def configure_step(self):
"""Configure build: set config options and configure"""
shlib_ext = get_shared_lib_ext()
if LooseVersion(self.version) < LooseVersion("4.3"):
self.cfg.update('configopts', "--enable-shared")
if self.toolchain.options['pic']:
self.cfg.update('configopts', '--with-pic')
tup = (os.getenv('FFLAGS'), os.getenv('MPICC'), os.getenv('F90'))
self.cfg.update('configopts', 'FCFLAGS="%s" CC="%s" FC="%s"' % tup)
# add -DgFortran to CPPFLAGS when building with GCC
if self.toolchain.comp_family() == toolchain.GCC: #@UndefinedVariable
self.cfg.update('configopts', 'CPPFLAGS="%s -DgFortran"' % os.getenv('CPPFLAGS'))
ConfigureMake.configure_step(self)
else:
for (dep, libname) in [('cURL', 'curl'), ('HDF5', 'hdf5'), ('Szip', 'sz'), ('zlib', 'z'),
('PnetCDF', 'pnetcdf')]:
dep_root = get_software_root(dep)
dep_libdir = get_software_libdir(dep)
if dep_root:
incdir = os.path.join(dep_root, 'include')
self.cfg.update('configopts', '-D%s_INCLUDE_DIR=%s ' % (dep.upper(), incdir))
if dep == 'HDF5':
env.setvar('HDF5_ROOT', dep_root)
self.cfg.update('configopts', '-DUSE_HDF5=ON')
hdf5cmvars = {
# library name: (cmake option suffix in netcdf<4.4, cmake option suffix in netcfd>=4.4)
'hdf5': ('LIB', 'C_LIBRARY'),
'hdf5_hl': ('HL_LIB', 'HL_LIBRARY'),
}
for libname in hdf5cmvars:
if LooseVersion(self.version) < LooseVersion("4.4"):
cmvar = hdf5cmvars[libname][0]
else:
cmvar = hdf5cmvars[libname][1]
libhdf5 = os.path.join(dep_root, dep_libdir, 'lib%s.%s' % (libname, shlib_ext))
self.cfg.update('configopts', '-DHDF5_%s=%s ' % (cmvar, libhdf5))
# 4.4 forgot to set HDF5_<lang>_LIBRARIES
if LooseVersion(self.version) == LooseVersion("4.4.0"):
lang = 'HL' if cmvar[0] == 'H' else 'C'
self.cfg.update('configopts', '-DHDF5_%s_LIBRARIES=%s ' % (lang, libhdf5))
elif dep == 'PnetCDF':
self.cfg.update('configopts', '-DENABLE_PNETCDF=ON')
else:
libso = os.path.join(dep_root, dep_libdir, 'lib%s.%s' % (libname, shlib_ext))
self.cfg.update('configopts', '-D%s_LIBRARY=%s ' % (dep.upper(), libso))
CMakeMake.configure_step(self)
def configure_step(self):
"""Configure build: set config options and configure"""
if LooseVersion(self.version) < LooseVersion("4.3"):
self.cfg.update('configopts', "--enable-shared")
if self.toolchain.options['pic']:
self.cfg.update('configopts', '--with-pic')
# tup = (os.getenv('FFLAGS'), os.getenv('MPICC'), os.getenv('F90'))
tup = (os.getenv('FFLAGS'), os.getenv('CC'), os.getenv('F90'))
self.cfg.update('configopts', 'FCFLAGS="%s" CC="%s" FC="%s"' % tup)
# add -DgFortran to CPPFLAGS when building with GCC
if self.toolchain.comp_family() == toolchain.GCC: #@UndefinedVariable
self.cfg.update('configopts', 'CPPFLAGS="%s -DgFortran"' % os.getenv('CPPFLAGS'))
ConfigureMake.configure_step(self)
else:
hdf5 = get_software_root('HDF5')
if hdf5:
env.setvar('HDF5_ROOT', hdf5)
CMakeMake.configure_step(self)
def configure_step(self):
"""Configure build: set config options and configure"""
if LooseVersion(self.version) < LooseVersion("4.3"):
self.cfg.update('configopts', "--enable-shared")
if self.toolchain.options['pic']:
self.cfg.update('configopts', '--with-pic')
tup = (os.getenv('FFLAGS'), os.getenv('MPICC'), os.getenv('F90'))
self.cfg.update('configopts', 'FCFLAGS="%s" CC="%s" FC="%s"' % tup)
# add -DgFortran to CPPFLAGS when building with GCC
if self.toolchain.comp_family(
) == toolchain.GCC: #@UndefinedVariable
self.cfg.update(
'configopts',
'CPPFLAGS="%s -DgFortran"' % os.getenv('CPPFLAGS'))
ConfigureMake.configure_step(self)
else:
hdf5 = get_software_root('HDF5')
if hdf5:
env.setvar('HDF5_ROOT', hdf5)
CMakeMake.configure_step(self)
def configure_step(self):
"""Custom configuration procedure for Eigen."""
