here. > > BTW, does the C++ version of the demo work? > > Johannes >
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