The problem is solved!
There was no error report, because the test program was compiling correctly! It
was not running due to “intended features" of OSX environment.
The problem was two fold: Apparently the clang does not like symlinks. My
solution: I modified the dolfin.py to dump a DYLD_LIBRARY_PATH with library
dirs of the artifacts. Somehow, sometimes the include flags are not passed
correctly. Again I modified dolfin.py to dump a CXXFLAGS.
For anyone that might experience a similar issue, the modified dolfin.py is
attached. Notice that I was NOT careful about multi system compatibility.
C.
Baris
from hashdist import build_stage
def rpath_flag(ctx, path):
if ctx.parameters['platform'] == 'linux':
return '-Wl,-rpath=%s' % path
else:
return ''
@build_stage()
def configure(ctx, stage_args):
"""
Generates DOLFIN cmake line.
Example::
- name: configure
build_type: Release
set_env_flags: true
Note: this is a fairly sophisticated build stage that inspects
the build artifacts available to decide what to enable in DOLFIN.
By default, this package builds DOLFIN with all required artifacts,
debugging support enabled, and shared libraries enabled. The
following extra keys are relevant:
* build_type: Release, Debug, RelWithDebInfo or Developer.
Release by default.
* set_env_flags: CPPFLAGS and LDFLAGS will be set, as appropriate
for the platform. Default is true.
"""
conf_lines = ['${CMAKE} -D CMAKE_INSTALL_PREFIX:PATH="${ARTIFACT}"',
'-D CMAKE_INSTALL_RPATH:STRING="${ARTIFACT}/lib"',
'-D CMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON',
'-D DOLFIN_ENABLE_DOCS:BOOL=OFF',
'-D
PKG_CONFIG_EXECUTABLE:FILEPATH="${PKG_CONFIG_EXECUTABLE}"',
'-D EIGEN3_INCLUDE_DIR:PATH="${EIGEN_DIR}/include/eigen3"',
'-D BOOST_ROOT:PATH="${BOOST_DIR}"',
'-D Boost_USE_MULTITHREADED:BOOL=${BOOST_USE_MULTITHREADED}',
'-D DOLFIN_ENABLE_UNIT_TESTS:BOOL=OFF']
# CMake needs to be given all the dependency dirs as prefix paths
# so that we search the HashDist directories before the system directories.
# CMake doesn't use the CPPFLAGS implicitly to find libraries.
prefix_paths = []
CPPFLAGS = []
LDFLAGS = []
DYLD_LIBRARY_PATH = []
CXXFLAGS = []
for dep_var in ctx.dependency_dir_vars:
prefix_paths.append('${%s_DIR}' % dep_var)
CPPFLAGS.append('-I${%s_DIR}/include' % dep_var)
CXXFLAGS.append('-I${%s_DIR}/include' % dep_var)
LDFLAGS.append('-L${%s_DIR}/lib' % dep_var)
DYLD_LIBRARY_PATH.append('${%s_DIR}/lib' % dep_var)
LDFLAGS.append(rpath_flag(ctx, '${%s_DIR}/lib' % dep_var))
conf_lines.append('-D CMAKE_PREFIX_PATH="%s"' % ';'.join(prefix_paths))
if ctx.parameters['platform'] == 'Cygwin':
libxml2 = '${LIBXML2_DIR}/lib/libxml2.dll.a'
conf_lines.append('-D LIBXML2_LIBRARIES:FILEPATH="%s"' % libxml2)
conf_lines.append('-D
LIBXML2_INCLUDE_DIR:PATH="${LIBXML2_DIR}/include/libxml2"')
if 'build_type' in stage_args and stage_args['build_type'] is not None:
conf_lines.append('-D CMAKE_BUILD_TYPE:STRING="%s"' %
stage_args['build_type'])
else:
conf_lines.append('-D CMAKE_BUILD_TYPE:STRING="Release"')
if 'CGAL' in ctx.dependency_dir_vars:
conf_lines.append('-D CGAL_DISABLE_ROUNDING_MATH_CHECK:BOOL=ON')
if 'SWIG' in ctx.dependency_dir_vars:
conf_lines.append('-D SWIG_EXECUTABLE:FILEPATH="${SWIG_EXECUTABLE}"')
