def configure():
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += ['petsc']
# PETSc for Python
INCLUDE_DIRS += [petsc4py.get_include()]
# NumPy
INCLUDE_DIRS += [numpy.get_include()]
return dict(
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS,
)
def configuration(parent_package='', top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [
join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')
]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += [ #'petscts', 'petscsnes', 'petscksp',
#'petscdm', 'petscmat', 'petscvec',
'petsc'
]
import os
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path)
config.add_extension(
'eSCAPE._fortran',
sources=['fortran/functions.pyf', 'fortran/functions.F90'],
depends=['fortran/functionsmodule.h'],
# f2py_options=['--quiet'],
define_macros=[], #[('F2PY_REPORT_ON_ARRAY_COPY',0)],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
extra_f90_compile_args=['-fPIC', '-O3'],
#extra_f90_compile_args = ['-fPIC', '-O0', '-g', '-fbacktrace','-fcheck=all'],
#extra_link_args = ['-shared '],
runtime_library_dirs=LIBRARY_DIRS)
#define_macros=[],
#include_dirs=[os.curdir],
# libraries=[],
# library_dirs=[],
# extra_f90_compile_args=['-fPIC','-O3'],
# extra_link_args = ['-shared '],
# runtime_library_dirs=[])
return config
def dijitso_jit(jitable,
name,
params,
generate=None,
send=None,
receive=None,
wait=None):
name = name.replace("dolfin", package_name)
params["build"]["include_dirs"].append(mpi4py.get_include())
params["build"]["include_dirs"].append(petsc4py.get_include())
params["build"]["include_dirs"].extend(include_dirs)
return original_dijitso_jit(jitable, name, params, generate, send,
receive, wait)
def configure():
if any(e not in os.environ
for e in ['PETSC_DIR', 'PETSC_ARCH', 'SLEPC_DIR']):
raise ValueError('Must set environment variables PETSC_DIR, '
'PETSC_ARCH and SLEPC_DIR before installing! '
'If executing with sudo, you may want the -E '
'flag to pass environment variables through '
'sudo.')
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ['PETSC_ARCH']
SLEPC_DIR = os.environ['SLEPC_DIR']
include = []
lib_paths = []
include += [
join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')
]
lib_paths += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
include += [
join(SLEPC_DIR, PETSC_ARCH, 'include'),
join(SLEPC_DIR, 'include')
]
lib_paths += [join(SLEPC_DIR, PETSC_ARCH, 'lib')]
libs = ['petsc', 'slepc']
# python package includes
include += [
petsc4py.get_include(),
slepc4py.get_include(),
numpy.get_include()
]
object_files = ['dynamite/backend/backend_impl.o']
# check if we have nvcc, and thus should link to
# the CUDA code
if HAVE_NVCC:
object_files = ['dynamite/backend/cuda_shell.o'] + object_files
return dict(include_dirs=include,
libraries=libs,
library_dirs=lib_paths,
runtime_library_dirs=lib_paths,
extra_objects=object_files)
def configuration(parent_package='', top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = find_petsc_dir()
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [
join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')
]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [
join(PETSC_DIR, 'include'),
join(PETSC_DIR, 'include\\petsc\\mpiuni')
]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += ['petsc']
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path)
config.add_extension(
'CompositeSimple1D',
sources=[
'CompositeSimple1D.pyx', 'CompositeSimple1Dimpl.c',
'multiblock/multiblock.c'
],
depends=['CompositeSimple1Dimpl.h'],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
extra_compile_args=["-Zi", "/Od"],
extra_link_args=["-debug"],
)
#runtime_library_dirs=LIBRARY_DIRS)
return config
def configuration(parent_package='', top_path=None):
INCLUDE_DIRS = [
'/usr/lib/openmpi/include/',
os.path.join(SUNDIALS_PATH, 'include')
]
LIBRARY_DIRS = [os.path.join(SUNDIALS_PATH, 'lib')]
LIBRARIES = [
'sundials_cvodes', 'sundials_nvecparallel', 'sundials_nvecserial'
]
# PETSc
PETSC_DIR = os.environ.get('PETSC_DIR', '/usr/lib/petsc')
PETSC_ARCH = os.environ.get('PETSC_ARCH', 'linux-gnu-c-opt')
if os.path.isdir(os.path.join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [os.path.join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [os.path.join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
raise Exception('Seems PETSC_DIR or PETSC_ARCH are wrong!')
