Hi there,
I am trying to use a code (https://bitbucket.org/finsberg/mesh_generation/src/master/demo/echo_mesh.py) available in this repo (https://bitbucket.org/finsberg/mesh_generation/src/master/). The repo ‘readme’ instructions says that the code would run with FEniCS 2016.1.0 which i have installed along side yaml, H5py and other dependencies however when ever i try to run the above mentioned demo example i.e. echo_mesh.py i get the following error:-
RuntimeError: In instant.recompile: The module did not compile with command ‘python setup.py build_ext install --install-platlib=.’, see ‘/home/fenics/.instant/error/instant_module_6845b426e05ff4716ec6f00dca3bd42f992f71cb/compile.log’
The complete error message is pasted below:-
fenics@c882ac520eaa:~/shared/meshgen/demo$ python echo_mesh.py
Round off Error
In instant.recompile: The module did not compile with command ‘python setup.py build_ext install --install-platlib=.’, see ‘/home/fenics/.instant/error/instant_module_6845b426e05ff4716ec6f00dca3bd42f992f71cb/compile.log’
Traceback (most recent call last):
File “echo_mesh.py”, line 52, in
main()
File “echo_mesh.py”, line 42, in main
M.mesh()
File “/usr/local/lib/python2.7/dist-packages/mesh_generation/generate_mesh.py”, line 163, in mesh
mesh = self.generate_mesh()
File “/usr/local/lib/python2.7/dist-packages/mesh_generation/generate_mesh.py”, line 224, in generate_mesh
mesh, markers, data = create_mesh(**self.parameters)
File “/usr/local/lib/python2.7/dist-packages/mesh_generation/generate_mesh.py”, line 131, in create_mesh
mesh_char_len)
File “/usr/local/lib/python2.7/dist-packages/mesh_generation/generate_mesh.py”, line 75, in estimate_round_off_buffer
bounds=(-1.0,1.0), options={“xatol” : 0.01})
File “/usr/lib/python2.7/dist-packages/scipy/optimize/_minimize.py”, line 611, in minimize_scalar
return _minimize_scalar_bounded(fun, bounds, args, **options)
File “/usr/lib/python2.7/dist-packages/scipy/optimize/optimize.py”, line 1601, in _minimize_scalar_bounded
fx = func(x, *args)
File “/usr/local/lib/python2.7/dist-packages/mesh_generation/generate_mesh.py”, line 66, in measured_vs_computed_volume
return_domain = False)
File “/usr/local/lib/python2.7/dist-packages/mesh_generation/generate_mesh.py”, line 104, in create_mesh_w_round_off_buffer
marker_ids=fiber_markers)
File “/usr/local/lib/python2.7/dist-packages/mesh_generation/mesh_utils.py”, line 904, in create_lv_geometry
mesh, markers = geo2dolfin(geocode, marker_ids=marker_ids)
File “/usr/local/lib/python2.7/dist-packages/mesh_generation/gmsh/geo2dolfin.py”, line 59, in geo2dolfin
gmsh_cpp_geo2msh(geoname, topological_dimension, mshname, logname)
File “/usr/local/lib/python2.7/dist-packages/mesh_generation/gmsh/inline_backend.py”, line 79, in gmsh_cpp_geo2msh
func = gmsh_cpp_inline(code, extra_system_headers=headers)
File “/usr/local/lib/python2.7/dist-packages/mesh_generation/gmsh/inline_backend.py”, line 43, in gmsh_cpp_inline
return inline(code, **p)
File “/usr/local/lib/python2.7/dist-packages/instant/inlining.py”, line 54, in inline
module = build_module(**kwargs)
File “/usr/local/lib/python2.7/dist-packages/instant/build.py”, line 563, in build_module
recompile(modulename, module_path, new_compilation_checksum, build_system)
File “/usr/local/lib/python2.7/dist-packages/instant/build.py”, line 137, in recompile
instant_error(msg % (cmd, compile_log_filename_dest))
File “/usr/local/lib/python2.7/dist-packages/instant/output.py”, line 85, in instant_error
raise RuntimeError(text)
RuntimeError: In instant.recompile: The module did not compile with command ‘python setup.py build_ext install --install-platlib=.’, see ‘/home/fenics/.instant/error/instant_module_6845b426e05ff4716ec6f00dca3bd42f992f71cb/compile.log’
Aborted
I would be thankful if someone from the community can very kindly point towards the reason of this error and possible remedy.
Best Regards,
Ovais