def configure_step(self):
"""Set extra configure options."""
self.cfg.update('configopts', "--with-threads --enable-shared")
modules_setup_dist = os.path.join(self.cfg['start_dir'], 'Modules', 'Setup.dist')
libreadline = get_software_root('libreadline')
if libreadline:
ncurses = get_software_root('ncurses')
if ncurses:
readline_libdir = get_software_libdir('libreadline')
ncurses_libdir = get_software_libdir('ncurses')
readline_static_lib = os.path.join(libreadline, readline_libdir, 'libreadline.a')
ncurses_static_lib = os.path.join(ncurses, ncurses_libdir, 'libncurses.a')
readline = "readline readline.c %s %s" % (readline_static_lib, ncurses_static_lib)
for line in fileinput.input(modules_setup_dist, inplace='1', backup='.readline'):
line = re.sub(r"^#readline readline.c.*", readline, line)
sys.stdout.write(line)
else:
self.log.error("Both libreadline and ncurses are required to ensure readline support")
openssl = get_software_root('OpenSSL')
if openssl:
for line in fileinput.input(modules_setup_dist, inplace='1', backup='.ssl'):
line = re.sub(r"^#SSL=.*", "SSL=%s" % openssl, line)
line = re.sub(r"^#(\s*-DUSE_SSL -I)", r"\1", line)
line = re.sub(r"^#(\s*-L\$\(SSL\)/lib )", r"\1 -L$(SSL)/lib64 ", line)
sys.stdout.write(line)
super(EB_Python, self).configure_step()
def configure_step(self):
"""Set extra configure options."""
self.cfg.update('configopts', "--with-threads --enable-shared")
# Need to be careful to match the unicode settings to the underlying python
if sys.maxunicode == 1114111:
self.cfg.update('configopts', "--enable-unicode=ucs4")
elif sys.maxunicode == 65535:
self.cfg.update('configopts', "--enable-unicode=ucs2")
else:
raise EasyBuildError("Unknown maxunicode value for your python: %d" % sys.maxunicode)
modules_setup_dist = os.path.join(self.cfg['start_dir'], 'Modules', 'Setup.dist')
libreadline = get_software_root('libreadline')
if libreadline:
ncurses = get_software_root('ncurses')
if ncurses:
readline_libdir = get_software_libdir('libreadline')
ncurses_libdir = get_software_libdir('ncurses')
readline_static_lib = os.path.join(libreadline, readline_libdir, 'libreadline.a')
ncurses_static_lib = os.path.join(ncurses, ncurses_libdir, 'libncurses.a')
readline = "readline readline.c %s %s" % (readline_static_lib, ncurses_static_lib)
for line in fileinput.input(modules_setup_dist, inplace='1', backup='.readline'):
line = re.sub(r"^#readline readline.c.*", readline, line)
sys.stdout.write(line)
else:
raise EasyBuildError("Both libreadline and ncurses are required to ensure readline support")
openssl = get_software_root('OpenSSL')
if openssl:
for line in fileinput.input(modules_setup_dist, inplace='1', backup='.ssl'):
line = re.sub(r"^#SSL=.*", "SSL=%s" % openssl, line)
line = re.sub(r"^#(\s*-DUSE_SSL -I)", r"\1", line)
line = re.sub(r"^#(\s*-L\$\(SSL\)/lib )", r"\1 -L$(SSL)/lib64 ", line)
sys.stdout.write(line)
tcl = get_software_root('Tcl')
tk = get_software_root('Tk')
if tcl and tk:
tclver = get_software_version('Tcl')
tkver = get_software_version('Tk')
tcltk_maj_min_ver = '.'.join(tclver.split('.')[:2])
if tcltk_maj_min_ver != '.'.join(tkver.split('.')[:2]):
raise EasyBuildError("Tcl and Tk major/minor versions don't match: %s vs %s", tclver, tkver)
self.cfg.update('configopts', "--with-tcltk-includes='-I%s/include -I%s/include'" % (tcl, tk))
tcl_libdir = os.path.join(tcl, get_software_libdir('Tcl'))
tk_libdir = os.path.join(tk, get_software_libdir('Tk'))
tcltk_libs = "-L%(tcl_libdir)s -L%(tk_libdir)s -ltcl%(maj_min_ver)s -ltk%(maj_min_ver)s" % {
'tcl_libdir': tcl_libdir,
'tk_libdir': tk_libdir,
'maj_min_ver': tcltk_maj_min_ver,
}
self.cfg.update('configopts', "--with-tcltk-libs='%s'" % tcltk_libs)
super(EB_Python, self).configure_step()
def configure_step(self):
"""Set extra configure options."""
self.cfg.update("configopts", "--with-threads --enable-shared")
modules_setup_dist = os.path.join(self.cfg["start_dir"], "Modules", "Setup.dist")
libreadline = get_software_root("libreadline")
if libreadline:
ncurses = get_software_root("ncurses")
if ncurses:
readline_libdir = get_software_libdir("libreadline")
ncurses_libdir = get_software_libdir("ncurses")
readline_static_lib = os.path.join(libreadline, readline_libdir, "libreadline.a")
ncurses_static_lib = os.path.join(ncurses, ncurses_libdir, "libncurses.a")
readline = "readline readline.c %s %s" % (readline_static_lib, ncurses_static_lib)
for line in fileinput.input(modules_setup_dist, inplace="1", backup=".readline"):
line = re.sub(r"^#readline readline.c.*", readline, line)
sys.stdout.write(line)
else:
raise EasyBuildError("Both libreadline and ncurses are required to ensure readline support")
openssl = get_software_root("OpenSSL")
if openssl:
for line in fileinput.input(modules_setup_dist, inplace="1", backup=".ssl"):
line = re.sub(r"^#SSL=.*", "SSL=%s" % openssl, line)
line = re.sub(r"^#(\s*-DUSE_SSL -I)", r"\1", line)
line = re.sub(r"^#(\s*-L\$\(SSL\)/lib )", r"\1 -L$(SSL)/lib64 ", line)
sys.stdout.write(line)
tcl = get_software_root("Tcl")
tk = get_software_root("Tk")
if tcl and tk:
tclver = get_software_version("Tcl")
tkver = get_software_version("Tk")
tcltk_maj_min_ver = ".".join(tclver.split(".")[:2])
if tcltk_maj_min_ver != ".".join(tkver.split(".")[:2]):
raise EasyBuildError("Tcl and Tk major/minor versions don't match: %s vs %s", tclver, tkver)
self.cfg.update("configopts", "--with-tcltk-includes='-I%s/include -I%s/include'" % (tcl, tk))
tcl_libdir = os.path.join(tcl, get_software_libdir("Tcl"))
tk_libdir = os.path.join(tk, get_software_libdir("Tk"))
tcltk_libs = "-L%(tcl_libdir)s -L%(tk_libdir)s -ltcl%(maj_min_ver)s -ltk%(maj_min_ver)s" % {
"tcl_libdir": tcl_libdir,
"tk_libdir": tk_libdir,
"maj_min_ver": tcltk_maj_min_ver,
}
self.cfg.update("configopts", "--with-tcltk-libs='%s'" % tcltk_libs)
super(EB_Python, self).configure_step()
def test_get_software_root_version_libdir(self):
"""Test get_software_X functions."""
tmpdir = tempfile.mkdtemp()
test_cases = [
('GCC', 'GCC'),
('grib_api', 'GRIB_API'),
('netCDF-C++', 'NETCDFMINCPLUSPLUS'),
('Score-P', 'SCOREMINP'),
]
for (name, env_var_name) in test_cases:
# mock stuff that get_software_X functions rely on
root = os.path.join(tmpdir, name)
os.makedirs(os.path.join(root, 'lib'))
os.environ['EBROOT%s' % env_var_name] = root
version = '0.0-%s' % root
os.environ['EBVERSION%s' % env_var_name] = version
self.assertEqual(get_software_root(name), root)
self.assertEqual(get_software_version(name), version)
self.assertEqual(get_software_libdir(name), 'lib')
os.environ.pop('EBROOT%s' % env_var_name)
os.environ.pop('EBVERSION%s' % env_var_name)
# check expected result of get_software_libdir with multiple lib subdirs
root = os.path.join(tmpdir, name)
os.makedirs(os.path.join(root, 'lib64'))
os.environ['EBROOT%s' % env_var_name] = root
self.assertErrorRegex(EasyBuildError, "Multiple library subdirectories found.*", get_software_libdir, name)
self.assertEqual(get_software_libdir(name, only_one=False), ['lib', 'lib64'])
# only directories containing files in specified list should be retained
open(os.path.join(root, 'lib64', 'foo'), 'w').write('foo')
self.assertEqual(get_software_libdir(name, fs=['foo']), 'lib64')
# clean up for previous tests
os.environ.pop('EBROOT%s' % env_var_name)
# if root/version for specified software package can not be found, these functions should return None
self.assertEqual(get_software_root('foo'), None)
self.assertEqual(get_software_version('foo'), None)
self.assertEqual(get_software_libdir('foo'), None)
# if no library subdir is found, get_software_libdir should return None
os.environ['EBROOTFOO'] = tmpdir
self.assertEqual(get_software_libdir('foo'), None)
os.environ.pop('EBROOTFOO')
shutil.rmtree(tmpdir)
def configure_step(self, *args, **kwargs):
"""Configure Score-P build, set configure options for compiler, MPI and dependencies."""