# start using CMake for Eigen 3.3.4 and newer versions
# not done for older versions, since this implies using (a dummy-built) CMake as a build dependency,
# which is a bit strange for a header-only library like Eigen...
if LooseVersion(self.version) >= LooseVersion('3.3.4'):
self.cfg['separate_build_dir'] = True
# avoid that include files are installed into include/eigen3/Eigen, should be include/Eigen
self.cfg.update('configopts', "-DINCLUDE_INSTALL_DIR=%s" % os.path.join(self.installdir, 'include'))
CMakeMake.configure_step(self)
def configure_step(self):
"""Custom configuration procedure for Eigen."""
# start using CMake for Eigen 3.3.4 and newer versions
# not done for older versions, since this implies using (a dummy-built) CMake as a build dependency,
# which is a bit strange for a header-only library like Eigen...
if LooseVersion(self.version) >= LooseVersion('3.3.4'):
self.cfg['separate_build_dir'] = True
# avoid that include files are installed into include/eigen3/Eigen, should be include/Eigen
self.cfg.update('configopts', "-DINCLUDE_INSTALL_DIR=%s" % os.path.join(self.installdir, 'include'))
CMakeMake.configure_step(self)
def configure_step(self):
"""Configure build: set config options and configure"""
shlib_ext = get_shared_lib_ext()
if LooseVersion(self.version) < LooseVersion("4.3"):
self.cfg.update('configopts', "--enable-shared")
if self.toolchain.options['pic']:
self.cfg.update('configopts', '--with-pic')
tup = (os.getenv('FFLAGS'), os.getenv('MPICC'), os.getenv('F90'))
self.cfg.update('configopts', 'FCFLAGS="%s" CC="%s" FC="%s"' % tup)
# add -DgFortran to CPPFLAGS when building with GCC
if self.toolchain.comp_family(
) == toolchain.GCC: #@UndefinedVariable
self.cfg.update(
'configopts',
'CPPFLAGS="%s -DgFortran"' % os.getenv('CPPFLAGS'))
ConfigureMake.configure_step(self)
else:
self.cfg.update(
'configopts',
'-DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG " '
)
for (dep, libname) in [('cURL', 'curl'), ('HDF5', 'hdf5'),
('Szip', 'sz'), ('zlib', 'z')]:
dep_root = get_software_root(dep)
dep_libdir = get_software_libdir(dep)
if dep_root:
incdir = os.path.join(dep_root, 'include')
self.cfg.update(
'configopts',
'-D%s_INCLUDE_DIR=%s ' % (dep.upper(), incdir))
if dep == 'HDF5':
env.setvar('HDF5_ROOT', dep_root)
libhdf5 = os.path.join(dep_root, dep_libdir,
'libhdf5.%s' % shlib_ext)
self.cfg.update('configopts',
'-DHDF5_LIB=%s ' % libhdf5)
libhdf5_hl = os.path.join(dep_root, dep_libdir,
'libhdf5_hl.%s' % shlib_ext)
self.cfg.update('configopts',
'-DHDF5_HL_LIB=%s ' % libhdf5_hl)
else:
libso = os.path.join(dep_root, dep_libdir,
'lib%s.%s' % (libname, shlib_ext))
self.cfg.update(
'configopts',
'-D%s_LIBRARY=%s ' % (dep.upper(), libso))
CMakeMake.configure_step(self)
def configure_step(self):
"""Configure BamTools build."""
# BamTools requires an out of source build.
builddir = os.path.join(self.cfg['start_dir'], 'build')
try:
mkdir(builddir)
os.chdir(builddir)
except OSError as err:
raise EasyBuildError("Failed to move to %s: %s", builddir, err)
CMakeMake.configure_step(self, srcdir='..')
def configure_step(self):
"""Custom configuration for ROOT, add configure options."""
