Building FEniCS from source - boost errors

[Justin Chang]

Hi all,

I am attempting to build FEniCS from source locally on my RHEL cluster. For building DOLFIN, it says one of the missing required packages was boost, so I installed boost 1.6.3. However when I get to the cmake step, this is the output:

$ cmake .. -DCMAKE_INSTALL_PREFIX=/home/jchang23/.local
-- The C compiler identification is GNU 4.9.2
-- The CXX compiler identification is GNU 4.9.2
-- Check for working C compiler: /share/apps/gcc-4.9.2/bin/gcc
-- Check for working C compiler: /share/apps/gcc-4.9.2/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /share/apps/gcc-4.9.2/bin/g++
-- Check for working CXX compiler: /share/apps/gcc-4.9.2/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of size_t
-- Check size of size_t - done
-- Found MPI_C: /share/apps/openmpi-1.8.3/lib/libmpi.so 
-- Found MPI_CXX: /share/apps/openmpi-1.8.3/lib/libmpi_cxx.so;/share/apps/openmpi-1.8.3/lib/libmpi.so 
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp 
-- Performing Test OPENMP_UINT_TEST_RUNS
-- Performing Test OPENMP_UINT_TEST_RUNS - Success
CMake Warning at cmake/modules/FindBoost.cmake:761 (message):
  Imported targets not available for Boost version 106300
Call Stack (most recent call first):
  cmake/modules/FindBoost.cmake:865 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/modules/FindBoost.cmake:1452 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:330 (find_package)


CMake Warning at cmake/modules/FindBoost.cmake:761 (message):
  Imported targets not available for Boost version 106300
Call Stack (most recent call first):
  cmake/modules/FindBoost.cmake:865 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/modules/FindBoost.cmake:1452 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:330 (find_package)


CMake Warning at cmake/modules/FindBoost.cmake:761 (message):
  Imported targets not available for Boost version 106300
Call Stack (most recent call first):
  cmake/modules/FindBoost.cmake:865 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/modules/FindBoost.cmake:1452 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:330 (find_package)


CMake Warning at cmake/modules/FindBoost.cmake:761 (message):
  Imported targets not available for Boost version 106300
Call Stack (most recent call first):
  cmake/modules/FindBoost.cmake:865 (_Boost_COMPONENT_DEPENDENCIES)
  cmake/modules/FindBoost.cmake:1452 (_Boost_MISSING_DEPENDENCIES)
  CMakeLists.txt:330 (find_package)


-- Boost version: 1.63.0
-- Found the following Boost libraries:
--   filesystem
--   program_options
--   iostreams
--   timer
-- Found Eigen3: /home/jchang23/.local/include/eigen3 (Required is at least version "3.2.0")
-- Found PythonInterp: /home/jchang23/.local/bin/python2.7 (found suitable version "2.7.10", minimum required is "2.7")
-- Found PythonLibs: /home/jchang23/.local/lib/libpython2.7.a (found suitable exact version "2.7.10")
-- NumPy header version 1.11.3 found
-- Found PY_ply: /home/jchang23/.local/lib/python2.7/site-packages/ply-3.9-py2.7.egg/ply 
-- Found SWIG: /home/jchang23/.local/bin/swig (found version "3.0.11")
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named ffc
-- UFC could not be found. (missing:  UFC_INCLUDE_DIRS UFC_VERSION UFC_VERSION_OK UFC_SIGNATURE) (Required is at least version "2017.1")
-- Checking for package 'PETSc'
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")
-- Checking for one of the modules 'craypetsc_real;PETSc'
-- PETSc could not be found. Be sure to set PETSC_DIR. (missing:  PETSC_FOUND) (Required is at least version "3.7")
-- ParMETIS could not be found/configured. (missing:  PARMETIS_LIBRARIES PARMETIS_TEST_RUNS PARMETIS_INCLUDE_DIRS PARMETIS_VERSION PARMETIS_VERSION_OK) (Required is at least version "4.0.2")
-- Checking for package 'SCOTCH-PT'
-- SCOTCH could not be found. Be sure to set SCOTCH_DIR. (missing:  SCOTCH_LIBRARIES SCOTCH_INCLUDE_DIRS SCOTCH_TEST_RUNS)
-- Checking for package 'AMD'
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE 
-- Checking for package 'UMFPACK'
-- Checking for package 'AMD'
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- Found BLAS: /usr/lib64/libblas.so
-- UMFPACK could not be found. Be sure to set UMFPACK_DIR. (missing:  UMFPACK_INCLUDE_DIRS AMD_LIBRARIES UMFPACK_TEST_RUNS)
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- Found BLAS: /usr/lib64/libblas.so
-- CHOLMOD could not be found. Be sure to set CHOLMOD_DIR. (missing:  CHOLMOD_INCLUDE_DIRS CHOLMOD_TEST_RUNS)
-- Could NOT find HDF5 (missing:  HDF5_LIBRARIES HDF5_INCLUDE_DIRS C)
-- Checking for Trilinos
CMake Warning at CMakeLists.txt:556 (find_package):
  Could not find a package configuration file provided by "Trilinos" with any
  of the following names:

    TrilinosConfig.cmake
    trilinos-config.cmake

  Add the installation prefix of "Trilinos" to CMAKE_PREFIX_PATH or set
  "Trilinos_DIR" to a directory containing one of the above files.  If
  "Trilinos" provides a separate development package or SDK, be sure it has
  been installed.


-- Unable to find Trilinos (>= 12.4.0)
-- Trilinos could not be found
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Checking for package 'Sphinx'
-- Could NOT find Sphinx (missing:  SPHINX_EXECUTABLE SPHINX_VERSION_OK) (Required is at least version "1.1.0")
CMake Warning at CMakeLists.txt:649 (find_package):
  Could not find a package configuration file provided by "VTK" with any of
  the following names:

    VTKConfig.cmake
    vtk-config.cmake

  Add the installation prefix of "VTK" to CMAKE_PREFIX_PATH or set "VTK_DIR"
  to a directory containing one of the above files.  If "VTK" provides a
  separate development package or SDK, be sure it has been installed.


--
-- The following features have been enabled:

 * BUILD_SHARED_LIBS , Build DOLFIN with shared libraries.
 * DOLFIN_AUTO_DETECT_MPI , Detect MPI automatically (turn this off to use the MPI compiler wrappers directly via setting CXX, CXX, FC).
 * DOLFIN_WITH_LIBRARY_VERSION , Build with library version information.
 * DOLFIN_ENABLE_GTEST , Enable C++ unit tests with Google Test if DOLFIN_ENABLE_TESTING is true (requires Internet connection to download Google Test when first configured).
 * DOLFIN_ENABLE_DOCS , Enable generation of documentation.
 * CMAKE_INSTALL_RPATH_USE_LINK_PATH , Add paths to linker search and installed rpath.
 * DOLFIN_ENABLE_OPENMP , Compile with support for OpenMP.
 * DOLFIN_ENABLE_MPI , Compile with support for MPI.
 * DOLFIN_ENABLE_PETSC , Compile with support for PETSc.
 * DOLFIN_ENABLE_PETSC4PY , Compile with support for PETSc4py.
 * DOLFIN_ENABLE_SLEPC , Compile with support for SLEPc.
 * DOLFIN_ENABLE_SLEPC4PY , Compile with support for SLEPc4py.
 * DOLFIN_ENABLE_TRILINOS , Compile with support for Trilinos.
 * DOLFIN_ENABLE_UMFPACK , Compile with support for UMFPACK.
 * DOLFIN_ENABLE_CHOLMOD , Compile with support for CHOLMOD.
 * DOLFIN_ENABLE_SCOTCH , Compile with support for SCOTCH.
 * DOLFIN_ENABLE_PARMETIS , Compile with support for ParMETIS.
 * DOLFIN_ENABLE_ZLIB , Compile with support for zlib.
 * DOLFIN_ENABLE_PYTHON , Compile with support for Python.
 * DOLFIN_ENABLE_SPHINX , Compile with support for Sphinx.
 * DOLFIN_ENABLE_HDF5 , Compile with support for HDF5.
 * DOLFIN_ENABLE_VTK , Compile with support for VTK.