# compiler and MPI suite should always be specified -- MUCH quicker and SAVER than autodetect
# --with-nocross-compiler-suite=(gcc|ibm|intel|pgi|studio)
# --with-mpi=(bullxmpi|hp|ibmpoe|intel|intel2|intelpoe|lam|mpibull2|mpich|mpich2|mpich3|openmpi|
# platform|scali|sgimpt|sun)
comp_opts = {
toolchain.GCC: 'gcc',
toolchain.INTELCOMP: 'intel',
}
comp_fam = self.toolchain.comp_family()
if comp_fam in comp_opts:
self.cfg.update('configopts', "--with-nocross-compiler-suite=%s" % comp_opts[comp_fam])
else:
raise EasyBuildError("Compiler family %s not supported yet (only: %s)",
comp_fam, ', '.join(comp_opts.keys()))
mpi_opts = {
toolchain.INTELMPI: 'intel2', # intel: Intel MPI v1.x (ancient); intelpoe: IBM POE MPI for Intel platforms
toolchain.OPENMPI: 'openmpi',
toolchain.MPICH: 'mpich3', # In EB terms, MPICH means MPICH 3.x; MPICH 1.x is ancient and unsupported
toolchain.MPICH2: 'mpich2',
}
mpi_fam = self.toolchain.mpi_family()
if mpi_fam is not None:
if mpi_fam in mpi_opts:
self.cfg.update('configopts', "--with-mpi=%s" % mpi_opts[mpi_fam])
else:
raise EasyBuildError("MPI family %s not supported yet (only: %s)",
mpi_fam, ', '.join(mpi_opts.keys()))
# auto-detection for dependencies mostly works fine, but hard specify paths anyway to have full control
deps = {
'binutils': ['--with-libbfd=%%s/%s' % get_software_libdir('binutils', fs=['libbfd.a'])],
'Cube': ['--with-cube=%s/bin'],
'CUDA': ['--with-libcudart=%s'],
'OTF2': ['--with-otf2=%s/bin'],
'OPARI2': ['--with-opari2=%s/bin'],
'PAPI': ['--with-papi-header=%s/include', '--with-papi-lib=%%s/%s' % get_software_libdir('PAPI')],
'PDT': ['--with-pdt=%s/bin'],
'Qt': ['--with-qt=%s'],
}
for (dep_name, dep_opts) in deps.items():
dep_root = get_software_root(dep_name)
if dep_root:
for dep_opt in dep_opts:
self.cfg.update('configopts', dep_opt % dep_root)
super(EB_Score_minus_P, self).configure_step(*args, **kwargs)
def configure_step(self):
"""Custom configuration procedure for binutils: statically link to zlib, configure options."""
# determine list of 'lib' directories to use rpath for;
# this should 'harden' the resulting binutils to bootstrap GCC (no trouble when other libstdc++ is build etc)
libdirs = []
for libdir in ['/usr/lib', '/usr/lib64', '/usr/lib/x86_64-linux-gnu/']:
# also consider /lib, /lib64
alt_libdir = libdir.replace('usr/', '')
if os.path.exists(libdir):
libdirs.append(libdir)
if os.path.exists(alt_libdir) and not os.path.samefile(libdir, alt_libdir):
libdirs.append(alt_libdir)
elif os.path.exists(alt_libdir):
libdirs.append(alt_libdir)
libs = ' '.join('-Wl,-rpath=%s' % libdir for libdir in libdirs)
# statically link to zlib if it is a (build) dependency
zlibroot = get_software_root('zlib')
if zlibroot:
self.cfg.update('configopts', '--with-system-zlib')
libz_path = os.path.join(zlibroot, get_software_libdir('zlib'), 'libz.a')
# for recent binutils versions, we need to override ZLIB in Makefile.in of components
if LooseVersion(self.version) >= LooseVersion('2.26'):
regex_subs = [
(r"^(ZLIB\s*=\s*).*$", r"\1%s" % libz_path),
(r"^(ZLIBINC\s*=\s*).*$", r"\1-I%s" % os.path.join(zlibroot, 'include')),
]
for makefile in glob.glob(os.path.join(self.cfg['start_dir'], '*', 'Makefile.in')):
apply_regex_substitutions(makefile, regex_subs)
# for older versions, injecting the path to the static libz library into $LIBS works
else:
libs += ' ' + libz_path
self.cfg.update('preconfigopts', "env LIBS='%s'" % libs)
self.cfg.update('prebuildopts', "env LIBS='%s'" % libs)
# use correct sysroot, to make sure 'ld' also considers system libraries
self.cfg.update('configopts', '--with-sysroot=/')
# build both static and shared libraries for recent binutils versions (default is only static)
if LooseVersion(self.version) > LooseVersion('2.24'):
self.cfg.update('configopts', "--enable-shared --enable-static")
# enable gold linker with plugin support, use ld as default linker (for recent versions of binutils)
if LooseVersion(self.version) > LooseVersion('2.24'):
self.cfg.update('configopts', "--enable-gold --enable-plugins --enable-ld=default")
# complete configuration with configure_method of parent
super(EB_binutils, self).configure_step()
def configure_step(self):
"""
Set the CMake options for SuperLU
"""
self.cfg['separate_build_dir'] = True
if self.cfg['build_shared_libs']:
self.cfg.update('configopts', '-DBUILD_SHARED_LIBS=ON')
self.lib_ext = get_shared_lib_ext()
else:
self.cfg.update('configopts', '-DBUILD_SHARED_LIBS=OFF')
self.lib_ext = 'a'
# Add -fPIC flag if necessary
pic_flag = ('OFF', 'ON')[self.toolchain.options['pic']]
self.cfg.update('configopts', '-DCMAKE_POSITION_INDEPENDENT_CODE=%s' % pic_flag)
# Make sure not to build the slow BLAS library included in the package
self.cfg.update('configopts', '-Denable_blaslib=OFF')
# Set the BLAS library to use
# For this, use the BLA_VENDOR option from the FindBLAS module of CMake
# Check for all possible values at https://cmake.org/cmake/help/latest/module/FindBLAS.html
toolchain_blas = self.toolchain.definition().get('BLAS', None)[0]
if toolchain_blas == 'imkl':
imkl_version = get_software_version('imkl')
if LooseVersion(imkl_version) >= LooseVersion('10'):
# 'Intel10_64lp' -> For Intel mkl v10 64 bit,lp thread model, lp64 model
# It should work for Intel MKL 10 and above, as long as the library names stay the same
# SuperLU requires thread, 'Intel10_64lp_seq' will not work!
self.cfg.update('configopts', '-DBLA_VENDOR="Intel10_64lp"')
else:
# 'Intel' -> For older versions of mkl 32 and 64 bit
self.cfg.update('configopts', '-DBLA_VENDOR="Intel"')
elif toolchain_blas in ['ACML', 'ATLAS']:
self.cfg.update('configopts', '-DBLA_VENDOR="%s"' % toolchain_blas)
elif toolchain_blas == 'OpenBLAS':
# Unfortunately, OpenBLAS is not recognized by FindBLAS from CMake,
# we have to specify the OpenBLAS library manually
openblas_lib = os.path.join( get_software_root('OpenBLAS'), get_software_libdir('OpenBLAS'), "libopenblas.a" )
self.cfg.update('configopts', '-DBLAS_LIBRARIES="%s;-pthread"' % openblas_lib)
elif toolchain_blas == None:
# This toolchain has no BLAS library
raise EasyBuildError("No BLAS library found in the toolchain")
else:
# This BLAS library is not supported yet
raise EasyBuildError("BLAS library '%s' is not supported yet", toolchain_blas)
super(EB_SuperLU, self).configure_step()
def prepare_step(self, *args, **kwargs):
"""Custom prepare step for Paraver: check required dependencies and collect information on them."""
super(EB_Paraver, self).prepare_step(*args, **kwargs)
# determine value to pass to --with-wxpropgrid (library name)
self.wxpropgrid = None
wxpropertygrid_root = get_software_root('wxPropertyGrid')
if wxpropertygrid_root:
wxpropertygrid_libdir = os.path.join(wxpropertygrid_root, get_software_libdir('wxPropertyGrid'))
libname_pattern = 'libwxcode_*_propgrid-*.so'
wxpropgrid_libs = glob.glob(os.path.join(wxpropertygrid_libdir, libname_pattern))
if len(wxpropgrid_libs) == 1:
# exclude the 'lib' prefix and '.so' suffix to determine value to be passed to --with-wxpropgrid
self.wxpropgrid = os.path.basename(wxpropgrid_libs[0])[3:-3]
else:
tup = (libname_pattern, wxpropertygrid_libdir, wxpropgrid_libs)
raise EasyBuildError("Expected to find exactly one %s library in %s, found %s" % tup)
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):
"""Custom configuration procedure for NWChem."""
# check whether a (valid) symlink to a .nwchemrc config file exists (via a dummy file if necessary)
# fail early if the link is not what's we expect, since running the test cases will likely fail in this case
try:
if os.path.exists(self.home_nwchemrc) or os.path.islink(
self.home_nwchemrc):
# create a dummy file to check symlink
if not os.path.exists(self.local_nwchemrc):
write_file(self.local_nwchemrc, 'dummy')
self.log.debug(
"Contents of %s: %s", os.path.dirname(self.local_nwchemrc),
os.listdir(os.path.dirname(self.local_nwchemrc)))
if os.path.islink(self.home_nwchemrc):
home_nwchemrc_target = os.readlink(self.home_nwchemrc)
if home_nwchemrc_target != self.local_nwchemrc:
raise EasyBuildError(
"Found %s, but it's not a symlink to %s. "
"Please (re)move %s while installing NWChem; it can be restored later",
self.home_nwchemrc, self.local_nwchemrc,
self.home_nwchemrc)
# ok to remove, we'll recreate it anyway
remove_file(self.local_nwchemrc)
except (IOError, OSError) as err:
raise EasyBuildError("Failed to validate %s symlink: %s",
self.home_nwchemrc, err)
# building NWChem in a long path name is an issue, so let's try to make sure we have a short one
try:
# NWChem insists that version is in name of build dir
tmpdir = tempfile.mkdtemp(suffix='-%s-%s' %
(self.name, self.version))
# remove created directory, since we're not going to use it as is
os.rmdir(tmpdir)
# avoid having '['/']' characters in build dir name, NWChem doesn't like that
start_dir = tmpdir.replace('[', '_').replace(']', '_')
mkdir(os.path.dirname(start_dir), parents=True)
symlink(self.cfg['start_dir'], start_dir)
change_dir(start_dir)
self.cfg['start_dir'] = start_dir
except OSError as err:
raise EasyBuildError(
"Failed to symlink build dir to a shorter path name: %s", err)
# change to actual build dir
change_dir('src')
nwchem_modules = self.cfg['modules']
# set required NWChem environment variables
env.setvar('NWCHEM_TOP', self.cfg['start_dir'])
if len(self.cfg['start_dir']) > 64:
# workaround for:
# "The directory name chosen for NWCHEM_TOP is longer than the maximum allowed value of 64 characters"
# see also https://svn.pnl.gov/svn/nwchem/trunk/src/util/util_nwchem_srcdir.F
self.setvar_env_makeopt('NWCHEM_LONG_PATHS', 'Y')
env.setvar('NWCHEM_TARGET', self.cfg['target'])
garoot = get_software_root('GlobalArrays')
if garoot:
self.setvar_env_makeopt('EXTERNAL_GA_PATH', garoot)
else:
env.setvar('MSG_COMMS', self.cfg['msg_comms'])
env.setvar('ARMCI_NETWORK', self.cfg['armci_network'])
if self.cfg['armci_network'] in ["OPENIB"]:
env.setvar('IB_INCLUDE', "/usr/include")
env.setvar('IB_LIB', "/usr/lib64")
env.setvar('IB_LIB_NAME', "-libumad -libverbs -lpthread")
if 'python' in self.cfg['modules']:
python_root = get_software_root('Python')
if not python_root:
raise EasyBuildError(
"Python module not loaded, you should add Python as a dependency."
