def set_as_default(self, module_folder_path, module_version):
"""
Create a symlink named 'default' inside the package's module folder in order to set the default module version
:param module_folder_path: module folder path, e.g. $HOME/easybuild/modules/all/Bison
:param module_version: module version, e.g. 3.0.4
"""
default_filepath = os.path.join(module_folder_path, 'default')
if os.path.islink(default_filepath):
link_target = resolve_path(default_filepath)
remove_file(default_filepath)
self.log.info("Removed default version marking from %s.", link_target)
elif os.path.exists(default_filepath):
raise EasyBuildError('Found an unexpected file named default in dir %s' % module_folder_path)
symlink(module_version + self.MODULE_FILE_EXTENSION, default_filepath, use_abspath_source=False)
self.log.info("Module default version file written to point to %s", default_filepath)
def set_as_default(self, module_folder_path, module_version):
"""
Create a symlink named 'default' inside the package's module folder in order to set the default module version
:param module_folder_path: module folder path, e.g. $HOME/easybuild/modules/all/Bison
:param module_version: module version, e.g. 3.0.4
"""
default_filepath = os.path.join(module_folder_path, 'default')
if os.path.islink(default_filepath):
link_target = resolve_path(default_filepath)
remove_file(default_filepath)
self.log.info("Removed default version marking from %s.", link_target)
elif os.path.exists(default_filepath):
raise EasyBuildError('Found an unexpected file named default in dir %s' % module_folder_path)
symlink(module_version + self.MODULE_FILE_EXTENSION, default_filepath, use_abspath_source=False)
self.log.info("Module default version file written to point to %s", default_filepath)
def get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None):
"""
Return a list of absolute paths where the specified subdir can be found, determined by the PYTHONPATH
"""
paths = []
# primary search path is robot path
path_list = []
if isinstance(robot_path, list):
path_list = robot_path[:]
elif robot_path is not None:
path_list = [robot_path]
# consider Python search path, e.g. setuptools install path for easyconfigs
path_list.extend(sys.path)
# figure out installation prefix, e.g. distutils install path for easyconfigs
eb_path = which('eb')
if eb_path is None:
_log.warning(
"'eb' not found in $PATH, failed to determine installation prefix")
else:
# real location to 'eb' should be <install_prefix>/bin/eb
eb_path = resolve_path(eb_path)
install_prefix = os.path.dirname(os.path.dirname(eb_path))
path_list.append(install_prefix)
_log.debug("Also considering installation prefix %s..." %
install_prefix)
# look for desired subdirs
for path in path_list:
path = os.path.join(path, "easybuild", subdir)
_log.debug("Checking for easybuild/%s at %s" % (subdir, path))
try:
if os.path.exists(path):
paths.append(os.path.abspath(path))
_log.debug("Added %s to list of paths for easybuild/%s" %
(path, subdir))
except OSError as err:
raise EasyBuildError(str(err))
return paths
def extract_compiler_version(compiler_name):
"""Extract compiler version for provided compiler_name."""
# look for 3-4 digit version number, surrounded by spaces
# examples:
# gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
# Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 15.0.1.133 Build 20141023
version_regex = re.compile(r'\s([0-9]+(?:\.[0-9]+){1,3})\s', re.M)
if compiler_name == 'gcc':
out, _ = run_cmd("gcc --version", simple=False)
res = version_regex.search(out)
if res is None:
raise EasyBuildError("Could not extract GCC version from %s", out)
compiler_version = res.group(1)
elif compiler_name in ['icc', 'ifort']:
# A fully resolved icc/ifort (without symlinks) includes the release version in the path
# e.g. .../composer_xe_2015.3.187/bin/intel64/icc
# Match the last incidence of _ since we don't know what might be in the path, then split it up on /
compiler_path = which(compiler_name)
if compiler_path:
compiler_version = resolve_path(compiler_path).split(
'_')[-1].split('/')[0]
else:
raise EasyBuildError("Compiler command '%s' not found",
compiler_name)
# Check what we have looks like a version number (the regex we use requires spaces around the version number)
if version_regex.search(' ' + compiler_version + ' ') is None:
error_msg = "Derived Intel compiler version '%s' doesn't look correct, " % compiler_version
error_msg += "is compiler installed in a path like '.../composer_xe_2015.3.187/bin/intel64/icc'?"
raise EasyBuildError(error_msg)
else:
raise EasyBuildError("Unknown compiler %s", compiler_name)
if compiler_version:
_log.debug("Extracted compiler version '%s' for %s", compiler_version,
compiler_name)
else:
raise EasyBuildError(
"Failed to extract compiler version for %s using regex pattern '%s' from: %s",
compiler_name, version_regex.pattern, out)
return compiler_version
def get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None):
"""
Return a list of absolute paths where the specified subdir can be found, determined by the PYTHONPATH
"""
paths = []
# primary search path is robot path
path_list = []
if isinstance(robot_path, list):
path_list = robot_path[:]
elif robot_path is not None:
path_list = [robot_path]
# consider Python search path, e.g. setuptools install path for easyconfigs
path_list.extend(sys.path)
# figure out installation prefix, e.g. distutils install path for easyconfigs
eb_path = which('eb')
if eb_path is None:
_log.warning("'eb' not found in $PATH, failed to determine installation prefix")
else:
# real location to 'eb' should be <install_prefix>/bin/eb
eb_path = resolve_path(eb_path)
install_prefix = os.path.dirname(os.path.dirname(eb_path))
path_list.append(install_prefix)
_log.debug("Also considering installation prefix %s..." % install_prefix)
# look for desired subdirs
for path in path_list:
path = os.path.join(path, "easybuild", subdir)
_log.debug("Checking for easybuild/%s at %s" % (subdir, path))
try:
if os.path.exists(path):
paths.append(os.path.abspath(path))
_log.debug("Added %s to list of paths for easybuild/%s" % (path, subdir))
except OSError as err:
raise EasyBuildError(str(err))
return paths
def extract_compiler_version(compiler_name):
"""Extract compiler version for provided compiler_name."""
