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):
"""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 install_step(self):
"""Custom install procedure for EggLib: first build/install C++ library, then build Python library."""
# build/install C++ library
cpp_subdir = os.path.join(self.builddir, 'egglib-cpp-%s' % self.version)
try:
os.chdir(cpp_subdir)
except OSError as err:
raise EasyBuildError("Failed to move to: %s", err)
ConfigureMake.configure_step(self)
ConfigureMake.build_step(self)
ConfigureMake.install_step(self)
# header files and libraries must be found when building Python library
for varname, subdir in [('CPATH', 'include'), ('LIBRARY_PATH', 'lib')]:
env.setvar(varname, '%s:%s' % (os.path.join(self.installdir, subdir), os.environ.get(varname, '')))
# build/install Python package
py_subdir = os.path.join(self.builddir, 'egglib-py-%s' % self.version)
try:
os.chdir(py_subdir)
except OSError as err:
raise EasyBuildError("Failed to move to: %s", err)
PythonPackage.build_step(self)
self.cfg.update('installopts', "--install-lib %s" % os.path.join(self.installdir, self.pylibdir))
self.cfg.update('installopts', "--install-scripts %s" % os.path.join(self.installdir, 'bin'))
PythonPackage.install_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:
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 and
Test if python module is loaded
"""
if not get_software_root('Python'):
raise EasyBuildError("Python module not loaded")
# We will do the python bindings ourselves so force them off
self.cfg.update('configopts', '--without-python')
ConfigureMake.configure_step(self)
def configure_step(self):
"""
Configure and
Test if python module is loaded
"""
if not get_software_root('Python'):
raise EasyBuildError("Python module not loaded")
# We will do the python bindings ourselves so force them off
self.cfg.update('configopts', '--without-python')
ConfigureMake.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):
"""Configuration step, we set FC, F77 is already set by EasyBuild to the right compiler,
FC is used for Fortan90"""
environment.setvar('FC', self.toolchain.get_variable('F90'))
# make sure correct config script is used for Tcl/Tk
for dep in ['Tcl', 'Tk']:
root = get_software_root(dep)
if root:
dep_config = os.path.join(root, 'lib', '%sConfig.sh' % dep.lower())
self.cfg.update('configopts', '-with-%s-config=%s' % (dep.lower(), dep_config))
ConfigureMake.configure_step(self)
def configure_step(self):
"""Configuration step, we set FC, F77 is already set by EasyBuild to the right compiler,
FC is used for Fortan90"""
environment.setvar('FC', self.toolchain.get_variable('F90'))
# make sure correct config script is used for Tcl/Tk
for dep in ['Tcl', 'Tk']:
root = get_software_root(dep)
if root:
dep_config = os.path.join(root, 'lib', '%sConfig.sh' % dep.lower())
self.cfg.update('configopts', '-with-%s-config=%s' % (dep.lower(), dep_config))
ConfigureMake.configure_step(self)
def configure_step(self):
"""
Configure and
Test if python module is loaded
"""
if not get_software_root('Python'):
self.log.error("Python module not loaded")
ConfigureMake.configure_step(self)
try:
os.chdir('python')
PythonPackage.configure_step(self)
os.chdir('..')
except OSError, err:
self.log.error("Failed to configure libxml2 Python bindings: %s" % err)
def configure_step(self):
"""
Configure libxml2 build
"""
# only build with Python bindings if Python is listed as a dependency
python = get_software_root('Python')
if python:
self.with_python_bindings = True
self.require_python = True
if not self.toolchain.is_system_toolchain():
self.cfg.update(
'configopts',
"CC='%s' CXX='%s'" % (os.getenv('CC'), os.getenv('CXX')))
if self.toolchain.options.get('pic', False):
self.cfg.update('configopts', '--with-pic')
zlib = get_software_root('zlib')
if zlib:
self.cfg.update('configopts', '--with-zlib=%s' % zlib)
xz_root = get_software_root('XZ')
if xz_root:
self.cfg.update('configopts', '--with-lzma=%s' % xz_root)
# enable building of Python bindings if Python is a dependency (or build them ourselves for old versions)
# disable building of Python bindings if Python is not a dependency
if self.with_python_bindings and LooseVersion(
self.version) >= LooseVersion('2.9.2'):
libxml2_pylibdir = os.path.join(self.installdir, self.pylibdir)
self.cfg.update(
'configopts',
"--with-python=%s" % os.path.join(python, 'bin', 'python'))
self.cfg.update('configopts',
"--with-python-install-dir=%s" % libxml2_pylibdir)
else:
self.cfg.update('configopts', '--without-python')
ConfigureMake.configure_step(self)
if self.with_python_bindings:
# prepare for installing Python package
PythonPackage.prepare_python(self)
# test using 'make check' (done via test_step)
self.cfg['runtest'] = 'check'
def configure_step(self):
"""
Configure and
Test if python module is loaded
"""
if not get_software_root('Python'):
raise EasyBuildError("Python module not loaded")
ConfigureMake.configure_step(self)
try:
os.chdir('python')
PythonPackage.configure_step(self)
os.chdir('..')
except OSError, err:
raise EasyBuildError(
"Failed to configure libxml2 Python bindings: %s", err)
def configure_step(self):
"""Custom configuration for R."""
# define $BLAS_LIBS to build R correctly against BLAS/LAPACK library
# $LAPACK_LIBS should *not* be specified since that may lead to using generic LAPACK
# see https://github.com/easybuilders/easybuild-easyconfigs/issues/1435
env.setvar('BLAS_LIBS', os.getenv('LIBBLAS'))
self.cfg.update('configopts', "--with-blas --with-lapack")
# make sure correct config script is used for Tcl/Tk
for dep in ['Tcl', 'Tk']:
root = get_software_root(dep)
if root:
dep_config = os.path.join(root, 'lib',
'%sConfig.sh' % dep.lower())
self.cfg.update(
'configopts',
'--with-%s-config=%s' % (dep.lower(), dep_config))
if "--with-x=" not in self.cfg['configopts'].lower():
if get_software_root('X11'):
self.cfg.update('configopts', '--with-x=yes')
else:
self.cfg.update('configopts', '--with-x=no')
# enable graphic capabilities for plotting, based on available dependencies
for dep in ['Cairo', 'libjpeg-turbo', 'libpng', 'libtiff']:
if get_software_root(dep):
if dep == 'libjpeg-turbo':
conf_opt = 'jpeglib'
else:
conf_opt = dep.lower()
self.cfg.update('configopts', '--with-%s' % conf_opt)
out = ConfigureMake.configure_step(self)
# check output of configure command to verify BLAS/LAPACK settings
ext_libs_regex = re.compile(
"External libraries:.*BLAS\((?P<BLAS>.*)\).*LAPACK\((?P<LAPACK>.*)\)"
)
res = ext_libs_regex.search(out)
if res:
for lib in ['BLAS', 'LAPACK']:
if res.group(lib) == 'generic':
warn_msg = "R will be built with generic %s, which will result in poor performance." % lib
self.log.warning(warn_msg)
print_warning(warn_msg)
else:
self.log.info("R is configured to use non-generic %s: %s",
lib, res.group(lib))
else:
warn_msg = "R is configured to be built without BLAS/LAPACK, which will result in (very) poor performance"
self.log.warning(warn_msg)
print_warning(warn_msg)
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 install_step(self):
"""Custom install procedure for EggLib: first build/install C++ library, then build Python library."""