)
env.setvar('PYTHONHOME', python_root)
pyver = '.'.join(get_software_version('Python').split('.')[0:2])
env.setvar('PYTHONVERSION', pyver)
# if libreadline is loaded, assume it was a dependency for Python
# pass -lreadline to avoid linking issues (libpython2.7.a doesn't include readline symbols)
libreadline = get_software_root('libreadline')
if libreadline:
libreadline_libdir = os.path.join(
libreadline, get_software_libdir('libreadline'))
ncurses = get_software_root('ncurses')
if not ncurses:
raise EasyBuildError(
"ncurses is not loaded, but required to link with libreadline"
)
ncurses_libdir = os.path.join(ncurses,
get_software_libdir('ncurses'))
readline_libs = ' '.join([
os.path.join(libreadline_libdir, 'libreadline.a'),
os.path.join(ncurses_libdir, 'libcurses.a'),
])
extra_libs = os.environ.get('EXTRA_LIBS', '')
env.setvar('EXTRA_LIBS', ' '.join([extra_libs, readline_libs]))
env.setvar('LARGE_FILES', 'TRUE')
env.setvar('USE_NOFSCHECK', 'TRUE')
env.setvar('CCSDTLR', 'y') # enable CCSDTLR
env.setvar(
'CCSDTQ',
'y') # enable CCSDTQ (compilation is long, executable is big)
if LooseVersion(self.version) >= LooseVersion("6.2"):
env.setvar('MRCC_METHODS',
'y') # enable multireference coupled cluster capability
if LooseVersion(self.version) >= LooseVersion("6.5"):
env.setvar(
'EACCSD', 'y'
) # enable EOM electron-attachemnt coupled cluster capability
env.setvar(
'IPCCSD', 'y'
) # enable EOM ionization-potential coupled cluster capability
env.setvar(
'USE_NOIO',
'TRUE') # avoid doing I/O for the ddscf, mp2 and ccsd modules
for var in ['USE_MPI', 'USE_MPIF', 'USE_MPIF4']:
env.setvar(var, 'y')
for var in ['CC', 'CXX', 'F90']:
env.setvar('MPI_%s' % var, os.getenv('MPI%s' % var))
libmpi = ""
# for NWChem 6.6 and newer, $LIBMPI & co should no longer be
# set, the correct values are determined by the NWChem build
# procedure automatically, see
# http://www.nwchem-sw.org/index.php/Compiling_NWChem#MPI_variables
if LooseVersion(self.version) < LooseVersion("6.6"):
env.setvar('MPI_LOC', os.path.dirname(os.getenv('MPI_INC_DIR')))
env.setvar('MPI_LIB', os.getenv('MPI_LIB_DIR'))
env.setvar('MPI_INCLUDE', os.getenv('MPI_INC_DIR'))
mpi_family = self.toolchain.mpi_family()
if mpi_family in toolchain.OPENMPI:
ompi_ver = get_software_version('OpenMPI')
if LooseVersion(ompi_ver) < LooseVersion("1.10"):
if LooseVersion(ompi_ver) < LooseVersion("1.8"):
libmpi = "-lmpi_f90 -lmpi_f77 -lmpi -ldl -Wl,--export-dynamic -lnsl -lutil"
else:
libmpi = "-lmpi_usempi -lmpi_mpifh -lmpi"
else:
libmpi = "-lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi"
elif mpi_family in [toolchain.INTELMPI]:
if self.cfg['armci_network'] in ["MPI-MT"]:
libmpi = "-lmpigf -lmpigi -lmpi_ilp64 -lmpi_mt"
else:
libmpi = "-lmpigf -lmpigi -lmpi_ilp64 -lmpi"
elif mpi_family in [toolchain.MPICH, toolchain.MPICH2]:
libmpi = "-lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread"
else:
raise EasyBuildError("Don't know how to set LIBMPI for %s",
mpi_family)
env.setvar('LIBMPI', libmpi)
if not garoot:
if self.cfg['armci_network'] in ["OPENIB"]:
libmpi += " -libumad -libverbs -lpthread"
# compiler optimization flags: set environment variables _and_ add them to list of make options
self.setvar_env_makeopt('COPTIMIZE', os.getenv('CFLAGS'))
self.setvar_env_makeopt('FOPTIMIZE', os.getenv('FFLAGS'))
# BLAS and ScaLAPACK
mpi_lib_dirs = ' '.join('-L' + d
for d in os.getenv('MPI_LIB_DIR').split())
self.setvar_env_makeopt(
'BLASOPT', ' '.join([
os.getenv('LDFLAGS'), mpi_lib_dirs,
os.getenv('LIBSCALAPACK_MT'), libmpi
]))
# Setting LAPACK_LIB is required from 7.0.0 onwards.
self.setvar_env_makeopt('LAPACK_LIB', os.getenv('LIBLAPACK'))
self.setvar_env_makeopt(
'SCALAPACK',
'%s %s' % (os.getenv('LDFLAGS'), os.getenv('LIBSCALAPACK_MT')))
if self.toolchain.options['i8']:
size = 8
self.setvar_env_makeopt('USE_SCALAPACK_I8', 'y')
self.cfg.update('lib_defines', '-DSCALAPACK_I8')
else:
self.setvar_env_makeopt('HAS_BLAS', 'yes')
self.setvar_env_makeopt('USE_SCALAPACK', 'y')
size = 4
# set sizes
for lib in ['BLAS', 'LAPACK', 'SCALAPACK']:
self.setvar_env_makeopt('%s_SIZE' % lib, str(size))
env.setvar('NWCHEM_MODULES', nwchem_modules)
env.setvar('LIB_DEFINES', self.cfg['lib_defines'])
# clean first (why not)
run_cmd("make clean", simple=True, log_all=True, log_ok=True)
# configure build
cmd = "make %s nwchem_config" % self.cfg['buildopts']
run_cmd(cmd, simple=True, log_all=True, log_ok=True, log_output=True)
env.setvar('IB_INCLUDE', "/usr/include")
env.setvar('IB_LIB', "/usr/lib64")
env.setvar('IB_LIB_NAME', "-libumad -libverbs -lpthread")
if 'python' in self.cfg['modules']:
python_root = get_software_root('Python')
if not python_root:
raise EasyBuildError("Python module not loaded, you should add Python as a dependency.")
env.setvar('PYTHONHOME', python_root)
pyver = '.'.join(get_software_version('Python').split('.')[0:2])
env.setvar('PYTHONVERSION', pyver)
# if libreadline is loaded, assume it was a dependency for Python
# pass -lreadline to avoid linking issues (libpython2.7.a doesn't include readline symbols)
libreadline = get_software_root('libreadline')
if libreadline:
libreadline_libdir = os.path.join(libreadline, get_software_libdir('libreadline'))
ncurses = get_software_root('ncurses')
if not ncurses:
raise EasyBuildError("ncurses is not loaded, but required to link with libreadline")
ncurses_libdir = os.path.join(ncurses, get_software_libdir('ncurses'))
readline_libs = ' '.join([
os.path.join(libreadline_libdir, 'libreadline.a'),
os.path.join(ncurses_libdir, 'libcurses.a'),
])
extra_libs = os.environ.get('EXTRA_LIBS', '')
env.setvar('EXTRA_LIBS', ' '.join([extra_libs, readline_libs]))
env.setvar('LARGE_FILES', 'TRUE')
env.setvar('USE_NOFSCHECK', 'TRUE')
env.setvar('CCSDTLR', 'y') # enable CCSDTLR
env.setvar('CCSDTQ', 'y') # enable CCSDTQ (compilation is long, executable is big)
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
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
self.cfg['build_shared_libs'] = True
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")
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:
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
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: 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:
if self.toolchain.options['debug']:
self.cfg.update('configopts', '-DCMAKE_BUILD_TYPE=DEBUG ')
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'),
('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 by patching UFconfig.mk or SuiteSparse_config.mk."""
if LooseVersion(self.version) < LooseVersion('4.0'):
self.config_name = 'UFconfig'
else:
self.config_name = 'SuiteSparse_config'
cfgvars = {
'CC': os.getenv('MPICC'),
'CFLAGS': os.getenv('CFLAGS'),
'CXX': os.getenv('MPICXX'),
'F77': os.getenv('MPIF77'),
'F77FLAGS': os.getenv('F77FLAGS'),
}
# Set BLAS and LAPACK libraries as specified in SuiteSparse README.txt
self.cfg.update('buildopts', 'BLAS="%s"' % os.getenv('LIBBLAS_MT'))
self.cfg.update('buildopts', 'LAPACK="%s"' % os.getenv('LIBLAPACK_MT'))
# Get METIS or ParMETIS settings
metis = get_software_root('METIS')
parmetis = get_software_root('ParMETIS')
if parmetis:
metis_path = parmetis
metis_include = os.path.join(parmetis, 'include')
metis_libs = os.path.join(parmetis,
get_software_libdir('ParMETIS'),
'libmetis.a')
elif metis:
metis_path = metis
metis_include = os.path.join(metis, 'include')
metis_libs = os.path.join(metis, get_software_libdir('METIS'),
'libmetis.a')
else:
raise EasyBuildError("Neither METIS or ParMETIS module loaded.")
