dolfin examples don't compile

[Sean Farley]

Trying to update and test dolfin 1.5.0, I run the poisson example only to get:

$ python /opt/local/share/dolfin/demo/documented/poisson/python/demo_poisson.py
Calling FFC just-in-time (JIT) compiler, this may take some time.
In instant.recompile: The module did not compile with command 'make VERBOSE=1', see '/Users/sean/.instant/error/ffc_form_746ebe8521dc9d314e6f65075dbc60d03cfee94b/compile.log'
Traceback (most recent call last):
  File "/opt/local/share/dolfin/demo/documented/poisson/python/demo_poisson.py", line 41, in <module>
    V = FunctionSpace(mesh, "Lagrange", 1)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/functions/functionspace.py", line 468, in __init__
    FunctionSpaceBase.__init__(self, mesh, element, constrained_domain)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/functions/functionspace.py", line 153, in __init__
    ufc_element, ufc_dofmap = jit(self._ufl_element, mpi_comm=mesh.mpi_comm())
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 64, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 128, in jit
    return form_compiler.jit(form, parameters=p)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/jitcompiler.py", line 72, in jit
    return jit_element(ufl_object, parameters)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/jitcompiler.py", line 177, in jit_element
    compiled_form, module, prefix = jit_form(form, parameters)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/jitcompiler.py", line 148, in jit_form
    cache_dir = cache_dir)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ffc/backends/ufc/build.py", line 73, in build_ufc_module
    **kwargs)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/instant/build.py", line 563, in build_module
    recompile(modulename, module_path, new_compilation_checksum, build_system)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/instant/build.py", line 165, in recompile
    instant_error(msg % (cmd, compile_log_filename_dest))
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/instant/output.py", line 85, in instant_error
    raise RuntimeError(text)
RuntimeError: In instant.recompile: The module did not compile with command 'make VERBOSE=1', see '/Users/sean/.instant/error/ffc_form_746ebe8521dc9d314e6f65075dbc60d03cfee94b/compile.log'

Attached is the error log.

[Chris Richardson]

Have you also updated ffc, ufl, instant and FIAT? Have you tried removing your ~/.instant folder?

[Jan Blechta]

There is for some reason missing -std=c++11 in compiler flags. This probably prevents interpreting curly brackets. It could happen because you have still instant, ffc 1.3.0 as @chris_richardson suggested.

Please, raise the issue at [e-mail].

[Sean Farley]

ffc, ufl, instant, and FIAT were all updated to 1.5.0 (in fact, I did not have any previous installations). The ~/.instant folder was removed many times previous to me opening this issue. Any other ideas? I can post this at [e-mail] if that's the workflow preferred.

[Jan Blechta]

Ok, maybe we can solve it here. Is there -std=c++11 in <prefix>/share/ufc/UFCConfig.cmake, variable UFC_CXX_FLAGS? If not, try recompiling FFC with

git clean -fdx
export CXXFLAGS='-std=c++11'
python setup.py install --prefix=<prefix>

[Sean Farley]

Interesting. You are right that the UFC_CXX_FLAGS variable is missing -std=c++11. Adding that does fix the demo compilations. The problem here was that I am testing this in a sandboxed environment (MacPorts) so exporting environment variables isn't as straight-forward. I've fixed this in the ffc port; thanks for the help!

[Jan Blechta]

Nevertheless, flag should be found by has_cxx_flag function in <ffc>/setup.py which is not working on your machine for some reason. Could you find a problem so that it can be patched?

[Sean Farley]

This might be a MacPorts bug in the Python portgroup with it not sending the environment variables to every phase.

[Jan Blechta]

I don't think so. <ffc>/setup.py tries to check whether compiler has -std=c++11 flag and writes it to UFCConfig.cmake if so. I don't think it has anything to do with environment.

It seems that has_cxx_flag('-std=c++11) returns false on your system while it should return true. This is what you could debug so that the bug can be fixed.

[Sean Farley]

Ah, I see what you mean now. Yeah, I can try to debug and see what's up.

[Jan Blechta]

@seanfarley, any progress here?

[Sean Farley]

Sorry, got side tracked at work. I'll try to work on this at lunch.

[Sean Farley]

Apologies for the delay! I finally got this pinned down. The issue turned out to be a macports one because we lock out access to using bare compilers (e.g. 'cc'). A quick check of passing CC through the environment (which is how MacPorts passing around this compiler variable) didn't seem to work either. Having a way to specify the compiler would be great but that's out of the scope of this bug report.

Hope that helps!

[Jan Blechta]

Thanks @seanfarley . I have suggested a solution https://bitbucket.org/fenics-project/ffc/issue/65/compiler-flags-detection-in-setuppy-is#comment-15793394, sorry for not letting known here.

[Sean Farley]

Aha, yep, something like that looks like it would work. Thanks!