# build/install C++ library
cpp_subdir = os.path.join(self.builddir,
'egglib-cpp-%s' % self.version)
try:
os.chdir(cpp_subdir)
except OSError as err:
raise EasyBuildError("Failed to move to: %s", err)
ConfigureMake.configure_step(self)
ConfigureMake.build_step(self)
ConfigureMake.install_step(self)
# header files and libraries must be found when building Python library
for varname, subdir in [('CPATH', 'include'), ('LIBRARY_PATH', 'lib')]:
env.setvar(
varname, '%s:%s' % (os.path.join(
self.installdir, subdir), os.environ.get(varname, '')))
# build/install Python package
py_subdir = os.path.join(self.builddir, 'egglib-py-%s' % self.version)
try:
os.chdir(py_subdir)
except OSError as err:
raise EasyBuildError("Failed to move to: %s", err)
PythonPackage.build_step(self)
self.cfg.update(
'installopts',
"--install-lib %s" % os.path.join(self.installdir, self.pylibdir))
self.cfg.update(
'installopts',
"--install-scripts %s" % os.path.join(self.installdir, 'bin'))
PythonPackage.install_step(self)
def configure_step(self):
"""
Configure libxml2 build
"""
# only build with Python bindings if Python is listed as a dependency
python = get_software_root('Python')
if python:
self.with_python_bindings = True
if self.toolchain.name != DUMMY_TOOLCHAIN_NAME:
self.cfg.update('configopts', "CC='%s' CXX='%s'" % (os.getenv('CC'), os.getenv('CXX')))
if self.toolchain.options.get('pic', False):
self.cfg.update('configopts', '--with-pic')
zlib = get_software_root('zlib')
if zlib:
self.cfg.update('configopts', '--with-zlib=%s' % zlib)
# enable building of Python bindings if Python is a dependency (or build them ourselves for old versions)
# disable building of Python bindings if Python is not a dependency
if self.with_python_bindings and LooseVersion(self.version) >= LooseVersion('2.9.2'):
libxml2_pylibdir = os.path.join(self.installdir, self.pylibdir)
self.cfg.update('configopts', "--with-python=%s" % os.path.join(python, 'bin', 'python'))
self.cfg.update('configopts', "--with-python-install-dir=%s" % libxml2_pylibdir)
else:
self.cfg.update('configopts', '--without-python')
ConfigureMake.configure_step(self)
if self.with_python_bindings:
# prepare for installing Python package
PythonPackage.prepare_python(self)
# test using 'make check' (done via test_step)
self.cfg['runtest'] = 'check'
def configure_step(self):
"""Custom configuration for R."""
# define $BLAS_LIBS to build R correctly against BLAS/LAPACK library
# $LAPACK_LIBS should *not* be specified since that may lead to using generic LAPACK
# see https://github.com/easybuilders/easybuild-easyconfigs/issues/1435
env.setvar('BLAS_LIBS', os.getenv('LIBBLAS'))
self.cfg.update('configopts', "--with-blas --with-lapack")
# make sure correct config script is used for Tcl/Tk
for dep in ['Tcl', 'Tk']:
root = get_software_root(dep)
if root:
dep_config = os.path.join(root, 'lib', '%sConfig.sh' % dep.lower())
self.cfg.update('configopts', '--with-%s-config=%s' % (dep.lower(), dep_config))
if "--with-x=" not in self.cfg['configopts'].lower():
if get_software_root('X11'):
self.cfg.update('configopts', '--with-x=yes')
else:
self.cfg.update('configopts', '--with-x=no')
# enable graphic capabilities for plotting, based on available dependencies
for dep in ['Cairo', 'libjpeg-turbo', 'libpng', 'libtiff']:
if get_software_root(dep):
if dep == 'libjpeg-turbo':
conf_opt = 'jpeglib'
else:
conf_opt = dep.lower()
self.cfg.update('configopts', '--with-%s' % conf_opt)
out = ConfigureMake.configure_step(self)
# check output of configure command to verify BLAS/LAPACK settings
ext_libs_regex = re.compile("External libraries:.*BLAS\((?P<BLAS>.*)\).*LAPACK\((?P<LAPACK>.*)\)")
res = ext_libs_regex.search(out)
if res:
for lib in ['BLAS', 'LAPACK']:
if res.group(lib) == 'generic':
warn_msg = "R will be built with generic %s, which will result in poor performance." % lib
self.log.warning(warn_msg)
print_warning(warn_msg)
else:
self.log.info("R is configured to use non-generic %s: %s", lib, res.group(lib))
else:
warn_msg = "R is configured to be built without BLAS/LAPACK, which will result in (very) poor performance"
self.log.warning(warn_msg)
print_warning(warn_msg)
class EB_EggLib(PythonPackage, ConfigureMake):
"""Support for building/installing EggLib."""
def configure_step(self):
"""Configure EggLib build/install procedure."""
# only need to configure Python library here, configuration of C++ library is done in install step
PythonPackage.configure_step(self)
def build_step(self):
"""No custom build procedure for EggLib; build/install is done in install_step."""
pass
def install_step(self):
"""Custom install procedure for EggLib: first build/install C++ library, then build Python library."""
# build/install C++ library
cpp_subdir = os.path.join(self.builddir,
'egglib-cpp-%s' % self.version)
try:
os.chdir(cpp_subdir)
except OSError, err:
raise EasyBuildError("Failed to move to: %s", err)
ConfigureMake.configure_step(self)
ConfigureMake.build_step(self)
ConfigureMake.install_step(self)
# header files and libraries must be found when building Python library
for varname, subdir in [('CPATH', 'include'), ('LIBRARY_PATH', 'lib')]:
env.setvar(
varname, '%s:%s' % (os.path.join(
self.installdir, subdir), os.environ.get(varname, '')))
# build/install Python package
py_subdir = os.path.join(self.builddir, 'egglib-py-%s' % self.version)
try:
os.chdir(py_subdir)
except OSError, err:
raise EasyBuildError("Failed to move to: %s", err)
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)
def configure_step(self):
"""Dedicated configure step for Mono: install Mono from RPM (if provided), then run configure."""