LIBRARIES += [ #'petscts', 'petscsnes', 'petscksp',
#'petscdm', 'petscmat', 'petscvec',
'petsc'
]
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
print "[DDD] INCLUDE_DIRS = {}".format(INCLUDE_DIRS)
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path)
config.add_extension('cvode_petsc',
sources=['cvode_petsc.pyx'],
depends=[''],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
config.add_extension('llg_petsc',
sources=['llg_petsc.pyx', 'llg.c'],
depends=[''],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
def build_sources(cmd):
from os.path import exists, isdir, join
if (exists(join('src', 'slepc4py.SLEPc.c')) and
not (isdir('.hg') or isdir('.git')) and
not cmd.force): return
# slepc4py.SLEPc
source = 'slepc4py.SLEPc.pyx'
depends = ("include/*/*.pxd",
"SLEPc/*.pyx",
"SLEPc/*.pxi",)
import petsc4py
includes = ['include', petsc4py.get_include()]
destdir_h = os.path.join('include', 'slepc4py')
run_cython(source, depends, includes,
destdir_c=None, destdir_h=destdir_h, wdir='src',
force=cmd.force, VERSION=CYTHON)
def configuration(parent_package="", top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ["PETSC_DIR"]
PETSC_ARCH = os.environ.get("PETSC_ARCH", "")
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [join(PETSC_DIR, PETSC_ARCH, "include"), join(PETSC_DIR, "include")]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, "lib")]
else:
if PETSC_ARCH:
pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, "include")]
LIBRARY_DIRS += [join(PETSC_DIR, "lib")]
LIBRARIES += [ #'petscts', 'petscsnes', 'petscksp',
#'petscdm', 'petscmat', 'petscvec',
"petsc"
]
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration("", parent_package, top_path)
config.add_extension(
"Bratu2D",
sources=["Bratu2D.pyf", "Bratu2D.F90"],
depends=["Bratu2Dmodule.h"],
f2py_options=["--quiet"],
define_macros=[("F2PY_REPORT_ON_ARRAY_COPY", 1)],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS,
)
return config
def get_ext_modules(Extension):
from os import walk, path
from glob import glob
depends = []
for pth, dirs, files in walk('src'):
depends += glob(path.join(pth, '*.h'))
depends += glob(path.join(pth, '*.c'))
try:
import petsc4py
petsc4py_includes = [petsc4py.get_include()]
except ImportError:
petsc4py_includes = []
return [Extension('slepc4py.lib.SLEPc',
sources=['src/SLEPc.c',],
include_dirs=['src/include',
] + petsc4py_includes,
depends=depends)]
def configuration(parent_package='',top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
def haslibrary(basename):
return ( os.path.exists(join(PETSC_DIR,PETSC_ARCH,'lib','%s.so' % basename))
or os.path.exists(join(PETSC_DIR,PETSC_ARCH,'lib','%s.dylib' % basename)))
if haslibrary('libpetsc'):
LIBRARIES += ['petsc']
elif haslibrary('libpetscts'):
LIBRARIES += ['petscts','petscsnes','petscksp','petscdm','petscmat','petscvec','petscsys']
else: raise DistutilsError('Cannot find valid PETSc libraries in PETSC_DIR=%s PETSC_ARCH=%s',PETSC_DIR,PETSC_ARCH)
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# Configuration
from numpy.distutils.misc_util import Configuration
module = 'assembly'
config = Configuration('', parent_package, top_path)
config.add_extension(module,
sources = [module+'.pyx',
module+'impl.c'],
depends = [module+'impl.h'],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
def configuration(parent_package='', top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [
join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')
]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += [ #'petscts', 'petscsnes', 'petscksp',
#'petscdm', 'petscmat', 'petscvec',
'petsc'
]
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
print INCLUDE_DIRS
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path)
config.add_extension('CavityFlow2D',
sources=['CavityFlow2D.pyx', 'CavityFlow2Dimpl.c'],
