I get the following runtime error while trying to import
fenicstools(https://github.com/mikaem/fenicstools)
RuntimeError: In instant.recompile: The module did not compile with
command 'make VERBOSE=1'
The compile log :
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found SWIG: /uio/hume/student-u29/imranal/Work/FEniCS/bin/swig
(found version "2.0.3")
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
DEBUG
-- Build files have been written to:
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393
/uio/hume/student-u29/imranal/Work/FEniCS/bin/cmake
-H/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393
-B/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393
--check-build-system CMakeFiles/Makefile.cmake 0
/uio/hume/student-u29/imranal/Work/FEniCS/bin/cmake -E
cmake_progress_start
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/CMakeFiles
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory
`/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393'
make -f CMakeFiles/source_file_lib.dir/build.make
CMakeFiles/source_file_lib.dir/depend
make[2]: Entering directory
`/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393'
cd
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393
&& /uio/hume/student-u29/imranal/Work/FEniCS/bin/cmake -E cmake_depends
"Unix Makefiles"
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/CMakeFiles/source_file_lib.dir/DependInfo.cmake
--color=
Dependee
"/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/CMakeFiles/source_file_lib.dir/DependInfo.cmake"
is newer than depender
"/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/CMakeFiles/source_file_lib.dir/depend.internal".
Dependee
"/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/CMakeFiles/CMakeDirectoryInformation.cmake"
is newer than depender
"/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/CMakeFiles/source_file_lib.dir/depend.internal".
Scanning dependencies of target source_file_lib
make[2]: Leaving directory
`/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393'
make -f CMakeFiles/source_file_lib.dir/build.make
CMakeFiles/source_file_lib.dir/build
make[2]: Entering directory
`/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393'
/uio/hume/student-u29/imranal/Work/FEniCS/bin/cmake -E
cmake_progress_report
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/CMakeFiles
3
[ 16%] Building CXX object CMakeFiles/source_file_lib.dir/Probe.cpp.o
/usr/bin/c++ -DDOLFIN_VERSION=\"1.3.0\" -DBOOST_UBLAS_NDEBUG
-DHAS_HDF5 -D_FORTIFY_SOURCE=2 -DHAS_SLEPC -DHAS_PETSC -DHAS_UMFPACK
-DHAS_SCOTCH -DHAS_PARMETIS -DHAS_CGAL
-DCGAL_DISABLE_ROUNDING_MATH_CHECK -DHAS_ZLIB -DHAS_MPI -DHAS_OPENMP
-DHAS_QT4 -DHAS_VTK -DNUMPY_VERSION_MAJOR="1 -DNUMPY_VERSION_MINOR=6
-DNUMPY_VERSION_MICRO=2 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION" -O2
-fpic -isystem /uio/hume/student-u29/imranal/Work/FEniCS/include
-isystem /usr/include/libxml2 -isystem
/uio/hume/student-u29/imranal/Work/FEniCS -isystem
/usr/include/openmpi-x86_64 -isystem
/uio/hume/student-u29/imranal/Work/FEniCS/include/eigen3 -isystem
/uio/hume/student-u29/imranal/Work/FEniCS/include/vtk-5.8
-I/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/.