if LooseVersion(self.version) >= LooseVersion('4.5.1'):
cfgvars.update({
'MY_METIS_LIB': metis_libs,
'MY_METIS_INC': metis_include,
})
else:
cfgvars.update({
'METIS_PATH': metis_path,
'METIS': metis_libs,
})
# patch file
fp = os.path.join(self.cfg['start_dir'], self.config_name,
'%s.mk' % self.config_name)
try:
for line in fileinput.input(fp, inplace=1, backup='.orig'):
for (var, val) in cfgvars.items():
orig_line = line
# for variables in cfgvars, substiture lines assignment
# in the file, whatever they are, by assignments to the
# values in cfgvars
line = re.sub(r"^\s*(%s\s*=\s*).*\n$" % var,
r"\1 %s # patched by EasyBuild\n" % val,
line)
if line != orig_line:
cfgvars.pop(var)
sys.stdout.write(line)
except IOError, err:
raise EasyBuildError("Failed to patch %s in: %s", fp, err)
env.setvar('IB_INCLUDE', "/usr/include")
env.setvar('IB_LIB', "/usr/lib64")
env.setvar('IB_LIB_NAME', "-libumad -libverbs -lpthread")
if 'python' in self.cfg['modules']:
python_root = get_software_root('Python')
if not python_root:
raise EasyBuildError("Python module not loaded, you should add Python as a dependency.")
env.setvar('PYTHONHOME', python_root)
pyver = '.'.join(get_software_version('Python').split('.')[0:2])
env.setvar('PYTHONVERSION', pyver)
# if libreadline is loaded, assume it was a dependency for Python
# pass -lreadline to avoid linking issues (libpython2.7.a doesn't include readline symbols)
libreadline = get_software_root('libreadline')
if libreadline:
libreadline_libdir = os.path.join(libreadline, get_software_libdir('libreadline'))
ncurses = get_software_root('ncurses')
if not ncurses:
raise EasyBuildError("ncurses is not loaded, but required to link with libreadline")
ncurses_libdir = os.path.join(ncurses, get_software_libdir('ncurses'))
readline_libs = ' '.join([
os.path.join(libreadline_libdir, 'libreadline.a'),
os.path.join(ncurses_libdir, 'libcurses.a'),
])
extra_libs = os.environ.get('EXTRA_LIBS', '')
env.setvar('EXTRA_LIBS', ' '.join([extra_libs, readline_libs]))
env.setvar('LARGE_FILES', 'TRUE')
env.setvar('USE_NOFSCHECK', 'TRUE')
env.setvar('CCSDTLR', 'y') # enable CCSDTLR
env.setvar('CCSDTQ', 'y') # enable CCSDTQ (compilation is long, executable is big)
def configure_step(self):
"""Set extra configure options."""
# Check for and report distutils user configs which may make the installation fail
# See https://github.com/easybuilders/easybuild-easyconfigs/issues/11009
for cfg in [
os.path.join(os.path.expanduser('~'), name)
for name in ('.pydistutils.cfg', 'pydistutils.cfg')
]:
if os.path.exists(cfg):
raise EasyBuildError(
"Legacy distutils user configuration file found at %s. Aborting.",
cfg)
self.cfg.update('configopts', "--enable-shared")
# Explicitely enable thread support on < 3.7 (always on 3.7+)
if LooseVersion(self.version) < LooseVersion('3.7'):
self.cfg.update('configopts', "--with-threads")
# Explicitely enable unicode on Python 2, always on for Python 3
# Need to be careful to match the unicode settings to the underlying python
if LooseVersion(self.version) < LooseVersion('3.0'):
if sys.maxunicode == 1114111:
self.cfg.update('configopts', "--enable-unicode=ucs4")
elif sys.maxunicode == 65535:
self.cfg.update('configopts', "--enable-unicode=ucs2")
else:
raise EasyBuildError(
"Unknown maxunicode value for your python: %d" %
sys.maxunicode)
# LTO introduced in 3.7.0
if LooseVersion(self.version) >= LooseVersion('3.7.0'):
use_lto = self.cfg['use_lto']
if use_lto is None:
use_lto = self.auto_detect_lto_support()
if use_lto:
self.cfg.update('configopts', "--with-lto")
# Enable further optimizations at the cost of a longer build
# Introduced in 3.5.3, fixed in 3.5.4: https://docs.python.org/3.5/whatsnew/changelog.html
if self.cfg['optimized'] and LooseVersion(
self.version) >= LooseVersion('3.5.4'):
# only configure with --enable-optimizations when compiling Python with (recent) GCC compiler
if self.toolchain.comp_family() == toolchain.GCC:
gcc_ver = get_software_version(
'GCCcore') or get_software_version('GCC')
if LooseVersion(gcc_ver) >= LooseVersion('8.0'):
self.cfg.update('configopts', "--enable-optimizations")
# When ensurepip is available we explicitely set this.
# E.g. in 3.4 it is by default "upgrade", i.e. on which is unexpected when we did set it to off
if self._has_ensure_pip():
self.cfg.update(
'configopts',
"--with-ensurepip=" + ('no', 'upgrade')[self.install_pip])
modules_setup = os.path.join(self.cfg['start_dir'], 'Modules', 'Setup')
if LooseVersion(self.version) < LooseVersion('3.8.0'):
modules_setup += '.dist'
libreadline = get_software_root('libreadline')
if libreadline:
ncurses = get_software_root('ncurses')
if ncurses:
readline_libdir = get_software_libdir('libreadline')
ncurses_libdir = get_software_libdir('ncurses')
readline_static_lib = os.path.join(libreadline,
readline_libdir,
'libreadline.a')
ncurses_static_lib = os.path.join(ncurses, ncurses_libdir,
'libncurses.a')
readline = "readline readline.c %s %s" % (readline_static_lib,
ncurses_static_lib)
for line in fileinput.input(modules_setup,
inplace='1',
backup='.readline'):
line = re.sub(r"^#readline readline.c.*", readline, line)
sys.stdout.write(line)
else:
raise EasyBuildError(
"Both libreadline and ncurses are required to ensure readline support"
)
openssl = get_software_root('OpenSSL')
if openssl:
for line in fileinput.input(modules_setup,
inplace='1',
backup='.ssl'):
line = re.sub(r"^#SSL=.*", "SSL=%s" % openssl, line)
line = re.sub(r"^#(\s*-DUSE_SSL -I)", r"\1", line)
line = re.sub(r"^#(\s*-L\$\(SSL\)/lib )",
r"\1 -L$(SSL)/lib64 ", line)
sys.stdout.write(line)
tcl = get_software_root('Tcl')
tk = get_software_root('Tk')
if tcl and tk:
tclver = get_software_version('Tcl')
tkver = get_software_version('Tk')
tcltk_maj_min_ver = '.'.join(tclver.split('.')[:2])
if tcltk_maj_min_ver != '.'.join(tkver.split('.')[:2]):
raise EasyBuildError(
"Tcl and Tk major/minor versions don't match: %s vs %s",
tclver, tkver)
self.cfg.update(
'configopts',
"--with-tcltk-includes='-I%s/include -I%s/include'" %
(tcl, tk))
tcl_libdir = os.path.join(tcl, get_software_libdir('Tcl'))
tk_libdir = os.path.join(tk, get_software_libdir('Tk'))
tcltk_libs = "-L%(tcl_libdir)s -L%(tk_libdir)s -ltcl%(maj_min_ver)s -ltk%(maj_min_ver)s" % {
'tcl_libdir': tcl_libdir,
'tk_libdir': tk_libdir,
'maj_min_ver': tcltk_maj_min_ver,
}
self.cfg.update('configopts',
"--with-tcltk-libs='%s'" % tcltk_libs)
# don't add user site directory to sys.path (equivalent to python -s)
# This matters e.g. when python installs the bundled pip & setuptools (for >= 3.4)
env.setvar('PYTHONNOUSERSITE', '1')
super(EB_Python, self).configure_step()
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)
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)
# 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 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")
# 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)
if 'python' in self.cfg['modules']:
python_root = get_software_root('Python')
if not python_root:
self.log.error(
"Python module not loaded, you should add Python as a dependency."
)
env.setvar('PYTHONHOME', python_root)
pyver = '.'.join(get_software_version('Python').split('.')[0:2])
env.setvar('PYTHONVERSION', pyver)
# if libreadline is loaded, assume it was a dependency for Python
# pass -lreadline to avoid linking issues (libpython2.7.a doesn't include readline symbols)
libreadline = get_software_root('libreadline')
if libreadline:
libreadline_libdir = os.path.join(
libreadline, get_software_libdir('libreadline'))
ncurses = get_software_root('ncurses')
if not ncurses:
self.log.error(
"ncurses is not loaded, but required to link with libreadline"
)
ncurses_libdir = os.path.join(ncurses,
get_software_libdir('ncurses'))
readline_libs = ' '.join([
os.path.join(libreadline_libdir, 'libreadline.a'),
os.path.join(ncurses_libdir, 'libcurses.a'),
])
extra_libs = os.environ.get('EXTRA_LIBS', '')
env.setvar('EXTRA_LIBS', ' '.join([extra_libs, readline_libs]))
env.setvar('LARGE_FILES', 'TRUE')
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)
def configure_step(self):
"""Set extra configure options."""