if 'PYTHON' in ctx.dependency_dir_vars:
conf_lines.append('-D PYTHON_EXECUTABLE:FILEPATH="${PYTHON}"')
conf_lines.append('-D
PYTHON_INCLUDE_DIR:PATH="${PYTHON_DIR}/include/python${PYVER}"')
# Some special variables are needed to find correct HDF5
if 'HDF5' in ctx.dependency_dir_vars:
conf_lines.append('-D HDF5_INCLUDE_DIRS="${HDF5_DIR}/include"')
conf_lines.append('-D HDF5_ROOT:PATH="${HDF5_DIR}"')
conf_lines.append('-D
HDF5_C_COMPILER_EXECUTABLE="${HDF5_DIR}/bin/h5pcc"')
# SuiteSparse provides UMFPACK and CHOLMOD
if 'SUITESPARSE' in ctx.dependency_dir_vars:
conf_lines.append('-D DOLFIN_ENABLE_UMFPACK:BOOL=ON')
conf_lines.append('-D DOLFIN_ENABLE_CHOLMOD:BOOL=ON')
conf_lines.append('-D UMFPACK_DIR:PATH="${SUITESPARSE_DIR}"')
conf_lines.append('-D CHOLMOD_DIR:PATH="${SUITESPARSE_DIR}"')
conf_lines.append('-D AMD_DIR:PATH="${SUITESPARSE_DIR}"')
conf_lines.append('-D CAMD_DIR:PATH="${SUITESPARSE_DIR}"')
conf_lines.append('-D COLAMD_DIR:PATH="${SUITESPARSE_DIR}"')
conf_lines.append('-D CCOLAMD_DIR:PATH="${SUITESPARSE_DIR}"')
else:
conf_lines.append('-D DOLFIN_ENABLE_UMFPACK:BOOL=OFF')
conf_lines.append('-D DOLFIN_ENABLE_CHOLMOD:BOOL=OFF')
if 'OPENBLAS' in ctx.dependency_dir_vars:
if ctx.parameters['platform'] == 'Darwin':
libopenblas = '${OPENBLAS_DIR}/lib/libopenblas.dylib'
else:
libopenblas = '${OPENBLAS_DIR}/lib/libopenblas.so'
conf_lines.append('-D LAPACK_LIBRARIES:FILEPATH="%s"' % libopenblas)
conf_lines.append('-D BLAS_LIBRARIES:FILEPATH="%s"' % libopenblas)
if 'ZLIB' in ctx.dependency_dir_vars:
conf_lines.append('-D ZLIB_ROOT="${ZLIB_DIR}"')
optional_deps = ['CGAL', 'HDF5', 'PETSC', 'PETSC4PY', 'SLEPC',
'TAO', 'TRILINOS', 'PASTIX', 'SCOTCH', 'PARMETIS',
'CGAL', 'ZLIB', 'PYTHON','SPHINX', 'VTK', 'QT']
for dep in optional_deps:
if dep in ctx.dependency_dir_vars:
conf_lines.append('-D DOLFIN_ENABLE_%s:BOOL=ON' % dep)
conf_lines.append('-D %s_DIR:PATH="${%s_DIR}"' % (dep, dep))
else:
conf_lines.append('-D DOLFIN_ENABLE_%s:BOOL=OFF' % dep)
builddir = '..'
if stage_args.get('build_in_source', False):
builddir = '.'
conf_lines.append(builddir)
for i in range(len(conf_lines) - 1):
conf_lines[i] = conf_lines[i] + ' \\'
conf_lines[i + 1] = ' ' + conf_lines[i + 1]
env_lines = []
if stage_args.get('set_env_flags', True):
env_lines.append('export CPPFLAGS="%s"' % ' '.join(CPPFLAGS))
env_lines.append('export LDFLAGS="%s"' % ' '.join(LDFLAGS))
env_lines.append('export CXXFLAGS="%s"' % ' '.join(CXXFLAGS))
env_lines.append('export DYLD_LIBRARY_PATH="%s"' %
':'.join(DYLD_LIBRARY_PATH))
return ['('] + env_lines + conf_lines + [')']
wit-amidst-folly:Fenics-clang-orig obm$ ls
fenics-hashstack fenics-osx-obm.yaml
fenics-install.sh fenics.custom
wit-amidst-folly:Fenics-clang-orig obm$ ls
fenics-hashstack/hashstack/pkgs/dolfin/dolfin.py
fenics-hashstack/hashstack/pkgs/dolfin/dolfin.py
wit-amidst-folly:Fenics-clang-orig obm$ clear
wit-amidst-folly:Fenics-clang-orig obm$ cat
fenics-hashstack/hashstack/pkgs/dolfin/dolfin.py
from hashdist import build_stage
def rpath_flag(ctx, path):
if ctx.parameters['platform'] == 'linux':
return '-Wl,-rpath=%s' % path
else:
return ''
@build_stage()
def configure(ctx, stage_args):
"""
Generates DOLFIN cmake line.
