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Re: pydolfin error

To: Gideon Simpson <grs2103@xxxxxxxxxxxx>
From: Ola Skavhaug <skavhaug@xxxxxxxxx>
Date: Sat, 16 Feb 2008 02:45:31 +0100
Cc: dolfin-dev@xxxxxxxxxx
Delivered-to: dolfin-dev@xxxxxxxxxx
In-reply-to: <61895F0F-8E9F-49D4-9629-80417F5441A2@columbia.edu>
Mail-followup-to: Ola Skavhaug <skavhaug@xxxxxxxxx>, Gideon Simpson <grs2103@xxxxxxxxxxxx>, dolfin-dev@xxxxxxxxxx
User-agent: Mutt/1.5.15+20070412 (2007-04-11)
Gideon Simpson skrev den 15/02-2008 følgende:
> No good.  Same errors.
> -gideon

OK; in that case, the header files included when constructing the wrapper code
with SWIG is not the ones from the source directories. Do you have DOLFIN
installed under /usr/local/include/dolfin or so? In that case, try deleting
the include/dolfin directory. Also, is SWIG run prior to the compilation
error?

Please include the full error log (staring with you issuing the make command).
To get the error messages as well, try:

(make 2>&1) | tee error.log

Ola
 
> On Feb 15, 2008, at 8:25 PM, Ola Skavhaug wrote:
> 
> > Gideon Simpson skrev den 15/02-2008 følgende:
> >> having pulled the latest repositories of everything, i'm getting the
> >> following error when it comes time for pydoflin:
> >
> > You need to touch the interface file:
> >
> > touch src/pydolfin/dolfin.i
> > make && make install
> >
> > This is a flaw in the build system in DOLFIN, and should be resolved  
> > as soon
> > as the new SCons build system is in place.
> >
> > Ola
> >
> >>  mpicxx -DPACKAGE_NAME=\"DOLFIN\" -DPACKAGE_TARNAME=\"dolfin\" -
> >> DPACKAGE_VERSION=\"0.7.1\" "-DPACKAGE_STRING=\"DOLFIN 0.7.1\"" -
> >> DPACKAGE_BUGREPORT=\"http://www.fenics.org/bugzilla/\"; -
> >> DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -
> >> DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -
> >> DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -
> >> DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_BOOST= -DHAVE_UMFPACK_H=1 - 
> >> I.
> >> -I/System/Library/Frameworks/Python.framework/Versions/2.5/include/
> >> python2.5 -I../../src/kernel/common -I../../src/kernel/elements -
> >> I../../src/kernel/fem -I../../src/kernel/function -I../../src/kernel/
> >> graph -I../../src/kernel/io -I../../src/kernel/la -I../../src/kernel/
> >> main -I../../src/kernel/math -I../../src/kernel/mesh -I../../src/
> >> kernel/mf -I../../src/kernel/nls -I../../src/kernel/ode -I../../src/
> >> kernel/pde -I../../src/kernel/quadrature -I../../src/kernel/ 
> >> parameter -
> >> I../../src/kernel/log -I../../src/kernel/plot -I/opt/petsc-2.3.3-p8/
> >> bmake/darwin9.1.0-cxx-debug -I/opt/petsc-2.3.3-p8/include -I/opt/
> >> include -I/opt/include -I/opt/include -I/opt/slepc-2.3.3 -I/opt/
> >> slepc-2.3.3/include -I/opt/include/boost-1_34_1 -I/sw/include/ 
> >> libxml2 -
> >> I/sw/include -I/opt/petsc-2.3.3-p8/externalpackages/UMFPACKv4.3/
> >> darwin9.1.0-cxx-debug/UMFPACK/Include -I/sw/include/glib-2.0 -I/sw/ 
> >> lib/
> >> glib-2.0/include -I/opt/include -I../../src/pydolfin -I/System/ 
> >> Library/
> >> Frameworks/Python.framework/Versions/2.5/include/python2.5 -I/opt/ 
> >> lib/
> >> python2.5/site-packages/numpy/core/include -DHAVE_MPI_H=1 -
> >> DMPICH_IGNORE_CXX_SEEK -DHAVE_SLEPC_H=1 -DHAVE_PETSC_H=1 -DNDEBUG - 
> >> g -
> >> O2 -fno-strict-aliasing -Wall -Werror -ansi -Wno-uninitialized -MT
> >> _dolfin_la-dolfin_wrap.lo -MD -MP -MF .deps/_dolfin_la- 
> >> dolfin_wrap.Tpo
> >> -c dolfin_wrap.cpp  -fno-common -DPIC -o .libs/_dolfin_la- 
> >> dolfin_wrap.o
> >> dolfin_wrap.cpp: In function 'PyObject* _wrap_add(PyObject*,
> >> PyObject*)':
> >> dolfin_wrap.cpp:27560: error: 'add' is not a member of 'dolfin'
> >> dolfin_wrap.cpp: In function 'PyObject* _wrap_set__SWIG_0(PyObject*,
> >> PyObject*)':