self.cfg.update('configopts', "--with-threads --enable-shared")
# Need to be careful to match the unicode settings to the underlying python
if sys.maxunicode == 1114111:
self.cfg.update('configopts', "--enable-unicode=ucs4")
elif sys.maxunicode == 65535:
self.cfg.update('configopts', "--enable-unicode=ucs2")
else:
raise EasyBuildError(
"Unknown maxunicode value for your python: %d" %
sys.maxunicode)
modules_setup_dist = os.path.join(self.cfg['start_dir'], 'Modules',
'Setup.dist')
libreadline = get_software_root('libreadline')
if libreadline:
ncurses = get_software_root('ncurses')
if ncurses:
readline_libdir = get_software_libdir('libreadline')
ncurses_libdir = get_software_libdir('ncurses')
readline_static_lib = os.path.join(libreadline,
readline_libdir,
'libreadline.a')
ncurses_static_lib = os.path.join(ncurses, ncurses_libdir,
'libncurses.a')
readline = "readline readline.c %s %s" % (readline_static_lib,
ncurses_static_lib)
for line in fileinput.input(modules_setup_dist,
inplace='1',
backup='.readline'):
line = re.sub(r"^#readline readline.c.*", readline, line)
sys.stdout.write(line)
else:
raise EasyBuildError(
"Both libreadline and ncurses are required to ensure readline support"
)
openssl = get_software_root('OpenSSL')
if openssl:
for line in fileinput.input(modules_setup_dist,
inplace='1',
backup='.ssl'):
line = re.sub(r"^#SSL=.*", "SSL=%s" % openssl, line)
line = re.sub(r"^#(\s*-DUSE_SSL -I)", r"\1", line)
line = re.sub(r"^#(\s*-L\$\(SSL\)/lib )",
r"\1 -L$(SSL)/lib64 ", line)
sys.stdout.write(line)
tcl = get_software_root('Tcl')
tk = get_software_root('Tk')
if tcl and tk:
tclver = get_software_version('Tcl')
tkver = get_software_version('Tk')
tcltk_maj_min_ver = '.'.join(tclver.split('.')[:2])
if tcltk_maj_min_ver != '.'.join(tkver.split('.')[:2]):
raise EasyBuildError(
"Tcl and Tk major/minor versions don't match: %s vs %s",
tclver, tkver)
self.cfg.update(
'configopts',
"--with-tcltk-includes='-I%s/include -I%s/include'" %
(tcl, tk))
tcl_libdir = os.path.join(tcl, get_software_libdir('Tcl'))
tk_libdir = os.path.join(tk, get_software_libdir('Tk'))
tcltk_libs = "-L%(tcl_libdir)s -L%(tk_libdir)s -ltcl%(maj_min_ver)s -ltk%(maj_min_ver)s" % {
'tcl_libdir': tcl_libdir,
'tk_libdir': tk_libdir,
'maj_min_ver': tcltk_maj_min_ver,
}
self.cfg.update('configopts',
"--with-tcltk-libs='%s'" % tcltk_libs)
super(EB_Python, self).configure_step()
aux_lib_gribex = os.path.join(tmp_installroot, gribdir, 'lib', 'libgribex.a')
aux_lib_ibm = os.path.join(tmp_installroot, gribdir, 'lib', 'libibmdummy.a')
grib_api_lib = os.path.join(get_software_root('grib_api'), 'lib', 'libgrib_api.a')
grib_api_f90_lib = os.path.join(get_software_root('grib_api'), 'lib', 'libgrib_api_f90.a')
grib_api_inc = os.path.join(get_software_root('grib_api'), 'include')
jasperlib = os.path.join(get_software_root('JasPer'), 'lib', 'libjasper.a')
mpilib = os.path.join(os.getenv('MPI_LIB_DIR'), os.getenv('MPI_LIB_SHARED'))
# netCDF
netcdf = get_software_root('netCDF')
netcdf_fortran = get_software_root('netCDF-Fortran')
if netcdf:
netcdfinc = os.path.join(netcdf, 'include')
if netcdf_fortran:
netcdflib = os.path.join(netcdf_fortran, get_software_libdir('netCDF-Fortran'), 'libnetcdff.a')
else:
netcdflib = os.path.join(netcdf, get_software_libdir('netCDF'), 'libnetcdff.a')
if not os.path.exists(netcdflib):
raise EasyBuildError("%s does not exist", netcdflib)
else:
raise EasyBuildError("netCDF(-Fortran) not available")
ldpaths = [ldflag[2:] for ldflag in os.getenv('LDFLAGS').split(' ')] # LDFLAGS have form '-L/path/to'
lapacklibs = []
for lib in os.getenv('LAPACK_STATIC_LIBS').split(','):
libpaths = [os.path.join(ldpath, lib) for ldpath in ldpaths]
lapacklibs.append([libpath for libpath in libpaths if os.path.exists(libpath)][0])
lapacklib = ' '.join(lapacklibs)
blaslibs = []
def configure_step(self):
"""Custom configuration procedure for ALADIN."""
# unset $LIBRARY_PATH set by modules of dependencies, because it may screw up linking
if 'LIBRARY_PATH' in os.environ:
self.log.debug("Unsetting $LIBRARY_PATH (was: %s)" % os.environ['LIBRARY_PATH'])
self.orig_library_path = os.environ.pop('LIBRARY_PATH')
# build auxiliary libraries
auxlibs_dir = None
my_gnu = None
if self.toolchain.comp_family() == toolchain.GCC:
my_gnu = 'y' # gfortran
for var in ['CFLAGS', 'CXXFLAGS', 'F90FLAGS', 'FFLAGS']:
flags = os.getenv(var)
env.setvar(var, "%s -fdefault-real-8 -fdefault-double-8" % flags)
self.log.info("Updated %s to '%s'" % (var, os.getenv(var)))
elif self.toolchain.comp_family() == toolchain.INTELCOMP:
my_gnu = 'i' # icc/ifort
else:
raise EasyBuildError("Don't know how to set 'my_gnu' variable in auxlibs build script.")
self.log.info("my_gnu set to '%s'" % my_gnu)
tmp_installroot = tempfile.mkdtemp(prefix='aladin_auxlibs_')
try:
cwd = os.getcwd()
os.chdir(self.builddir)
builddirs = os.listdir(self.builddir)
auxlibs_dir = [x for x in builddirs if x.startswith('auxlibs_installer')][0]
os.chdir(auxlibs_dir)
auto_driver = 'driver_automatic'
for line in fileinput.input(auto_driver, inplace=1, backup='.orig.eb'):
line = re.sub(r"^(my_gnu\s*=\s*).*$", r"\1%s" % my_gnu, line)
line = re.sub(r"^(my_r32\s*=\s*).*$", r"\1n", line) # always 64-bit real precision
line = re.sub(r"^(my_readonly\s*=\s*).*$", r"\1y", line) # make libs read-only after build
line = re.sub(r"^(my_installroot\s*=\s*).*$", r"\1%s" % tmp_installroot, line)
sys.stdout.write(line)
run_cmd("./%s" % auto_driver)
os.chdir(cwd)
except OSError as err:
raise EasyBuildError("Failed to build ALADIN: %s", err)
# build gmkpack, update PATH and set GMKROOT
# we build gmkpack here because a config file is generated in the gmkpack isntall path
try:
gmkpack_dir = [x for x in builddirs if x.startswith('gmkpack')][0]
os.chdir(os.path.join(self.builddir, gmkpack_dir))
qa = {
'Do you want to run the configuration file maker assistant now (y) or later [n] ?': 'n',
}
run_cmd_qa("./build_gmkpack", qa)
os.chdir(cwd)
paths = os.getenv('PATH').split(':')
paths.append(os.path.join(self.builddir, gmkpack_dir, 'util'))
env.setvar('PATH', ':'.join(paths))
env.setvar('GMKROOT', os.path.join(self.builddir, gmkpack_dir))
except OSError as err:
raise EasyBuildError("Failed to build gmkpack: %s", err)
# generate gmkpack configuration file
self.conf_file = 'ALADIN_%s' % self.version
self.conf_filepath = os.path.join(self.builddir, 'gmkpack_support', 'arch', '%s.x' % self.conf_file)
try:
if os.path.exists(self.conf_filepath):
os.remove(self.conf_filepath)
self.log.info("Removed existing gmpack config file %s" % self.conf_filepath)
archdir = os.path.dirname(self.conf_filepath)
if not os.path.exists(archdir):
mkdir(archdir, parents=True)
except OSError as err:
raise EasyBuildError("Failed to remove existing file %s: %s", self.conf_filepath, err)
mpich = 'n'
known_mpi_libs = [toolchain.MPICH, toolchain.MPICH2, toolchain.INTELMPI]
if self.toolchain.options.get('usempi', None) and self.toolchain.mpi_family() in known_mpi_libs:
mpich = 'y'
qpref = 'Please type the ABSOLUTE name of '
qsuff = ', or ignore (environment variables allowed) :'
qsuff2 = ', or ignore : (environment variables allowed) :'
comp_fam = self.toolchain.comp_family()
if comp_fam == toolchain.GCC:
gribdir = 'GNU'
elif comp_fam == toolchain.INTELCOMP:
gribdir = 'INTEL'
else:
raise EasyBuildError("Don't know which grib lib dir to use for compiler %s", comp_fam)
aux_lib_gribex = os.path.join(tmp_installroot, gribdir, 'lib', 'libgribex.a')
aux_lib_ibm = os.path.join(tmp_installroot, gribdir, 'lib', 'libibmdummy.a')
grib_api_lib = os.path.join(get_software_root('grib_api'), 'lib', 'libgrib_api.a')
grib_api_f90_lib = os.path.join(get_software_root('grib_api'), 'lib', 'libgrib_api_f90.a')
grib_api_inc = os.path.join(get_software_root('grib_api'), 'include')
jasperlib = os.path.join(get_software_root('JasPer'), 'lib', 'libjasper.a')
mpilib = os.path.join(os.getenv('MPI_LIB_DIR'), os.getenv('MPI_LIB_SHARED'))
# netCDF
netcdf = get_software_root('netCDF')
netcdf_fortran = get_software_root('netCDF-Fortran')
if netcdf:
netcdfinc = os.path.join(netcdf, 'include')
if netcdf_fortran:
netcdflib = os.path.join(netcdf_fortran, get_software_libdir('netCDF-Fortran'), 'libnetcdff.a')
else:
netcdflib = os.path.join(netcdf, get_software_libdir('netCDF'), 'libnetcdff.a')
if not os.path.exists(netcdflib):
raise EasyBuildError("%s does not exist", netcdflib)
else:
raise EasyBuildError("netCDF(-Fortran) not available")
ldpaths = [ldflag[2:] for ldflag in os.getenv('LDFLAGS').split(' ')] # LDFLAGS have form '-L/path/to'
lapacklibs = []
for lib in os.getenv('LAPACK_STATIC_LIBS').split(','):
libpaths = [os.path.join(ldpath, lib) for ldpath in ldpaths]
lapacklibs.append([libpath for libpath in libpaths if os.path.exists(libpath)][0])
lapacklib = ' '.join(lapacklibs)
blaslibs = []
for lib in os.getenv('BLAS_STATIC_LIBS').split(','):
libpaths = [os.path.join(ldpath, lib) for ldpath in ldpaths]
blaslibs.append([libpath for libpath in libpaths if os.path.exists(libpath)][0])
blaslib = ' '.join(blaslibs)
qa = {
'Do you want to run the configuration file maker assistant now (y) or later [n] ?': 'y',
'Do you want to setup your configuration file for MPICH (y/n) [n] ?': mpich,
'Please type the directory name where to find a dummy file mpif.h or ignore :': os.getenv('MPI_INC_DIR'),
'%sthe library gribex or emos%s' % (qpref, qsuff2): aux_lib_gribex,
'%sthe library ibm%s' % (qpref, qsuff): aux_lib_ibm,
'%sthe library grib_api%s' % (qpref, qsuff): grib_api_lib,
'%sthe library grib_api_f90%s' % (qpref, qsuff): grib_api_f90_lib,
'%sthe JPEG auxilary library if enabled by Grib_api%s' % (qpref, qsuff2): jasperlib,
'%sthe library netcdf%s' % (qpref, qsuff): netcdflib,
'%sthe library lapack%s' % (qpref, qsuff): lapacklib,
'%sthe library blas%s' % (qpref, qsuff): blaslib,
'%sthe library mpi%s' % (qpref, qsuff): mpilib,
'%sa MPI dummy library for serial executions, or ignore :' % qpref: '',
'Please type the directory name where to find grib_api headers, or ignore :': grib_api_inc,
'Please type the directory name where to find fortint.h or ignore :': '',
'Please type the directory name where to find netcdf headers, or ignore :': netcdfinc,
'Do you want to define CANARI (y/n) [y] ?': 'y',
'Please type the name of the script file used to generate a preprocessed blacklist file, or ignore :': '',
'Please type the name of the script file used to recover local libraries (gget), or ignore :': '',
'Please type the options to tune the gnu compilers, or ignore :': os.getenv('F90FLAGS'),
}
f90_seq = os.getenv('F90_SEQ')
if not f90_seq:
# F90_SEQ is only defined when usempi is enabled
f90_seq = os.getenv('F90')
stdqa = OrderedDict([
(r'Confirm library .* is .*', 'y'), # this one needs to be tried first!
