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Miscellaneous cleanup

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This commit is contained in:
Ray Speth 2012-06-12 22:48:28 +00:00
parent 2806907060
commit 5a2e2567f5
4 changed files with 79 additions and 11403 deletions
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5
AUTHORS
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@ -1,5 +1,6 @@
cantera developers: Cantera developers:
Dave Goodwin
Nicholas Malaya Nicholas Malaya
Harry Moffat Harry Moffat
Ray Speth Raymond Speth

11274
ChangeLog
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File diff suppressed because it is too large Load diff

181
SConstruct
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@ -152,8 +152,6 @@ class defaults: pass
if os.name == 'posix': if os.name == 'posix':
defaults.prefix = '/usr/local' defaults.prefix = '/usr/local'
# defaults.boostIncDir = '/usr/include'
# defaults.boostLibDir = '/usr/lib'
defaults.boostIncDir = '' defaults.boostIncDir = ''
defaults.boostLibDir = '' defaults.boostLibDir = ''
env['INSTALL_MANPAGES'] = True env['INSTALL_MANPAGES'] = True
@ -259,17 +257,16 @@ opts.AddVariables(
'default', ('full', 'minimal', 'none','default')), 'default', ('full', 'minimal', 'none','default')),
PathVariable( PathVariable(
'python_cmd', 'python_cmd',
"""Cantera needs to know where to find the Python """Cantera needs to know where to find the Python interpreter. If
interpreter. If PYTHON_CMD is not set, then the PYTHON_CMD is not set, then the configuration process will use the
configuration process will use the same Python interpreter same Python interpreter being used by SCons.""",
being used by SCons.""",
sys.executable), sys.executable),
EnumVariable( EnumVariable(
'python_array', 'python_array',
"""The Cantera Python interface requires one of the Python """The Cantera Python interface requires one of the Python array
array packages listed. Support for the legacy 'numeric' and packages listed. Support for the legacy 'numeric' and 'numarray'
'numarray' packages is deprecated, and will be removed in a packages is deprecated, and will be removed in a future version
future version of Cantera.""", of Cantera.""",
'numpy', ('numpy', 'numarray', 'numeric')), 'numpy', ('numpy', 'numarray', 'numeric')),
PathVariable( PathVariable(
'python_array_home', 'python_array_home',
@ -278,18 +275,17 @@ opts.AddVariables(
'', PathVariable.PathAccept), '', PathVariable.PathAccept),
PathVariable( PathVariable(
'python_prefix', 'python_prefix',
"""If you want to install the Cantera Python package somewhere """If you want to install the Cantera Python package somewhere other
other than the default 'site-packages' directory within the than the default 'site-packages' directory within the Python library
Python library directory, then set this to the desired directory, then set this to the desired directory. This is useful
directory. This is useful when you do not have write access when you do not have write access to the Python library directory.""",
to the Python library directory.""",
'', PathVariable.PathAccept), '', PathVariable.PathAccept),
EnumVariable( EnumVariable(
'matlab_toolbox', 'matlab_toolbox',
"""This variable controls whether the Matlab toolbox will be """This variable controls whether the Matlab toolbox will be built. If
built. If set to 'y', you will also need to set the value set to 'y', you will also need to set the value of the 'matlab_path'
of the 'matlab_path' variable. If set to 'default', the Matlab variable. If set to 'default', the Matlab toolbox will be built if
toolbox will be built if 'matlab_path' is set.""", 'matlab_path' is set.""",
'default', ('y', 'n', 'default')), 'default', ('y', 'n', 'default')),
PathVariable( PathVariable(
'matlab_path', 'matlab_path',
@ -301,16 +297,15 @@ opts.AddVariables(
'', PathVariable.PathAccept), '', PathVariable.PathAccept),
EnumVariable( EnumVariable(
'f90_interface', 'f90_interface',
"""This variable controls whether the Fortran 90/95 interface """This variable controls whether the Fortran 90/95 interface will be
will be built. If set to 'default', the builder will look built. If set to 'default', the builder will look for a compatible
for a compatible Fortran compiler in the $PATH, and compile Fortran compiler in the $PATH, and compile the Fortran 90 interface
the Fortran 90 interface if one is found.""", if one is found.""",
'default', ('y', 'n', 'default')), 'default', ('y', 'n', 'default')),
PathVariable( PathVariable(
'F90', 'F90',