-- The following OPTIONAL packages have been found:

 * MPI , Message Passing Interface (MPI)
   Enables DOLFIN to run in parallel with MPI
 * OpenMP , Open Multi-Processing API
   Enables DOLFIN to run in parallel with OpenMP
 * BLAS , Basic Linear Algebra Subprograms , <http://netlib.org/blas/>
 * Threads
 * ZLIB , Compression library , <http://www.zlib.net>

-- The following REQUIRED packages have been found:

 * Boost , Boost C++ libraries , <http://www.boost.org>
 * Eigen3 (required version >= 3.2.0) , Lightweight C++ template library for linear algebra , <http://eigen.tuxfamily.org>
 * PythonInterp (required version >= 2.7) , Interactive high-level object-oriented language , <http://www.python.org>
   Needed for the Python interface to DOLFIN
 * PythonLibs (required version == 2.7.10) , Include paths and libraries for Python
 * NumPy , Array processing for numbers, strings, records, and objects in Python. , <http://www.numpy.org>
   Needed for the Python interface to DOLFIN
 * SWIG , Tool to wrap C/C++ libraries in high-level languages , <http://swig.org>
   Needed for the Python interface to DOLFIN
 * PkgConfig

-- The following features have been disabled:

 * CMAKE_USE_RELATIVE_PATHS , Use relative paths in makefiles and projects.
 * DOLFIN_ENABLE_CODE_COVERAGE , Enable code coverage.
 * DOLFIN_ENABLE_TESTING , Enable testing.
 * DOLFIN_ENABLE_BENCHMARKS , Enable benchmark programs.
 * DOLFIN_SKIP_BUILD_TESTS , Skip build tests for testing usability of dependency packages.
 * DOLFIN_DEPRECATION_ERROR , Turn deprecation warnings into errors.
 * DOLFIN_IGNORE_PETSC4PY_VERSION , Ignore version of PETSc4py.

-- The following OPTIONAL packages have not been found:

 * PETSc (required version >= 3.7) , Portable, Extensible Toolkit for Scientific Computation , <https://www.mcs.anl.gov/petsc/>
   Enables the PETSc linear algebra backend
 * SCOTCH , Programs and libraries for graph, mesh and hypergraph partitioning , <https://www.labri.fr/perso/pelegrin/scotch>
   Enables parallel graph partitioning
 * UMFPACK , Sparse LU factorization library , <http://faculty.cse.tamu.edu/davis/suitesparse.html>
 * CHOLMOD , Sparse Cholesky factorization library for sparse matrices , <http://faculty.cse.tamu.edu/davis/suitesparse.html>
 * HDF5 , Hierarchical Data Format 5 (HDF5) , <https://www.hdfgroup.org/HDF5>
 * Trilinos , Object-oriented framework for large-scale problems , <https://trilinos.org>
 * Sphinx (required version >= 1.1.0) , Python documentation generator , <http://www.sphinx-doc.org>
   Needed to build documentation
 * VTK , The Visualization Toolkit - A high level 3D visualization library , <https://www.vtk.org>
   Enables plotting with VTK as backend

-- The following REQUIRED packages have not been found:

 * UFC (required version >= 2017.1) , Unified language for form-compilers (part of FFC) , <https://bitbucket.org/fenics-project/ffc>