-I/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/fenicstools/Probe
-I/uio/hume/student-u29/imranal/Work/FEniCS/include/python2.7
-I/uio/hume/student-u29/imranal/Work/FEniCS/lib64/python2.6/site-packages/petsc4py/include
-I/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/numpy/core/include
-I/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393
-o CMakeFiles/source_file_lib.dir/Probe.cpp.o -c
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp
In file included from
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:1:
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/fenicstools/Probe/Probe.h:73:
error: ISO C++ forbids declaration of ‘shared_ptr’ with no type
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/fenicstools/Probe/Probe.h:73:
error: invalid use of ‘::’
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/fenicstools/Probe/Probe.h:73:
error: expected ‘;’ before ‘<’ token
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/fenicstools/Probe/Probe.h:79:
error: ISO C++ forbids declaration of ‘unique_ptr’ with no type
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/fenicstools/Probe/Probe.h:79:
error: invalid use of ‘::’
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/fenicstools/Probe/Probe.h:79:
error: expected ‘;’ before ‘<’ token
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:
In constructor ‘dolfin::Probe::Probe(const dolfin::Array<double>&,
const dolfin::FunctionSpace&)’:
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:11:
error: class ‘dolfin::Probe’ does not have any field named ‘_element’
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:31:
error: ‘_element’ was not declared in this scope
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:37:
error: ‘dolfin_cell’ was not declared in this scope
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:40:
error: ‘_element’ was not declared in this scope
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:
In copy constructor ‘dolfin::Probe::Probe(const dolfin::Probe&)’:
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:72:
error: ‘_element’ was not declared in this scope
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:72:
error: ‘const class dolfin::Probe’ has no member named ‘_element’
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:73:
error: ‘dolfin_cell’ was not declared in this scope
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:73:
error: ‘const class dolfin::Probe’ has no member named ‘dolfin_cell’
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:73:
error: ‘const class dolfin::Probe’ has no member named ‘dolfin_cell’
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:
In member function ‘virtual void dolfin::Probe::eval(const
dolfin::Function&)’:
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:83:
error: ‘_element’ was not declared in this scope
/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/Probe.cpp:83:
error: ‘dolfin_cell’ was not declared in this scope
make[2]: *** [CMakeFiles/source_file_lib.dir/Probe.cpp.o] Error 1
make[2]: Leaving directory
`/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393'
make[1]: *** [CMakeFiles/source_file_lib.dir/all] Error 2
make[1]: Leaving directory
`/tmp/tmpqFAr1h2014-4-5-16-21_instant_a6caf104558e8b034b4d643ae7006f696bf2d3a3/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393'
make: *** [all] Error 2
_______________________________________________________
Here is the entire error message :
In [3]: from fenicstools import *
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
In instant.recompile: The module did not compile with command 'make
VERBOSE=1', see
'/uio/hume/student-u29/imranal/.instant/error/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/compile.log'
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call
last)
/uio/hume/student-u29/imranal/<ipython-input-3-989c67bf6f60> in
<module>()
----> 1 from fenicstools import *
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/fenicstools/__init__.py
in <module>()
----> 1 from Probe import Probe, Probes, StatisticsProbe,
StatisticsProbes
2 from StructuredGrid import StructuredGrid, ChannelGrid
3 from WeightedGradient import weighted_gradient_matrix,
compiled_gradient_module
4 from Interpolation import interpolate_nonmatching_mesh
5 from getMemoryUsage import getMemoryUsage
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/fenicstools/Probe.py
in <module>()
24 code = strip_essential_code(headers)
25 compiled_module = compile_extension_module(code=code,
source_directory=os.path.abspath(dolfin_folder),
---> 26 sources=sources,
include_dirs=[".", os.path.abspath(dolfin_folder)])
27
28 # Give the compiled classes some additional pythonic
functionality
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/compilemodules/jit.pyc
in mpi_jit(*args, **kwargs)
58 # Just call JIT compiler when running in serial
59 if MPI.num_processes() == 1:
---> 60 return local_jit(*args, **kwargs)
61
62 # Compile first on process 0
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.pyc
in compile_extension_module(code, module_name, additional_declarations,
additional_system_headers, **instant_kwargs)
446 code = code,
447 additional_declarations = _additional_declarations %
declaration_strs,
--> 448 **instant_kwargs)
449
450 sys.stdout.flush()
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/instant/build.pyc
in build_module(modulename, source_directory, code, init_code,
additional_definitions, additional_declarations, sources, wrap_headers,
local_headers, system_headers, include_dirs, library_dirs, libraries,
swigargs, swig_include_dirs, cppargs, lddargs, object_files, arrays,
generate_interface, generate_setup, cmake_packages, signature,
cache_dir)
540
541 # Recompile if necessary
--> 542 recompile(modulename, module_path,
new_compilation_checksum, build_system)
543
544 # --- Load, cache, and return module
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/instant/build.pyc
in recompile(modulename, module_path, new_compilation_checksum,
build_system)
149 os.remove(compilation_checksum_filename)
150 msg = "In instant.recompile: The module did not
compile with command '%s', see '%s'"
--> 151 instant_error(msg % (cmd,
compile_log_filename_dest))
152
153 finally:
/uio/hume/student-u29/imranal/Work/FEniCS/lib/python2.7/site-packages/instant/output.pyc
in instant_error(*message)
55 _log.error(*message)
56 text = message[0] % message[1:]
---> 57 raise RuntimeError(text)
58
59 def instant_assert(condition, *message):
RuntimeError: In instant.recompile: The module did not compile with
command 'make VERBOSE=1', see
'/uio/hume/student-u29/imranal/.instant/error/dolfin_compile_code_81c70be75d9c6745ab2e66980ac24393/compile.log'
_______________________________________________________
Imran
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