# install Mono from RPMs if provided (because we need Mono to build Mono)
if self.rpms:
# prepare path for installing RPMs in
monorpms_path = os.path.join(self.builddir, "monorpms")
try:
os.makedirs(os.path.join(monorpms_path, 'rpm'))
except OSError as err:
raise EasyBuildError(
"Failed to create directories for installing Mono RPMs in: %s",
err)
self.src = self.rpms
self.rebuildRPM = True
# rebuild RPMs to make them relocatable
Rpm.configure_step(self)
# prepare to install RPMs
self.log.debug(
"Initializing temporary RPM repository to install to...")
cmd = "rpm --initdb --dbpath /rpm --root %s" % monorpms_path
run_cmd(cmd, log_all=True, simple=True)
# install RPMs one by one
for rpm in self.src:
self.log.debug("Installing RPM %s ..." % rpm['name'])
if os.path.exists(rpm['path']):
cmd = ' '.join([
"rpm -i",
"--dbpath %(inst)s/rpm",
"--force",
"--relocate /=%(inst)s",
"--badreloc",
"--nodeps --nopost",
"%(rpm)s",
]) % {
'inst': monorpms_path,
'rpm': rpm['path'],
}
run_cmd(cmd, log_all=True, simple=True)
else:
raise EasyBuildError("RPM file %s not found", rpm['path'])
# create patched version of gmcs command
self.log.debug("Making our own copy of gmcs (one that works).")
mygmcs_path = os.path.join(monorpms_path, 'usr', 'bin', 'mygmcs')
try:
shutil.copy(os.path.join(monorpms_path, 'usr', 'bin', 'gmcs'),
mygmcs_path)
except OSError as err:
raise EasyBuildError("Failed to copy gmcs to %s: %s",
mygmcs_path, err)
rpls = [
("exec /usr/bin/mono", "exec %s/usr/bin/mono" % monorpms_path),
("`/usr/bin/monodir`", "%s/usr/lib64/mono" % monorpms_path),
]
apply_regex_substitutions(mygmcs_path, rpls)
self.log.debug("Patched version of gmcs (%s): %s" %
(mygmcs_path, read_file(mygmcs_path)))
# initiate bootstrap: build/install Mono with installed RPMs to temporary path
tmp_mono_path = os.path.join(self.builddir, "tmp_mono")
self.log.debug(
"Build/install temporary Mono version in %s using installed RPMs..."
% tmp_mono_path)
par = ''
if self.cfg['parallel']:
par = "-j %s" % self.cfg['parallel']
config_cmd = "%s ./configure --prefix=%s %s" % (
self.cfg['preconfigopts'], tmp_mono_path,
self.cfg['configopts'])
build_cmd = ' '.join([
"%(prebuildopts)s"
"make %(par)s",
"EXTERNAL_MCS=%(path)s/usr/bin/mygmcs",
"EXTERNAL_RUNTIME=%(path)s/usr/bin/mono",
"%(buildopts)s",
]) % {
'prebuildopts': self.cfg['prebuildopts'],
'par': par,
'path': monorpms_path,
'buildopts': self.cfg['buildopts'],
}
install_cmd = "make install"
for cmd in [config_cmd, build_cmd, install_cmd]:
run_cmd(cmd, log_all=True, simple=True)
more_buildopts = ' '.join([
"EXTERNAL_MCS=%(path)s/bin/gmcs",
"EXTERNAL_RUNTIME=%(path)s/bin/mono",
]) % {
'path': tmp_mono_path
}
self.cfg.update('buildopts', more_buildopts)
self.src = self.mono_srcs
# continue with normal configure, and subsequent make, make install
ConfigureMake.configure_step(self)
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 procedure for GROMACS: set configure options for configure or cmake."""
if LooseVersion(self.version) >= LooseVersion('4.6'):
cuda = get_software_root('CUDA')
if cuda:
# CUDA with double precision is currently not supported in GROMACS yet
# If easyconfig explicitly have double_precision=True error out,
# otherwise warn about it and skip the double precision build
if self.cfg.get('double_precision'):
raise EasyBuildError("Double precision is not available for GPU build. " +
"Please explicitly set \"double_precision = False\" " +
"or remove it in the easyconfig file.")
if self.double_prec_pattern in self.cfg['configopts']:
if self.cfg.get('double_precision') is None:
# Only print warning once when trying double precision
# build the first time
self.cfg['double_precision'] = False
self.log.info("Double precision is not available for " +
"GPU build. Skipping the double precision build.")
self.log.info("skipping configure step")
return
if LooseVersion(self.version) >= LooseVersion('2021'):
self.cfg.update('configopts', "-DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=%s" % cuda)
else:
self.cfg.update('configopts', "-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=%s" % cuda)
else:
# explicitly disable GPU support if CUDA is not available,
# to avoid that GROMACS find and uses a system-wide CUDA compiler
self.cfg.update('configopts', "-DGMX_GPU=OFF")
# check whether PLUMED is loaded as a dependency
plumed_root = get_software_root('PLUMED')
if plumed_root:
# Need to check if PLUMED has an engine for this version
engine = 'gromacs-%s' % self.version
(out, _) = run_cmd("plumed-patch -l", log_all=True, simple=False)
if not re.search(engine, out):
raise EasyBuildError("There is no support in PLUMED version %s for GROMACS %s: %s",
get_software_version('PLUMED'), self.version, out)
# PLUMED patching must be done at different stages depending on
# version of GROMACS. Just prepare first part of cmd here
plumed_cmd = "plumed-patch -p -e %s" % engine
if LooseVersion(self.version) < LooseVersion('4.6'):
self.log.info("Using configure script for configuring GROMACS build.")
if self.cfg['build_shared_libs']:
self.cfg.update('configopts', "--enable-shared --disable-static")
else:
self.cfg.update('configopts', "--enable-static")
# Use external BLAS and LAPACK
self.cfg.update('configopts', "--with-external-blas --with-external-lapack")
env.setvar('LIBS', "%s %s" % (os.environ['LIBLAPACK'], os.environ['LIBS']))
# Don't use the X window system
self.cfg.update('configopts', "--without-x")