"""The Fortran 90 compiler. If unspecified, the builder will """The Fortran 90 compiler. If unspecified, the builder will look for a
look for a compatible compiler (gfortran, ifort, g95) in compatible compiler (gfortran, ifort, g95) in the $PATH.""",
the $PATH.""",
'', PathVariable.PathAccept), '', PathVariable.PathAccept),
('F90FLAGS', ('F90FLAGS',
'Compilation options for the Fortran 90 compiler.', 'Compilation options for the Fortran 90 compiler.',
@ -340,60 +335,54 @@ opts.AddVariables(
False), False),
BoolVariable( BoolVariable(
'with_html_log_files', 'with_html_log_files',
"""write HTML log files. Some multiphase equilibrium """write HTML log files. Some multiphase equilibrium procedures can
procedures can write copious diagnostic log messages. Set write copious diagnostic log messages. Set this to 'n' to disable
this to 'n' to disable this capability. (results in this capability. (results in slightly faster equilibrium calculations)""",
slightly faster equilibrium calculations)""",
True), True),
EnumVariable( EnumVariable(
'use_sundials', 'use_sundials',
"""Cantera uses the CVODE or CVODES ODE integrator to """Cantera uses the CVODE or CVODES ODE integrator to time-integrate
time-integrate reactor network ODE's and for various other reactor network ODE's and for various other purposes. An older
purposes. An older version of CVODE comes with Cantera, but version of CVODE comes with Cantera, but it is possible to use the
it is possible to use the latest version as well, which now latest version as well, which now supports sensitivity analysis
supports sensitivity analysis (CVODES). CVODES is a part of (CVODES). CVODES is a part of the 'sundials' package from Lawrence
the 'sundials' package from Lawrence Livermore National Livermore National Laboratory. Sundials is not distributed with
Laboratory. Sundials is not distributed with Cantera, but Cantera, but it is free software that may be downloaded and
it is free software that may be downloaded and installed installed separately. If you leave USE_SUNDIALS = 'default', then it
separately. If you leave USE_SUNDIALS = 'default', then it will be used if you have it, and if not the older CVODE will be
will be used if you have it, and if not the older CVODE used. Or set USE_SUNDIALS to 'y' or 'n' to force using it or not.
will be used. Or set USE_SUNDIALS to 'y' or 'n' to force Note that sensitivity analysis with Cantera requires use of
using it or not. Note that sensitivity analysis with sundials. See: http://www.llnl.gov/CASC/sundials""",
Cantera requires use of sundials. See:
http://www.llnl.gov/CASC/sundials""",
'default', ('default', 'y', 'n')), 'default', ('default', 'y', 'n')),
PathVariable( PathVariable(
'sundials_include', 'sundials_include',
"""The directory where the Sundials header files are """The directory where the Sundials header files are installed. This
installed. This should be the directory that contains the should be the directory that contains the "cvodes", "nvector", etc.
"cvodes", "nvector", etc. subdirectories. Not needed if the subdirectories. Not needed if the headers are installed in a
headers are installed in a standard location, standard location, e.g. /usr/include.""",
e.g. /usr/include.""",
'', PathVariable.PathAccept), '', PathVariable.PathAccept),
PathVariable( PathVariable(
'sundials_libdir', 'sundials_libdir',
"""The directory where the sundials static libraries are """The directory where the sundials static libraries are installed.
installed. Not needed if the libraries are installed in a Not needed if the libraries are installed in a standard location,
standard location, e.g. /usr/lib.""", e.g. /usr/lib.""",
'', PathVariable.PathAccept), '', PathVariable.PathAccept),
('blas_lapack_libs', ('blas_lapack_libs',
"""Cantera comes with Fortran (or C) versions of those parts of """Cantera comes with Fortran (or C) versions of those parts of BLAS and
BLAS and LAPACK it requires. But performance may be better if LAPACK it requires. But performance may be better if you use a version
you use a version of these libraries optimized for your of these libraries optimized for your machine hardware. If you want to
machine hardware. If you want to use your own libraries, set use your own libraries, set blas_lapack_libs to the the list of
blas_lapack_libs to the the list of libraries that should be libraries that should be passed to the linker, separated by commas,
passed to the linker, separated by commas, e.g. "lapack,blas" e.g. "lapack,blas" or "lapack,f77blas,cblas,atlas". """,
or "lapack,f77blas,cblas,atlas". """,
''), ''),
PathVariable('blas_lapack_dir', PathVariable('blas_lapack_dir',
