def configuration(parent_package='', top_path=None):
global config
from numpy.distutils.misc_util import Configuration
from numpy.distutils.fcompiler import get_default_fcompiler, CompilerNotFound
compiler = get_default_fcompiler()
# set some fortran compiler-dependent flags
f90flags = []
if compiler == 'gnu95':
f90flags.append('-fdefault-real-8')
elif compiler == 'intel' or compiler == 'intelem':
f90flags.append('-132')
f90flags.append('-r8')
# Set aggressive optimization level
f90flags.append('-O3')
# Suppress all compiler warnings (avoid huge CI log files)
f90flags.append('-w')
config = Configuration('minimalf2py',
parent_name=parent_package,
top_path=top_path)
config.add_subpackage('tests')
config.add_extension(
name='add',
sources=['add.f', 'add.pyf'],
extra_f90_compile_args=f90flags,
)
return config
def configuration(parent_package='', top_path=None):
global config
from numpy.distutils.misc_util import Configuration
from numpy.distutils.fcompiler import get_default_fcompiler, CompilerNotFound
build = True
try:
# figure out which compiler we're going to use
compiler = get_default_fcompiler()
# set some fortran compiler-dependent flags
f90flags = []
if compiler == 'gnu95':
f90flags.append('-fdefault-real-8')
elif compiler == 'intel' or compiler == 'intelem':
f90flags.append('-132')
f90flags.append('-r8')
# Suppress all compiler warnings (avoid huge CI log files)
f90flags.append('-w')
except CompilerNotFound:
print(
'No Fortran compiler found, not building the CAM3 radiation module!'
)
build = False
config = Configuration(package_name='cam3',
parent_name=parent_package,
top_path=top_path)
config.add_data_files(join('data', 'abs_ems_factors_fastvx.c030508.nc'))
if build:
config.add_extension(name='_cam3',
sources=[cam3_gen_source],
extra_f90_compile_args=f90flags,
f2py_options=['--quiet'])
config.add_include_dirs('src')
return config
def check_f2py_compiler():
from numpy.distutils.fcompiler import get_default_fcompiler
f2py_compiler = get_default_fcompiler()
if 'gnu' not in f2py_compiler:
print(' GNU compiler not installed. Checking f2py comompiler - this is UNTESTED' )
print(' Speculatively setting flags - if compile fails, or OpenMP doesn\'t work install gfortran and retry')
if 'gnu' in f2py_compiler:
print('Found gnu compiler. Setting OpenMP flag to \'-fopenmp\'')
compile_args = ['-fopenmp', '-lgomp', '-O3']
link_args = ['-lgomp']
elif 'intel' in f2py_compiler:
print('Found intel compiler. Setting OpenMP flag to \'-openmp\'')
compile_args = ['-openmp', '-O3']
link_args = []
elif 'pg' in f2py_comopiler:
print('Found portland compiler. Setting OpenMP flag to \'-mp\'')
compile_args = ['-mp', '-O3']
link_args = []
elif 'nag' in f2py_compiler:
print('Found NAG compiler. Setting OpenMP flag to \'-openmp\'')
compile_args = ['-openmp', '-O3']
link_args = []
else:
print('Not sure what compiler f2py uses. Speculatively setting OpenMP flag to \'-openmp\'')
compile_args = ['-openmp', '-O3']
link_args = []
args = {'link_args':link_args,'compile_args':compile_args}
return args
def configuration(parent_package='', top_path=None):
global config
from numpy.distutils.misc_util import Configuration
from numpy.distutils.fcompiler import get_default_fcompiler, CompilerNotFound
build = True
try:
# figure out which compiler we're going to use
compiler = get_default_fcompiler()
# set some fortran compiler-dependent flags
f90flags = []
if compiler == 'gnu95':
f90flags.append('-fno-range-check')
f90flags.append('-ffree-form')
f90flags.append('-fPIC')
elif compiler == 'intel' or compiler == 'intelem':
f90flags.append('-132')
# Need zero-level optimization to avoid build problems with rrtmg_lw_k_g.f90
#f90flags.append('-O2')
# Suppress all compiler warnings (avoid huge CI log files)
f90flags.append('-w')
except CompilerNotFound:
print('No Fortran compiler found, not building the RRTMG_LW radiation module!')
build = False
config = Configuration(package_name='_rrtmg_lw', parent_name=parent_package, top_path=top_path)
if build:
config.add_extension(
name='_rrtmg_lw',
sources=[rrtmg_lw_gen_source],
extra_f90_compile_args=f90flags,
f2py_options=['--quiet'],
)
return config
def configuration(parent_package='', top_path=None):
global config
from numpy.distutils.misc_util import Configuration
from numpy.distutils.fcompiler import get_default_fcompiler, CompilerNotFound
build = True
try:
# figure out which compiler we're going to use
compiler = get_default_fcompiler()
# set some fortran compiler-dependent flags
f90flags = []
if compiler == 'gnu95':
f90flags.append('-fno-range-check')
f90flags.append('-ffree-form')
elif compiler == 'intel' or compiler == 'intelem':
f90flags.append('-132')
# Set aggressive optimization level
f90flags.append('-O3')
# Suppress all compiler warnings (avoid huge CI log files)
f90flags.append('-w')
except CompilerNotFound:
print('No Fortran compiler found, not building the RRTMG_LW radiation module!')