--
-- Generating SWIG interface.
-- --------------------------
--
-- Generating demo source files from reStructuredText
-- --------------------------------------------------
extract written to /home/jchang23/dolfin/demo/documented/auto-adaptive-poisson/python/demo_auto-adaptive-poisson.py
extract written to /home/jchang23/dolfin/demo/documented/biharmonic/python/demo_biharmonic.py
extract written to /home/jchang23/dolfin/demo/documented/built-in-meshes/python/demo_built-in-meshes.py
extract written to /home/jchang23/dolfin/demo/documented/cahn-hilliard/python/demo_cahn-hilliard.py
extract written to /home/jchang23/dolfin/demo/documented/eigenvalue/python/demo_eigenvalue.py
extract written to /home/jchang23/dolfin/demo/documented/hyperelasticity/python/demo_hyperelasticity.py
extract written to /home/jchang23/dolfin/demo/documented/maxwell-eigenvalues/python/demo_maxwell-eigenvalues.py
extract written to /home/jchang23/dolfin/demo/documented/mixed-poisson/python/demo_mixed-poisson.py
extract written to /home/jchang23/dolfin/demo/documented/nonlinear-poisson/python/demo_nonlinear-poisson.py
extract written to /home/jchang23/dolfin/demo/documented/nonmatching-interpolation/python/demo_nonmatching-interpolation.py
extract written to /home/jchang23/dolfin/demo/documented/poisson/python/demo_poisson.py
extract written to /home/jchang23/dolfin/demo/documented/singular-poisson-rst/python/demo_singular-poisson-rst.py
extract written to /home/jchang23/dolfin/demo/documented/auto-adaptive-poisson/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/biharmonic/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/built-in-meshes/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/eigenvalue/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/mixed-poisson/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/nonmatching-interpolation/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/poisson/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/auto-adaptive-poisson/cpp/AdaptivePoisson.ufl
extract written to /home/jchang23/dolfin/demo/documented/biharmonic/cpp/Biharmonic.ufl
extract written to /home/jchang23/dolfin/demo/documented/eigenvalue/cpp/StiffnessMatrix.ufl
extract written to /home/jchang23/dolfin/demo/documented/mixed-poisson/cpp/MixedPoisson.ufl
extract written to /home/jchang23/dolfin/demo/documented/nonmatching-interpolation/cpp/P1.ufl
extract written to /home/jchang23/dolfin/demo/documented/nonmatching-interpolation/cpp/P3.ufl
extract written to /home/jchang23/dolfin/demo/documented/poisson/cpp/Poisson.ufl
--
-- Generating demo source files
-- --------------------------------------------------
extract written to /home/jchang23/dolfin/demo/documented/auto-adaptive-poisson/python/demo_auto-adaptive-poisson.py
extract written to /home/jchang23/dolfin/demo/documented/biharmonic/python/demo_biharmonic.py
extract written to /home/jchang23/dolfin/demo/documented/built-in-meshes/python/demo_built-in-meshes.py
extract written to /home/jchang23/dolfin/demo/documented/cahn-hilliard/python/demo_cahn-hilliard.py
extract written to /home/jchang23/dolfin/demo/documented/eigenvalue/python/demo_eigenvalue.py
extract written to /home/jchang23/dolfin/demo/documented/hyperelasticity/python/demo_hyperelasticity.py
extract written to /home/jchang23/dolfin/demo/documented/maxwell-eigenvalues/python/demo_maxwell-eigenvalues.py
extract written to /home/jchang23/dolfin/demo/documented/mixed-poisson/python/demo_mixed-poisson.py
extract written to /home/jchang23/dolfin/demo/documented/nonlinear-poisson/python/demo_nonlinear-poisson.py
extract written to /home/jchang23/dolfin/demo/documented/nonmatching-interpolation/python/demo_nonmatching-interpolation.py
extract written to /home/jchang23/dolfin/demo/documented/poisson/python/demo_poisson.py
extract written to /home/jchang23/dolfin/demo/documented/singular-poisson-rst/python/demo_singular-poisson-rst.py
extract written to /home/jchang23/dolfin/demo/documented/auto-adaptive-poisson/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/biharmonic/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/built-in-meshes/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/eigenvalue/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/mixed-poisson/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/nonmatching-interpolation/cpp/main.cpp
extract written to /home/jchang23/dolfin/demo/documented/poisson/cpp/main.cpp
-- Performing Test HAVE_NO_MULTLINE
-- Performing Test HAVE_NO_MULTLINE - Success
-- Disabling generation of documentation because Sphinx is missing.
-- Configuring done
CMake Error at dolfin/CMakeLists.txt:60 (add_library):
  Target "dolfin" links to target "Boost::filesystem" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?