# using ./configure is deprecated/broken in recent versions, need to use CMake instead
if LooseVersion(self.version.lstrip('v')) >= LooseVersion('6.10'):
if self.cfg['arch']:
raise EasyBuildError("Specified value '%s' for 'arch' is not used, should not be set", self.cfg['arch'])
cfitsio_root = get_software_root('CFITSIO')
if cfitsio_root:
self.cfg.update('configopts', '-DCFITSIO=%s' % cfitsio_root)
fftw_root = get_software_root('FFTW')
if fftw_root:
self.cfg.update('configopts', '-Dbuiltin_fftw3=OFF -DFFTW_DIR=%s' % fftw_root)
gsl_root = get_software_root('GSL')
if gsl_root:
self.cfg.update('configopts', '-DGSL_DIR=%s' % gsl_root)
mesa_root = get_software_root('Mesa')
if mesa_root:
self.cfg.update('configopts', '-DDOPENGL_INCLUDE_DIR=%s' % os.path.join(mesa_root, 'include'))
self.cfg.update('configopts', '-DOPENGL_gl_LIBRARY=%s' % os.path.join(mesa_root, 'lib', 'libGL.so'))
python_root = get_software_root('Python')
if python_root:
pyshortver = '.'.join(get_software_version('Python').split('.')[:2])
self.cfg.update('configopts', '-DPYTHON_EXECUTABLE=%s' % os.path.join(python_root, 'bin', 'python'))
python_inc_dir = os.path.join(python_root, 'include', 'python%s' % pyshortver)
self.cfg.update('configopts', '-DPYTHON_INCLUDE_DIR=%s' % python_inc_dir)
python_lib = os.path.join(python_root, 'lib', 'libpython%s.so' % pyshortver)
self.cfg.update('configopts', '-DPYTHON_LIBRARY=%s' % python_lib)
if get_software_root('X11'):
self.cfg.update('configopts', '-Dx11=ON')
self.cfg['separate_build_dir'] = True
CMakeMake.configure_step(self)
else:
if self.cfg['arch'] is None:
raise EasyBuildError("No architecture specified to pass to configure script")
self.cfg.update('configopts', "--etcdir=%s/etc/root " % self.installdir)
cmd = "%s ./configure %s --prefix=%s %s" % (self.cfg['preconfigopts'],
self.cfg['arch'],
self.installdir,
self.cfg['configopts'])
run_cmd(cmd, log_all=True, log_ok=True, simple=True)
def configure_step(self):
"""Custom configuration procedure for Eigen."""
# start using CMake for Eigen 3.3.4 and newer versions
# not done for older versions, since this implies using CMake as a build dependency
if LooseVersion(self.version) >= LooseVersion('3.3.4'):
# Install headers as include/Eigen/*.h instead of the default include/eigen3/Eigen/*.h to make it easier
# for dependencies to find the headers without setting anything in addition
# Note: Path must be relative to the install prefix!
self.cfg.update('configopts',
"-DINCLUDE_INSTALL_DIR=%s" % 'include')
# Patch to make the relative path actually work.
regex_subs = [
('CACHE PATH ("The directory relative to CMAKE.*PREFIX)',
r'CACHE STRING \1')
]
apply_regex_substitutions(
os.path.join(self.cfg['start_dir'], 'CMakeLists.txt'),
regex_subs)
CMakeMake.configure_step(self)
def configure_step(self):
"""Configure build: set config options and configure"""
shlib_ext = get_shared_lib_ext()
if LooseVersion(self.version) < LooseVersion("4.3"):
self.cfg.update('configopts', "--enable-shared")
if self.toolchain.options['pic']:
self.cfg.update('configopts', '--with-pic')
tup = (os.getenv('FFLAGS'), os.getenv('MPICC'), os.getenv('F90'))
self.cfg.update('configopts', 'FCFLAGS="%s" CC="%s" FC="%s"' % tup)
# add -DgFortran to CPPFLAGS when building with GCC
if self.toolchain.comp_family() == toolchain.GCC: #@UndefinedVariable
self.cfg.update('configopts', 'CPPFLAGS="%s -DgFortran"' % os.getenv('CPPFLAGS'))
ConfigureMake.configure_step(self)
else:
self.cfg.update('configopts', '-DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_C_FLAGS_RELEASE="-DNDEBUG " ')
for (dep, libname) in [('cURL', 'curl'), ('HDF5', 'hdf5'), ('Szip', 'sz'), ('zlib', 'z')]:
dep_root = get_software_root(dep)
dep_libdir = get_software_libdir(dep)
if dep_root:
incdir = os.path.join(dep_root, 'include')
self.cfg.update('configopts', '-D%s_INCLUDE_DIR=%s ' % (dep.upper(), incdir))
if dep == 'HDF5':
env.setvar('HDF5_ROOT', dep_root)
libhdf5 = os.path.join(dep_root, dep_libdir, 'libhdf5.%s' % shlib_ext)
self.cfg.update('configopts', '-DHDF5_LIB=%s ' % libhdf5)
libhdf5_hl = os.path.join(dep_root, dep_libdir, 'libhdf5_hl.%s' % shlib_ext)
self.cfg.update('configopts', '-DHDF5_HL_LIB=%s ' % libhdf5_hl)
else:
libso = os.path.join(dep_root, dep_libdir, 'lib%s.%s' % (libname, shlib_ext))
self.cfg.update('configopts', '-D%s_LIBRARY=%s ' % (dep.upper(), libso))
CMakeMake.configure_step(self)
class EB_BamTools(MakeCp, CMakeMake):
"""Support for building and installing BamTools."""
def configure_step(self):
"""Configure BamTools build."""
# BamTools requires an out of source build.
builddir = os.path.join(self.cfg['start_dir'], 'build')
try:
mkdir(builddir)
os.chdir(builddir)
except OSError, err:
raise EasyBuildError("Failed to move to %s: %s", builddir, err)
CMakeMake.configure_step(self, srcdir='..')
class EB_BamTools(MakeCp, CMakeMake):
"""Support for building and installing BamTools."""
def configure_step(self):
"""Configure BamTools build."""