# OpenMP is not supported for versions older than 4.5.
if LooseVersion(self.version) >= LooseVersion('4.5'):
# enable OpenMP support if desired
if self.toolchain.options.get('openmp', None):
self.cfg.update('configopts', "--enable-threads")
else:
self.cfg.update('configopts', "--disable-threads")
elif self.toolchain.options.get('openmp', None):
raise EasyBuildError("GROMACS version %s does not support OpenMP" % self.version)
# GSL support
if get_software_root('GSL'):
self.cfg.update('configopts', "--with-gsl")
else:
self.cfg.update('configopts', "--without-gsl")
# actually run configure via ancestor (not direct parent)
self.cfg['configure_cmd'] = "./configure"
ConfigureMake.configure_step(self)
# Now patch GROMACS for PLUMED between configure and build
if plumed_root:
run_cmd(plumed_cmd, log_all=True, simple=True)
else:
if '-DGMX_MPI=ON' in self.cfg['configopts']:
mpi_numprocs = self.cfg.get('mpi_numprocs', 0)
if mpi_numprocs == 0:
self.log.info("No number of test MPI tasks specified -- using default: %s",
self.cfg['parallel'])
mpi_numprocs = self.cfg['parallel']
elif mpi_numprocs > self.cfg['parallel']:
self.log.warning("Number of test MPI tasks (%s) is greater than value for 'parallel': %s",
mpi_numprocs, self.cfg['parallel'])
mpiexec = self.cfg.get('mpiexec')
if mpiexec:
mpiexec_path = which(mpiexec)
if mpiexec_path:
self.cfg.update('configopts', "-DMPIEXEC=%s" % mpiexec_path)
self.cfg.update('configopts', "-DMPIEXEC_NUMPROC_FLAG=%s" %
self.cfg.get('mpiexec_numproc_flag'))
self.cfg.update('configopts', "-DNUMPROC=%s" % mpi_numprocs)
elif self.cfg['runtest']:
raise EasyBuildError("'%s' not found in $PATH", mpiexec)
else:
raise EasyBuildError("No value found for 'mpiexec'")
self.log.info("Using %s as MPI executable when testing, with numprocs flag '%s' and %s tasks",
mpiexec_path, self.cfg.get('mpiexec_numproc_flag'),
mpi_numprocs)
if LooseVersion(self.version) >= LooseVersion('2019'):
# Building the gmxapi interface requires shared libraries,
# this is handled in the class initialisation so --module-only works
self.cfg.update('configopts', "-DGMXAPI=ON")
if LooseVersion(self.version) >= LooseVersion('2020'):
# build Python bindings if Python is loaded as a dependency
python_root = get_software_root('Python')
if python_root:
bin_python = os.path.join(python_root, 'bin', 'python')
self.cfg.update('configopts', "-DPYTHON_EXECUTABLE=%s" % bin_python)
self.cfg.update('configopts', "-DGMX_PYTHON_PACKAGE=ON")
# Now patch GROMACS for PLUMED before cmake
if plumed_root:
if LooseVersion(self.version) >= LooseVersion('5.1'):
# Use shared or static patch depending on
# setting of self.cfg['build_shared_libs']
# and adapt cmake flags accordingly as per instructions
# from "plumed patch -i"
if self.cfg['build_shared_libs']:
mode = 'shared'
else:
mode = 'static'
plumed_cmd = plumed_cmd + ' -m %s' % mode
run_cmd(plumed_cmd, log_all=True, simple=True)
# prefer static libraries, if available
if self.cfg['build_shared_libs']:
self.cfg.update('configopts', "-DGMX_PREFER_STATIC_LIBS=OFF")
else:
self.cfg.update('configopts', "-DGMX_PREFER_STATIC_LIBS=ON")
# always specify to use external BLAS/LAPACK
self.cfg.update('configopts', "-DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON")
# disable GUI tools
self.cfg.update('configopts', "-DGMX_X11=OFF")
# convince to build for an older architecture than present on the build node by setting GMX_SIMD CMake flag
# it does not make sense for Cray, because OPTARCH is defined by the Cray Toolchain
if self.toolchain.toolchain_family() != toolchain.CRAYPE:
gmx_simd = self.get_gromacs_arch()
if gmx_simd:
if LooseVersion(self.version) < LooseVersion('5.0'):
self.cfg.update('configopts', "-DGMX_CPU_ACCELERATION=%s" % gmx_simd)
else:
self.cfg.update('configopts', "-DGMX_SIMD=%s" % gmx_simd)
# set regression test path
prefix = 'regressiontests'
if any([src['name'].startswith(prefix) for src in self.src]):
self.cfg.update('configopts', "-DREGRESSIONTEST_PATH='%%(builddir)s/%s-%%(version)s' " % prefix)
# enable OpenMP support if desired
if self.toolchain.options.get('openmp', None):
self.cfg.update('configopts', "-DGMX_OPENMP=ON")
else:
self.cfg.update('configopts', "-DGMX_OPENMP=OFF")
imkl_root = get_software_root('imkl')
if imkl_root:
# using MKL for FFT, so it will also be used for BLAS/LAPACK
imkl_include = os.path.join(os.getenv('MKLROOT'), 'mkl', 'include')
self.cfg.update('configopts', '-DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR="%s" ' % imkl_include)
libs = os.getenv('LAPACK_STATIC_LIBS').split(',')
mkl_libs = [os.path.join(os.getenv('LAPACK_LIB_DIR'), lib) for lib in libs if lib != 'libgfortran.a']
mkl_libs = ['-Wl,--start-group'] + mkl_libs + ['-Wl,--end-group -lpthread -lm -ldl']
self.cfg.update('configopts', '-DMKL_LIBRARIES="%s" ' % ';'.join(mkl_libs))
else:
for libname in ['BLAS', 'LAPACK']:
libdir = os.getenv('%s_LIB_DIR' % libname)
if self.toolchain.toolchain_family() == toolchain.CRAYPE:
libsci_mpi_mp_lib = glob.glob(os.path.join(libdir, 'libsci_*_mpi_mp.a'))
if libsci_mpi_mp_lib:
self.cfg.update('configopts', '-DGMX_%s_USER=%s' % (libname, libsci_mpi_mp_lib[0]))
else:
raise EasyBuildError("Failed to find libsci library to link with for %s", libname)
else:
# -DGMX_BLAS_USER & -DGMX_LAPACK_USER require full path to library
# prefer shared libraries when using FlexiBLAS-based toolchain
if self.toolchain.blas_family() == toolchain.FLEXIBLAS:
libs = os.getenv('%s_SHARED_LIBS' % libname).split(',')
else:
libs = os.getenv('%s_STATIC_LIBS' % libname).split(',')
libpaths = [os.path.join(libdir, lib) for lib in libs if not lib.startswith('libgfortran')]
self.cfg.update('configopts', '-DGMX_%s_USER="******"' % (libname, ';'.join(libpaths)))
# if libgfortran.a is listed, make sure it gets linked in too to avoiding linking issues
if 'libgfortran.a' in libs:
env.setvar('LDFLAGS', "%s -lgfortran -lm" % os.environ.get('LDFLAGS', ''))
# no more GSL support in GROMACS 5.x, see http://redmine.gromacs.org/issues/1472
if LooseVersion(self.version) < LooseVersion('5.0'):
# enable GSL when it's provided
if get_software_root('GSL'):
self.cfg.update('configopts', "-DGMX_GSL=ON")
else:
self.cfg.update('configopts', "-DGMX_GSL=OFF")
# include flags for linking to zlib/XZ in $LDFLAGS if they're listed as a dep;
# this is important for the tests, to correctly link against libxml2
for dep, link_flag in [('XZ', '-llzma'), ('zlib', '-lz')]:
root = get_software_root(dep)
if root:
libdir = get_software_libdir(dep)
ldflags = os.environ.get('LDFLAGS', '')
env.setvar('LDFLAGS', "%s -L%s %s" % (ldflags, os.path.join(root, libdir), link_flag))
# complete configuration with configure_method of parent
out = super(EB_GROMACS, self).configure_step()
# for recent GROMACS versions, make very sure that a decent BLAS, LAPACK and FFT is found and used
if LooseVersion(self.version) >= LooseVersion('4.6.5'):
patterns = [
r"Using external FFT library - \S*",
r"Looking for dgemm_ - found",
r"Looking for cheev_ - found",
]
for pattern in patterns:
regex = re.compile(pattern, re.M)
if not regex.search(out):
raise EasyBuildError("Pattern '%s' not found in GROMACS configuration output.", pattern)
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 procedure for GROMACS: set configure options for configure or cmake."""
# check whether PLUMED is loaded as a dependency
plumed_root = get_software_root('PLUMED')
if plumed_root:
# Need to check if PLUMED has an engine for this version
engine = 'gromacs-%s' % self.version
(out, _) = run_cmd("plumed-patch -l", log_all=True, simple=False)
if not re.search(engine, out):
raise EasyBuildError(
"There is no support in PLUMED version %s for GROMACS %s: %s",
get_software_version('PLUMED'), self.version, out)
# PLUMED patching must be done at different stages depending on
# version of GROMACS. Just prepare first part of cmd here
plumed_cmd = "plumed-patch -p -e %s" % engine
if LooseVersion(self.version) < LooseVersion('4.6'):
self.log.info(
"Using configure script for configuring GROMACS build.")