Example::
- name: configure
build_type: Release
set_env_flags: true
Note: this is a fairly sophisticated build stage that inspects
the build artifacts available to decide what to enable in DOLFIN.
By default, this package builds DOLFIN with all required artifacts,
debugging support enabled, and shared libraries enabled. The
following extra keys are relevant:
* build_type: Release, Debug, RelWithDebInfo or Developer.
Release by default.
* set_env_flags: CPPFLAGS and LDFLAGS will be set, as appropriate
for the platform. Default is true.
"""
conf_lines = ['${CMAKE} -D CMAKE_INSTALL_PREFIX:PATH="${ARTIFACT}"',
'-D CMAKE_INSTALL_RPATH:STRING="${ARTIFACT}/lib"',
'-D CMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON',
'-D DOLFIN_ENABLE_DOCS:BOOL=OFF',
'-D
PKG_CONFIG_EXECUTABLE:FILEPATH="${PKG_CONFIG_EXECUTABLE}"',
'-D EIGEN3_INCLUDE_DIR:PATH="${EIGEN_DIR}/include/eigen3"',
'-D BOOST_ROOT:PATH="${BOOST_DIR}"',
'-D Boost_USE_MULTITHREADED:BOOL=${BOOST_USE_MULTITHREADED}',
'-D DOLFIN_ENABLE_UNIT_TESTS:BOOL=OFF']
# CMake needs to be given all the dependency dirs as prefix paths
# so that we search the HashDist directories before the system directories.
# CMake doesn't use the CPPFLAGS implicitly to find libraries.
prefix_paths = []
CPPFLAGS = []
LDFLAGS = []
DYLD_LIBRARY_PATH = []
CXXFLAGS = []
for dep_var in ctx.dependency_dir_vars:
prefix_paths.append('${%s_DIR}' % dep_var)
CPPFLAGS.append('-I${%s_DIR}/include' % dep_var)
CXXFLAGS.append('-I${%s_DIR}/include' % dep_var)
LDFLAGS.append('-L${%s_DIR}/lib' % dep_var)
DYLD_LIBRARY_PATH.append('${%s_DIR}/lib' % dep_var)
LDFLAGS.append(rpath_flag(ctx, '${%s_DIR}/lib' % dep_var))
conf_lines.append('-D CMAKE_PREFIX_PATH="%s"' % ';'.join(prefix_paths))
if ctx.parameters['platform'] == 'Cygwin':
libxml2 = '${LIBXML2_DIR}/lib/libxml2.dll.a'
conf_lines.append('-D LIBXML2_LIBRARIES:FILEPATH="%s"' % libxml2)
conf_lines.append('-D
LIBXML2_INCLUDE_DIR:PATH="${LIBXML2_DIR}/include/libxml2"')
if 'build_type' in stage_args and stage_args['build_type'] is not None:
conf_lines.append('-D CMAKE_BUILD_TYPE:STRING="%s"' %
stage_args['build_type'])
else:
conf_lines.append('-D CMAKE_BUILD_TYPE:STRING="Release"')
if 'CGAL' in ctx.dependency_dir_vars:
conf_lines.append('-D CGAL_DISABLE_ROUNDING_MATH_CHECK:BOOL=ON')
if 'SWIG' in ctx.dependency_dir_vars:
conf_lines.append('-D SWIG_EXECUTABLE:FILEPATH="${SWIG_EXECUTABLE}"')
if 'PYTHON' in ctx.dependency_dir_vars:
conf_lines.append('-D PYTHON_EXECUTABLE:FILEPATH="${PYTHON}"')
conf_lines.append('-D
PYTHON_INCLUDE_DIR:PATH="${PYTHON_DIR}/include/python${PYVER}"')
# Some special variables are needed to find correct HDF5
if 'HDF5' in ctx.dependency_dir_vars:
conf_lines.append('-D HDF5_INCLUDE_DIRS="${HDF5_DIR}/include"')
conf_lines.append('-D HDF5_ROOT:PATH="${HDF5_DIR}"')
conf_lines.append('-D
HDF5_C_COMPILER_EXECUTABLE="${HDF5_DIR}/bin/h5pcc"')
# SuiteSparse provides UMFPACK and CHOLMOD
if 'SUITESPARSE' in ctx.dependency_dir_vars:
