Neil Hopcroft

Build #338 of dolfin failed with this error:

[ 98%] Building CXX object dolfin/swig/modules/function/CMakeFiles/_function.dir/modulePYTHON_wrap.cxx.o
/usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/function/modulePYTHON_wrap.cxx: In function ‘PyObject* _wrap_Function_non_matching_eval(PyObject*, PyObject*)’:
/usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/function/modulePYTHON_wrap.cxx:11623:41: error: ‘const class dolfin::Function’ has no member named ‘non_matching_eval’
((dolfin::Function const *)arg1)->non_matching_eval(*arg2,(dolfin::Array< double > const &)*arg3,(ufc::cell const &)*arg4);
^

Which seems like it is probably caused by this commit:

Commit 88a38a716b887b9d8d7ba0d5ce9e33a410907bbf by gnw20
Remove deprecated functions slated for removal with 1.7 release.

Then, in build #340 the error becomes:

CMake Error at CMakeLists.txt:889 (message):
Generation of form files failed:

Traceback (most recent call last):

File “/usr/local/bin/ffc”, line 213, in
sys.exit(main(sys.argv[1:]))
File “/usr/local/bin/ffc”, line 187, in main
compile_form(ufd.forms, ufd.object_names, prefix, parameters)
File “/usr/local/lib64/python2.7/site-packages/ffc/compiler.py”, line 154, in compile_form
analysis = analyze_forms(forms, parameters)
File “/usr/local/lib64/python2.7/site-packages/ffc/analysis.py”, line 67, in analyze_forms
unique_elements = sort_elements(unique_elements)
File “/usr/local/lib/python2.7/site-packages/ufl/algorithms/analysis.py”, line 205, in sort_elements
sorted_elements = topological_sorting(nodes, edges)
File “/usr/local/lib/python2.7/site-packages/ufl/utils/sorting.py”, line 36, in topological_sorting
S = nodes[:]

TypeError: ‘set’ object has no attribute ‘__getitem__’

Traceback (most recent call last):

File “/usr/share/tomcat7/.jenkins/workspace/dolfin/cmake/scripts/generate-form-files”, line 80, in
raise RuntimeError(“Unable to compile form: %s/%s” % (root, f))

RuntimeError: Unable to compile form: dolfin/ale/Poisson2D.ufl

This build was caused by completion of ffc build #45, looking at the changelog for ffc, this change is the most likely candidate:

Commit bd892c555ed4f751e7dc149c15b2b0799da75a68 by martinal
Fixes and simplifications of element analysis.

I notice the ffc build doesn’t include a clean step, so trying to add that before investigating further.
This error was fixed in build #352, but I can’t see a specific change that would have caused the fix – this always worries me, having something magically fix itself without really understanding why. But I’m not going to investigate too much further – there were a lot of upstream changes feeding into this build, so it could be any one of those.
However, we are still left with a further error:

/usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/function/modulePYTHON_wrap.cxx: In function ‘PyObject* _wrap_Function_non_matching_eval(PyObject*, PyObject*)’:
/usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/function/modulePYTHON_wrap.cxx:11551:41: error: ‘const class dolfin::Function’ has no member named ‘non_matching_eval’
((dolfin::Function const *)arg1)->non_matching_eval(*arg2,(dolfin::Array< double > const &)*arg3,(ufc::cell const &)*arg4);
^
make[2]: *** [dolfin/swig/modules/function/CMakeFiles/_function.dir/modulePYTHON_wrap.cxx.o] Error 1

This changes in build #362, to become:

/usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:27303:64: error: no matching function for call to ‘dolfin::Cell::get_vertex_coordinates(double*&) const’
((dolfin::Cell const *)arg1)->get_vertex_coordinates(arg2);
^
/usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:27303:64: note: candidate is:
In file included from /usr/share/tomcat7/.jenkins/workspace/dolfin/dolfin/function/FunctionSpace.h:38:0,
from /usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:3862:
/usr/share/tomcat7/.jenkins/workspace/dolfin/dolfin/mesh/Cell.h:338:10: note: void dolfin::Cell::get_vertex_coordinates(std::vector&) const
void get_vertex_coordinates(std::vector& coordinates) const
^
/usr/share/tomcat7/.jenkins/workspace/dolfin/dolfin/mesh/Cell.h:338:10: note: no known conversion for argument 1 from ‘double*’ to ‘std::vector&’
make[2]: *** [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/modulePYTHON_wrap.cxx.o] Error 1

And, finally, in build #366 to become:

Linking CXX shared library libdolfin.so
/usr/bin/ld: cannot find -lvtkftgl
/usr/bin/ld: cannot find -lvtkftgl
collect2: error: ld returned 1 exit status

Which looks to be something missing from the vtk build. Again, vtk doesn’t include a clean step (why is this missing from the default Jenkins project setup?), so I’m going to try adding that and rebuilding before I do any further investigating.
Build #375 introduces:

[ 79%] Building CXX object dolfin/CMakeFiles/dolfin.dir/fem/FiniteElement.cpp.o
/usr/share/tomcat7/.jenkins/workspace/dolfin/dolfin/fem/FiniteElement.cpp: In member function ‘void dolfin::FiniteElement::tabulate_dof_coordinates(boost::multi_array&, const std::vector&, const dolfin::Cell&) const’:
/usr/share/tomcat7/.jenkins/workspace/dolfin/dolfin/fem/FiniteElement.cpp:52:17: error: ‘const class ufc::finite_element’ has no member named ‘tabulate_dof_coordinates’
_ufc_element->tabulate_dof_coordinates(coordinates.data(),
^
make[2]: *** [dolfin/CMakeFiles/dolfin.dir/fem/FiniteElement.cpp.o] Error 1

