Hello,
I installed FEniCS 1.5.0 (for Mac OS 10.9) and I cannot run any of the old codes I had any more. The error seems to be when compiling the Expressions.
For example, for the following (which is actually an example I copied from one of the FEniCS demos):
from dolfin import *
mesh = UnitSquareMesh(3, 3)
# Mark boundaries of original mesh
bdry = FacetFunction('size_t', mesh, 0)
DomainBoundary().mark(bdry, 10)
# Function space for displacement u
V = VectorFunctionSpace(mesh, 'CG', 1)
# Shear displacement
u = interpolate(Expression(('0.25*x[1]', '0')), V)
plot(bdry, title='Initial', interactive=True)
# Move the mesh
mesh.move(u)
plot(bdry, title='Moved', interactive=True)
# Revert manually
x, y = mesh.coordinates()[:, 0], mesh.coordinates()[:, 1]
x -= 0.25*y
plot(bdry, title='And back', interactive=True)
The error message I get is as follows:
In instant.recompile: The module did not compile with command 'make VERBOSE=1', see '/Users/debanjan-shaddenlab/.instant/error/dolfin_compile_code_5295871d33b17b4758523c206c35ce895941b320/compile.log'
Traceback (most recent call last):
File "mesh-move-fenics-forum.py", line 11, in <module>
u = interpolate(Expression(('0.25*x[1]', '0')), V)
File "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/functions/expression.py", line 602, in __new__
mpi_comm=mpi_comm)
File "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 217, in compile_expressions
mpi_comm=mpi_comm)
File "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", line 145, in compile_expression_code
mpi_comm=mpi_comm)
File "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 64, in mpi_jit
return local_jit(*args, **kwargs)
File "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.py", line 458, in compile_extension_module
**instant_kwargs)
File "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/instant/build.py", line 563, in build_module
recompile(modulename, module_path, new_compilation_checksum, build_system)
File "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/instant/build.py", line 165, in recompile
instant_error(msg % (cmd, compile_log_filename_dest))
File "/Applications/FEniCS.app/Contents/Resources/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/debanjan-shaddenlab/.instant/error/dolfin_compile_code_5295871d33b17b4758523c206c35ce895941b320/compile.log'
I also checked the log file, and it seems like the error is originating from the following:
fatal error: 'numpy/arrayobject.h' file not found
71 #include <numpy/arrayobject.h>
72 ^
73 1 error generated.
74 make[2]: *** [CMakeFiles/_dolfin_compile_code_21b017147821a4e96e4d0e94f3a17c6708c1f661.dir/dolfin_compile_code_21b017147821a4e96e4d0e94f3a17c6708c1f661PYTHON_wrap.cxx.o] Error 1
75 make[1]: *** [CMakeFiles/_dolfin_compile_code_21b017147821a4e96e4d0e94f3a17c6708c1f661.dir/all] Error 2
76 make: *** [all] Error 2
I have however not yet been able to work out the issue. I have checked and I have the latest numpy installed, and also latest scipy. Can someone provide some tips, or help creating a cleaner alternative installation?
Thanks
Further Information
Tried installing FEniCS 1.4.0 - and this gives an error saying module python-scientific is not installed.
Tried installing from source by running
curl -s http://fenicsproject.org/fenics-install.sh | bash
This did not complete the installation - and gave an error when the python build was initiated.
Any help will be very valuable.
Thanks