CMake Error at dolfin/CMakeLists.txt:60 (add_library):
  Target "dolfin" links to target "Boost::program_options" but the target was
  not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?


CMake Error at dolfin/CMakeLists.txt:60 (add_library):
  Target "dolfin" links to target "Boost::iostreams" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?


CMake Error at dolfin/CMakeLists.txt:60 (add_library):
  Target "dolfin" links to target "Boost::timer" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?


CMake Error at dolfin/CMakeLists.txt:60 (add_library):
  Target "dolfin" links to target "Boost::filesystem" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?


CMake Error at dolfin/CMakeLists.txt:60 (add_library):
  Target "dolfin" links to target "Boost::program_options" but the target was
  not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?


CMake Error at dolfin/CMakeLists.txt:60 (add_library):
  Target "dolfin" links to target "Boost::iostreams" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?


CMake Error at dolfin/CMakeLists.txt:60 (add_library):
  Target "dolfin" links to target "Boost::timer" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?


-- Generating done
-- Build files have been written to: /home/jchang23/dolfin/build

========

But I thought I already installed boost with those four missing libraries, what I did for that was:

$ ./bootstrap.sh --with-libraries=filesystem,iostreams,program_options,timer --prefix=/home/jchang23/.local
$ ./b2
$ ./b2 install

And the message above says it detected said libraries, yet I still get the CMake errors saying those targets were not found. Any suggestions what to do here?

Thanks!
Justin

[Jan Blechta]

I don't about boost issue but required UFC headers were not found as
well. You should be able to import ffc python package, i.e.

python -c"import ffc"

before running cmake. Have you installed ffc and is it in PYTHONPATH?

Jan

[Justin Chang]

Jan,

Yes I have installed ffc and others but I forgot to set PYTHONPATH. Now I have. But I still get the boost error:

-- Found UFC: /home/jchang23/.local/lib/python2.7/site-packages/FFC-2017.1.0.dev0-py2.7.egg/ffc/backends/ufc (Required is at least version "2017.1") 

 * UFC (required version >= 2017.1) , Unified language for form-compilers (part of FFC) , <https://bitbucket.org/fenics-project/ffc>

 * PkgConfig

-- The following features have been disabled:

 * CMAKE_USE_RELATIVE_PATHS , Use relative paths in makefiles and projects.

 * DOLFIN_ENABLE_CODE_COVERAGE , Enable code coverage.

 * DOLFIN_ENABLE_TESTING , Enable testing.

 * DOLFIN_ENABLE_BENCHMARKS , Enable benchmark programs.

 * DOLFIN_SKIP_BUILD_TESTS , Skip build tests for testing usability of dependency packages.

 * DOLFIN_DEPRECATION_ERROR , Turn deprecation warnings into errors.

 * DOLFIN_IGNORE_PETSC4PY_VERSION , Ignore version of PETSc4py.