> >> dolfin_wrap.cpp:27624: error: 'set' is not a member of 'dolfin'
> >> dolfin_wrap.cpp: In function 'PyObject* _wrap_set__SWIG_1(PyObject*,
> >> PyObject*)':
> >> dolfin_wrap.cpp:27682: error: 'set' is not a member of 'dolfin'
> >> dolfin_wrap.cpp: In function 'PyObject* _wrap_get(PyObject*,
> >> PyObject*)':
> >> dolfin_wrap.cpp:27776: error: 'get' is not a member of 'dolfin'
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_0(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:85644: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:85644: error: 'arg3' was not declared in this scope
> >> dolfin_wrap.cpp:85680: error: expected type-specifier
> >> dolfin_wrap.cpp:85680: error: expected `>'
> >> dolfin_wrap.cpp:85680: error: expected `('
> >> dolfin_wrap.cpp:85680: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:85680: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:85680: error: expected `)' before ';' token
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_1(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:85721: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:85721: error: 'arg3' was not declared in this scope
> >> dolfin_wrap.cpp:85753: error: expected type-specifier
> >> dolfin_wrap.cpp:85753: error: expected `>'
> >> dolfin_wrap.cpp:85753: error: expected `('
> >> dolfin_wrap.cpp:85753: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:85753: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:85753: error: expected `)' before ';' token
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_2(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:85789: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:85789: error: 'arg3' was not declared in this scope
> >> dolfin_wrap.cpp:85829: error: expected type-specifier
> >> dolfin_wrap.cpp:85829: error: expected `>'
> >> dolfin_wrap.cpp:85829: error: expected `('
> >> dolfin_wrap.cpp:85829: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:85829: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:85829: error: expected `)' before ';' token
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_3(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:85878: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:85878: error: 'arg3' was not declared in this scope
> >> dolfin_wrap.cpp:85914: error: expected type-specifier
> >> dolfin_wrap.cpp:85914: error: expected `>'
> >> dolfin_wrap.cpp:85914: error: expected `('
> >> dolfin_wrap.cpp:85914: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:85914: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:85914: error: expected `)' before ';' token
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_4(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:85958: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:85958: error: 'arg3' was not declared in this scope
> >> dolfin_wrap.cpp:86006: error: expected type-specifier
> >> dolfin_wrap.cpp:86006: error: expected `>'
> >> dolfin_wrap.cpp:86006: error: expected `('
> >> dolfin_wrap.cpp:86006: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:86006: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:86006: error: expected `)' before ';' token
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_5(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:86071: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:86071: error: 'arg3' was not declared in this scope
> >> dolfin_wrap.cpp:86115: error: expected type-specifier
> >> dolfin_wrap.cpp:86115: error: expected `>'
> >> dolfin_wrap.cpp:86115: error: expected `('
> >> dolfin_wrap.cpp:86115: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:86115: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:86115: error: expected `)' before ';' token