build = False
config = Configuration(package_name='_emanuel_convection', parent_name=parent_package, top_path=top_path)
if build:
config.add_extension(name='_emanuel_convection',
sources=[gen_source],
extra_f90_compile_args=f90flags,
f2py_options=['--quiet'],
)
return config
def get_fc():
''' get Fortran compiler '''
fc = fcompiler.get_default_fcompiler()
for i in range(len(sys.argv)):
if '--fcompiler' in sys.argv[i]:
fc = sys.argv.pop(i)
fc = fc[fc.index('=') + 1:]
return fc
def configuration(parent_package='', top_path=None):
"""Configure all packages that need to be built."""
config = Configuration('', parent_package, top_path)
F95FLAGS = get_compiler_flags()
kwargs = {}
kwargs['extra_compile_args'] = F95FLAGS
kwargs['f2py_options'] = ['--quiet']
# numpy.distutils.fcompiler.FCompiler doesn't support .F95 extension
compiler = FCompiler(get_default_fcompiler())
compiler.src_extensions.append('.F95')
compiler.language_map['.F95'] = 'f90'
# collect all Fortran sources
files = os.listdir('src')
exclude_sources = ['PlanetsConstants.f95', 'PythonWrapper.f95']
sources = [
os.path.join('src', file) for file in files
if file.lower().endswith('.f95') and file not in exclude_sources
]
# (from http://stackoverflow.com/questions/14320220/
# testing-python-c-libraries-get-build-path)):
build_lib_dir = "{dirname}.{platform}-{version[0]}.{version[1]}"
dirparams = {
'dirname': 'temp',
'platform': sysconfig.get_platform(),
'version': sys.version_info
}
libdir = os.path.join('build', build_lib_dir.format(**dirparams))
print('searching SHTOOLS in:', libdir)
# Fortran compilation
config.add_library('SHTOOLS', sources=sources, **kwargs)
# SHTOOLS
config.add_extension(
'pyshtools._SHTOOLS',
include_dirs=[libdir],
library_dirs=[libdir],
libraries=['SHTOOLS', 'fftw3', 'm', 'lapack', 'blas'],
sources=['src/pyshtools.pyf', 'src/PythonWrapper.f95'],
**kwargs)
# constants
config.add_extension('pyshtools._constant',
sources=['src/PlanetsConstants.f95'],
**kwargs)
return config
def configuration(parent_package='', top_path=None):
"""Configure all packages that need to be built."""
config = Configuration('', parent_package, top_path)
F95FLAGS = get_compiler_flags()
kwargs = {}
kwargs['extra_compile_args'] = F95FLAGS
kwargs['f2py_options'] = ['--quiet']
# numpy.distutils.fcompiler.FCompiler doesn't support .F95 extension
compiler = FCompiler(get_default_fcompiler())
compiler.src_extensions.append('.F95')
compiler.language_map['.F95'] = 'f90'
# collect all Fortran sources
files = os.listdir('src')
exclude_sources = ['PlanetsConstants.f95', 'PythonWrapper.f95']
sources = [os.path.join('src', file) for file in files if
file.lower().endswith('.f95') and file not in exclude_sources]
# (from http://stackoverflow.com/questions/14320220/
# testing-python-c-libraries-get-build-path)):
build_lib_dir = "{dirname}.{platform}-{version[0]}.{version[1]}"
dirparams = {'dirname': 'temp',
'platform': sysconfig.get_platform(),
'version': sys.version_info}
libdir = os.path.join('build', build_lib_dir.format(**dirparams))
print('searching SHTOOLS in:', libdir)
# Fortran compilation
config.add_library('SHTOOLS',
sources=sources,
**kwargs)
# SHTOOLS
config.add_extension('pyshtools._SHTOOLS',
include_dirs=[libdir],
library_dirs=[libdir],
libraries=['SHTOOLS', 'fftw3', 'm', 'lapack', 'blas'],
sources=['src/pyshtools.pyf',
'src/PythonWrapper.f95'],
**kwargs)
# constants
config.add_extension('pyshtools._constant',
sources=['src/PlanetsConstants.f95'],
**kwargs)
return config
def check_f2py_compiler():
from numpy.distutils.fcompiler import get_default_fcompiler, CompilerNotFound
from numpy.distutils.fcompiler import CompilerNotFound
f2py_compiler = get_default_fcompiler()
if f2py_compiler == None:
raise CompilerNotFound(
'You don\'t have a Fortran compiler installed. Please install one and try again'
)
sys.exit()
if 'gnu' not in f2py_compiler:
print(
' GNU compiler not installed. Checking f2py compiler - this is UNTESTED'
)
print(
' Speculatively setting flags - if compile fails, or OpenMP doesn\'t work install gfortran and retry'
)
if 'gnu' in f2py_compiler:
print('Found gnu compiler. Setting OpenMP flag to \'-fopenmp\'')
compile_args = ['-fopenmp', '-lgomp', '-O3']
link_args = ['-lgomp']
elif f2py_compiler == 'intel':
print('Found intel compiler. Setting OpenMP flag to \'-openmp\'')
compile_args = ['-qopenmp', '-O3']
link_args = []
elif f2py_compiler == 'intelem':
print('Found intel compiler. Setting OpenMP flag to \'-openmp\'')
compile_args = ['-qopenmp', '-O3']
link_args = []
elif 'pg' in f2py_comopiler:
print('Found portland compiler. Setting OpenMP flag to \'-mp\'')
compile_args = ['-mp', '-O3']
link_args = []
elif 'nag' in f2py_compiler:
print('Found NAG compiler. Setting OpenMP flag to \'-openmp\'')
compile_args = ['-openmp', '-O3']
link_args = []
else:
print(
'Not sure what compiler f2py uses. Speculatively setting OpenMP flag to \'-openmp\''
)
compile_args = ['-openmp', '-O3']
link_args = []
args = {'link_args': link_args, 'compile_args': compile_args}
return args
def configuration(parent_package='', top_path=None):
import os
from numpy.distutils.misc_util import Configuration
from numpy.distutils import fcompiler
# figure out which compiler we're going to use
compiler = fcompiler.get_default_fcompiler()
# set some fortran compiler-dependent flags
f90flags = []
if compiler == 'gnu95':
f90flags.append('-fdefault-real-8')
elif compiler == 'intel' or compiler == 'intelem':
f90flags.append('-132')
f90flags.append('-r8')
# Suppress all compiler warnings (avoid huge CI log files)
f90flags.append('-w')
sourcelist = ['_cam3.pyf',
'src/pmgrid.F90',
'src/prescribed_aerosols.F90',
'src/quicksort.F90',
'src/abortutils.F90',
'src/shr_kind_mod.F90',
'src/absems.F90',
'src/wv_saturation.F90',
'src/aer_optics.F90',
'src/cmparray_mod.F90',
'src/shr_const_mod.F90',
'src/physconst.F90',
'src/pkg_cldoptics.F90',
'src/gffgch.F90',
'src/chem_surfvals.F90',
'src/volcrad.F90',
'src/radae.F90',
'src/radlw.F90',
'src/radsw.F90',
'src/crm.F90',
'Driver.f90']
config = Configuration(package_name='cam3', parent_name=parent_package, top_path=top_path)
config.add_extension(name='_cam3',
sources=sourcelist,
extra_f90_compile_args=f90flags,
f2py_options=['--quiet'])
config.add_include_dirs('src')
config.add_data_files(os.path.join('data', 'abs_ems_factors_fastvx.c030508.nc'))
return config
def get_compiler_flags():
"""Set fortran flags depending on the compiler."""