depends=['CavityFlow2Dimpl.h'],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
def configuration(parent_package='',top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += [#'petscts', 'petscsnes', 'petscksp',
#'petscdm', 'petscmat', 'petscvec',
'petsc']
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path)
config.add_extension('Bratu2D',
sources = ['Bratu2D.pyf',
'Bratu2D.F90'],
depends = ['Bratu2Dmodule.h'],
f2py_options=['--quiet'],
define_macros=[('F2PY_REPORT_ON_ARRAY_COPY',1)],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
def configuration(parent_package='',top_path=None):
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# PETSc
import os
PETSC_DIR = os.environ['PETSC_DIR']
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += [#'petscts', 'petscsnes', 'petscksp',
#'petscdm', 'petscmat', 'petscvec',
'petsc']
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
print INCLUDE_DIRS
# Configuration
from numpy.distutils.misc_util import Configuration
config = Configuration('', parent_package, top_path)
config.add_extension('CavityFlow2D',
sources = ['CavityFlow2D.pyx',
'CavityFlow2Dimpl.c'],
depends = ['CavityFlow2Dimpl.h'],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
from os.path import join, isdir
if PETSC_ARCH and isdir(join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'include'),
join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += [#'petscts', 'petscsnes', 'petscksp',
#'petscdm', 'petscmat', 'petscvec',
'petsc']
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# CUDA
from setup_cuda import locate_cuda
CUDA = locate_cuda()
print CUDA
LIBRARY_DIRS += [CUDA['lib64']]
LIBRARIES += ['cudart']
INCLUDE_DIRS += [CUDA['include']]
# Obtain the numpy include directory:
import numpy
numpy_include = numpy.get_include()
INCLUDE_DIRS += [numpy_include]
ext = Extension('GPUArray',
}
namespace pybind11
{
namespace detail
{
PETSC_CASTER_MACRO(IS, is);
}
}
"""
# Load and wrap compiled function dofmap_dofs_is
path = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(__file__)))
module_dofs = compile_cpp_code(dofmap_dofs_is_cpp_code,
include_dirs=[path,
petsc4py.get_include()])
def dofmap_dofs_is(dofmap):
"""Converts DofMap::dofs() to IS.
This function is intended to circumvent NumPy which would be
involved in code like::
iset = PETSc.IS().createGeneral(dofmap.dofs(),
comm=dofmap.index_map().mpi_comm())
"""
iset = module_dofs.dofmap_dofs_is(dofmap)
iset.decRef()
assert iset.getRefCount() == 1
return iset
def MPIpackage(config):
try:
from numpy.distutils.fcompiler import FCompiler
def runtime_library_dir_option(self, dir):
return self.c_compiler.runtime_library_dir_option(dir)
FCompiler.runtime_library_dir_option = \
runtime_library_dir_option
except Exception:
pass
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# Get PETSc environment variables
try:
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
PETSC_DIR = os.environ['PETSC_DIR']
if PETSC_DIR == '':
raise KeyError
elif not (os.path.isfile(PETSC_DIR+'/'+PETSC_ARCH+'/lib/libpetsc.so') or os.path.isfile(PETSC_DIR+'/'+PETSC_ARCH+'/lib/libpetsc.a')):
raise dirError
except KeyError:
raise Exception("ERROR: PETSC_DIR environment variable not set")
except dirError:
raise Exception("ERROR: PETSC_DIR does not point towards a valid directory")
# get PETSc include and library directories
if PETSC_ARCH and os.path.isdir(os.path.join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [os.path.join(PETSC_DIR, PETSC_ARCH, 'include'),
os.path.join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [os.path.join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass
INCLUDE_DIRS += [os.path.join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [os.path.join(PETSC_DIR, 'lib')]
LIBRARIES += ['petsc']
# PETSc for Python
try:
import petsc4py
except ImportError:
raise Exception("""ERROR: petsc4py 3.4 not installed.