# BamTools requires an out of source build.
try:
builddir = os.path.join(self.cfg['start_dir'], 'build')
mkdir(builddir)
os.chdir(builddir)
except OSError, err:
self.log.error("")
CMakeMake.configure_step(self, srcdir='..')
class EB_BamTools(MakeCp, CMakeMake):
"""Support for building and installing BamTools."""
@staticmethod
def extra_options(extra_vars=None):
"""Extra easyconfig parameters for BamTools."""
extra = MakeCp.extra_options()
# files_to_copy is not mandatory here, since we overwrite it in install_step
extra['files_to_copy'][2] = CUSTOM
return extra
def configure_step(self):
"""Configure BamTools build."""
# BamTools requires an out of source build.
builddir = os.path.join(self.cfg['start_dir'], 'build')
try:
mkdir(builddir)
os.chdir(builddir)
except OSError, err:
raise EasyBuildError("Failed to move to %s: %s", builddir, err)
CMakeMake.configure_step(self, srcdir='..')
def configure_step(self):
"""
Configure build outside of source directory.
"""
try:
objdir = os.path.join(self.builddir, 'obj')
os.makedirs(objdir)
os.chdir(objdir)
except OSError as err:
raise EasyBuildError("Failed to prepare for configuration of PSI build: %s", err)
env.setvar('F77FLAGS', os.getenv('F90FLAGS'))
# In order to create new plugins with PSI, it needs to know the location of the source
# and the obj dir after install. These env vars give that information to the configure script.
self.psi_srcdir = os.path.basename(self.cfg['start_dir'].rstrip(os.sep))
self.install_psi_objdir = os.path.join(self.installdir, 'obj')
self.install_psi_srcdir = os.path.join(self.installdir, self.psi_srcdir)
env.setvar('PSI_OBJ_INSTALL_DIR', self.install_psi_objdir)
env.setvar('PSI_SRC_INSTALL_DIR', self.install_psi_srcdir)
# explicitely specify Python binary to use
pythonroot = get_software_root('Python')
if not pythonroot:
raise EasyBuildError("Python module not loaded.")
# pre 4.0b5, they were using autotools, on newer it's CMake
if LooseVersion(self.version) <= LooseVersion("4.0b5") and self.name == "PSI":
# Use EB Boost
boostroot = get_software_root('Boost')
if not boostroot:
raise EasyBuildError("Boost module not loaded.")
self.log.info("Using configure based build")
env.setvar('PYTHON', os.path.join(pythonroot, 'bin', 'python'))
env.setvar('USE_SYSTEM_BOOST', 'TRUE')
if self.toolchain.options.get('usempi', None):
# PSI doesn't require a Fortran compiler itself, but may require it to link to BLAS/LAPACK correctly
# we should always specify the sequential Fortran compiler,
# to avoid problems with -lmpi vs -lmpi_mt during linking
fcompvar = 'F77_SEQ'
else:
fcompvar = 'F77'
# update configure options
# using multi-threaded BLAS/LAPACK is important for performance,
# cfr. http://sirius.chem.vt.edu/psi4manual/latest/installfile.html#sec-install-iii
opt_vars = [
('cc', 'CC'),
('cxx', 'CXX'),
('fc', fcompvar),
('libdirs', 'LDFLAGS'),
('blas', 'LIBBLAS_MT'),
('lapack', 'LIBLAPACK_MT'),
]
for (opt, var) in opt_vars:
self.cfg.update('configopts', "--with-%s='%s'" % (opt, os.getenv(var)))
# -DMPICH_IGNORE_CXX_SEEK dances around problem with order of stdio.h and mpi.h headers
# both define SEEK_SET, this makes the one for MPI be ignored
self.cfg.update('configopts', "--with-opt='%s -DMPICH_IGNORE_CXX_SEEK'" % os.getenv('CFLAGS'))
# specify location of Boost
self.cfg.update('configopts', "--with-boost=%s" % boostroot)
# enable support for plugins
self.cfg.update('configopts', "--with-plugins")
ConfigureMake.configure_step(self, cmd_prefix=self.cfg['start_dir'])
else:
self.log.info("Using CMake based build")
self.cfg.update('configopts', ' -DPYTHON_INTERPRETER=%s' % os.path.join(pythonroot, 'bin', 'python'))
if self.name == 'PSI4' and LooseVersion(self.version) >= LooseVersion("1.2"):
self.log.info("Remove the CMAKE_BUILD_TYPE test in PSI4 source and the downloaded dependencies!")