conf_lines.append('-D DOLFIN_ENABLE_UMFPACK:BOOL=ON')
conf_lines.append('-D DOLFIN_ENABLE_CHOLMOD:BOOL=ON')
conf_lines.append('-D UMFPACK_DIR:PATH="${SUITESPARSE_DIR}"')
conf_lines.append('-D CHOLMOD_DIR:PATH="${SUITESPARSE_DIR}"')
conf_lines.append('-D AMD_DIR:PATH="${SUITESPARSE_DIR}"')
conf_lines.append('-D CAMD_DIR:PATH="${SUITESPARSE_DIR}"')
conf_lines.append('-D COLAMD_DIR:PATH="${SUITESPARSE_DIR}"')
conf_lines.append('-D CCOLAMD_DIR:PATH="${SUITESPARSE_DIR}"')
else:
conf_lines.append('-D DOLFIN_ENABLE_UMFPACK:BOOL=OFF')
conf_lines.append('-D DOLFIN_ENABLE_CHOLMOD:BOOL=OFF')
if 'OPENBLAS' in ctx.dependency_dir_vars:
if ctx.parameters['platform'] == 'Darwin':
libopenblas = '${OPENBLAS_DIR}/lib/libopenblas.dylib'
else:
libopenblas = '${OPENBLAS_DIR}/lib/libopenblas.so'
conf_lines.append('-D LAPACK_LIBRARIES:FILEPATH="%s"' % libopenblas)
conf_lines.append('-D BLAS_LIBRARIES:FILEPATH="%s"' % libopenblas)
if 'ZLIB' in ctx.dependency_dir_vars:
conf_lines.append('-D ZLIB_ROOT="${ZLIB_DIR}"')
optional_deps = ['CGAL', 'HDF5', 'PETSC', 'PETSC4PY', 'SLEPC',
'TAO', 'TRILINOS', 'PASTIX', 'SCOTCH', 'PARMETIS',
'CGAL', 'ZLIB', 'PYTHON','SPHINX', 'VTK', 'QT']
for dep in optional_deps:
if dep in ctx.dependency_dir_vars:
conf_lines.append('-D DOLFIN_ENABLE_%s:BOOL=ON' % dep)
conf_lines.append('-D %s_DIR:PATH="${%s_DIR}"' % (dep, dep))
else:
conf_lines.append('-D DOLFIN_ENABLE_%s:BOOL=OFF' % dep)
builddir = '..'
if stage_args.get('build_in_source', False):
builddir = '.'
conf_lines.append(builddir)
for i in range(len(conf_lines) - 1):
conf_lines[i] = conf_lines[i] + ' \\'
conf_lines[i + 1] = ' ' + conf_lines[i + 1]
env_lines = []
if stage_args.get('set_env_flags', True):
env_lines.append('export CPPFLAGS="%s"' % ' '.join(CPPFLAGS))
env_lines.append('export LDFLAGS="%s"' % ' '.join(LDFLAGS))
env_lines.append('export CXXFLAGS="%s"' % ' '.join(CXXFLAGS))
env_lines.append('export DYLD_LIBRARY_PATH="%s"' %
':'.join(DYLD_LIBRARY_PATH))
return ['('] + env_lines + conf_lines + [')']
> 19 Şub 2015 tarihinde 17:41 saatinde, Baris Malcioglu
> <[email protected]> şunları yazdı:
>
> Dear developers,
> I am trying to compile FEniCS in Mac OSX 10.10 with hashdist. I modified the
> supplied script so that petsc is compiled with
> petsc:
> build_with: |
> parmetis, openblas, scotch, suitesparse, trilinos
> download: |
> superlu, superlu_dist, hypre, mumps, scalapack
>
> However, dolfin can not detect PETSC, and I was unable to find a log file
> that tells me why. I see
> Performing test PETSC_TEST_RUNS - Failed
> in the logs
> however, CMakeError.log contains only a failure about PETSC_CUSP_FOUND, no
> errors whatsoever anywhere regarding PETSC_TEST_RUNS
>
> at the moment, I searched for petsc in every single text file in dolfin
> directory, but there are no indications of what failed and why.
>
> a nm to the petsc artifact library suggests it compiled successfully.
>
> best,
> Baris
>
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