This can be installed by running
pip install https://bitbucket.org/petsc/petsc4py/downloads/petsc4py-3.4.tar.gz
Please see http://pythonhosted.org/petsc4py/ for more info.""")
INCLUDE_DIRS += [petsc4py.get_include()]
# Get SLEPc environment variables
try:
SLEPC_DIR = os.environ['SLEPC_DIR']
if SLEPC_DIR == '':
raise KeyError
elif not (os.path.isfile(SLEPC_DIR+'/'+PETSC_ARCH+'/lib/libslepc.so') or os.path.isfile(SLEPC_DIR+'/'+PETSC_ARCH+'/lib/libslepc.a')):
raise dirError
except KeyError:
raise Exception("ERROR: SLEPC_DIR environment variable not set")
except dirError:
raise Exception("ERROR: SLEPC_DIR does not point towards a valid directory")
# get SLEPc include and library directories
if PETSC_ARCH and os.path.isdir(os.path.join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [os.path.join(SLEPC_DIR, PETSC_ARCH, 'include'),
os.path.join(SLEPC_DIR, 'include')]
LIBRARY_DIRS += [os.path.join(SLEPC_DIR, PETSC_ARCH, 'lib')]
else:
INCLUDE_DIRS += [os.path.join(SLEPC_DIR, 'include')]
LIBRARY_DIRS += [os.path.join(SLEPC_DIR, 'lib')]
LIBRARIES += ['slepc']
# set the compiler to mpi
if os.getenv('LDSHARED', '') == '':
os.environ["CC"] = "mpicc"
os.environ["F90"] = "mpif90"
os.environ["LDSHARED"] = "mpif90"
# create the extension
config.add_extension('libpyctqw_MPI',
sources = ['src/ctqwMPI.F90','src/ctqwMPI.pyf'],
f2py_options=['--quiet'],
extra_f90_compile_args=['-Wno-unused-variable','-Wno-conversion','-Wno-unused-dummy-argument'],
#define_macros=[('F2PY_REPORT_ON_ARRAY_COPY',1)],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
try:
os.remove(output)
except OSError:
pass
return 1
# move ouputs
for destdir, outputs in ((destdir_c, outputs_c), (destdir_h,
outputs_h)):
if destdir is None: continue
for output in outputs:
dest = os.path.join(destdir, os.path.basename(output))
try:
os.remove(dest)
except OSError:
pass
os.rename(output, dest)
#
return 0
#
finally:
os.chdir(cwd)
if __name__ == "__main__":
import petsc4py
sys.exit(
cythonize('slepc4py.SLEPc.pyx',
includes=['include', petsc4py.get_include()],
destdir_h=os.path.join('include', 'slepc4py'),
wdir='src'))
mg_sources = ["firedrake/mg/impl.pyx"]
except ImportError:
# No cython, dmplex.c must be generated in distributions.
dmplex_sources = ["firedrake/dmplex.c"]
spatialindex_sources = ["firedrake/spatialindex.cpp"]
h5iface_sources = ["firedrake/hdf5interface.c"]
mg_sources = ["firedrake/mg/impl.c"]
if 'CC' not in env:
env['CC'] = "mpicc"
if 'CXX' not in env:
env['CXX'] = "mpic++"
petsc_dirs = get_petsc_dir()
include_dirs = [np.get_include(), petsc4py.get_include()]
include_dirs += ["%s/include" % d for d in petsc_dirs]
setup(name='firedrake',
version=versioneer.get_version(),
cmdclass=cmdclass,
description="""Firedrake is an automated system for the portable solution
of partial differential equations using the finite element method
(FEM)""",
author="Imperial College London and others",
author_email="*****@*****.**",
url="http://firedrakeproject.org",
packages=["firedrake", "firedrake.mg"],
package_data={"firedrake": ["firedrake_geometry.h",
"evaluate.h",
"locate.cpp"]},
join(PETSC_DIR, 'include')
]
LIBRARY_DIRS += [join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += ['petsc']
# NumPy
INCLUDE_DIRS += [numpy.get_include()]
# PETSc for Python
import petsc4py
INCLUDE_DIRS += [petsc4py.get_include()]
# Intel MPI
IMPI_DIR = '/afs/@cell/common/soft/intel/ics2013/impi/4.1.3/intel64'
if isdir(IMPI_DIR):
INCLUDE_DIRS += [join(IMPI_DIR, 'include')]
LIBRARY_DIRS += [join(IMPI_DIR, 'lib')]
# MacPorts OpenMPI
if isdir('/opt/local/include/openmpi-gcc6'):
INCLUDE_DIRS += ['/opt/local/include/openmpi-gcc6']
if isdir('/opt/local/lib/openmpi-gcc6'):
LIBRARY_DIRS += ['/opt/local/lib/openmpi-gcc6']
# MPI library
]
dep_links = ['git+https://github.com/coneoproject/COFFEE#egg=COFFEE-dev']
version = sys.version_info[:2]
if version < (2, 7) or (3, 0) <= version <= (3, 1):
install_requires += ['argparse', 'ordereddict']
test_requires = [
'flake8>=2.1.0',
'pytest>=2.3',
]
petsc_dirs = get_petsc_dir()
numpy_includes = [np.get_include()]
includes = numpy_includes + [petsc4py.get_include()]
includes += ["%s/include" % d for d in petsc_dirs]
if 'CC' not in env:
env['CC'] = "mpicc"
class sdist(_sdist):
def run(self):
# Make sure the compiled Cython files in the distribution are up-to-date
from Cython.Build import cythonize
cythonize(sparsity_sources, language="c", include_path=includes)
cythonize(computeind_sources)
_sdist.run(self)
class MakeBuildExt(build_ext):
def run(self):
# build the backend_impl.o object file
make = check_output(['make', 'backend_impl.o'], cwd='dynamite/backend')
print(make.decode())
# if we have nvcc, build the CUDA backend
if HAVE_NVCC:
make = check_output(['make', 'cuda_shell.o'],
cwd='dynamite/backend')
print(make.decode())
build_ext.run(self)
setup(name="dynamite",
version="0.0.2",
author="Greg Meyer",
author_email="*****@*****.**",
description="Fast direct evolution of quantum spin chains.",
packages=['dynamite'],
classifiers=[
"Development Status :: 4 - Beta",
],
ext_modules=cythonize(
extensions(),
include_path=[petsc4py.get_include(),
slepc4py.get_include()]),
cmdclass={'build_ext': MakeBuildExt})
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += ['petsc']
# PETSc for Python
INCLUDE_DIRS += [petsc4py.get_include()]
# NumPy
INCLUDE_DIRS += [numpy.get_include()]
return dict(
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS,
)
extensions = [
Extension(
'pcdeflation',
sources=['pcdeflation.pyx'],
#depends = ['Bratu3Dimpl.h'],
**configure()),
]
setup(
name="pcdeflation",
ext_modules=cythonize(extensions, include_path=[petsc4py.get_include()]),
)
'mpi4py',
'numpy>=1.6',
]
version = sys.version_info[:2]
if version < (2, 7) or (3, 0) <= version <= (3, 1):