self.log.info("Use PATCH_COMMAND in the corresponding CMakeLists.txt")
self.cfg.update('configopts', ' -DCMAKE_BUILD_TYPE=EasyBuildRelease')
else:
self.cfg.update('configopts', ' -DCMAKE_BUILD_TYPE=Release')
if self.toolchain.options.get('usempi', None):
self.cfg.update('configopts', " -DENABLE_MPI=ON")
if get_software_root('imkl'):
self.cfg.update('configopts', " -DENABLE_CSR=ON -DBLAS_TYPE=MKL")
if self.name == 'PSI4':
pcmsolverroot = get_software_root('PCMSolver')
if pcmsolverroot:
self.cfg.update('configopts', " -DENABLE_PCMSOLVER=ON")
if LooseVersion(self.version) < LooseVersion("1.2"):
self.cfg.update('configopts', " -DPCMSOLVER_ROOT=%s" % pcmsolverroot)
else:
self.cfg.update('configopts', " -DCMAKE_INSIST_FIND_PACKAGE_PCMSolver=ON "
"-DPCMSolver_DIR=%s/share/cmake/PCMSolver" % pcmsolverroot)
chempsroot = get_software_root('CheMPS2')
if chempsroot:
self.cfg.update('configopts', " -DENABLE_CHEMPS2=ON")
if LooseVersion(self.version) < LooseVersion("1.2"):
self.cfg.update('configopts', " -DCHEMPS2_ROOT=%s" % chempsroot)
else:
self.cfg.update('configopts', " -DCMAKE_INSIST_FIND_PACKAGE_CheMPS2=ON "
"-DCheMPS2_DIR=%s/share/cmake/CheMPS2" % chempsroot)
# Be aware, PSI4 wants exact versions of the following deps! built with CMake!!
# If you want to use non-CMake build versions, the you have to provide the
# corresponding Find<library-name>.cmake scripts
# In PSI4 version 1.2.1, you can check the corresponding CMakeLists.txt file
# in external/upstream/<library-name>/
if LooseVersion(self.version) >= LooseVersion("1.2"):
for dep in ['libxc', 'Libint', 'pybind11', 'gau2grid']:
deproot = get_software_root(dep)
if deproot:
self.cfg.update('configopts', " -DCMAKE_INSIST_FIND_PACKAGE_%s=ON" % dep)
dep_dir = os.path.join(deproot, 'share', 'cmake', dep)
self.cfg.update('configopts', " -D%s_DIR=%s " % (dep, dep_dir))
CMakeMake.configure_step(self, srcdir=self.cfg['start_dir'])
def configure_step(self):
"""Custom configuration for ROOT, add configure options."""
# ROOT includes an (old) copy of LLVM;
# if LLVM is loaded as an indirect dep, we need to make sure
# the location to its header files is not included in $CPATH
llvm_root = get_software_root('LLVM')
if llvm_root:
llvm_inc = os.path.join(llvm_root, 'include')
cpath = os.getenv('CPATH')
if cpath:
new_cpath = [
p for p in cpath.split(os.pathsep) if p != llvm_inc
]
self.log.info(
"Filtered %s from $CPATH to avoid using LLVM loaded as indirect dependency",
llvm_inc)
setvar('CPATH', os.pathsep.join(new_cpath))
# using ./configure is deprecated/broken in recent versions, need to use CMake instead
if LooseVersion(self.version.lstrip('v')) >= LooseVersion('6.10'):
if self.cfg['arch']:
raise EasyBuildError(
"Specified value '%s' for 'arch' is not used, should not be set",
self.cfg['arch'])
cfitsio_root = get_software_root('CFITSIO')
if cfitsio_root:
self.cfg.update('configopts', '-DCFITSIO=%s' % cfitsio_root)
fftw_root = get_software_root('FFTW')
if fftw_root:
self.cfg.update(
'configopts',
'-Dbuiltin_fftw3=OFF -DFFTW_DIR=%s' % fftw_root)
gsl_root = get_software_root('GSL')
if gsl_root:
self.cfg.update('configopts', '-DGSL_DIR=%s' % gsl_root)
mesa_root = get_software_root('Mesa')
if mesa_root:
self.cfg.update(
'configopts', '-DDOPENGL_INCLUDE_DIR=%s' %
os.path.join(mesa_root, 'include'))
self.cfg.update(
'configopts', '-DOPENGL_gl_LIBRARY=%s' %
os.path.join(mesa_root, 'lib', 'libGL.so'))
python_root = get_software_root('Python')
if python_root:
pyshortver = '.'.join(
get_software_version('Python').split('.')[:2])
self.cfg.update(
'configopts', '-DPYTHON_EXECUTABLE=%s' %
os.path.join(python_root, 'bin', 'python'))
python_inc_dir = find_glob_pattern(
os.path.join(python_root, 'include',
'python%s*' % pyshortver))
self.cfg.update('configopts',
'-DPYTHON_INCLUDE_DIR=%s' % python_inc_dir)
python_lib = find_glob_pattern(
os.path.join(python_root, 'lib',
'libpython%s*.so' % pyshortver))
self.cfg.update('configopts',
'-DPYTHON_LIBRARY=%s' % python_lib)
if get_software_root('X11'):
self.cfg.update('configopts', '-Dx11=ON')
CMakeMake.configure_step(self)
else:
if self.cfg['arch'] is None:
raise EasyBuildError(
"No architecture specified to pass to configure script")
self.cfg.update('configopts',
"--etcdir=%s/etc/root " % self.installdir)
cmd = "%s ./configure %s --prefix=%s %s" % (
self.cfg['preconfigopts'], self.cfg['arch'], self.installdir,
self.cfg['configopts'])
run_cmd(cmd, log_all=True, log_ok=True, simple=True)
def configure_step(self, *args, **kwargs):
"""Main configuration using cmake"""
PythonPackage.configure_step(self, *args, **kwargs)
return CMakeMake.configure_step(self, *args, **kwargs)
def configure_step(self, srcdir=None, builddir=None):
"""Configure build using CMake"""
return CMakeMake.configure_step(self, srcdir=srcdir, builddir=builddir)
def configure_step(self, *args, **kwargs):
CMakeMake.configure_step(self, *args, **kwargs)
def configure_step(self, *args, **kwargs):
"""Main configuration using cmake"""
PythonPackage.configure_step(self, *args, **kwargs)
return CMakeMake.configure_step(self, *args, **kwargs)
def configure_step(self, srcdir=None, builddir=None):
CMakeMake.configure_step(self, srcdir=srcdir, builddir=builddir)
def configure_step(self, *args, **kwargs):
"""Configure using CMake."""
