segfault with iterative linear solvers

Asked by Chaffra Affouda

I am getting the error below when running the demo-nonlinear-poisson.py wiht the iterative solver: gmres and others. I have tried PETSc and Epetra without success. Can anyone reproduce? I am using ubuntu oneiric with the trunk version of dolfin.

*** glibc detected *** /usr/bin/python: free(): invalid pointer: 0x0000000002fb7328 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7a6e6)[0x7f952bc996e6]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f952bc9d9cc]
/home/chaffra/Projects/Fenics/dolfin/build/dolfin/libdolfin.so.1.0(_ZN6dolfin26NonlinearVariationalSolver5solveEv+0xb0b)[0x7f9504e62beb]
/usr/local/lib/python2.7/dist-packages/dolfin/cpp/_fem.so(+0x498cf)[0x7f94f679a8cf]
/usr/bin/python(PyEval_EvalFrameEx+0x43f6)[0x4ba666]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python[0x449098]
/usr/bin/python(PyObject_Call+0x3a)[0x41ad2a]
/usr/bin/python(PyEval_EvalFrameEx+0x2246)[0x4b84b6]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalCode+0x32)[0x4bd802]
/usr/bin/python[0x4dcc22]
/usr/bin/python(PyRun_FileExFlags+0x84)[0x4dd7e4]
/usr/bin/python[0x4b3fe6]
/usr/bin/python(PyEval_EvalFrameEx+0x3ee1)[0x4ba151]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python[0x448edf]
/usr/bin/python(PyObject_Call+0x3a)[0x41ad2a]
/usr/bin/python(PyEval_EvalFrameEx+0x2246)[0x4b84b6]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalCode+0x32)[0x4bd802]
/usr/bin/python(PyEval_EvalFrameEx+0x339b)[0x4b960b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
/usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
/usr/bin/python(PyEval_EvalCode+0x32)[0x4bd802]
/usr/bin/python[0x4dcc22]
/usr/bin/python(PyRun_FileExFlags+0x84)[0x4dd7e4]
/usr/bin/python(PyRun_SimpleFileExFlags+0x17e)[0x4de2ee]
/usr/bin/python(Py_Main+0x4fd)[0x4ee6dd]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f952bc4030d]
/usr/bin/python[0x41cb69]
======= Memory map: ========

Question information

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Solved by:
Anders Logg
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Revision history for this message
Best Anders Logg (logg) said :
#1

It works fine for me. It also runs fine on our buildbots and one of
them is running Oneiric.

--
Anders

On Tue, Apr 03, 2012 at 04:41:17PM -0000, Chaffra Affouda wrote:
> New question #192533 on DOLFIN:
> https://answers.launchpad.net/dolfin/+question/192533
>
> I am getting the error below when running the demo-nonlinear-poisson.py wiht the iterative solver: gmres and others. I have tried PETSc and Epetra without success. Can anyone reproduce? I am using ubuntu oneiric with the trunk version of dolfin.
>
>
> *** glibc detected *** /usr/bin/python: free(): invalid pointer: 0x0000000002fb7328 ***
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(+0x7a6e6)[0x7f952bc996e6]
> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f952bc9d9cc]
> /home/chaffra/Projects/Fenics/dolfin/build/dolfin/libdolfin.so.1.0(_ZN6dolfin26NonlinearVariationalSolver5solveEv+0xb0b)[0x7f9504e62beb]
> /usr/local/lib/python2.7/dist-packages/dolfin/cpp/_fem.so(+0x498cf)[0x7f94f679a8cf]
> /usr/bin/python(PyEval_EvalFrameEx+0x43f6)[0x4ba666]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python[0x449098]
> /usr/bin/python(PyObject_Call+0x3a)[0x41ad2a]
> /usr/bin/python(PyEval_EvalFrameEx+0x2246)[0x4b84b6]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalCode+0x32)[0x4bd802]
> /usr/bin/python[0x4dcc22]
> /usr/bin/python(PyRun_FileExFlags+0x84)[0x4dd7e4]
> /usr/bin/python[0x4b3fe6]
> /usr/bin/python(PyEval_EvalFrameEx+0x3ee1)[0x4ba151]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python[0x448edf]
> /usr/bin/python(PyObject_Call+0x3a)[0x41ad2a]
> /usr/bin/python(PyEval_EvalFrameEx+0x2246)[0x4b84b6]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalCode+0x32)[0x4bd802]
> /usr/bin/python(PyEval_EvalFrameEx+0x339b)[0x4b960b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalFrameEx+0x7eb)[0x4b6a5b]
> /usr/bin/python(PyEval_EvalCodeEx+0x13d)[0x4bcd2d]
> /usr/bin/python(PyEval_EvalCode+0x32)[0x4bd802]
> /usr/bin/python[0x4dcc22]
> /usr/bin/python(PyRun_FileExFlags+0x84)[0x4dd7e4]
> /usr/bin/python(PyRun_SimpleFileExFlags+0x17e)[0x4de2ee]
> /usr/bin/python(Py_Main+0x4fd)[0x4ee6dd]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f952bc4030d]
> /usr/bin/python[0x41cb69]
> ======= Memory map: ========
>
>

Revision history for this message
Chaffra Affouda (chaffra) said :
#2

Thanks. I made a fresh install of dolfin and it is working now.

Revision history for this message
Chaffra Affouda (chaffra) said :
#3

Thanks Anders Logg, that solved my question.