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_6(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:86174: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:86174: error: 'arg2' was not declared in this scope
> >> dolfin_wrap.cpp:86196: error: expected type-specifier
> >> dolfin_wrap.cpp:86196: error: expected `>'
> >> dolfin_wrap.cpp:86196: error: expected `('
> >> dolfin_wrap.cpp:86196: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:86196: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:86196: error: expected `)' before ';' token
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_7(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:86231: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:86231: error: 'arg2' was not declared in this scope
> >> dolfin_wrap.cpp:86257: error: expected type-specifier
> >> dolfin_wrap.cpp:86257: error: expected `>'
> >> dolfin_wrap.cpp:86257: error: expected `('
> >> dolfin_wrap.cpp:86257: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:86257: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:86257: error: expected `)' before ';' token
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_8(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:86300: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:86300: error: 'arg2' was not declared in this scope
> >> dolfin_wrap.cpp:86334: error: expected type-specifier
> >> dolfin_wrap.cpp:86334: error: expected `>'
> >> dolfin_wrap.cpp:86334: error: expected `('
> >> dolfin_wrap.cpp:86334: error: 'pForm' is not a member of 'dolfin'
> >> dolfin_wrap.cpp:86334: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:86334: error: expected `)' before ';' token
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_9(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:86396: error: 'pDofMapSet' is not a member of  
> >> 'dolfin'
> >> dolfin_wrap.cpp:86396: error: 'arg5' was not declared in this scope
> >> dolfin_wrap.cpp:86466: error: expected type-specifier
> >> dolfin_wrap.cpp:86466: error: expected `>'
> >> dolfin_wrap.cpp:86466: error: expected `('
> >> dolfin_wrap.cpp:86466: error: 'pDofMapSet' is not a member of  
> >> 'dolfin'
> >> dolfin_wrap.cpp:86466: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:86466: error: expected `)' before ';' token
> >> dolfin_wrap.cpp:86489: error: 'pDofMapSet' is not a member of  
> >> 'dolfin'
> >> dolfin_wrap.cpp:86489: error: expected `)' before 'const'
> >> dolfin_wrap.cpp: In function 'PyObject*
> >> _wrap_pAssembler_assemble__SWIG_10(PyObject*, PyObject*)':
> >> dolfin_wrap.cpp:86524: error: 'pDofMapSet' is not a member of  
> >> 'dolfin'
> >> dolfin_wrap.cpp:86524: error: 'arg5' was not declared in this scope
> >> dolfin_wrap.cpp:86590: error: expected type-specifier
> >> dolfin_wrap.cpp:86590: error: expected `>'
> >> dolfin_wrap.cpp:86590: error: expected `('
> >> dolfin_wrap.cpp:86590: error: 'pDofMapSet' is not a member of  
> >> 'dolfin'
> >> dolfin_wrap.cpp:86590: error: expected primary-expression before '>'
> >> token
> >> dolfin_wrap.cpp:86590: error: expected `)' before ';' token
> >> dolfin_wrap.cpp:86608: error: 'pDofMapSet' is not a member of  
> >> 'dolfin'
> >> dolfin_wrap.cpp:86608: error: expected `)' before 'const'
> >> make[3]: *** [_dolfin_la-dolfin_wrap.lo] Error 1
> >> make[2]: *** [all] Error 2
> >> make[1]: *** [all-recursive] Error 1
> >> make: *** [all-recursive] Error 1
> >>
> >> _______________________________________________
> >> DOLFIN-dev mailing list
> >> DOLFIN-dev@xxxxxxxxxx
> >> http://www.fenics.org/mailman/listinfo/dolfin-dev
> 
> _______________________________________________
> DOLFIN-dev mailing list
> DOLFIN-dev@xxxxxxxxxx
> http://www.fenics.org/mailman/listinfo/dolfin-dev
References

pydolfin error
From: Gideon Simpson, 2008-02-16
Re: pydolfin error
From: Ola Skavhaug, 2008-02-16
Re: pydolfin error
From: Gideon Simpson, 2008-02-16