CMakeMake.configure_step(self, *args, **kwargs)
def configure_step(self):
"""
Configure build outside of source directory.
"""
try:
objdir = os.path.join(self.builddir, 'obj')
os.makedirs(objdir)
os.chdir(objdir)
except OSError as err:
raise EasyBuildError(
"Failed to prepare for configuration of PSI build: %s", err)
env.setvar('F77FLAGS', os.getenv('F90FLAGS'))
# In order to create new plugins with PSI, it needs to know the location of the source
# and the obj dir after install. These env vars give that information to the configure script.
self.psi_srcdir = os.path.basename(self.cfg['start_dir'].rstrip(
os.sep))
self.install_psi_objdir = os.path.join(self.installdir, 'obj')
self.install_psi_srcdir = os.path.join(self.installdir,
self.psi_srcdir)
env.setvar('PSI_OBJ_INSTALL_DIR', self.install_psi_objdir)
env.setvar('PSI_SRC_INSTALL_DIR', self.install_psi_srcdir)
# explicitely specify Python binary to use
pythonroot = get_software_root('Python')
if not pythonroot:
raise EasyBuildError("Python module not loaded.")
# pre 4.0b5, they were using autotools, on newer it's CMake
if LooseVersion(
self.version) <= LooseVersion("4.0b5") and self.name == "PSI":
# Use EB Boost
boostroot = get_software_root('Boost')
if not boostroot:
raise EasyBuildError("Boost module not loaded.")
self.log.info("Using configure based build")
env.setvar('PYTHON', os.path.join(pythonroot, 'bin', 'python'))
env.setvar('USE_SYSTEM_BOOST', 'TRUE')
if self.toolchain.options.get('usempi', None):
# PSI doesn't require a Fortran compiler itself, but may require it to link to BLAS/LAPACK correctly
# we should always specify the sequential Fortran compiler,
# to avoid problems with -lmpi vs -lmpi_mt during linking
fcompvar = 'F77_SEQ'
else:
fcompvar = 'F77'
# update configure options
# using multi-threaded BLAS/LAPACK is important for performance,
# cfr. http://sirius.chem.vt.edu/psi4manual/latest/installfile.html#sec-install-iii
opt_vars = [
('cc', 'CC'),
('cxx', 'CXX'),
('fc', fcompvar),
('libdirs', 'LDFLAGS'),
('blas', 'LIBBLAS_MT'),
('lapack', 'LIBLAPACK_MT'),
]
for (opt, var) in opt_vars:
self.cfg.update('configopts',
"--with-%s='%s'" % (opt, os.getenv(var)))
# -DMPICH_IGNORE_CXX_SEEK dances around problem with order of stdio.h and mpi.h headers
# both define SEEK_SET, this makes the one for MPI be ignored
self.cfg.update(
'configopts', "--with-opt='%s -DMPICH_IGNORE_CXX_SEEK'" %
os.getenv('CFLAGS'))
# specify location of Boost
self.cfg.update('configopts', "--with-boost=%s" % boostroot)
# enable support for plugins
self.cfg.update('configopts', "--with-plugins")
ConfigureMake.configure_step(self,
cmd_prefix=self.cfg['start_dir'])
else:
self.log.info("Using CMake based build")
self.cfg.update(
'configopts', ' -DPYTHON_INTERPRETER=%s' %
os.path.join(pythonroot, 'bin', 'python'))
if self.name == 'PSI4' and LooseVersion(
self.version) >= LooseVersion("1.2"):
self.log.info(
"Remove the CMAKE_BUILD_TYPE test in PSI4 source and the downloaded dependencies!"