(r'.*fortran 90 compiler name .*\s*:\n\(suggestions\s*: .*\)', f90_seq),
(r'.*fortran 90 compiler interfaced with .*\s*:\n\(suggestions\s*: .*\)', f90_seq),
(r'Please type the ABSOLUTE name of .*library.*, or ignore\s*[:]*\s*[\n]*.*', ''),
(r'Please .* to save this draft configuration file :\n.*', '%s.x' % self.conf_file),
])
no_qa = [
".*ignored.",
]
env.setvar('GMKTMP', self.builddir)
env.setvar('GMKFILE', self.conf_file)
run_cmd_qa("gmkfilemaker", qa, std_qa=stdqa, no_qa=no_qa)
# set environment variables for installation dirs
env.setvar('ROOTPACK', os.path.join(self.installdir, 'rootpack'))
env.setvar('ROOTBIN', os.path.join(self.installdir, 'rootpack'))
env.setvar('HOMEPACK', os.path.join(self.installdir, 'pack'))
env.setvar('HOMEBIN', os.path.join(self.installdir, 'pack'))
# patch config file to include right Fortran compiler flags
regex_subs = [(r"^(FRTFLAGS\s*=.*)$", r"\1 %s" % os.getenv('FFLAGS'))]
apply_regex_substitutions(self.conf_filepath, regex_subs)
def configure_step(self, *args, **kwargs):
"""Configure the build, set configure options for compiler, MPI and dependencies."""
# On non-cross-compile platforms, specify compiler and MPI suite explicitly. This is much quicker and safer
# than autodetection. In Score-P build-system terms, the following platforms are considered cross-compile
# architectures:
#
# - Cray XT/XE/XK/XC series
# - Fujitsu FX10, FX100 & K computer
# - IBM Blue Gene series
#
# Of those, only Cray is supported right now.
tc_fam = self.toolchain.toolchain_family()
if tc_fam != toolchain.CRAYPE:
# --with-nocross-compiler-suite=(gcc|ibm|intel|pgi|studio)
comp_opts = {
toolchain.DUMMY: 'gcc', # Assume that dummy toolchain uses a system-provided GCC
toolchain.GCC: 'gcc',
toolchain.IBMCOMP: 'ibm',
toolchain.INTELCOMP: 'intel',
toolchain.PGI: 'pgi',
}
comp_fam = self.toolchain.comp_family()
if comp_fam in comp_opts:
self.cfg.update('configopts', "--with-nocross-compiler-suite=%s" % comp_opts[comp_fam])
else:
raise EasyBuildError("Compiler family %s not supported yet (only: %s)",
comp_fam, ', '.join(comp_opts.keys()))
# --with-mpi=(bullxmpi|hp|ibmpoe|intel|intel2|intelpoe|lam|mpibull2|mpich|mpich2|mpich3|openmpi|
# platform|scali|sgimpt|sun)
#
# Notes:
# - intel: Intel MPI v1.x (ancient & unsupported)
# - intel2: Intel MPI v2.x and higher
# - intelpoe: IBM POE MPI for Intel platforms
# - mpich: MPICH v1.x (ancient & unsupported)
# - mpich2: MPICH2 v1.x
# - mpich3: MPICH v3.x & MVAPICH2
# This setting actually only affects options passed to the MPI (Fortran) compiler wrappers.
# And since MPICH v3.x-compatible options were already supported in MVAPICH2 v1.7, it is
# safe to use 'mpich3' for all supported versions although MVAPICH2 is based on MPICH v3.x
# only since v1.9b.
#
# With minimal toolchains, packages using this easyblock may be built with a non-MPI toolchain (e.g., OTF2).
# In this case, skip passing the '--with-mpi' option.
mpi_opts = {
toolchain.INTELMPI: 'intel2',
toolchain.OPENMPI: 'openmpi',
toolchain.MPICH: 'mpich3', # In EB terms, MPICH means MPICH 3.x
toolchain.MPICH2: 'mpich2',
toolchain.MVAPICH2: 'mpich3',
}
mpi_fam = self.toolchain.mpi_family()
if mpi_fam is not None:
if mpi_fam in mpi_opts:
self.cfg.update('configopts', "--with-mpi=%s" % mpi_opts[mpi_fam])
else:
raise EasyBuildError("MPI family %s not supported yet (only: %s)",
mpi_fam, ', '.join(mpi_opts.keys()))
# Auto-detection for dependencies mostly works fine, but hard specify paths anyway to have full control
#
# Notes:
# - binutils: Pass include/lib directories separately, as different directory layouts may break Score-P's
# configure, see https://github.com/geimer/easybuild-easyblocks/pull/4#issuecomment-219284755
deps = {
'binutils': ['--with-libbfd-include=%s/include',
'--with-libbfd-lib=%%s/%s' % get_software_libdir('binutils', fs=['libbfd.a'])],
'libunwind': ['--with-libunwind=%s'],
'Cube': ['--with-cube=%s/bin'],
'CUDA': ['--with-libcudart=%s'],
'OTF2': ['--with-otf2=%s/bin'],
'OPARI2': ['--with-opari2=%s/bin'],
'PAPI': ['--with-papi-header=%s/include', '--with-papi-lib=%%s/%s' % get_software_libdir('PAPI')],
'PDT': ['--with-pdt=%s/bin'],
'Qt': ['--with-qt=%s'],
'SIONlib': ['--with-sionlib=%s/bin'],
}
for (dep_name, dep_opts) in deps.items():
dep_root = get_software_root(dep_name)
if dep_root:
for dep_opt in dep_opts:
self.cfg.update('configopts', dep_opt % dep_root)
super(EB_Score_minus_P, self).configure_step(*args, **kwargs)
def configure_step(self):
"""Custom configuration procedure for OpenCV."""
# enable Python support if unspecified and Python is a dependency
if 'BUILD_PYTHON_SUPPORT' not in self.cfg['configopts']:
if get_software_root('Python'):
self.cfg.update(
'configopts',
"-DBUILD_PYTHON_SUPPORT=ON -DBUILD_NEW_PYTHON_SUPPORT=ON")
# recent OpenCV 3.x versions (and newer) use an alternative configure option to specify the location
# where the OpenCV Python bindings should be installed
py_pkgs_path = os.path.join(self.installdir, self.pylibdir)
if LooseVersion(self.version) >= LooseVersion('3.4.4'):
self.cfg.update(
'configopts',
'-DOPENCV_PYTHON_INSTALL_PATH=%s' % py_pkgs_path)
else:
self.cfg.update('configopts',
'-DPYTHON_PACKAGES_PATH=%s' % py_pkgs_path)
else:
self.cfg.update(
'configopts',
"-DBUILD_PYTHON_SUPPORT=OFF -DBUILD_NEW_PYTHON_SUPPORT=OFF"
)
# enable CUDA support if CUDA is a dependency
if 'WITH_CUDA' not in self.cfg['configopts']:
if get_software_root('CUDA'):
self.cfg.update('configopts', '-DWITH_CUDA=ON')
else:
self.cfg.update('configopts', '-DWITH_CUDA=OFF')
# configure for dependency libraries
for dep in ['JasPer', 'libjpeg-turbo', 'libpng', 'LibTIFF', 'zlib']:
if dep in ['libpng', 'LibTIFF']:
# strip off 'lib'
opt_name = dep[3:].upper()
elif dep == 'libjpeg-turbo':
opt_name = 'JPEG'
else:
opt_name = dep.upper()
shlib_ext = get_shared_lib_ext()
if dep == 'zlib':
lib_file = 'libz.%s' % shlib_ext
else:
lib_file = 'lib%s.%s' % (opt_name.lower(), shlib_ext)
dep_root = get_software_root(dep)
if dep_root:
self.cfg.update(
'configopts', '-D%s_INCLUDE_DIR=%s' %
(opt_name, os.path.join(dep_root, 'include')))
libdir = get_software_libdir(dep, only_one=True)
self.cfg.update(
'configopts', '-D%s_LIBRARY=%s' %
(opt_name, os.path.join(dep_root, libdir, lib_file)))
# configure optimisation for CPU architecture
# see https://github.com/opencv/opencv/wiki/CPU-optimizations-build-options
if self.toolchain.options.get(
'optarch') and 'CPU_BASELINE' not in self.cfg['configopts']:
optarch = build_option('optarch')
if optarch is None:
# optimize for host arch (let OpenCV detect it)
self.cfg.update('configopts', '-DCPU_BASELINE=DETECT')
elif optarch == OPTARCH_GENERIC:
# optimize for generic x86 architecture (lowest supported by OpenCV is SSE3)
self.cfg.update('configopts', '-DCPU_BASELINE=SSE3')
else:
raise EasyBuildError(
"Don't know how to configure OpenCV in accordance with --optarch='%s'",
optarch)
if self.cfg['cpu_dispatch']:
# using 'NONE' as value is equivalent with disabling the build of fat binaries (which is done by default)
self.cfg.update('configopts',
'-DCPU_DISPATCH=%s' % self.cfg['cpu_dispatch'])