"""Directory containing the libraries specified by 'blas_lapack_libs'.""", """Directory containing the libraries specified by 'blas_lapack_libs'.""",
'', PathVariable.PathAccept), '', PathVariable.PathAccept),
EnumVariable( EnumVariable(
'lapack_names', 'lapack_names',
"""Set depending on whether the procedure names in the """Set depending on whether the procedure names in the specified
specified libraries are lowercase or uppercase. If you libraries are lowercase or uppercase. If you don't know, run 'nm' on
don't know, run 'nm' on the library file (e.g. 'nm the library file (e.g. 'nm libblas.a').""",
libblas.a').""",
'lower', ('lower','upper')), 'lower', ('lower','upper')),
BoolVariable( BoolVariable(
'lapack_ftn_trailing_underscore', '', True), 'lapack_ftn_trailing_underscore', '', True),
@ -415,8 +404,9 @@ opts.AddVariables(
defaults.threadFlags), defaults.threadFlags),
BoolVariable( BoolVariable(
'optimize', 'optimize',
"""Enable extra compiler optimizations specified by the "optimize_flags" variable, """Enable extra compiler optimizations specified by the
instead of the flags specified by the "debug_flags" variable""", "optimize_flags" variable, instead of the flags specified by the
"debug_flags" variable""",
True), True),
('optimize_flags', ('optimize_flags',
'Additional compiler flags passed to the C/C++ compiler when optimize=yes.', 'Additional compiler flags passed to the C/C++ compiler when optimize=yes.',
@ -442,12 +432,11 @@ opts.AddVariables(
defaults.noDebugLinkFlags), defaults.noDebugLinkFlags),
BoolVariable( BoolVariable(
'build_thread_safe', 'build_thread_safe',
"""Cantera can be built so that it is thread safe. Doing so """Cantera can be built so that it is thread safe. Doing so requires
requires using procedures from the Boost library, so if you using procedures from the Boost library, so if you want thread
want thread safety then you need to get and install Boost safety then you need to get and install Boost (http://www.boost.org)
(http://www.boost.org) if you don't have it. This is if you don't have it. This is turned off by default, in which case
turned off by default, in which case Boost is not required Boost is not required to build Cantera.""",
to build Cantera.""",
False), False),
PathVariable( PathVariable(
'boost_inc_dir', 'boost_inc_dir',
@ -492,7 +481,7 @@ opts.AddVariables(
False), False),
BoolVariable( BoolVariable(
'renamed_shared_libraries', 'renamed_shared_libraries',
"""If this option is turned on, which is the default, the shared libraries that are created """If this option is turned on, the shared libraries that are created
will be renamed to have a "_shared" extension added to their base name. will be renamed to have a "_shared" extension added to their base name.
If not, the base names will be the same as the static libraries. If not, the base names will be the same as the static libraries.
In some cases this simplifies subsequent linking environments with In some cases this simplifies subsequent linking environments with
@ -513,19 +502,18 @@ opts.AddVariables(
'standard', ('standard','debian')), 'standard', ('standard','debian')),
PathVariable( PathVariable(
'graphvizdir', 'graphvizdir',
"""The directory location of the graphviz program, "dot". dot is """The directory location of the graphviz program, "dot". dot is used
used for creating the documentation, and for making for creating the documentation, and for making reaction path
reaction path diagrams. If "dot" is in your path, you can diagrams. If "dot" is in your path, you can leave this unspecified.
leave this unspecified. NOTE: Matlab comes with a NOTE: Matlab comes with a stripped-down version of 'dot'. If 'dot'
stripped-down version of 'dot'. If 'dot' is on your path, is on your path, make sure it is not the Matlab version!""",
make sure it is not the Matlab version!""",
'', PathVariable.PathAccept), '', PathVariable.PathAccept),
('rpfont', ('rpfont',
"""The font to use in reaction path diagrams. This must be a font """The font to use in reaction path diagrams. This must be a font
name recognized by the 'dot' program. On linux systems, this name recognized by the 'dot' program. On linux systems, this
should be lowercase 'helvetica'.""", should be lowercase 'helvetica'.""",
'Helvetica'), 'Helvetica'),
('cantera_version', '', '2.0.0b3') ('cantera_version', '', '2.0.0b4')
) )
opts.Update(env) opts.Update(env)
@ -544,11 +532,10 @@ build process. They should be given in the form:
scons build option1=value1 option2=value2 scons build option1=value1 option2=value2