install_requires += ['argparse', 'ordereddict']
test_requires = [
'flake8>=2.1.0',
'pytest>=2.3',
]
petsc_dirs = get_petsc_dir()
numpy_includes = [np.get_include()]
includes = numpy_includes + [petsc4py.get_include()]
includes += ["%s/include" % d for d in petsc_dirs]
if 'CC' not in env:
env['CC'] = "mpicc"
class sdist(_sdist):
def run(self):
# Make sure the compiled Cython files in the distribution are up-to-date
from Cython.Build import cythonize
cythonize(plan_sources)
cythonize(sparsity_sources, language="c++", include_path=includes)
cythonize(computeind_sources)
_sdist.run(self)
import os
import petsc4py
import numpy
include_dirs = [os.path.join(os.getenv('PETSC_DIR'), 'include'),
petsc4py.get_include(),numpy.get_include(),
# May need to add extras here depending on your environment
'/usr/lib/openmpi/include', '/usr/lib/openmpi/include/openmpi',
]
swig_include_dirs = [petsc4py.get_include()]
library_dirs = [os.path.join(os.getenv('PETSC_DIR'),'lib')] # os.getenv('PETSC_ARCH')
libraries = ['petsc']
os.getenv("FOAM_SRC") + "/transportModels/compressible/lnInclude",
os.getenv("FOAM_SRC") + "/thermophysicalModels/basic/lnInclude",
os.getenv("FOAM_SRC") +
"/TurbulenceModels/turbulenceModels/lnInclude",
os.getenv("FOAM_SRC") + "/TurbulenceModels/compressible/lnInclude",
os.getenv("FOAM_SRC") + "/finiteVolume/cfdTools",
os.getenv("FOAM_SRC") + "/finiteVolume/lnInclude",
os.getenv("FOAM_SRC") + "/meshTools/lnInclude",
os.getenv("FOAM_SRC") + "/sampling/lnInclude",
# These are common for all OpenFOAM executives
os.getenv("FOAM_SRC") + "/OpenFOAM/lnInclude",
os.getenv("FOAM_SRC") + "/OSspecific/POSIX/lnInclude",
os.getenv("FOAM_LIBBIN"),
# DAFoam include
os.getenv("PETSC_DIR") + "/include",
petsc4py.get_include(),
os.getenv("PETSC_DIR") + "/" + os.getenv("PETSC_ARCH") +
"/include",
"../../ofLibs/adjoint/lnInclude",
"../../ofLibs/boundaryConditions/tractionDisplacement",
"./"
"../../include"
],
# These are from Make/options:EXE_LIBS
libraries=[
"compressibleTransportModels", "fluidThermophysicalModels",
"specie", "turbulenceModels", "compressibleTurbulenceModels",
"finiteVolume", "sampling", "meshTools", "fvOptions",
"AdjointDerivativeCompressible", "petsc"
],
# These are pathes of linked libraries
def MPIpackage(config):
try:
from numpy.distutils.fcompiler import FCompiler
def runtime_library_dir_option(self, dir):
return self.c_compiler.runtime_library_dir_option(dir)
FCompiler.runtime_library_dir_option = \
runtime_library_dir_option
except Exception:
pass
INCLUDE_DIRS = []
LIBRARY_DIRS = []
LIBRARIES = []
# Get PETSc environment variables
try:
PETSC_ARCH = os.environ.get('PETSC_ARCH', '')
PETSC_DIR = os.environ['PETSC_DIR']
if PETSC_DIR == '':
raise KeyError
elif not (os.path.isfile(PETSC_DIR + '/' + PETSC_ARCH +
'/lib/libpetsc.so')
or os.path.isfile(PETSC_DIR + '/' + PETSC_ARCH +
'/lib/libpetsc.a')):
raise dirError
except KeyError:
raise Exception("ERROR: PETSC_DIR environment variable not set")
except dirError:
raise Exception(
"ERROR: PETSC_DIR does not point towards a valid directory")
# get PETSc include and library directories
if PETSC_ARCH and os.path.isdir(os.path.join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [
os.path.join(PETSC_DIR, PETSC_ARCH, 'include'),
os.path.join(PETSC_DIR, 'include')
]
LIBRARY_DIRS += [os.path.join(PETSC_DIR, PETSC_ARCH, 'lib')]
else:
if PETSC_ARCH: pass
INCLUDE_DIRS += [os.path.join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [os.path.join(PETSC_DIR, 'lib')]
LIBRARIES += ['petsc']
# PETSc for Python
try:
import petsc4py
except ImportError:
raise Exception("""ERROR: petsc4py 3.4 not installed.
