dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Thursday 05 March 2009 14:31:23 Aron Wahlberg wrote:
> Finally...
>
> I have now managed to install FEniCS, but without trilinos and scotch
> (as you recommended Anders Logg).
>
> I have tried running the demo provided on the homepage but run into
> some errors, lots of them about malloc.
> I have then tried to run the different lines from the demo
> separateley - you'll see it below.  Do you see what I need to do?
>
> E.g. what to do about this:
> "C API version mismatch for module _cpp: This Python has API version
> 1013, module _cpp has version 1012"?

It looks like you have several versions of Python installed, or you have 
upgraded Python after you compiled your PyDOLFIN.

It also seems like you do not have pkg-config installed, see the last error 
message. 

Johan

> Aron
>
> ########################################################################
> ####################
>
>  >>> from dolfin import*
>
> /Users/aronwahlberg/Work/FEniCS/build/lib/python2.5/site-packages/
> dolfin/cpp.py:7: RuntimeWarning: Python
> C API version mismatch for module _cpp: This Python has API version
> 1013, module _cpp has version 1012.
>    import _cpp
>
>  >>> mesh = UnitSquare(32,32)
>
> Checking mesh ordering (finished).
>
>  >>> V = FunctionSpace(mesh, "CG", 1)
>
> python(5057) malloc: ***  Deallocation of a pointer not malloced:
> 0xa0b0da94; This could be a double free
> ), or free() called with the middle of an allocated block; Try
> setting environment variable MallocHelp to
> see tools to help debug
>
>  >>> class DirichletBoundary(SubDomain):
>
> ... def inside(self, x, on_boundary):
>    File "<stdin>", line 2
>      def inside(self, x, on_boundary):
>        ^
> IndentationError: expected an indented block
>
>  >>> class DirichletBoundary(SubDomain):
>
> ...     def inside(self, x, on_boundary):
> ...             return x[0] < DOLFIN_EPS or x[0] >1.0-DOLFIN_EPS
> ...
>
>  >>> u0 = Constant(mesh, 0.0)
>
> python(5057) malloc: ***  Deallocation of a pointer not malloced:
> 0xa0b0da94; This could be a double free
> ), or free() called with the middle of an allocated block; Try
> setting environment variable MallocHelp to
> see tools to help debug
> /Users/aronwahlberg/.instant/cache/
> dolfin_compile_function_c2c6ca28e8e29b2498da8bbcedb6ff5e/dolfin_compil
> _function_c2c6ca28e8e29b2498da8bbcedb6ff5e.py:7: RuntimeWarning:
> Python C API version mismatch for module
> _dolfin_compile_function_c2c6ca28e8e29b2498da8bbcedb6ff5e: This
> Python has API version 1013, module _dolf
> n_compile_function_c2c6ca28e8e29b2498da8bbcedb6ff5e has version 1012.
>    import _dolfin_compile_function_c2c6ca28e8e29b2498da8bbcedb6ff5e
>
>  >>> bc = DirichletBV(V, u0, DirichletBoundary())
>
> Traceback (most recent call last):
>    File "<stdin>", line 1, in <module>
> NameError: name 'DirichletBV' is not defined
>
>  >>> bc = DirichletBC(V, u0, DirichletBoundary())
>  >>> v = TestFunction(V)
>  >>> u = TrialFunction(V)
>  >>> f = Function(V, "500.0 * exp(-(pow(x[0] - 0.5, 2) + pow(x[1] -
>
> 0.5,2)) / 0.02)")
> Calling just-in-time (JIT) compiler, this may take some time...
> Traceback (most recent call last):
>    File "<stdin>", line 1, in <module>
>    File "/Users/aronwahlberg/Work/FEniCS/build/lib/python2.5/site-
> packages/dolfin/function.py", line 498,
> n __new__
>      cpp_base = compile_function([cpparg],[defaults])[0]
>    File "/Users/aronwahlberg/Work/FEniCS/build/lib/python2.5/site-
> packages/dolfin/compile_function.py", li
> e 335, in compile_function
>      function_classes = compile_function_code("\n\n".join
> (code_snippets),classnames)
>    File "/Users/aronwahlberg/Work/FEniCS/build/lib/python2.5/site-
> packages/dolfin/compile_function.py", li
> e 222, in compile_function_code
>      (includes, flags, libraries, libdirs) =
> instant.header_and_libs_from_pkgconfig("dolfin")
>    File "/Users/aronwahlberg/Work/FEniCS/build/lib/python2.5/site-
> packages/instant/config.py", line 13, in
> header_and_libs_from_pkgconfig
>      raise OSError("The pkg-config package is not installed on the
> system.")
> OSError: The pkg-config package is not installed on the system.
>
>  >>> a = dot(grad(v),grad(u))*dx
>
> _______________________________________________
> DOLFIN-dev mailing list
> DOLFIN-dev@xxxxxxxxxx
> http://www.fenics.org/mailman/listinfo/dolfin-dev