Variables set in this way will be stored in the 'cantera.conf' file Variables set in this way will be stored in the 'cantera.conf' file and reused
and reused automatically on subsequent invocations of automatically on subsequent invocations of scons. Alternatively, the
scons. Alternatively, the configuration options can be entered configuration options can be entered directly into 'cantera.conf' before
directly into 'cantera.conf' before running 'scons build'. The format running 'scons build'. The format of this file is:
of this file is:
option1 = 'value1' option1 = 'value1'
option2 = 'value2' option2 = 'value2'
@ -675,7 +662,6 @@ if env['coverage']:
if env['CC'] == 'gcc': if env['CC'] == 'gcc':
env.Append(CCFLAGS=['-fprofile-arcs', '-ftest-coverage']) env.Append(CCFLAGS=['-fprofile-arcs', '-ftest-coverage'])
env.Append(LINKFLAGS=['-fprofile-arcs', '-ftest-coverage']) env.Append(LINKFLAGS=['-fprofile-arcs', '-ftest-coverage'])
# ipdb()
else: else:
print 'Error: coverage testing is only available with GCC' print 'Error: coverage testing is only available with GCC'
@ -704,10 +690,7 @@ ret = SCons.Conftest.CheckLib(SCons.SConf.CheckContext(conf),
env['HAS_SUNDIALS'] = not ret # CheckLib returns False to indicate success env['HAS_SUNDIALS'] = not ret # CheckLib returns False to indicate success
env['NEED_LIBM'] = not conf.CheckLibWithHeader(None, 'math.h', 'C', env['NEED_LIBM'] = not conf.CheckLibWithHeader(None, 'math.h', 'C',
'double x; log(x);', False) 'double x; log(x);', False)
if env['NEED_LIBM']: env['LIBM'] = ['m'] if env['NEED_LIBM'] else []
env['LIBM'] = ['m']
else:
env['LIBM'] = []
if env['HAS_SUNDIALS'] and env['use_sundials'] != 'n': if env['HAS_SUNDIALS'] and env['use_sundials'] != 'n':
# Determine Sundials version # Determine Sundials version
@ -1061,41 +1044,29 @@ if not env['single_library']:
linkLibs.append('execstream') linkLibs.append('execstream')
linkSharedLibs.append('execstream_shared') linkSharedLibs.append('execstream_shared')
#
# Add lapack and blas to the link line # Add lapack and blas to the link line
#
if env['blas_lapack_libs']: if env['blas_lapack_libs']:
linkLibs.extend(env['blas_lapack_libs']) linkLibs.extend(env['blas_lapack_libs'])
elif not env['single_library']: elif not env['single_library']:
linkLibs.extend(('ctlapack', 'ctblas')) linkLibs.extend(('ctlapack', 'ctblas'))
linkSharedLibs.extend(('ctlapack_shared', 'ctblas_shared')) linkSharedLibs.extend(('ctlapack_shared', 'ctblas_shared'))
#
# Add the f2c library if it is necessary to link fortran libraries
#
if not env['build_with_f2c']: if not env['build_with_f2c']:
# # TODO: This is not the correct library to link if the fortran sources
# Early gcc compilers will fail on this line as they use g77 and not gfortran # are compiled with a different fortran compiler.
#
linkLibs.append('gfortran') linkLibs.append('gfortran')
linkSharedLibs.append('gfortran') linkSharedLibs.append('gfortran')
elif not env['single_library']: elif not env['single_library']:
# Add the f2c library when f2c is requested # Add the f2c library when f2c is requested
#
linkLibs.append('ctf2c') linkLibs.append('ctf2c')
linkSharedLibs.append('ctf2c_shared') linkSharedLibs.append('ctf2c_shared')
#
# Store the list of needed static link libraries in the environment # Store the list of needed static link libraries in the environment
#
env['cantera_libs'] = linkLibs env['cantera_libs'] = linkLibs
env['cantera_shared_libs'] = linkSharedLibs env['cantera_shared_libs'] = linkSharedLibs
if env['renamed_shared_libraries'] == False : if env['renamed_shared_libraries'] == False :
env['cantera_shared_libs'] = linkLibs env['cantera_shared_libs'] = linkLibs
# Add targets from the SConscript files in the various subdirectories # Add targets from the SConscript files in the various subdirectories
Export('env', 'build', 'libraryTargets', 'install', 'buildSample') Export('env', 'build', 'libraryTargets', 'install', 'buildSample')

22
cantera.pc.in
View file

@ -1,22 +0,0 @@
# @PACKAGE_NAME@ installation details
prefix=@prefix@
exec_prefix=@exec_prefix@
libdir=@libdir@
includedir=@includedir@
# Fortran compilation and linking information
# Retrieve these using `pkg-config --variable=name @PACKAGE_NAME@`
fflags=-I@libdir@
flibs=-L@libdir@ -lf@PACKAGE_NAME@ -l@PACKAGE_NAME@
Name: @PACKAGE_NAME@
Description: @PACKAGE_DESCRIPTION@
URL: @PACKAGE_URL@
Requires:
Version: @VERSION@
LINK = -lctcxx -luser -loneD -lzeroD -lequil -lkinetics -ltransport -lthermo
LINK += -lctnumerics -lctmath -ltpx -lctspectra -lconverters -lctbase -lcvode
LINK += -lctlapack -lctblas -lctf2c -lm -lstdc++
Libs: -L${libdir} ${LINK}
Cflags: -I${includedir}