This can be installed by running
pip install https://bitbucket.org/petsc/petsc4py/downloads/petsc4py-3.4.tar.gz
Please see http://pythonhosted.org/petsc4py/ for more info.""")
INCLUDE_DIRS += [petsc4py.get_include()]
# Get SLEPc environment variables
try:
SLEPC_DIR = os.environ['SLEPC_DIR']
if SLEPC_DIR == '':
raise KeyError
elif not (os.path.isfile(SLEPC_DIR + '/' + PETSC_ARCH +
'/lib/libslepc.so')
or os.path.isfile(SLEPC_DIR + '/' + PETSC_ARCH +
'/lib/libslepc.a')):
raise dirError
except KeyError:
raise Exception("ERROR: SLEPC_DIR environment variable not set")
except dirError:
raise Exception(
"ERROR: SLEPC_DIR does not point towards a valid directory")
# get SLEPc include and library directories
if PETSC_ARCH and os.path.isdir(os.path.join(PETSC_DIR, PETSC_ARCH)):
INCLUDE_DIRS += [
os.path.join(SLEPC_DIR, PETSC_ARCH, 'include'),
os.path.join(SLEPC_DIR, 'include')
]
LIBRARY_DIRS += [os.path.join(SLEPC_DIR, PETSC_ARCH, 'lib')]
else:
INCLUDE_DIRS += [os.path.join(SLEPC_DIR, 'include')]
LIBRARY_DIRS += [os.path.join(SLEPC_DIR, 'lib')]
LIBRARIES += ['slepc']
# set the compiler to mpi
if os.getenv('LDSHARED', '') == '':
os.environ["CC"] = "mpicc"
os.environ["F90"] = "mpif90"
os.environ["LDSHARED"] = "mpif90"
# create the extension
config.add_extension(
'libpyctqw_MPI',
sources=['src/ctqwMPI.F90', 'src/ctqwMPI.pyf'],
f2py_options=['--quiet'],
extra_f90_compile_args=[
'-Wno-unused-variable', '-Wno-conversion',
'-Wno-unused-dummy-argument'
],
#define_macros=[('F2PY_REPORT_ON_ARRAY_COPY',1)],
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS)
return config
except KeyError:
try:
import petsc
return (petsc.get_petsc_dir(), )
except ImportError:
sys.exit("""Error: Could not find PETSc library.
Set the environment variable PETSC_DIR / PETSC_ARCH to your local
PETSc base directory or install PETSc via pip.""")
if 'CC' not in env:
env['CC'] = "mpicc"
petsc_dirs = get_petsc_dir()
include_dirs = [np.get_include(), petsc4py.get_include()]
include_dirs += ["%s/include" % d for d in petsc_dirs]
link_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "ssc"))
setup(name='ssc',
cmdclass={'build_ext': build_ext},
packages=["ssc"],
ext_modules=[Extension('ssc.PatchPC',
sources=["ssc/PatchPC.pyx"],
include_dirs=include_dirs,
extra_link_args=["-L" + link_dir] +
["-Wl,-rpath," + link_dir],
extra_compile_args=["-O3"],
libraries=["ssc"])])
if PETSC_ARCH: pass # XXX should warn ...
INCLUDE_DIRS += [join(PETSC_DIR, 'include')]
LIBRARY_DIRS += [join(PETSC_DIR, 'lib')]
LIBRARIES += ['petsc']
# PETSc for Python
INCLUDE_DIRS += [petsc4py.get_include()]
# NumPy
INCLUDE_DIRS += [numpy.get_include()]
return dict(
include_dirs=INCLUDE_DIRS + [os.curdir],
libraries=LIBRARIES,
library_dirs=LIBRARY_DIRS,
runtime_library_dirs=LIBRARY_DIRS,
)
extensions = [
Extension('Bratu3D',
sources = ['Bratu3D.pyx',
'Bratu3Dimpl.c'],
depends = ['Bratu3Dimpl.h'],
**configure()),
]
setup(name = "Bratu3D",
ext_modules = cythonize(
extensions, include_path=[petsc4py.get_include()]),
)