-- The following OPTIONAL packages have not been found:

 * PETSc (required version >= 3.7) , Portable, Extensible Toolkit for Scientific Computation , <https://www.mcs.anl.gov/petsc/>

   Enables the PETSc linear algebra backend

 * SCOTCH , Programs and libraries for graph, mesh and hypergraph partitioning , <https://www.labri.fr/perso/pelegrin/scotch>

   Enables parallel graph partitioning

 * UMFPACK , Sparse LU factorization library , <http://faculty.cse.tamu.edu/davis/suitesparse.html>

 * CHOLMOD , Sparse Cholesky factorization library for sparse matrices , <http://faculty.cse.tamu.edu/davis/suitesparse.html>

 * HDF5 , Hierarchical Data Format 5 (HDF5) , <https://www.hdfgroup.org/HDF5>

 * Trilinos , Object-oriented framework for large-scale problems , <https://trilinos.org>

 * Sphinx (required version >= 1.1.0) , Python documentation generator , <http://www.sphinx-doc.org>

   Needed to build documentation

 * VTK , The Visualization Toolkit - A high level 3D visualization library , <https://www.vtk.org>

   Enables plotting with VTK as backend

-- 

-- Generating SWIG interface.

-- --------------------------

-- 

-- Generating demo source files from reStructuredText

-- --------------------------------------------------

extract written to /home/jchang23/Software/dolfin/demo/documented/auto-adaptive-poisson/python/demo_auto-adaptive-poisson.py

extract written to /home/jchang23/Software/dolfin/demo/documented/biharmonic/python/demo_biharmonic.py

extract written to /home/jchang23/Software/dolfin/demo/documented/built-in-meshes/python/demo_built-in-meshes.py

extract written to /home/jchang23/Software/dolfin/demo/documented/cahn-hilliard/python/demo_cahn-hilliard.py

extract written to /home/jchang23/Software/dolfin/demo/documented/eigenvalue/python/demo_eigenvalue.py

extract written to /home/jchang23/Software/dolfin/demo/documented/hyperelasticity/python/demo_hyperelasticity.py

extract written to /home/jchang23/Software/dolfin/demo/documented/maxwell-eigenvalues/python/demo_maxwell-eigenvalues.py

extract written to /home/jchang23/Software/dolfin/demo/documented/mixed-poisson/python/demo_mixed-poisson.py

extract written to /home/jchang23/Software/dolfin/demo/documented/nonlinear-poisson/python/demo_nonlinear-poisson.py

extract written to /home/jchang23/Software/dolfin/demo/documented/nonmatching-interpolation/python/demo_nonmatching-interpolation.py

extract written to /home/jchang23/Software/dolfin/demo/documented/poisson/python/demo_poisson.py

extract written to /home/jchang23/Software/dolfin/demo/documented/singular-poisson-rst/python/demo_singular-poisson-rst.py

extract written to /home/jchang23/Software/dolfin/demo/documented/auto-adaptive-poisson/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/biharmonic/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/built-in-meshes/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/eigenvalue/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/mixed-poisson/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/nonmatching-interpolation/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/poisson/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/auto-adaptive-poisson/cpp/AdaptivePoisson.ufl

extract written to /home/jchang23/Software/dolfin/demo/documented/biharmonic/cpp/Biharmonic.ufl

extract written to /home/jchang23/Software/dolfin/demo/documented/eigenvalue/cpp/StiffnessMatrix.ufl

extract written to /home/jchang23/Software/dolfin/demo/documented/mixed-poisson/cpp/MixedPoisson.ufl

extract written to /home/jchang23/Software/dolfin/demo/documented/nonmatching-interpolation/cpp/P1.ufl

extract written to /home/jchang23/Software/dolfin/demo/documented/nonmatching-interpolation/cpp/P3.ufl

extract written to /home/jchang23/Software/dolfin/demo/documented/poisson/cpp/Poisson.ufl