compiler = get_default_fcompiler()
if compiler == 'absoft':
flags = ['-m64', '-O3', '-YEXT_NAMES=LCS', '-YEXT_SFX=_',
'-fpic', '-speed_math=10']
elif compiler == 'gnu95':
flags = ['-m64', '-fPIC', '-O3', '-ffast-math']
elif compiler == 'intel':
flags = ['-m64', '-fpp', '-free', '-O3', '-Tf']
elif compiler == 'g95':
flags = ['-O3', '-fno-second-underscore']
elif compiler == 'pg':
flags = ['-fast']
else:
flags = ['-m64', '-O3']
return flags
def configuration(parent_package='', top_path=None):
global config
from numpy.distutils.misc_util import Configuration
from numpy.distutils.fcompiler import get_default_fcompiler, CompilerNotFound
build = True
try:
# figure out which compiler we're going to use
compiler = get_default_fcompiler()
# set some fortran compiler-dependent flags
f90flags = []
if compiler == 'gnu95':
f90flags.append('-fno-range-check')
f90flags.append('-ffree-form')
elif compiler == 'intel' or compiler == 'intelem':
f90flags.append('-132')
# Need zero-level optimization to avoid build problems with rrtmg_sw_k_g.f90
f90flags.append('-O0')
# Suppress all compiler warnings (avoid huge CI log files)
f90flags.append('-w')
except CompilerNotFound:
print(
'No Fortran compiler found, not building the RRTMG_SW radiation module!'
)
build = False
config = Configuration(package_name='_rrtmg_sw',
parent_name=parent_package,
top_path=top_path)
if build:
config.add_extension(
name='_rrtmg_sw',
sources=[rrtmg_sw_gen_source],
extra_f90_compile_args=f90flags,
f2py_options=['--quiet'],
)
# Not currently initializing from nc data file, so there's no reason to include it
#config.add_data_files(join('rrtmg_sw_v4.0', 'gcm_model', 'data', 'rrtmg_sw.nc'))
return config
'cppflags':'-DPLON=%i -DPLEV=%i' % (IM,KM)},
{'name':'simple_turbulence',
'dir':'src/turbulence/simple'},
{'name':'rrtm_radiation_fortran',
'dir':'src/radiation/rrtm'}
]
# define extensions that will be built when the --lite option is used
LiteExtensionsNames = ['grid','timestep','insolation','ozone','thermodyn','ccm3_radiation']
ExtensionsLite = []
for ext in Extensions:
if ext['name'] in LiteExtensionsNames:
ExtensionsLite.append(ext)
# figure out which compiler we're goint to use
compiler = fcompiler.get_default_fcompiler()
for i in range(len(sys.argv)):
if '--fcompiler' in sys.argv[i]:
compiler = sys.argv.pop(i)
compiler = compiler[compiler.index('=')+1:]
print 'Using %s compiler' % compiler
# set some fortran compiler-dependent flags
if compiler == 'gnu95':
f77flags='-ffixed-line-length-132 -fdefault-real-8'
f90flags='-fdefault-real-8 -fno-range-check -ffree-form'
elif compiler == 'intel' or compiler == 'intelem':
f77flags='-132 -r8'
f90flags='-132 -r8'
elif compiler == 'ibm':
f77flags='-qautodbl=dbl4 -qsuffix=f=f:cpp=F -qfixed=132'
def get_options(args=None, get_parser=False):
import optparse
import os
from glob import glob
import kmos
parser = optparse.OptionParser('Usage: %prog [help] (' +
'|'.join(sorted(usage.keys())) +
') [options]',
version=kmos.__version__)
parser.add_option('-s',
'--source-only',
dest='source_only',
action='store_true',
default=False)
parser.add_option('-p',
'--path-to-f2py',
dest='path_to_f2py',
default='f2py')
parser.add_option('-b', '--backend', dest='backend', default='local_smart')
parser.add_option(
'-a',
'--avoid-default-state',
dest='avoid_default_state',
action='store_true',
default=False,
)
parser.add_option('-v',
'--steps-per-frame',
dest='steps_per_frame',
type='int',
default='50000')
parser.add_option('-d',
'--debug',
default=False,
dest='debug',
action='store_true')
parser.add_option('-n',
'--no-compiler-optimization',
default=False,
dest='no_optimize',
action='store_true')
parser.add_option('-o', '--overwrite', default=False, action='store_true')
parser.add_option('-l',
'--variable-length',
dest='variable_length',
default=95,
type='int')
parser.add_option('-c', '--catmap', default=False, action='store_true')
parser.add_option(
'--acf',
dest='acf',
action='store_true',
default=False,
)
try:
from numpy.distutils.fcompiler import get_default_fcompiler
from numpy.distutils import log
log.set_verbosity(-1, True)
fcompiler = get_default_fcompiler()
except:
fcompiler = 'gfortran'
parser.add_option('-f',
'--fcompiler',
dest='fcompiler',
default=os.environ.get('F2PY_FCOMPILER', fcompiler))
if args is not None:
options, args = parser.parse_args(args.split())
else:
options, args = parser.parse_args()
if len(args) < 1:
parser.error('Command expected')
if get_parser:
return options, args, parser
else:
return options, args
def get_options(args=None, get_parser=False):
import optparse
import os
from glob import glob
import kmos
parser = optparse.OptionParser(
'Usage: %prog [help] ('
+ '|'.join(sorted(usage.keys()))
+ ') [options]',
version=kmos.__version__)
parser.add_option('-s', '--source-only',
dest='source_only',
action='store_true',
default=False)
parser.add_option('-p', '--path-to-f2py',
dest='path_to_f2py',
default='f2py')
parser.add_option('-b', '--backend',
dest='backend',
default='local_smart')
parser.add_option('-v', '--steps-per-frame',
dest='steps_per_frame',
type='int',
default='50000')
parser.add_option('-d', '--debug',
default=False,
dest='debug',
action='store_true')
parser.add_option('-n', '--no-compiler-optimization',
default=False,
dest='no_optimize',
action='store_true')
try:
from numpy.distutils.fcompiler import get_default_fcompiler
from numpy.distutils import log
log.set_verbosity(-1, True)
fcompiler = get_default_fcompiler()
except:
fcompiler = 'gfortran'
parser.add_option('-f', '--fcompiler',
dest='fcompiler',
default=os.environ.get('F2PY_FCOMPILER', fcompiler))
if args is not None:
options, args = parser.parse_args(args.split())
else:
options, args = parser.parse_args()
if len(args) < 1:
parser.error('Command expected')
if get_parser:
return options, args, parser
else:
return options, args
def main(args=None):
"""The CLI main entry point function.
The optional arguemnts args, can be used to
directly supply command line argument like
$ kmos <args>
otherwise args will be taken from STDIN.
"""
import optparse
import os
from glob import glob
import kmos
parser = optparse.OptionParser('Usage: %prog [help] (' +
'|'.join(sorted(usage.keys())) +
') [options]',
version=kmos.__version__)
parser.add_option('-s',
'--source-only',
dest='source_only',
action='store_true',
default=False)
parser.add_option('-p',
'--path-to-f2py',
dest='path_to_f2py',
default='f2py')
try:
from numpy.distutils.fcompiler import get_default_fcompiler
from numpy.distutils import log
log.set_verbosity(-1, True)
fcompiler = get_default_fcompiler()
except:
fcompiler = 'gfortran'
parser.add_option('-f',
'--fcompiler',
dest='fcompiler',
default=os.environ.get('F2PY_FCOMPILER', fcompiler))
if args is not None:
options, args = parser.parse_args(args.split())
else:
options, args = parser.parse_args()
if len(args) < 1:
parser.error('Command expected')
if args[0] == 'benchmark':
from sys import path
path.append(os.path.abspath(os.curdir))
nsteps = 1000000
from time import time
from kmos.run import KMC_Model
with KMC_Model(print_rates=False, banner=False) as model:
time0 = time()
model.do_steps(nsteps)
needed_time = time() - time0
print('%s steps took %.2f seconds' % (nsteps, needed_time))
print('Or %.2e steps/s' % (1e6 / needed_time))
elif args[0] == 'build':
from kmos.utils import build
build(options)
elif args[0] == 'edit':
from kmos import gui
gui.main()
elif args[0] == 'export-settings':
import kmos.types
import kmos.io
from kmos.utils import build
import shutil
from kmos.io import ProcListWriter
if len(args) < 2:
parser.error('XML file and export path expected.')
if len(args) < 3:
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting to %s' % out_dir)
args.append(out_dir)
xml_file = args[1]
export_dir = args[2]
project = kmos.types.Project()
project.import_xml_file(xml_file)
writer = ProcListWriter(project, export_dir)
writer.write_settings()
elif args[0] == 'export':
import kmos.types
import kmos.io
from kmos.utils import build
import shutil
if len(args) < 2:
parser.error('XML file and export path expected.')
if len(args) < 3:
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting to %s' % out_dir)
args.append(out_dir)
xml_file = args[1]
export_dir = os.path.join(args[2], 'src')
project = kmos.types.Project()
project.import_xml_file(xml_file)
kmos.io.export_source(project, export_dir)
if ((os.name == 'posix'
and os.uname()[0] == 'Linux')
or os.name == 'nt') \
and not options.source_only:
os.chdir(export_dir)
build(options)
for out in glob('kmc_*'):
if os.path.exists('../%s' % out):
overwrite = raw_input(('Should I overwrite existing %s ?'