# Use static libraries if possible
self.cfg.update('configopts', "--enable-static")
# Use external BLAS and LAPACK
self.cfg.update('configopts',
"--with-external-blas --with-external-lapack")
env.setvar('LIBS',
"%s %s" % (os.environ['LIBLAPACK'], os.environ['LIBS']))
# Don't use the X window system
self.cfg.update('configopts', "--without-x")
# OpenMP is not supported for versions older than 4.5.
if LooseVersion(self.version) >= LooseVersion('4.5'):
# enable OpenMP support if desired
if self.toolchain.options.get('openmp', None):
self.cfg.update('configopts', "--enable-threads")
else:
self.cfg.update('configopts', "--disable-threads")
elif self.toolchain.options.get('openmp', None):
raise EasyBuildError(
"GROMACS version %s does not support OpenMP" %
self.version)
# GSL support
if get_software_root('GSL'):
self.cfg.update('configopts', "--with-gsl")
else:
self.cfg.update('configopts', "--without-gsl")
# actually run configure via ancestor (not direct parent)
self.cfg['configure_cmd'] = "./configure"
ConfigureMake.configure_step(self)
# Now patch GROMACS for PLUMED between configure and build
if plumed_root:
run_cmd(plumed_cmd, log_all=True, simple=True)
else:
# Now patch GROMACS for PLUMED before cmake
if plumed_root:
if LooseVersion(self.version) >= LooseVersion('5.1'):
# Use shared or static patch depending on
# setting of self.toolchain.options.get('dynamic')
# and adapt cmake flags accordingly as per instructions
# from "plumed patch -i"
if self.toolchain.options.get('dynamic', False):
mode = 'shared'
else:
mode = 'static'
plumed_cmd = plumed_cmd + ' -m %s' % mode
run_cmd(plumed_cmd, log_all=True, simple=True)
# Select debug or release build
if self.toolchain.options.get('debug', None):
self.cfg.update('configopts', "-DCMAKE_BUILD_TYPE=Debug")
else:
self.cfg.update('configopts', "-DCMAKE_BUILD_TYPE=Release")
# prefer static libraries, if available
if self.toolchain.options.get('dynamic', False):
self.cfg.update('configopts', "-DGMX_PREFER_STATIC_LIBS=OFF")
else:
self.cfg.update('configopts', "-DGMX_PREFER_STATIC_LIBS=ON")
if plumed_root:
self.cfg.update('configopts', "-DBUILD_SHARED_LIBS=OFF")
if self.cfg['double_precision']:
self.cfg.update('configopts', "-DGMX_DOUBLE=ON")
# always specify to use external BLAS/LAPACK
self.cfg.update('configopts',
"-DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON")
# disable GUI tools
self.cfg.update('configopts', "-DGMX_X11=OFF")
# convince to build for an older architecture than present on the build node by setting GMX_SIMD CMake flag
gmx_simd = self.get_gromacs_arch()
if gmx_simd:
if LooseVersion(self.version) < LooseVersion('5.0'):
self.cfg.update('configopts',
"-DGMX_CPU_ACCELERATION=%s" % gmx_simd)
else:
self.cfg.update('configopts', "-DGMX_SIMD=%s" % gmx_simd)
# set regression test path
prefix = 'regressiontests'
if any([src['name'].startswith(prefix) for src in self.src]):
major_minor_version = '.'.join(self.version.split('.')[:2])
self.cfg.update(
'configopts',
"-DREGRESSIONTEST_PATH='%%(builddir)s/%s-%%(version)s' " %
prefix)
# enable OpenMP support if desired
if self.toolchain.options.get('openmp', None):
self.cfg.update('configopts', "-DGMX_OPENMP=ON")
else:
self.cfg.update('configopts', "-DGMX_OPENMP=OFF")
# disable MPI support for initial, serial/SMP build; actual MPI build is done later
self.cfg.update('configopts', "-DGMX_MPI=OFF")
# explicitly disable GPU support if CUDA is not available,
# to avoid that GROMACS find and uses a system-wide CUDA compiler
cuda = get_software_root('CUDA')
if cuda:
self.cfg.update(
'configopts',
"-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=%s" % cuda)
else:
self.cfg.update('configopts', "-DGMX_GPU=OFF")
if get_software_root('imkl'):
# using MKL for FFT, so it will also be used for BLAS/LAPACK
self.cfg.update(
'configopts',
'-DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR="$EBROOTMKL/mkl/include" '
)
libs = os.getenv('LAPACK_STATIC_LIBS').split(',')
mkl_libs = [
os.path.join(os.getenv('LAPACK_LIB_DIR'), lib)
for lib in libs if lib != 'libgfortran.a'
]
mkl_libs = ['-Wl,--start-group'
] + mkl_libs + ['-Wl,--end-group']
self.cfg.update('configopts',
'-DMKL_LIBRARIES="%s" ' % ';'.join(mkl_libs))
else:
shlib_ext = get_shared_lib_ext()
for libname in ['BLAS', 'LAPACK']:
libdir = os.getenv('%s_LIB_DIR' % libname)
if self.toolchain.toolchain_family() == toolchain.CRAYPE:
libsci_mpi_mp_lib = glob.glob(
os.path.join(libdir, 'libsci_*_mpi_mp.a'))
if libsci_mpi_mp_lib:
self.cfg.update(
'configopts', '-DGMX_%s_USER=%s' %
(libname, libsci_mpi_mp_lib[0]))
else:
raise EasyBuildError(
"Failed to find libsci library to link with for %s",
libname)
else:
# -DGMX_BLAS_USER & -DGMX_LAPACK_USER require full path to library
libs = os.getenv('%s_STATIC_LIBS' % libname).split(',')
libpaths = [
os.path.join(libdir, lib) for lib in libs
if lib != 'libgfortran.a'
]
self.cfg.update(
'configopts', '-DGMX_%s_USER="******"' %
(libname, ';'.join(libpaths)))
# if libgfortran.a is listed, make sure it gets linked in too to avoiding linking issues
if 'libgfortran.a' in libs:
env.setvar(
'LDFLAGS', "%s -lgfortran -lm" %
os.environ.get('LDFLAGS', ''))
# no more GSL support in GROMACS 5.x, see http://redmine.gromacs.org/issues/1472
if LooseVersion(self.version) < LooseVersion('5.0'):
# enable GSL when it's provided
if get_software_root('GSL'):
self.cfg.update('configopts', "-DGMX_GSL=ON")
else:
self.cfg.update('configopts', "-DGMX_GSL=OFF")
# include flags for linking to zlib/XZ in $LDFLAGS if they're listed as a dep;
# this is important for the tests, to correctly link against libxml2
for dep, link_flag in [('XZ', '-llzma'), ('zlib', '-lz')]:
root = get_software_root(dep)
if root:
libdir = get_software_libdir(dep)
ldflags = os.environ.get('LDFLAGS', '')
env.setvar(
'LDFLAGS', "%s -L%s %s" %
(ldflags, os.path.join(root, libdir), link_flag))
# complete configuration with configure_method of parent
self.cfg['separate_build_dir'] = True
out = super(EB_GROMACS, self).configure_step()
# for recent GROMACS versions, make very sure that a decent BLAS, LAPACK and FFT is found and used
if LooseVersion(self.version) >= LooseVersion('4.6.5'):
patterns = [
r"Using external FFT library - \S*",
r"Looking for dgemm_ - found",
r"Looking for cheev_ - found",
]
for pattern in patterns:
regex = re.compile(pattern, re.M)
if not regex.search(out):
raise EasyBuildError(
"Pattern '%s' not found in GROMACS configuration output.",
pattern)
def install_step(self):
"""
Custom install step for GROMACS; figure out where libraries were installed to.