# make sure that host CPU supports FP16 (unless -DCPU_BASELINE_DISABLE is already specified)
# Intel Sandy Bridge does not support FP16!
if 'CPU_BASELINE_DISABLE' not in self.cfg['configopts']:
avail_cpu_features = get_cpu_features()
if 'f16c' not in avail_cpu_features:
self.cfg.update('configopts', '-DCPU_BASELINE_DISABLE=FP16')
super(EB_OpenCV, self).configure_step()
def configure_step(self):
"""Configure build by patching UFconfig.mk or SuiteSparse_config.mk."""
if LooseVersion(self.version) < LooseVersion('4.0'):
self.config_name = 'UFconfig'
else:
self.config_name = 'SuiteSparse_config'
cfgvars = {
'CC': os.getenv('MPICC'),
'CFLAGS': os.getenv('CFLAGS'),
'CXX': os.getenv('MPICXX'),
'F77': os.getenv('MPIF77'),
'F77FLAGS': os.getenv('F77FLAGS'),
}
# Set BLAS and LAPACK libraries as specified in SuiteSparse README.txt
self.cfg.update('buildopts', 'BLAS="%s"' % os.getenv('LIBBLAS_MT'))
self.cfg.update('buildopts', 'LAPACK="%s"' % os.getenv('LIBLAPACK_MT'))
# Get METIS or ParMETIS settings
metis = get_software_root('METIS')
parmetis = get_software_root('ParMETIS')
if parmetis:
metis_path = parmetis
metis_include = os.path.join(parmetis, 'include')
metis_libs = os.path.join(parmetis, get_software_libdir('ParMETIS'), 'libmetis.a')
elif metis:
metis_path = metis
metis_include = os.path.join(metis, 'include')
metis_libs = os.path.join(metis, get_software_libdir('METIS'), 'libmetis.a')
else:
raise EasyBuildError("Neither METIS or ParMETIS module loaded.")
if LooseVersion(self.version) >= LooseVersion('4.5.1'):
cfgvars.update({
'MY_METIS_LIB': metis_libs,
'MY_METIS_INC': metis_include,
})
else:
cfgvars.update({
'METIS_PATH': metis_path,
'METIS': metis_libs,
})
# patch file
fp = os.path.join(self.cfg['start_dir'], self.config_name, '%s.mk' % self.config_name)
try:
for line in fileinput.input(fp, inplace=1, backup='.orig'):
for (var, val) in cfgvars.items():
orig_line = line
# for variables in cfgvars, substiture lines assignment
# in the file, whatever they are, by assignments to the
# values in cfgvars
line = re.sub(r"^\s*(%s\s*=\s*).*\n$" % var,
r"\1 %s # patched by EasyBuild\n" % val,
line)
if line != orig_line:
cfgvars.pop(var)
sys.stdout.write(line)
except IOError, err:
raise EasyBuildError("Failed to patch %s in: %s", fp, err)
def configure_step(self):
"""Custom configuration procedure for ALADIN."""
# unset $LIBRARY_PATH set by modules of dependencies, because it may screw up linking
if 'LIBRARY_PATH' in os.environ:
self.log.debug("Unsetting $LIBRARY_PATH (was: %s)" %
os.environ['LIBRARY_PATH'])
self.orig_library_path = os.environ.pop('LIBRARY_PATH')
# build auxiliary libraries
auxlibs_dir = None
my_gnu = None
if self.toolchain.comp_family() == toolchain.GCC:
my_gnu = 'y' # gfortran
for var in ['CFLAGS', 'CXXFLAGS', 'F90FLAGS', 'FFLAGS']:
flags = os.getenv(var)
env.setvar(var,
"%s -fdefault-real-8 -fdefault-double-8" % flags)
self.log.info("Updated %s to '%s'" % (var, os.getenv(var)))
elif self.toolchain.comp_family() == toolchain.INTELCOMP:
my_gnu = 'i' # icc/ifort
else:
raise EasyBuildError(
"Don't know how to set 'my_gnu' variable in auxlibs build script."
)
self.log.info("my_gnu set to '%s'" % my_gnu)
tmp_installroot = tempfile.mkdtemp(prefix='aladin_auxlibs_')
try:
cwd = os.getcwd()
os.chdir(self.builddir)
builddirs = os.listdir(self.builddir)
auxlibs_dir = [
x for x in builddirs if x.startswith('auxlibs_installer')
][0]
os.chdir(auxlibs_dir)
auto_driver = 'driver_automatic'
for line in fileinput.input(auto_driver,
inplace=1,
backup='.orig.eb'):
line = re.sub(r"^(my_gnu\s*=\s*).*$", r"\1%s" % my_gnu, line)
line = re.sub(r"^(my_r32\s*=\s*).*$", r"\1n",
line) # always 64-bit real precision
line = re.sub(r"^(my_readonly\s*=\s*).*$", r"\1y",
line) # make libs read-only after build
line = re.sub(r"^(my_installroot\s*=\s*).*$",
r"\1%s" % tmp_installroot, line)
sys.stdout.write(line)
run_cmd("./%s" % auto_driver)
os.chdir(cwd)
except OSError as err:
raise EasyBuildError("Failed to build ALADIN: %s", err)
# build gmkpack, update PATH and set GMKROOT
# we build gmkpack here because a config file is generated in the gmkpack isntall path
try:
gmkpack_dir = [x for x in builddirs if x.startswith('gmkpack')][0]
os.chdir(os.path.join(self.builddir, gmkpack_dir))
qa = {
'Do you want to run the configuration file maker assistant now (y) or later [n] ?':
'n',
}
run_cmd_qa("./build_gmkpack", qa)
os.chdir(cwd)
paths = os.getenv('PATH').split(':')
paths.append(os.path.join(self.builddir, gmkpack_dir, 'util'))
env.setvar('PATH', ':'.join(paths))
env.setvar('GMKROOT', os.path.join(self.builddir, gmkpack_dir))
except OSError as err:
raise EasyBuildError("Failed to build gmkpack: %s", err)
# generate gmkpack configuration file
self.conf_file = 'ALADIN_%s' % self.version
self.conf_filepath = os.path.join(self.builddir, 'gmkpack_support',
'arch', '%s.x' % self.conf_file)
try:
if os.path.exists(self.conf_filepath):
os.remove(self.conf_filepath)
self.log.info("Removed existing gmpack config file %s" %
self.conf_filepath)
archdir = os.path.dirname(self.conf_filepath)
if not os.path.exists(archdir):
mkdir(archdir, parents=True)
except OSError as err:
raise EasyBuildError("Failed to remove existing file %s: %s",
self.conf_filepath, err)
mpich = 'n'
known_mpi_libs = [
toolchain.MPICH, toolchain.MPICH2, toolchain.INTELMPI
]
if self.toolchain.options.get(
'usempi',
None) and self.toolchain.mpi_family() in known_mpi_libs:
mpich = 'y'
qpref = 'Please type the ABSOLUTE name of '
qsuff = ', or ignore (environment variables allowed) :'
qsuff2 = ', or ignore : (environment variables allowed) :'
comp_fam = self.toolchain.comp_family()
if comp_fam == toolchain.GCC:
gribdir = 'GNU'
elif comp_fam == toolchain.INTELCOMP:
gribdir = 'INTEL'
else:
raise EasyBuildError(
"Don't know which grib lib dir to use for compiler %s",
comp_fam)
aux_lib_gribex = os.path.join(tmp_installroot, gribdir, 'lib',
'libgribex.a')
aux_lib_ibm = os.path.join(tmp_installroot, gribdir, 'lib',
'libibmdummy.a')
grib_api_lib = os.path.join(get_software_root('grib_api'), 'lib',
'libgrib_api.a')
grib_api_f90_lib = os.path.join(get_software_root('grib_api'), 'lib',
'libgrib_api_f90.a')
grib_api_inc = os.path.join(get_software_root('grib_api'), 'include')
jasperlib = os.path.join(get_software_root('JasPer'), 'lib',
'libjasper.a')
mpilib = os.path.join(os.getenv('MPI_LIB_DIR'),
os.getenv('MPI_LIB_SHARED'))
# netCDF
netcdf = get_software_root('netCDF')
netcdf_fortran = get_software_root('netCDF-Fortran')
if netcdf:
netcdfinc = os.path.join(netcdf, 'include')
if netcdf_fortran:
netcdflib = os.path.join(netcdf_fortran,
get_software_libdir('netCDF-Fortran'),
'libnetcdff.a')
else:
netcdflib = os.path.join(netcdf, get_software_libdir('netCDF'),
'libnetcdff.a')
if not os.path.exists(netcdflib):
raise EasyBuildError("%s does not exist", netcdflib)
else:
raise EasyBuildError("netCDF(-Fortran) not available")
ldpaths = [ldflag[2:] for ldflag in os.getenv('LDFLAGS').split(' ')
] # LDFLAGS have form '-L/path/to'
lapacklibs = []
for lib in os.getenv('LAPACK_STATIC_LIBS').split(','):
libpaths = [os.path.join(ldpath, lib) for ldpath in ldpaths]
lapacklibs.append([
libpath for libpath in libpaths if os.path.exists(libpath)
][0])
lapacklib = ' '.join(lapacklibs)
blaslibs = []
for lib in os.getenv('BLAS_STATIC_LIBS').split(','):
libpaths = [os.path.join(ldpath, lib) for ldpath in ldpaths]
blaslibs.append([
libpath for libpath in libpaths if os.path.exists(libpath)
][0])
blaslib = ' '.join(blaslibs)
qa = {
'Do you want to run the configuration file maker assistant now (y) or later [n] ?':
'y',
'Do you want to setup your configuration file for MPICH (y/n) [n] ?':
mpich,
'Please type the directory name where to find a dummy file mpif.h or ignore :':
os.getenv('MPI_INC_DIR'),
'%sthe library gribex or emos%s' % (qpref, qsuff2):
aux_lib_gribex,
'%sthe library ibm%s' % (qpref, qsuff):
aux_lib_ibm,
'%sthe library grib_api%s' % (qpref, qsuff):
grib_api_lib,
'%sthe library grib_api_f90%s' % (qpref, qsuff):
grib_api_f90_lib,
'%sthe JPEG auxilary library if enabled by Grib_api%s' % (qpref, qsuff2):
jasperlib,
'%sthe library netcdf%s' % (qpref, qsuff):
netcdflib,
'%sthe library lapack%s' % (qpref, qsuff):
lapacklib,
'%sthe library blas%s' % (qpref, qsuff):
blaslib,
'%sthe library mpi%s' % (qpref, qsuff):
mpilib,
'%sa MPI dummy library for serial executions, or ignore :' % qpref:
'',
'Please type the directory name where to find grib_api headers, or ignore :':
grib_api_inc,
'Please type the directory name where to find fortint.h or ignore :':
'',
'Please type the directory name where to find netcdf headers, or ignore :':
netcdfinc,
'Do you want to define CANARI (y/n) [y] ?':
'y',
'Please type the name of the script file used to generate a preprocessed blacklist file, or ignore :':
'',
'Please type the name of the script file used to recover local libraries (gget), or ignore :':
'',
'Please type the options to tune the gnu compilers, or ignore :':
os.getenv('F90FLAGS'),
}
f90_seq = os.getenv('F90_SEQ')
if not f90_seq:
# F90_SEQ is only defined when usempi is enabled
f90_seq = os.getenv('F90')
stdqa = OrderedDict([
(r'Confirm library .* is .*',
'y'), # this one needs to be tried first!