'[y/N] ') % out).lower()
if overwrite.startswith('y'):
os.remove('../%s' % out)
shutil.move(out, '..')
else:
shutil.move(out, '..')
elif args[0] == 'export-settings':
import kmos.io
pt = kmos.io.import_xml_file(args[1])
if len(args) < 3:
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting kmc_settings.py to %s' %
out_dir)
args.append(out_dir)
if not os.path.exists(args[2]):
os.mkdir(args[2])
elif not os.path.isdir(args[2]):
raise UserWarning("Cannot overwrite %s; Exiting;" % args[2])
writer = kmos.io.ProcListWriter(pt, args[2])
writer.write_settings()
elif args[0] == 'export-view':
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting to %s' % out_dir)
args.append(out_dir)
os.system('kmos-export-program %s %s' % (args[1], args[2]))
os.chdir(out_dir)
main('view')
elif args[0] == 'all':
print('Interpreting: all -> help all\n\n')
main('help all')
elif args[0] == 'help':
if len(args) < 2:
parser.error('Which help do you want?')
if args[1] == 'all':
for command in sorted(usage):
print(usage[command])
elif args[1] in usage:
print('Usage: %s\n' % usage[args[1]])
else:
raise Exception('Command "%s" not known or not documented.' %
args[1])
elif args[0] == 'import':
import kmos.io
if not len(args) >= 2:
raise UserWarning('XML file name expected.')
global pt
pt = kmos.io.import_xml_file(args[1])
sh(banner='Note: pt = kmos.io.import_xml(\'%s\')' % args[1])
elif args[0] == 'rebuild':
from sys import path
path.append(os.path.abspath(os.curdir))
from tempfile import mktemp
if not os.path.exists('kmc_model.so') \
and not os.path.exists('kmc_model.pyd'):
raise Exception('No kmc_model.so found.')
if not os.path.exists('kmc_settings.py'):
raise Exception('No kmc_settings.py found.')
from kmos.run import KMC_Model
with KMC_Model(print_rates=False, banner=False) as model:
tempfile = mktemp()
f = file(tempfile, 'w')
f.write(model.xml())
f.close()
for kmc_model in glob('kmc_model.*'):
os.remove(kmc_model)
os.remove('kmc_settings.py')
main('export %s .' % tempfile)
os.remove(tempfile)
elif args[0] == 'run':
from sys import path
path.append(os.path.abspath(os.curdir))
from kmos.run import KMC_Model
with KMC_Model(print_rates=False) as model:
global model
sh(banner='Note: model = KMC_Model(print_rates=False)')
elif args[0] == 'view':
from sys import path
path.append(os.path.abspath(os.curdir))
from kmos import view
view.main()
else:
parser.error('Command "%s" not understood.' % args[0])
from numpy.distutils.fcompiler import get_default_fcompiler
import sys
import os
fcompile = get_default_fcompiler(os.name,sys.platform,True)
install_dir = sys.argv[1]
os.system("python setup.py config_fc --fcompiler="+str(fcompile)+" build_clib --fcompiler="+str(fcompile)+" build_ext --fcompiler="+str(fcompile)+" install --prefix='"+str(install_dir)+"'")
direct = os.path.dirname(direct)
if base=='lib' or base=='lib64':
root = direct
if 'bin' in os.listdir(root):
f2py_exec_path = os.path.join(root,'bin')
if 'f2py' in os.listdir(f2py_exec_path):
f2py_bin = os.path.join(f2py_exec_path,'f2py')
break
Extensions = [
{'name':'disort',
'dir':'src/disort'},
]
# figure out which compiler we're goint to use
compiler = fcompiler.get_default_fcompiler(requiref90=True)
compiler = 'gnu95' # ensure gfortran
for i in range(len(sys.argv)):
if '--fcompiler' in sys.argv[i]:
compiler = sys.argv.pop(i)
compiler = compiler[compiler.index('=')+1:]
print 'Using %s compiler' % compiler
# set some fortran compiler-dependent flags
if compiler == 'gnu95' or compiler == 'gnu':
# f77flags='-ffixed-line-length-132 -fdefault-real-8'
# f90flags='-fdefault-real-8'
f77flags='-O3'
f90flags='-O3'
elif compiler == 'intel' or compiler == 'intelem':
f77flags='-132 -r8 -w95 -w90 -mp'
def configuration(parent_package='', top_path=None):
import os
from numpy.distutils.misc_util import Configuration
from numpy.distutils import fcompiler
# figure out which compiler we're going to use
compiler = fcompiler.get_default_fcompiler()
# set some fortran compiler-dependent flags
f90flags = []
if compiler == 'gnu95':
f90flags.append('-fno-range-check')
f90flags.append('-ffree-form')
elif compiler == 'intel' or compiler == 'intelem':
f90flags.append('-132')
# Need zero-level optimization to avoid build problems with rrtmg_sw_k_g.f90
f90flags.append('-O0')
# Suppress all compiler warnings (avoid huge CI log files)
f90flags.append('-w')
sourcelist = ['_rrtmg_sw.pyf',
'rrtmg_sw_v4.0/gcm_model/modules/parkind.f90',
'rrtmg_sw_v4.0/gcm_model/modules/parrrsw.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_aer.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_cld.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_con.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg16.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg17.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg18.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg19.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg20.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg21.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg22.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg23.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg24.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg25.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg26.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg27.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg28.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_kg29.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_ncpar.f90',
'rrtmg_sw_v4.0/gcm_model/src/rrtmg_sw_k_g.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_ref.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_tbl.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_vsn.f90',
'rrtmg_sw_v4.0/gcm_model/modules/rrsw_wvn.f90',
'rrtmg_sw_v4.0/gcm_model/src/mcica_random_numbers.f90',
'rrtmg_sw_v4.0/gcm_model/src/mcica_subcol_gen_sw.f90',
'rrtmg_sw_v4.0/gcm_model/src/rrtmg_sw_vrtqdr.f90',
'rrtmg_sw_v4.0/gcm_model/src/rrtmg_sw_reftra.f90',
'rrtmg_sw_v4.0/gcm_model/src/rrtmg_sw_taumol.f90',
'rrtmg_sw_v4.0/gcm_model/src/rrtmg_sw_spcvmc.f90',
'rrtmg_sw_v4.0/gcm_model/src/rrtmg_sw_setcoef.f90',
'rrtmg_sw_v4.0/gcm_model/src/rrtmg_sw_init.f90',
'rrtmg_sw_v4.0/gcm_model/src/rrtmg_sw_cldprmc.f90',
'sourcemods/rrtmg_sw_rad.f90',
'Driver.f90']
config = Configuration(package_name='_rrtmg_sw', parent_name=parent_package, top_path=top_path)
config.add_extension(name='_rrtmg_sw',
sources=sourcelist,
extra_f90_compile_args=f90flags,
f2py_options=['--quiet'],
)
# Not currently initializing from nc data file, so there's no reason to include it
#config.add_data_files(os.path.join('rrtmg_sw_v4.0', 'gcm_model', 'data', 'rrtmg_sw.nc'))
return config
def main(args=None):
"""The CLI main entry point function.