Also, install the MPI version of the executable in a separate step.
"""
# run 'make install' in parallel since it involves more compilation
self.cfg.update('installopts', "-j %s" % self.cfg['parallel'])
super(EB_GROMACS, self).install_step()
# the GROMACS libraries get installed in different locations (deeper subdirectory), depending on the platform;
# this is determined by the GNUInstallDirs CMake module;
# rather than trying to replicate the logic, we just figure out where the library was placed
if self.toolchain.options.get('dynamic', False):
self.libext = get_shared_lib_ext()
else:
self.libext = 'a'
if LooseVersion(self.version) < LooseVersion('5.0'):
libname = 'libgmx*.%s' % self.libext
else:
libname = 'libgromacs*.%s' % self.libext
for libdir in ['lib', 'lib64']:
if os.path.exists(os.path.join(self.installdir, libdir)):
for subdir in [libdir, os.path.join(libdir, '*')]:
libpaths = glob.glob(
os.path.join(self.installdir, subdir, libname))
if libpaths:
self.lib_subdir = os.path.dirname(
libpaths[0])[len(self.installdir) + 1:]
self.log.info(
"Found lib subdirectory that contains %s: %s",
libname, self.lib_subdir)
break
if not self.lib_subdir:
raise EasyBuildError("Failed to determine lib subdirectory in %s",
self.installdir)
# Install a version with the MPI suffix
if self.toolchain.options.get('usempi', None):
if LooseVersion(self.version) < LooseVersion('4.6'):
cmd = "make distclean"
(out, _) = run_cmd(cmd, log_all=True, simple=False)
self.cfg.update(
'configopts', "--enable-mpi --program-suffix={0}".format(
self.cfg['mpisuffix']))
ConfigureMake.configure_step(self)
super(EB_GROMACS, self).build_step()
super(EB_GROMACS, self).install_step()
else:
self.cfg['configopts'] = re.sub(r'-DGMX_MPI=OFF', r'',
self.cfg['configopts'])
if self.cfg['mpi_numprocs'] == 0:
self.log.info(
"No number of test MPI tasks specified -- using default: %s"
% self.cfg['parallel'])
self.cfg['mpi_numprocs'] = self.cfg['parallel']
elif self.cfg['mpi_numprocs'] > self.cfg['parallel']:
self.log.warning(
"Number of test MPI tasks (%s) is greater than value for 'parallel': %s",
self.cfg['mpi_numprocs'], self.cfg['parallel'])
self.cfg.update('configopts',
"-DGMX_MPI=ON -DGMX_THREAD_MPI=OFF")
mpiexec = which(self.cfg['mpiexec'])
if mpiexec:
self.cfg.update('configopts', "-DMPIEXEC=%s" % mpiexec)
self.cfg.update(
'configopts', "-DMPIEXEC_NUMPROC_FLAG=%s" %
self.cfg['mpiexec_numproc_flag'])
self.cfg.update('configopts',
"-DNUMPROC=%s" % self.cfg['mpi_numprocs'])
elif self.cfg['runtest']:
raise EasyBuildError("'%s' not found in $PATH",
self.cfg['mpiexec'])
self.log.info(
"Using %s as MPI executable when testing, with numprocs flag '%s' and %s tasks",
self.cfg['mpiexec'], self.cfg['mpiexec_numproc_flag'],
self.cfg['mpi_numprocs'])
# clean up obj dir before reconfiguring
shutil.rmtree(os.path.join(self.builddir, 'easybuild_obj'))
# rebuild/test/install with MPI options
super(EB_GROMACS, self).configure_step()
super(EB_GROMACS, self).build_step()
super(EB_GROMACS, self).test_step()
super(EB_GROMACS, self).install_step()
self.log.info(
"A full regression test suite is available from the GROMACS web site"
)
def configure_step(self):
"""Add some extra configure options."""
if LooseVersion(self.version) >= LooseVersion('2.6.0'):
# Libint 2.6.0 requires first compiling the Libint compiler,
# by running configure with appropriate options, followed by 'make export'
# and unpacking the resulting source tarball;
# see https://github.com/evaleev/libint/wiki#compiling-libint-compiler
# CMake is recommended, but configuring with Fortran support doesn't work correctly yet in Libint 2.6.0
# so stick to traditional configure script for now
print_msg("configuring Libint compiler...")
# first run autogen.sh script to generate initial configure script
run_cmd("./autogen.sh")
cmd = ' '.join([
self.cfg['preconfigopts'],
'./configure',
self.cfg['configopts'],
self.cfg['libint_compiler_configopts'],
])
run_cmd(cmd)
print_msg("generating Libint library...")
run_cmd("make export")
source_fn = 'libint-%s.tgz' % self.version
if os.path.exists(source_fn):
extract_file(source_fn, os.getcwd(), change_into_dir=False)
change_dir('libint-%s' % self.version)
else:
raise EasyBuildError(
"Could not find generated source tarball after 'make export'!"
)
# Libint < 2.7.0 can be configured using configure script,
# Libint >= 2.7.0 should be configured via cmake
if LooseVersion(self.version) < LooseVersion('2.7.0'):
# also build shared libraries (not enabled by default)
self.cfg.update('configopts', "--enable-shared")
if self.toolchain.options['pic']:
# Enforce consistency.
self.cfg.update('configopts', "--with-pic")
if LooseVersion(
self.version) >= LooseVersion('2.0') and LooseVersion(
self.version) < LooseVersion('2.1'):
# the code in libint is automatically generated and hence it is in some
# parts so complex that -O2 or -O3 compiler optimization takes forever
self.cfg.update('configopts', "--with-cxx-optflags='-O1'")
elif LooseVersion(self.version) >= LooseVersion('2.1'):
# pass down $CXXFLAGS to --with-cxxgen-optflags configure option;
# mainly to avoid warning about it not being set (but $CXXFLAGS is picked up anyway in practice)
self.cfg.update(
'configopts',
"--with-cxxgen-optflags='%s'" % os.getenv('CXXFLAGS'))
# --enable-fortran is only a known configure option for Libint library, not for Libint compiler,
# so only add --enable-fortran *after* configuring & generating Libint compiler
if self.cfg['with_fortran']:
self.cfg.update('configopts', '--enable-fortran')
self.cfg['configure_cmd'] = DEFAULT_CONFIGURE_CMD
ConfigureMake.configure_step(self)
else:
if self.cfg['with_fortran']:
self.cfg.update('configopts', '-DENABLE_FORTRAN=ON')
# also build shared libraries (not enabled by default)
self.cfg.update('configopts',
"-DLIBINT2_BUILD_SHARED_AND_STATIC_LIBS=ON")
# specify current directory as source directory (that contains CMakeLists.txt),
# since that's the path to the unpacked source tarball for Libint library (created by 'make export')
super(EB_Libint, self).configure_step(srcdir=os.getcwd())
def configure_step(self):
"""Dedicated configure step for Mono: install Mono from RPM (if provided), then run configure."""