)
self.log.info(
"Use PATCH_COMMAND in the corresponding CMakeLists.txt")
self.cfg.update('configopts',
' -DCMAKE_BUILD_TYPE=EasyBuildRelease')
else:
self.cfg.update('configopts', ' -DCMAKE_BUILD_TYPE=Release')
if self.toolchain.options.get('usempi', None):
self.cfg.update('configopts', " -DENABLE_MPI=ON")
if get_software_root('imkl'):
self.cfg.update('configopts',
" -DENABLE_CSR=ON -DBLAS_TYPE=MKL")
if self.name == 'PSI4':
pcmsolverroot = get_software_root('PCMSolver')
if pcmsolverroot:
self.cfg.update('configopts', " -DENABLE_PCMSOLVER=ON")
if LooseVersion(self.version) < LooseVersion("1.2"):
self.cfg.update('configopts',
" -DPCMSOLVER_ROOT=%s" % pcmsolverroot)
else:
self.cfg.update(
'configopts',
" -DCMAKE_INSIST_FIND_PACKAGE_PCMSolver=ON "
"-DPCMSolver_DIR=%s/share/cmake/PCMSolver" %
pcmsolverroot)
chempsroot = get_software_root('CheMPS2')
if chempsroot:
self.cfg.update('configopts', " -DENABLE_CHEMPS2=ON")
if LooseVersion(self.version) < LooseVersion("1.2"):
self.cfg.update('configopts',
" -DCHEMPS2_ROOT=%s" % chempsroot)
else:
self.cfg.update(
'configopts',
" -DCMAKE_INSIST_FIND_PACKAGE_CheMPS2=ON "
"-DCheMPS2_DIR=%s/share/cmake/CheMPS2" %
chempsroot)
# Be aware, PSI4 wants exact versions of the following deps! built with CMake!!
# If you want to use non-CMake build versions, the you have to provide the
# corresponding Find<library-name>.cmake scripts
# In PSI4 version 1.2.1, you can check the corresponding CMakeLists.txt file
# in external/upstream/<library-name>/
if LooseVersion(self.version) >= LooseVersion("1.2"):
for dep in ['libxc', 'Libint', 'pybind11', 'gau2grid']:
deproot = get_software_root(dep)
if deproot:
self.cfg.update(
'configopts',
" -DCMAKE_INSIST_FIND_PACKAGE_%s=ON" % dep)
dep_dir = os.path.join(deproot, 'share', 'cmake',
dep)
self.cfg.update('configopts',
" -D%s_DIR=%s " % (dep, dep_dir))
CMakeMake.configure_step(self, srcdir=self.cfg['start_dir'])
def configure_step(self):
PythonPackage.configure_step(self)
return CMakeMake.configure_step(self)
class EB_PSI(CMakeMake):
"""
Support for building and installing PSI
"""
def __init__(self, *args, **kwargs):
"""Initialize class variables custom to PSI."""
super(EB_PSI, self).__init__(*args, **kwargs)
self.psi_srcdir = None
self.install_psi_objdir = None
self.install_psi_srcdir = None
@staticmethod
def extra_options():
"""Extra easyconfig parameters specific to PSI."""
extra_vars = {
# always include running PSI unit tests (takes about 2h or less)
'runtest': ["tests TESTFLAGS='-u -q'", "Run tests included with PSI, without interruption.", BUILD],
}
return CMakeMake.extra_options(extra_vars)
def configure_step(self):
"""
Configure build outside of source directory.
"""
try:
objdir = os.path.join(self.builddir, 'obj')
os.makedirs(objdir)
os.chdir(objdir)
except OSError, err:
raise EasyBuildError("Failed to prepare for configuration of PSI build: %s", err)
env.setvar('F77FLAGS', os.getenv('F90FLAGS'))
# In order to create new plugins with PSI, it needs to know the location of the source
# and the obj dir after install. These env vars give that information to the configure script.
self.psi_srcdir = os.path.basename(self.cfg['start_dir'].rstrip(os.sep))
self.install_psi_objdir = os.path.join(self.installdir, 'obj')
self.install_psi_srcdir = os.path.join(self.installdir, self.psi_srcdir)
env.setvar('PSI_OBJ_INSTALL_DIR', self.install_psi_objdir)
env.setvar('PSI_SRC_INSTALL_DIR', self.install_psi_srcdir)
# explicitely specify Python binary to use
pythonroot = get_software_root('Python')
if not pythonroot:
raise EasyBuildError("Python module not loaded.")
# Use EB Boost
boostroot = get_software_root('Boost')
if not boostroot:
raise EasyBuildError("Boost module not loaded.")