The optional arguemnts args, can be used to
directly supply command line argument like
$ kmos <args>
otherwise args will be taken from STDIN.
"""
import optparse
import os
from glob import glob
import kmos
parser = optparse.OptionParser(
'Usage: %prog [help] ('
+ '|'.join(sorted(usage.keys()))
+ ') [options]',
version=kmos.__version__)
parser.add_option('-s', '--source-only',
dest='source_only',
action='store_true',
default=False)
parser.add_option('-p', '--path-to-f2py',
dest='path_to_f2py',
default='f2py')
try:
from numpy.distutils.fcompiler import get_default_fcompiler
from numpy.distutils import log
log.set_verbosity(-1, True)
fcompiler = get_default_fcompiler()
except:
fcompiler = 'gfortran'
parser.add_option('-f', '--fcompiler',
dest='fcompiler',
default=os.environ.get('F2PY_FCOMPILER', fcompiler ))
if args is not None:
options, args = parser.parse_args(args.split())
else:
options, args = parser.parse_args()
if len(args) < 1:
parser.error('Command expected')
if args[0] == 'benchmark':
from sys import path
path.append(os.path.abspath(os.curdir))
nsteps = 1000000
from time import time
from kmos.run import KMC_Model
with KMC_Model(print_rates=False, banner=False) as model:
time0 = time()
model.do_steps(nsteps)
needed_time = time() - time0
print('%s steps took %.2f seconds' % (nsteps, needed_time))
print('Or %.2e steps/s' % (1e6 / needed_time))
elif args[0] == 'build':
from kmos.utils import build
build(options)
elif args[0] == 'edit':
from kmos import gui
gui.main()
elif args[0] == 'export-settings':
import kmos.types
import kmos.io
from kmos.utils import build
import shutil
from kmos.io import ProcListWriter
if len(args) < 2:
parser.error('XML file and export path expected.')
if len(args) < 3:
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting to %s' % out_dir)
args.append(out_dir)
xml_file = args[1]
export_dir = args[2]
project = kmos.types.Project()
project.import_xml_file(xml_file)
writer = ProcListWriter(project, export_dir)
writer.write_settings()
elif args[0] == 'export':
import kmos.types
import kmos.io
from kmos.utils import build
import shutil
if len(args) < 2:
parser.error('XML file and export path expected.')
if len(args) < 3:
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting to %s' % out_dir)
args.append(out_dir)
xml_file = args[1]
export_dir = os.path.join(args[2], 'src')
project = kmos.types.Project()
project.import_xml_file(xml_file)
kmos.io.export_source(project, export_dir)
if ((os.name == 'posix'
and os.uname()[0] == 'Linux')
or os.name == 'nt') \
and not options.source_only:
os.chdir(export_dir)
build(options)
for out in glob('kmc_*'):
if os.path.exists('../%s' % out):
overwrite = raw_input(('Should I overwrite existing %s ?'
'[y/N] ') % out).lower()
if overwrite.startswith('y'):
os.remove('../%s' % out)
shutil.move(out, '..')
else:
shutil.move(out, '..')
elif args[0] == 'export-settings':
import kmos.io
pt = kmos.io.import_xml_file(args[1])
if len(args) < 3:
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting kmc_settings.py to %s'
% out_dir)
args.append(out_dir)
if not os.path.exists(args[2]):
os.mkdir(args[2])
elif not os.path.isdir(args[2]):
raise UserWarning("Cannot overwrite %s; Exiting;" % args[2])
writer = kmos.io.ProcListWriter(pt, args[2])
writer.write_settings()
elif args[0] == 'export-view':
out_dir = os.path.splitext(args[1])[0]
print('No export path provided. Exporting to %s' % out_dir)
args.append(out_dir)
os.system('kmos-export-program %s %s' % (args[1], args[2]))
os.chdir(out_dir)
main('view')
elif args[0] == 'all':
print('Interpreting: all -> help all\n\n')
main('help all')
elif args[0] == 'help':
if len(args) < 2:
parser.error('Which help do you want?')
if args[1] == 'all':
for command in sorted(usage):
print(usage[command])
elif args[1] in usage:
print('Usage: %s\n' % usage[args[1]])
else:
raise Exception('Command "%s" not known or not documented.'