# install Mono from RPMs if provided (because we need Mono to build Mono)
if self.rpms:
# prepare path for installing RPMs in
monorpms_path = os.path.join(self.builddir, "monorpms")
try:
os.makedirs(os.path.join(monorpms_path, 'rpm'))
except OSError as err:
raise EasyBuildError("Failed to create directories for installing Mono RPMs in: %s", err)
self.src = self.rpms
self.rebuildRPM = True
# rebuild RPMs to make them relocatable
Rpm.configure_step(self)
# prepare to install RPMs
self.log.debug("Initializing temporary RPM repository to install to...")
cmd = "rpm --initdb --dbpath /rpm --root %s" % monorpms_path
run_cmd(cmd, log_all=True, simple=True)
# install RPMs one by one
for rpm in self.src:
self.log.debug("Installing RPM %s ..." % rpm['name'])
if os.path.exists(rpm['path']):
cmd = ' '.join([
"rpm -i",
"--dbpath %(inst)s/rpm",
"--force",
"--relocate /=%(inst)s",
"--badreloc",
"--nodeps --nopost",
"%(rpm)s",
]) % {
'inst': monorpms_path,
'rpm': rpm['path'],
}
run_cmd(cmd,log_all=True,simple=True)
else:
raise EasyBuildError("RPM file %s not found", rpm['path'])
# create patched version of gmcs command
self.log.debug("Making our own copy of gmcs (one that works).")
mygmcs_path = os.path.join(monorpms_path, 'usr', 'bin', 'mygmcs')
try:
shutil.copy(os.path.join(monorpms_path, 'usr' ,'bin', 'gmcs'), mygmcs_path)
except OSError as err:
raise EasyBuildError("Failed to copy gmcs to %s: %s", mygmcs_path, err)
rpls = [
("exec /usr/bin/mono", "exec %s/usr/bin/mono" % monorpms_path),
("`/usr/bin/monodir`", "%s/usr/lib64/mono" % monorpms_path),
]
apply_regex_substitutions(mygmcs_path, rpls)
self.log.debug("Patched version of gmcs (%s): %s" % (mygmcs_path, read_file(mygmcs_path)))
# initiate bootstrap: build/install Mono with installed RPMs to temporary path
tmp_mono_path = os.path.join(self.builddir, "tmp_mono")
self.log.debug("Build/install temporary Mono version in %s using installed RPMs..." % tmp_mono_path)
par = ''
if self.cfg['parallel']:
par = "-j %s" % self.cfg['parallel']
config_cmd = "%s ./configure --prefix=%s %s" % (self.cfg['preconfigopts'], tmp_mono_path, self.cfg['configopts'])
build_cmd = ' '.join([
"%(prebuildopts)s"
"make %(par)s",
"EXTERNAL_MCS=%(path)s/usr/bin/mygmcs",
"EXTERNAL_RUNTIME=%(path)s/usr/bin/mono",
"%(buildopts)s",
]) %{
'prebuildopts': self.cfg['prebuildopts'],
'par': par,
'path': monorpms_path,
'buildopts': self.cfg['buildopts'],
}
install_cmd = "make install"
for cmd in [config_cmd, build_cmd, install_cmd]:
run_cmd(cmd, log_all=True, simple=True)
more_buildopts = ' '.join([
"EXTERNAL_MCS=%(path)s/bin/gmcs",
"EXTERNAL_RUNTIME=%(path)s/bin/mono",
]) % {'path': tmp_mono_path}
self.cfg.update('buildopts', more_buildopts)
self.src = self.mono_srcs
# continue with normal configure, and subsequent make, make install
ConfigureMake.configure_step(self)
def configure_step(self):
"""Configuration step, we set FC, F77 is already set by EasyBuild to the right compiler,
FC is used for Fortan90"""
environment.setvar("FC", self.toolchain.get_variable('F90'))
ConfigureMake.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):
"""Configuration step, we set FC, F77 is already set by EasyBuild to the right compiler,
FC is used for Fortan90"""
environment.setvar("FC", self.toolchain.get_variable('F90'))
ConfigureMake.configure_step(self)
def install_step(self):
"""
Custom install step for GROMACS; figure out where libraries were installed to.
Also, install the MPI version of the executable in a separate step.
"""
# run 'make install' in parallel since it involves more compilation
self.cfg.update('installopts', "-j %s" % self.cfg['parallel'])
super(EB_GROMACS, self).install_step()
# the GROMACS libraries get installed in different locations (deeper subdirectory), depending on the platform;
# this is determined by the GNUInstallDirs CMake module;
# rather than trying to replicate the logic, we just figure out where the library was placed
if self.toolchain.options.get('dynamic', False):
self.libext = get_shared_lib_ext()
else:
self.libext = 'a'
if LooseVersion(self.version) < LooseVersion('5.0'):
libname = 'libgmx*.%s' % self.libext
else:
libname = 'libgromacs*.%s' % self.libext
for libdir in ['lib', 'lib64']:
if os.path.exists(os.path.join(self.installdir, libdir)):
for subdir in [libdir, os.path.join(libdir, '*')]:
libpaths = glob.glob(os.path.join(self.installdir, subdir, libname))
if libpaths:
self.lib_subdir = os.path.dirname(libpaths[0])[len(self.installdir)+1:]
self.log.info("Found lib subdirectory that contains %s: %s", libname, self.lib_subdir)
break
if not self.lib_subdir:
raise EasyBuildError("Failed to determine lib subdirectory in %s", self.installdir)
# Install a version with the MPI suffix
if self.toolchain.options.get('usempi', None):
if LooseVersion(self.version) < LooseVersion('4.6'):
cmd = "make distclean"
(out, _) = run_cmd(cmd, log_all=True, simple=False)
self.cfg.update('configopts', "--enable-mpi --program-suffix={0}".format(self.cfg['mpisuffix']))
ConfigureMake.configure_step(self)
super(EB_GROMACS, self).build_step()
super(EB_GROMACS, self).install_step()
else:
self.cfg['configopts'] = re.sub(r'-DGMX_MPI=OFF', r'', self.cfg['configopts'])
if self.cfg['mpi_numprocs'] == 0:
self.log.info("No number of test MPI tasks specified -- using default: %s" % self.cfg['parallel'])
self.cfg['mpi_numprocs'] = self.cfg['parallel']
elif self.cfg['mpi_numprocs'] > self.cfg['parallel']:
self.log.warning("Number of test MPI tasks (%s) is greater than value for 'parallel': %s",
self.cfg['mpi_numprocs'], self.cfg['parallel'])
self.cfg.update('configopts', "-DGMX_MPI=ON -DGMX_THREAD_MPI=OFF")
mpiexec = which(self.cfg['mpiexec'])
if mpiexec:
self.cfg.update('configopts', "-DMPIEXEC=%s" % mpiexec)
self.cfg.update('configopts', "-DMPIEXEC_NUMPROC_FLAG=%s" % self.cfg['mpiexec_numproc_flag'])
self.cfg.update('configopts', "-DNUMPROC=%s" % self.cfg['mpi_numprocs'])
elif self.cfg['runtest']:
raise EasyBuildError("'%s' not found in $PATH", self.cfg['mpiexec'])
self.log.info("Using %s as MPI executable when testing, with numprocs flag '%s' and %s tasks",
self.cfg['mpiexec'], self.cfg['mpiexec_numproc_flag'], self.cfg['mpi_numprocs'])
# clean up obj dir before reconfiguring
shutil.rmtree(os.path.join(self.builddir, 'easybuild_obj'))
# rebuild/test/install with MPI options
super(EB_GROMACS, self).configure_step()
super(EB_GROMACS, self).build_step()
super(EB_GROMACS, self).test_step()
super(EB_GROMACS, self).install_step()
self.log.info("A full regression test suite is available from the GROMACS web site")
def configure_step(self):
"""Custom configuration procedure for GROMACS: set configure options for configure or cmake."""
