10. apr. 2014 kl. 16:02 skrev Miroslav Kuchta <[email protected]>: > On 04/10/2014 03:56 PM, Imran Ali wrote: >> 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 >> >> _______________________________________________ >> fenics-support mailing list >> [email protected] >> http://fenicsproject.org/mailman/listinfo/fenics-support > Hi Imran, > > this should be addressed to Mikael and not the fenics mailing list as > fenicstools is not an official part of fenics (despite the name :)). > Did you clone master branch or 1.3.0 branch? Judging from the error I'd say > master. Try 1.3.0 which is compatible with 1.3.0 release > of dolfin. > > Regards, Miro
Thanks for the heads-up and for helping me fix the problem. Using the branch I managed to install fenicstools successfully. I also found that I was missing some python modules and installed them as well. Kind regards, Imran _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