% args[1])
elif args[0] == 'import':
import kmos.io
if not len(args) >= 2:
raise UserWarning('XML file name expected.')
global pt
pt = kmos.io.import_xml_file(args[1])
sh(banner='Note: pt = kmos.io.import_xml(\'%s\')' % args[1])
elif args[0] == 'rebuild':
from sys import path
path.append(os.path.abspath(os.curdir))
from tempfile import mktemp
if not os.path.exists('kmc_model.so') \
and not os.path.exists('kmc_model.pyd'):
raise Exception('No kmc_model.so found.')
if not os.path.exists('kmc_settings.py'):
raise Exception('No kmc_settings.py found.')
from kmos.run import KMC_Model
with KMC_Model(print_rates=False, banner=False) as model:
tempfile = mktemp()
f = file(tempfile, 'w')
f.write(model.xml())
f.close()
for kmc_model in glob('kmc_model.*'):
os.remove(kmc_model)
os.remove('kmc_settings.py')
main('export %s .' % tempfile)
os.remove(tempfile)
elif args[0] == 'run':
from sys import path
path.append(os.path.abspath(os.curdir))
from kmos.run import KMC_Model
with KMC_Model(print_rates=False) as model:
global model
sh(banner='Note: model = KMC_Model(print_rates=False)')
elif args[0] == 'view':
from sys import path
path.append(os.path.abspath(os.curdir))
from kmos import view
view.main()
else:
parser.error('Command "%s" not understood.' % args[0])
def configuration(parent_package='', top_path=None):
"""Configure all packages that need to be built."""
config = Configuration('', parent_package, top_path)
kwargs = {'libraries': [], 'include_dirs': [], 'library_dirs': []}
# numpy.distutils.fcompiler.FCompiler doesn't support .F95 extension
compiler = FCompiler(get_default_fcompiler())
compiler.src_extensions.append('.F95')
compiler.language_map['.F95'] = 'f90'
# collect all Fortran sources
files = os.listdir('src')
exclude_sources = ['PlanetsConstants.f95', 'PythonWrapper.f95']
sources = [
os.path.join('src', file) for file in files
if file.lower().endswith(('.f95',
'.c')) and file not in exclude_sources
]
# (from http://stackoverflow.com/questions/14320220/
# testing-python-c-libraries-get-build-path)):
build_lib_dir = "{dirname}.{platform}-{version[0]}.{version[1]}"
dirparams = {
'dirname': 'temp',
'platform': sysconfig.get_platform(),
'version': sys.version_info
}
libdir = os.path.join('build', build_lib_dir.format(**dirparams))
print('searching SHTOOLS in:', libdir)
# Fortran compilation
config.add_library('SHTOOLS', sources=sources)
# SHTOOLS
kwargs['libraries'].extend(['SHTOOLS'])
kwargs['include_dirs'].extend([libdir])
kwargs['library_dirs'].extend([libdir])
kwargs['f2py_options'] = ['--quiet']
# FFTW info
fftw_info = get_info('fftw', notfound_action=2)
dict_append(kwargs, **fftw_info)
if sys.platform != 'win32':
kwargs['libraries'].extend(['m'])
# BLAS / Lapack info
lapack_info = get_info('lapack_opt', notfound_action=2)
blas_info = get_info('blas_opt', notfound_action=2)
dict_append(kwargs, **blas_info)
dict_append(kwargs, **lapack_info)
if sys.platform == 'win32':
kwargs['runtime_library_dirs'] = []
config.add_extension(
'pyshtools._SHTOOLS',
sources=['src/pyshtools.pyf', 'src/PythonWrapper.f95'],
**kwargs)
return config
def _build_extension(KM,JM,IM):
name = 'cam3_radiation'
# Temporarily move to the source directory
here = os.getcwd()
pydir = os.path.dirname(os.path.abspath(__file__))
srcdir = pydir + '/src/cam3'
# need to change to srcdir so f2py sees the .f2py_f2cmap file
os.chdir(srcdir)
srcdir = os.getcwd()
# figure out which compiler we're goint to use
compiler = fcompiler.get_default_fcompiler()
# set some fortran compiler-dependent flags
if compiler == 'gnu95':
f77flags='-ffixed-line-length-132 -fdefault-real-8'
f90flags='-fdefault-real-8 -fno-range-check -ffree-form'
elif compiler == 'intel' or compiler == 'intelem':
f77flags='-132 -r8'
f90flags='-132 -r8'
elif compiler == 'ibm':
f77flags='-qautodbl=dbl4 -qsuffix=f=f:cpp=F -qfixed=132'
f90flags='-qautodbl=dbl4 -qsuffix=f=f90:cpp=F90 -qfree=f90'
else:
print 'Sorry, compiler %s not supported' % compiler
#cppflags = '-DPLEV=%i -DIM=%i -DJM=%i -DKM=%i' % (KM,IM,JM,KM)
# only the vertical dimension needs to be set by pre-processor
cppflags = '-DPLEV=%i' %KM
src = getSources(srcdir)
target = '_%s.so' % name
#target = '_cam3_radiation.so'
driver = glob.glob(os.path.join(srcdir,'Driver.f*'))[0]
f77flags = '"%s %s"' % (cppflags,f77flags)
f90flags = '"%s %s"' % (cppflags,f90flags)
if buildNeeded(src, KM):
#if True:
print '\n Building %s ... \n' % os.path.basename(target)
# generate signature file
if os.path.exists(os.path.join(srcdir, 'sources_signature_file')):
src_pyf = getSources(srcdir, source_file_name='sources_signature_file')
src_pyf_str = string.join(src_pyf)
else:
src_pyf_str = driver
subprocess.call('f2py --quiet --overwrite-signature %s -m _%s -h _%s.pyf'%(src_pyf_str,name,name), shell=True)