-- 

-- Generating demo source files

-- --------------------------------------------------

extract written to /home/jchang23/Software/dolfin/demo/documented/auto-adaptive-poisson/python/demo_auto-adaptive-poisson.py

extract written to /home/jchang23/Software/dolfin/demo/documented/biharmonic/python/demo_biharmonic.py

extract written to /home/jchang23/Software/dolfin/demo/documented/built-in-meshes/python/demo_built-in-meshes.py

extract written to /home/jchang23/Software/dolfin/demo/documented/cahn-hilliard/python/demo_cahn-hilliard.py

extract written to /home/jchang23/Software/dolfin/demo/documented/eigenvalue/python/demo_eigenvalue.py

extract written to /home/jchang23/Software/dolfin/demo/documented/hyperelasticity/python/demo_hyperelasticity.py

extract written to /home/jchang23/Software/dolfin/demo/documented/maxwell-eigenvalues/python/demo_maxwell-eigenvalues.py

extract written to /home/jchang23/Software/dolfin/demo/documented/mixed-poisson/python/demo_mixed-poisson.py

extract written to /home/jchang23/Software/dolfin/demo/documented/nonlinear-poisson/python/demo_nonlinear-poisson.py

extract written to /home/jchang23/Software/dolfin/demo/documented/nonmatching-interpolation/python/demo_nonmatching-interpolation.py

extract written to /home/jchang23/Software/dolfin/demo/documented/poisson/python/demo_poisson.py

extract written to /home/jchang23/Software/dolfin/demo/documented/singular-poisson-rst/python/demo_singular-poisson-rst.py

extract written to /home/jchang23/Software/dolfin/demo/documented/auto-adaptive-poisson/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/biharmonic/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/built-in-meshes/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/eigenvalue/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/mixed-poisson/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/nonmatching-interpolation/cpp/main.cpp

extract written to /home/jchang23/Software/dolfin/demo/documented/poisson/cpp/main.cpp

-- Build files have been written to: /home/jchang23/Software/dolfin/build

[Justin Chang]

Okay I think I figured it out.

I was using boost_1_63_0, but in the file cmake/modules/FindBoost.cmake it seems only up to _1_62_0 is supported. So I installed boost_1_62_0, and cmake seems to work. However, i get a different error, now in the "make install" step:

[ 94%] Built target dolfin
[ 94%] Built target copy_swig_files
[ 94%] Building CXX object dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/modulePYTHON_wrap.cxx.o
In file included from /home/jchang23/Software/dolfin/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:3925:0:
/home/jchang23/Software/dolfin/dolfin/function/Function.h:29:43: fatal error: boost/ptr_container/ptr_map.hpp: No such file or directory
 #include <boost/ptr_container/ptr_map.hpp>
                                           ^
compilation terminated.
make[2]: *** [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/modulePYTHON_wrap.cxx.o] Error 1
make[1]: *** [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/all] Error 2
make: *** [all] Error 2

So it seems boost/ptr_container/ptr_map.hpp was not included in cmake/modules/FindBoost.cmake. How do I "properly" add this dependency, or is there something else I am missing here?

Thanks,

Justin

[Francesco Ballarin]

Hi Justin,

I have encountered the same problem recently. It seems that boost include dirs are correctly passed when compiling c++ objects in dolfin, but not when calling swig. I am not capable of pinpointing the source of the problem in the cmake build system, but I can offer you a simple workaround that has worked for me: add $BOOST_HOME/include to your CPATH.

Best regards,

Francesco

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[Garth N. Wells]

I copied the latest FindBoost.cmake from CMake into the dev version of
DOLFIN recently to deal with the issue of FindBoost.cmake from recent
(but not latest) CMake not handling Boost 1.63.

Are you building DOLFIN dev or 2016.2?

On 4 January 2017 at 06:08, Justin Chang <jych...@gmail.com> wrote:
> Okay I think I figured it out.
>
> I was using boost_1_63_0, but in the file cmake/modules/FindBoost.cmake it
> seems only up to _1_62_0 is supported. So I installed boost_1_62_0, and
> cmake seems to work. However, i get a different error, now in the "make
> install" step:
>
> [ 94%] Built target dolfin
> [ 94%] Built target copy_swig_files
> [ 94%] Building CXX object
> dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/modulePYTHON_wrap.cxx.o
> In file included from
> /home/jchang23/Software/dolfin/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:3925:0:
> /home/jchang23/Software/dolfin/dolfin/function/Function.h:29:43: fatal
> error: boost/ptr_container/ptr_map.hpp: No such file or directory
> #include <boost/ptr_container/ptr_map.hpp>
> ^
> compilation terminated.
> make[2]: ***
> [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/modulePYTHON_wrap.cxx.o]
> Error 1
> make[1]: *** [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/all] Error 2
> make: *** [all] Error 2
>

I haven't seen this before. Which version of CMake are you using?