Which is fixed again in #376.
Then #380 gives a lot more library problems:

Linking CXX shared library libdolfin.so
/usr/bin/ld: cannot find -lvtkGUISupportQtOpenGL
/usr/bin/ld: cannot find -lvtkRenderingOpenGL
/usr/bin/ld: cannot find -lvtkRenderingLIC
/usr/bin/ld: cannot find -lvtkgl2ps
/usr/bin/ld: cannot find -lvtkRenderingContextOpenGL
/usr/bin/ld: cannot find -lvtkRenderingVolumeOpenGL
/usr/bin/ld: cannot find -lvtkftgl
/usr/bin/ld: cannot find -lvtkRenderingGL2PS
/usr/bin/ld: cannot find -lvtkGUISupportQtOpenGL
/usr/bin/ld: cannot find -lvtkRenderingOpenGL
/usr/bin/ld: cannot find -lvtkRenderingLIC
/usr/bin/ld: cannot find -lvtkgl2ps
/usr/bin/ld: cannot find -lvtkRenderingContextOpenGL
/usr/bin/ld: cannot find -lvtkRenderingVolumeOpenGL
/usr/bin/ld: cannot find -lvtkftgl
/usr/bin/ld: cannot find -lvtkRenderingGL2PS
collect2: error: ld returned 1 exit status

These were introduced by changes in vtk build #92. The most likely candidate for this error is “Commit 7bb212d348f7e913edc6504b14fbec797ee44f78 FindPythonLibs Py3k fixes from cmake master.” which alters library and include directories for python 3, but we’re using 2.7.
Build #431 introduces another error:

CMake Error at CMakeLists.txt:883 (message):
Generation of form files failed:

Traceback (most recent call last):

File “/usr/local/bin/ffc”, line 213, in
sys.exit(main(sys.argv[1:]))
File “/usr/local/bin/ffc”, line 187, in main
compile_form(ufd.forms, ufd.object_names, prefix, parameters)
File “/usr/local/lib64/python2.7/site-packages/ffc/compiler.py”, line 174, in compile_form
wrapper_code = generate_wrapper_code(analysis, prefix, object_names, parameters)
File “/usr/local/lib64/python2.7/site-packages/ffc/wrappers.py”, line 40, in generate_wrapper_code
return _generate_dolfin_wrapper(analysis, prefix, object_names, parameters)
File “/usr/local/lib64/python2.7/site-packages/ffc/wrappers.py”, line 47, in _generate_dolfin_wrapper
(capsules, common_space) = _encapsulate(prefix, object_names, analysis, parameters)
File “/usr/local/lib64/python2.7/site-packages/ffc/wrappers.py”, line 80, in _encapsulate
(i, form_data) in enumerate(form_datas)]
File “/usr/local/lib64/python2.7/site-packages/ffc/wrappers.py”, line 100, in _encapsule_form
make_classname(prefix, “form”, i),

NameError: global name ‘make_classname’ is not defined

Which was probably introduced by changes in ffc build #65 and persists until build #441, when we return to the missing vtk libraries error.
Build #468 again introduces what appears to be an ffc error:

CMake Error at CMakeLists.txt:883 (message):
Generation of form files failed:

Traceback (most recent call last):

File “/usr/local/bin/ffc”, line 213, in
sys.exit(main(sys.argv[1:]))
File “/usr/local/bin/ffc”, line 187, in main
compile_form(ufd.forms, ufd.object_names, prefix, parameters)
File “/usr/local/lib64/python2.7/site-packages/ffc/compiler.py”, line 159, in compile_form
ir = compute_ir(analysis, prefix, parameters)
File “/usr/local/lib64/python2.7/site-packages/ffc/representation.py”, line 108, in compute_ir
for (i, fd) in enumerate(form_datas)]
File “/usr/local/lib64/python2.7/site-packages/ffc/representation.py”, line 381, in _compute_form_ir
ir[“max_%s_subdomain_id” % integral_type] = form_data.max_subdomain_ids.get(integral_type, 0)

AttributeError: ‘FormData’ object has no attribute ‘max_subdomain_ids’

Which remains in build #472.
To attempt to resolve the link errors for vtk libraries, I have made a number of symlinks removing the version numbers from the library names, but I can’t test this until the most recent ffc error has been resolved.
The symlinks resolve the link errors in build #475, but I’m left with some further errors:

/usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx: In function ‘PyObject* _wrap_CellType_refine_cell(PyObject*, PyObject*)’:
/usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:16065:41: error: ‘const class dolfin::CellType’ has no member named ‘refine_cell’
((dolfin::CellType const *)arg1)->refine_cell(*arg2,*arg3,*arg4);
^
/usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx: In function ‘PyObject* _wrap_MeshGeometry_x__SWIG_0(PyObject*, int, PyObject**)’:
/usr/share/tomcat7/.jenkins/workspace/dolfin/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:18402:47: error: lvalue required as unary ‘&’ operand
result = (double *) &(arg1)->x(arg2,arg3);
^

I’ll tackle this in another post – this has gotten long enough already.