# compile extension
F2pyCommand = []
F2pyCommand.append('f2py -c -m _%s' % name)
F2pyCommand.append('--fcompiler=%s --noopt' % compiler)
#F2pyCommand.append('-I%s' % dir)
#F2pyCommand.append('-I%s' % os.path.join(dir,'include'))
F2pyCommand.append('-I%s' % os.path.join(srcdir,'src'))
#F2pyCommand.append('-I%s' % os.path.join(dir,'src','include'))
F2pyCommand.append('--f77flags=%s' % f77flags)
F2pyCommand.append('--f90flags=%s' % f90flags)
F2pyCommand.append('_%s.pyf' % name)
F2pyCommand.append('%s' % string.join(src))
F2pyCommand.append('--quiet')
F2pyCommand = string.join(F2pyCommand)
print F2pyCommand
if subprocess.call(F2pyCommand, shell=True) > 0:
raise StandardError('+++ Compilation failed')
# delete signature file
subprocess.call('rm -f _%s.pyf' % name, shell=True)
# Copy shared object file to pydir
subprocess.call('cp %s %s'%(target, pydir), shell=True)
# Switch back to original working directory
os.chdir(here)
dependency_graph = {
filename: {
module_sources[module]
for module in scan_regexp(filename, r"use (\w+)")
}
for filename in f90_sources
}
return f77_sources + topological_sort(dependency_graph)
src_dir = "src"
source_files = get_sorted_source_files(src_dir)
compiler = fcompiler.get_default_fcompiler()
for arg in sys.argv:
if "--fcompiler" in arg:
compiler = arg[arg.index("=") + 1:]
print("Using %s compiler" % compiler, file=sys.stderr)
if compiler == "gnu95":
f77flags = []
f90flags = ["-ffree-line-length-none"]
opt = ["-Ofast", "-march=native", "-funroll-loops", "-flto", "-fopenmp"]
elif compiler.startswith("intel"):
f77flags = []
f90flags = ["-assume realloc_lhs"]
opt = ["-fast", "-openmp"]
else:
print("Compiler %s not supported. Let's hope things just work." % compiler,
f77_compiler_flags = {
'gnu': '-Wall -ffixed-form -fno-second-underscore -fno-automatic',
'gnu95': '-Wall -ffixed-form -fno-second-underscore -fno-automatic',
}
# Check if we need to configure a compile.
config_index = 0
for i, arg in enumerate(sys.argv):
if arg == 'config_fc':
break
elif arg.startswith(('build', 'bdist', 'develop', 'install')):
config_index = i
break
if config_index > 0:
f77 = get_default_fcompiler()
f77flags = f77_compiler_flags.get(f77, None)
if f77flags:
# Configure compiler options using setup's 'config_fc' command.
sys.argv[config_index:config_index] = \
['config_fc', '--f77flags=%s' % f77flags]
kwds = {
'description': 'AXOD - axial turbine off-design analysis.',
'version': version,
'license': 'public domain',
'install_requires': ['numpy'],
'zip_safe': False,
}
kwds.update(config.todict())
'language_level': 3,
'cdivision': False,
"boundscheck": True
}))
# from https://github.com/pytest-dev/pytest-runner#conditional-requirement
needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
pytest_runner = ["pytest-runner"] if needs_pytest else []
try:
with open("README.md", "r") as handle:
long_description = handle.read()
except Exception:
long_description = "\n".join(short_description[2:])
if get_default_fcompiler() != None:
fortran_list = glob.glob(os.path.join(fpath, "*.f90"))
for fext in fortran_list:
name = os.path.split(fext)[-1].split(".")[-2]
ext1 = Extension(name=name, sources=[fext], include_dirs=[fpath])
extensions.append(ext1)
else:
print("Fortran compiler is not found, default will use numba")
# try Extension and compile
# !!!! Note that we have Fortran modules that need to be compiled with "f2py3 -m solv_assoc -c solve_assoc.f90" and the same with solve_assoc_matrix.f90
setup(
# Self-descriptive entries which should always be present
name="despasito",
author="Jennifer A Clark",
f77_compiler_flags = {
'gnu': '-Wall -ffixed-form -fno-second-underscore -fno-automatic',
'gnu95': '-Wall -ffixed-form -fno-second-underscore -fno-automatic',
}
# Check if we need to configure a compile.
config_index = 0
for i, arg in enumerate(sys.argv):
if arg == 'config_fc':
break
elif arg.startswith(('build', 'bdist', 'develop', 'install')):
config_index = i
break
if config_index > 0:
f77 = get_default_fcompiler()
f77flags = f77_compiler_flags.get(f77, None)
if f77flags:
# Configure compiler options using setup's 'config_fc' command.
sys.argv[config_index:config_index] = \
['config_fc', '--f77flags=%s' % f77flags]
kwds = {'description':'AXOD - axial turbine off-design analysis.',
'version':version,
'license': 'public domain',
'install_requires':['numpy'],
'zip_safe':False,
}
kwds.update(config.todict())
from numpy.distutils.fcompiler import get_default_fcompiler
import sys
import os
fcompile = get_default_fcompiler(os.name, sys.platform, True)
install_dir = sys.argv[1]
os.system("python setup.py config_fc --fcompiler=" + str(fcompile) +
" build_clib --fcompiler=" + str(fcompile) +
" build_ext --fcompiler=" + str(fcompile) + " install --prefix='" +
str(install_dir) + "'")