Garth

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[Justin Chang]

Following Francesco's suggestion of adding $BOOST_HOME/include to my CPATH resolves the issue. The CMake version I was using was 3.7.1

I can't tell whether I am using DOLFIN dev or 2016.2, I just did 'git clone https://bitbucket.org/fenics-project/dolfin' to obtain the source file.

Anyhow, everything installed correctly (I think), and when I run any FEniCS code, I get this warning message:

"subprocess32 module not found! Using unsafe built-in subprocess module instead. Install subprocess32 for thread-safety and safe usage on OFED/Infiniband networks."

I manually installed my own python (version 2.7.10 into $HOME/.local with enable-shared turned on). Any idea why this is happening?

Thanks,

Justin

> email to fenics-support+unsubscribe@googlegroups.com.
> To post to this group, send email to fenics-support@googlegroups.com.

[Jan Blechta]

On Thu, 5 Jan 2017 03:23:49 -0600
Justin Chang <jych...@gmail.com> wrote:

> Following Francesco's suggestion of adding $BOOST_HOME/include to my
> CPATH resolves the issue. The CMake version I was using was 3.7.1
>
> I can't tell whether I am using DOLFIN dev or 2016.2, I just did 'git
> clone https://bitbucket.org/fenics-project/dolfin' to obtain the
> source file.
>
> Anyhow, everything installed correctly (I think), and when I run any
> FEniCS code, I get this warning message:
>
> "subprocess32 module not found! Using unsafe built-in subprocess
> module instead. Install subprocess32 for thread-safety and safe usage
> on OFED/Infiniband networks."

Unless your machine is Infiniband cluster (very unlikely) or you'd
like to deal with threads in your applications (very unlikely), you can
just ignore the message.

If you want to get rid of it, just install subprocess32 python package

pip install subprocess32

and the message will go away.

Jan

> > > send an email to fenics-suppor...@googlegroups.com.

> > > To post to this group, send email to

> > > fenics-...@googlegroups.com. To view this discussion on the

[David Ham]

On Thu, 5 Jan 2017 at 09:51 Jan Blechta <ble...@karlin.mff.cuni.cz> wrote:

On Thu, 5 Jan 2017 03:23:49 -0600
Justin Chang <jych...@gmail.com> wrote:

> Following Francesco's suggestion of adding $BOOST_HOME/include to my
> CPATH resolves the issue. The CMake version I was using was 3.7.1
>
> I can't tell whether I am using DOLFIN dev or 2016.2, I just did 'git
> clone https://bitbucket.org/fenics-project/dolfin' to obtain the
> source file.
>
> Anyhow, everything installed correctly (I think), and when I run any
> FEniCS code, I get this warning message:
>
> "subprocess32 module not found! Using unsafe built-in subprocess
> module instead. Install subprocess32 for thread-safety and safe usage
> on OFED/Infiniband networks."

Unless your machine is Infiniband cluster (very unlikely) or you'd
like to deal with threads in your applications (very unlikely), you can
just ignore the message.

The original post specified "RHEL cluster". Infiniband sounds not unlikely...

 

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Department of Mathematics

Imperial College London

[Balázs Tóth]

Hi all,

I am trying to install FEniCS on mac and have the same issue with cmake and boost 1.63. I pulled the latest versions of the libraries from bitbucket. My $BOOST_HOME variable is empty and adding '/usr/local/include/boost' to CPATH doesn't help. Does anyone have a clue how could I resolve this issue?

Thanks,

Balázs