if LooseVersion(self.version) < LooseVersion('4.6'):
self.log.info("Using configure script for configuring GROMACS build.")
# Use static libraries if possible
self.cfg.update('configopts', "--enable-static")
# Use external BLAS and LAPACK
self.cfg.update('configopts', "--with-external-blas --with-external-lapack")
env.setvar('LIBS', "%s %s" % (os.environ['LIBLAPACK'], os.environ['LIBS']))
# Don't use the X window system
self.cfg.update('configopts', "--without-x")
# OpenMP is not supported for versions older than 4.5.
if LooseVersion(self.version) >= LooseVersion('4.5'):
# enable OpenMP support if desired
if self.toolchain.options.get('openmp', None):
self.cfg.update('configopts', "--enable-threads")
else:
self.cfg.update('configopts', "--disable-threads")
elif self.toolchain.options.get('openmp', None):
raise EasyBuildError("GROMACS version %s does not support OpenMP" % self.version)
# GSL support
if get_software_root('GSL'):
self.cfg.update('configopts', "--with-gsl")
else:
self.cfg.update('configopts', "--without-gsl")
# actually run configure via ancestor (not direct parent)
ConfigureMake.configure_step(self)
else:
# build a release build
self.cfg.update('configopts', "-DCMAKE_BUILD_TYPE=Release")
# prefer static libraries, if available
if self.toolchain.options.get('dynamic', False):
self.cfg.update('configopts', "-DGMX_PREFER_STATIC_LIBS=OFF")
else:
self.cfg.update('configopts', "-DGMX_PREFER_STATIC_LIBS=ON")
if self.cfg['double_precision']:
self.cfg.update('configopts', "-DGMX_DOUBLE=ON")
# always specify to use external BLAS/LAPACK
self.cfg.update('configopts', "-DGMX_EXTERNAL_BLAS=ON -DGMX_EXTERNAL_LAPACK=ON")
# disable GUI tools
self.cfg.update('configopts', "-DGMX_X11=OFF")
# set regression test path
prefix = 'regressiontests'
if any([src['name'].startswith(prefix) for src in self.src]):
major_minor_version = '.'.join(self.version.split('.')[:2])
self.cfg.update('configopts', "-DREGRESSIONTEST_PATH='%%(builddir)s/%s-%%(version)s' " % prefix)
# enable OpenMP support if desired
if self.toolchain.options.get('openmp', None):
self.cfg.update('configopts', "-DGMX_OPENMP=ON")
else:
self.cfg.update('configopts', "-DGMX_OPENMP=OFF")
# disable MPI support for initial, serial/SMP build; actual MPI build is done later
self.cfg.update('configopts', "-DGMX_MPI=OFF")
# explicitly disable GPU support if CUDA is not available,
# to avoid that GROMACS find and uses a system-wide CUDA compiler
cuda = get_software_root('CUDA')
if cuda:
self.cfg.update('configopts', "-DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=%s" % cuda)
else:
self.cfg.update('configopts', "-DGMX_GPU=OFF")
if get_software_root('imkl'):
# using MKL for FFT, so it will also be used for BLAS/LAPACK
self.cfg.update('configopts', '-DGMX_FFT_LIBRARY=mkl -DMKL_INCLUDE_DIR="$EBROOTMKL/mkl/include" ')
mkl_libs = [os.path.join(os.getenv('LAPACK_LIB_DIR'), lib) for lib in ['libmkl_lapack.a']]
self.cfg.update('configopts', '-DMKL_LIBRARIES="%s" ' % ';'.join(mkl_libs))
else:
shlib_ext = get_shared_lib_ext()
for libname in ['BLAS', 'LAPACK']:
libdir = os.getenv('%s_LIB_DIR' % libname)
if self.toolchain.toolchain_family() == toolchain.CRAYPE:
libsci_mpi_mp_lib = glob.glob(os.path.join(libdir, 'libsci_*_mpi_mp.a'))
if libsci_mpi_mp_lib:
self.cfg.update('configopts', '-DGMX_%s_USER=%s' % (libname, libsci_mpi_mp_lib[0]))
else:
raise EasyBuildError("Failed to find libsci library to link with for %s", libname)
else:
# -DGMX_BLAS_USER & -DGMX_LAPACK_USER require full path to library
libs = os.getenv('%s_STATIC_LIBS' % libname).split(',')
libpaths = [os.path.join(libdir, lib) for lib in libs if lib != 'libgfortran.a']
self.cfg.update('configopts', '-DGMX_%s_USER="******"' % (libname, ';'.join(libpaths)))
# if libgfortran.a is listed, make sure it gets linked in too to avoiding linking issues
if 'libgfortran.a' in libs:
env.setvar('LDFLAGS', "%s -lgfortran -lm" % os.environ.get('LDFLAGS', ''))
# no more GSL support in GROMACS 5.x, see http://redmine.gromacs.org/issues/1472
if LooseVersion(self.version) < LooseVersion('5.0'):
# enable GSL when it's provided
if get_software_root('GSL'):
self.cfg.update('configopts', "-DGMX_GSL=ON")
else:
self.cfg.update('configopts', "-DGMX_GSL=OFF")
# include flags for linking to zlib/XZ in $LDFLAGS if they're listed as a dep;
# this is important for the tests, to correctly link against libxml2
for dep, link_flag in [('XZ', '-llzma'), ('zlib', '-lz')]:
root = get_software_root(dep)
if root:
libdir = get_software_libdir(dep)
ldflags = os.environ.get('LDFLAGS', '')
env.setvar('LDFLAGS', "%s -L%s %s" % (ldflags, os.path.join(root, libdir), link_flag))
# complete configuration with configure_method of parent
self.cfg['separate_build_dir'] = True
out = super(EB_GROMACS, self).configure_step()
# for recent GROMACS versions, make very sure that a decent BLAS, LAPACK and FFT is found and used
if LooseVersion(self.version) >= LooseVersion('4.6.5'):
patterns = [
r"Using external FFT library - \S*",
r"Looking for dgemm_ - found",
r"Looking for cheev_ - found",
]
for pattern in patterns:
regex = re.compile(pattern, re.M)
if not regex.search(out):
raise EasyBuildError("Pattern '%s' not found in GROMACS configuration output.", pattern)