# pre 4.0b5, they were using autotools, on newer it's CMake
if LooseVersion(self.version) <= LooseVersion("4.0b5"):
env.setvar('PYTHON', os.path.join(pythonroot, 'bin', 'python'))
env.setvar('USE_SYSTEM_BOOST', 'TRUE')
if self.toolchain.options.get('usempi', None):
# PSI doesn't require a Fortran compiler itself, but may require it to link to BLAS/LAPACK correctly
# we should always specify the sequential Fortran compiler,
# to avoid problems with -lmpi vs -lmpi_mt during linking
fcompvar = 'F77_SEQ'
else:
fcompvar = 'F77'
# update configure options
# using multi-threaded BLAS/LAPACK is important for performance,
# cfr. http://sirius.chem.vt.edu/psi4manual/latest/installfile.html#sec-install-iii
opt_vars = [
('cc', 'CC'),
('cxx', 'CXX'),
('fc', fcompvar),
('libdirs', 'LDFLAGS'),
('blas', 'LIBBLAS_MT'),
('lapack', 'LIBLAPACK_MT'),
]
for (opt, var) in opt_vars:
self.cfg.update('configopts', "--with-%s='%s'" % (opt, os.getenv(var)))
# -DMPICH_IGNORE_CXX_SEEK dances around problem with order of stdio.h and mpi.h headers
# both define SEEK_SET, this makes the one for MPI be ignored
self.cfg.update('configopts', "--with-opt='%s -DMPICH_IGNORE_CXX_SEEK'" % os.getenv('CFLAGS'))
# specify location of Boost
self.cfg.update('configopts', "--with-boost=%s" % boostroot)
# enable support for plugins
self.cfg.update('configopts', "--with-plugins")
ConfigureMake.configure_step(self, cmd_prefix=self.cfg['start_dir'])
else:
self.cfg['configopts'] += "-DPYTHON_INTERPRETER=%s " % os.path.join(pythonroot, 'bin', 'python')
self.cfg['configopts'] += "-DCMAKE_BUILD_TYPE=Release "
if self.toolchain.options.get('usempi', None):
self.cfg['configopts'] += "-DENABLE_MPI=ON "
if get_software_root('impi'):
self.cfg['configopts'] += "-DENABLE_CSR=ON -DBLAS_TYPE=MKL "
CMakeMake.configure_step(self, srcdir=self.cfg['start_dir'])
def configure_step(self):
"""Configure BamTools build."""
CMakeMake.configure_step(self)
def configure_step(self):
"""Custom configuration procedure for NEURON."""
if LooseVersion(self.version) < LooseVersion('7.8.1'):
# make sure we're using the correct configure command
# (required because custom easyconfig parameters from CMakeMake are picked up)
self.cfg['configure_cmd'] = "./configure"
# enable support for distributed simulations if desired
if self.cfg['paranrn']:
self.cfg.update('configopts', '--with-paranrn')
# specify path to InterViews if it is available as a dependency
interviews_root = get_software_root('InterViews')
if interviews_root:
self.cfg.update('configopts', "--with-iv=%s" % interviews_root)
else:
self.cfg.update('configopts', "--without-iv")
# optionally enable support for Python as alternative interpreter
python_root = get_software_root('Python')
if python_root:
self.with_python = True
self.cfg.update('configopts', "--with-nrnpython=%s/bin/python" % python_root)
# determine host CPU type
cmd = "./config.guess"
(out, ec) = run_cmd(cmd, simple=False)
self.hostcpu = out.split('\n')[0].split('-')[0]
self.log.debug("Determined host CPU type as %s" % self.hostcpu)
# determine Python lib dir
self.pylibdir = det_pylibdir()
# complete configuration with configure_method of parent
ConfigureMake.configure_step(self)
else:
# enable support for distributed simulations if desired
if self.cfg['paranrn']:
self.cfg.update('configopts', '-DNRN_ENABLE_MPI=ON')
else:
self.cfg.update('configopts', '-DNRN_ENABLE_MPI=OFF')
# specify path to InterViews if it is available as a dependency
interviews_root = get_software_root('InterViews')
if interviews_root:
self.cfg.update('configopts', "-DIV_DIR=%s -DNRN_ENABLE_INTERVIEWS=ON" % interviews_root)
else:
self.cfg.update('configopts', "-DNRN_ENABLE_INTERVIEWS=OFF")
# no longer used it seems
self.hostcpu = ''
# optionally enable support for Python as alternative interpreter
python_root = get_software_root('Python')
if python_root:
self.with_python = True
self.cfg.update('configopts', "-DNRN_ENABLE_PYTHON=ON -DPYTHON_EXECUTABLE=%s/bin/python" % python_root)
self.cfg.update('configopts', "-DNRN_ENABLE_MODULE_INSTALL=ON "
"-DNRN_MODULE_INSTALL_OPTIONS='--prefix=%s'" % self.installdir)
else:
self.cfg.update('configopts', "-DNRN_ENABLE_PYTHON=OFF")
# determine Python lib dir
self.pylibdir = det_pylibdir()
# complete configuration with configure_method of parent
CMakeMake.configure_step(self)