(r'.*fortran 90 compiler name .*\s*:\n\(suggestions\s*: .*\)',
f90_seq),
(r'.*fortran 90 compiler interfaced with .*\s*:\n\(suggestions\s*: .*\)',
f90_seq),
(r'Please type the ABSOLUTE name of .*library.*, or ignore\s*[:]*\s*[\n]*.*',
''),
(r'Please .* to save this draft configuration file :\n.*',
'%s.x' % self.conf_file),
])
no_qa = [
".*ignored.",
]
env.setvar('GMKTMP', self.builddir)
env.setvar('GMKFILE', self.conf_file)
run_cmd_qa("gmkfilemaker", qa, std_qa=stdqa, no_qa=no_qa)
# set environment variables for installation dirs
env.setvar('ROOTPACK', os.path.join(self.installdir, 'rootpack'))
env.setvar('ROOTBIN', os.path.join(self.installdir, 'rootpack'))
env.setvar('HOMEPACK', os.path.join(self.installdir, 'pack'))
env.setvar('HOMEBIN', os.path.join(self.installdir, 'pack'))
# patch config file to include right Fortran compiler flags
regex_subs = [(r"^(FRTFLAGS\s*=.*)$", r"\1 %s" % os.getenv('FFLAGS'))]
apply_regex_substitutions(self.conf_filepath, regex_subs)
def configure_step(self):
"""Custom configuration procedure for OpenCV."""
if 'CMAKE_BUILD_TYPE' not in self.cfg['configopts']:
self.cfg.update('configopts', '-DCMAKE_BUILD_TYPE=Release')
# enable Python support if unspecified and Python is a dependency
if 'BUILD_PYTHON_SUPPORT' not in self.cfg['configopts']:
if get_software_root('Python'):
self.cfg.update('configopts', "-DBUILD_PYTHON_SUPPORT=ON -DBUILD_NEW_PYTHON_SUPPORT=ON")
py_pkgs_path = os.path.join(self.installdir, self.pylibdir)
self.cfg.update('configopts', '-DPYTHON_PACKAGES_PATH=%s' % py_pkgs_path)
else:
self.cfg.update('configopts', "-DBUILD_PYTHON_SUPPORT=OFF -DBUILD_NEW_PYTHON_SUPPORT=OFF")
# enable CUDA support if CUDA is a dependency
if 'WITH_CUDA' not in self.cfg['configopts']:
if get_software_root('CUDA'):
self.cfg.update('configopts', '-DWITH_CUDA=ON')
else:
self.cfg.update('configopts', '-DWITH_CUDA=OFF')
# configure for dependency libraries
for dep in ['JasPer', 'libjpeg-turbo', 'libpng', 'LibTIFF', 'zlib']:
if dep in ['libpng', 'LibTIFF']:
# strip off 'lib'
opt_name = dep[3:].upper()
elif dep == 'libjpeg-turbo':
opt_name = 'JPEG'
else:
opt_name = dep.upper()
shlib_ext = get_shared_lib_ext()
if dep == 'zlib':
lib_file = 'libz.%s' % shlib_ext
else:
lib_file = 'lib%s.%s' % (opt_name.lower(), shlib_ext)
dep_root = get_software_root(dep)
if dep_root:
self.cfg.update('configopts', '-D%s_INCLUDE_DIR=%s' % (opt_name, os.path.join(dep_root, 'include')))
libdir = get_software_libdir(dep, only_one=True)
self.cfg.update('configopts', '-D%s_LIBRARY=%s' % (opt_name, os.path.join(dep_root, libdir, lib_file)))
# configure optimisation for CPU architecture
# see https://github.com/opencv/opencv/wiki/CPU-optimizations-build-options
if self.toolchain.options.get('optarch') and 'CPU_BASELINE' not in self.cfg['configopts']:
optarch = build_option('optarch')
if optarch is None:
# optimize for host arch (let OpenCV detect it)
self.cfg.update('configopts', '-DCPU_BASELINE=DETECT')
elif optarch == OPTARCH_GENERIC:
# optimize for generic x86 architecture (lowest supported by OpenCV is SSE3)
self.cfg.update('configopts', '-DCPU_BASELINE=SSE3')
else:
raise EasyBuildError("Don't know how to configure OpenCV in accordance with --optarch='%s'", optarch)
if self.cfg['cpu_dispatch']:
# using 'NONE' as value is equivalent with disabling the build of fat binaries (which is done by default)
self.cfg.update('configopts', '-DCPU_DISPATCH=%s' % self.cfg['cpu_dispatch'])
# make sure that host CPU supports FP16 (unless -DCPU_BASELINE_DISABLE is already specified)
# Intel Sandy Bridge does not support FP16!
if 'CPU_BASELINE_DISABLE' not in self.cfg['configopts']:
avail_cpu_features = get_cpu_features()
if 'f16c' not in avail_cpu_features:
self.cfg.update('configopts', '-DCPU_BASELINE_DISABLE=FP16')
super(EB_OpenCV, self).configure_step()
def configure_step(self):
"""Custom configuration procedure for binutils: statically link to zlib, configure options."""
libs = ''
if self.toolchain.name == DUMMY_TOOLCHAIN_NAME:
# determine list of 'lib' directories to use rpath for;
# this should 'harden' the resulting binutils to bootstrap GCC
# (no trouble when other libstdc++ is build etc)
libdirs = []
for libdir in ['/usr/lib', '/usr/lib64', '/usr/lib/x86_64-linux-gnu/']:
# also consider /lib, /lib64
alt_libdir = libdir.replace('usr/', '')
if os.path.exists(libdir):
libdirs.append(libdir)
if os.path.exists(alt_libdir) and not os.path.samefile(libdir, alt_libdir):
libdirs.append(alt_libdir)
elif os.path.exists(alt_libdir):
libdirs.append(alt_libdir)
libs += ' '.join('-Wl,-rpath=%s' % libdir for libdir in libdirs)
# statically link to zlib if it is a (build) dependency
zlibroot = get_software_root('zlib')
if zlibroot:
self.cfg.update('configopts', '--with-system-zlib')
libz_path = os.path.join(zlibroot, get_software_libdir('zlib'), 'libz.a')
# for recent binutils versions, we need to override ZLIB in Makefile.in of components
if LooseVersion(self.version) >= LooseVersion('2.26'):
regex_subs = [
(r"^(ZLIB\s*=\s*).*$", r"\1%s" % libz_path),
(r"^(ZLIBINC\s*=\s*).*$", r"\1-I%s" % os.path.join(zlibroot, 'include')),
]
for makefile in glob.glob(os.path.join(self.cfg['start_dir'], '*', 'Makefile.in')):
apply_regex_substitutions(makefile, regex_subs)
# for older versions, injecting the path to the static libz library into $LIBS works
else:
libs += ' ' + libz_path
self.cfg.update('preconfigopts', "env LIBS='%s'" % libs)
self.cfg.update('prebuildopts', "env LIBS='%s'" % libs)
# use correct sysroot, to make sure 'ld' also considers system libraries
self.cfg.update('configopts', '--with-sysroot=/')
# build both static and shared libraries for recent binutils versions (default is only static)
if LooseVersion(self.version) > LooseVersion('2.24'):
self.cfg.update('configopts', "--enable-shared --enable-static")
# enable gold linker with plugin support, use ld as default linker (for recent versions of binutils)
if LooseVersion(self.version) > LooseVersion('2.24'):
self.cfg.update('configopts', "--enable-gold --enable-plugins --enable-ld=default")
# complete configuration with configure_method of parent
super(EB_binutils, self).configure_step()
if self.cfg['install_libiberty']:
cflags = os.getenv('CFLAGS')
if cflags:
self.cfg.update('buildopts', 'CFLAGS="$CFLAGS -fPIC"')
else:
# if $CFLAGS is not defined, make sure we retain "-g -O2",
# since not specifying any optimization level implies -O0...
self.cfg.update('buildopts', 'CFLAGS="-g -O2 -fPIC"')