# look for 3-4 digit version number, surrounded by spaces
# examples:
# gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
# Intel(R) C Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 15.0.1.133 Build 20141023
version_regex = re.compile(r'\s([0-9]+(?:\.[0-9]+){1,3})\s', re.M)
if compiler_name == 'gcc':
out, _ = run_cmd("gcc --version", simple=False)
res = version_regex.search(out)
if res is None:
raise EasyBuildError("Could not extract GCC version from %s", out)
compiler_version = res.group(1)
elif compiler_name in ['icc', 'ifort']:
# A fully resolved icc/ifort (without symlinks) includes the release version in the path
# e.g. .../composer_xe_2015.3.187/bin/intel64/icc
# Match the last incidence of _ since we don't know what might be in the path, then split it up on /
compiler_path = which(compiler_name)
if compiler_path:
compiler_version = resolve_path(compiler_path).split('_')[-1].split('/')[0]
else:
raise EasyBuildError("Compiler command '%s' not found", compiler_name)
# Check what we have looks like a version number (the regex we use requires spaces around the version number)
if version_regex.search(' ' + compiler_version + ' ') is None:
error_msg = "Derived Intel compiler version '%s' doesn't look correct, " % compiler_version
error_msg += "is compiler installed in a path like '.../composer_xe_2015.3.187/bin/intel64/icc'?"
raise EasyBuildError(error_msg)
else:
raise EasyBuildError("Unknown compiler %s", compiler_name)
if compiler_version:
_log.debug("Extracted compiler version '%s' for %s", compiler_version, compiler_name)
else:
raise EasyBuildError("Failed to extract compiler version for %s using regex pattern '%s' from: %s",
compiler_name, version_regex.pattern, out)
return compiler_version
def build_step(self):
"""Custom build procedure for TensorFlow."""
# pre-create target installation directory
mkdir(os.path.join(self.installdir, self.pylibdir), parents=True)
binutils_root = get_software_root('binutils')
if binutils_root:
binutils_bin = os.path.join(binutils_root, 'bin')
else:
raise EasyBuildError(
"Failed to determine installation prefix for binutils")
gcc_root = get_software_root('GCCcore') or get_software_root('GCC')
if gcc_root:
gcc_lib64 = os.path.join(gcc_root, 'lib64')
gcc_ver = get_software_version('GCCcore') or get_software_version(
'GCC')
# figure out location of GCC include files
res = glob.glob(
os.path.join(gcc_root, 'lib', 'gcc', '*', gcc_ver, 'include'))
if res and len(res) == 1:
gcc_lib_inc = res[0]
else:
raise EasyBuildError(
"Failed to pinpoint location of GCC include files: %s",
res)
# make sure include-fixed directory is where we expect it to be
gcc_lib_inc_fixed = os.path.join(os.path.dirname(gcc_lib_inc),
'include-fixed')
if not os.path.exists(gcc_lib_inc_fixed):
raise EasyBuildError("Derived directory %s does not exist",
gcc_lib_inc_fixed)
# also check on location of include/c++/<gcc version> directory
gcc_cplusplus_inc = os.path.join(gcc_root, 'include', 'c++',
gcc_ver)
if not os.path.exists(gcc_cplusplus_inc):
raise EasyBuildError("Derived directory %s does not exist",
gcc_cplusplus_inc)
else:
raise EasyBuildError(
"Failed to determine installation prefix for GCC")
inc_paths = [gcc_lib_inc, gcc_lib_inc_fixed, gcc_cplusplus_inc]
lib_paths = [gcc_lib64]
cuda_root = get_software_root('CUDA')
if cuda_root:
inc_paths.append(os.path.join(cuda_root, 'include'))
lib_paths.append(os.path.join(cuda_root, 'lib64'))
# fix hardcoded locations of compilers & tools
cxx_inc_dir_lines = '\n'.join(r'cxx_builtin_include_directory: "%s"' %
resolve_path(p) for p in inc_paths)
cxx_inc_dir_lines_no_resolv_path = '\n'.join(
r'cxx_builtin_include_directory: "%s"' % p for p in inc_paths)
regex_subs = [
(r'-B/usr/bin/',
'-B%s/ %s' % (binutils_bin, ' '.join('-L%s/' % p
for p in lib_paths))),
(r'(cxx_builtin_include_directory:).*', ''),
(r'^toolchain {', 'toolchain {\n' + cxx_inc_dir_lines + '\n' +
cxx_inc_dir_lines_no_resolv_path),
]
for tool in [
'ar', 'cpp', 'dwp', 'gcc', 'gcov', 'ld', 'nm', 'objcopy',
'objdump', 'strip'
]:
path = which(tool)
if path:
regex_subs.append((os.path.join('/usr', 'bin', tool), path))
else:
raise EasyBuildError("Failed to determine path to '%s'", tool)
# -fPIE/-pie and -fPIC are not compatible, so patch out hardcoded occurences of -fPIE/-pie if -fPIC is used
if self.toolchain.options.get('pic', None):
regex_subs.extend([('-fPIE', '-fPIC'), ('"-pie"', '"-fPIC"')])
# patch all CROSSTOOL* scripts to fix hardcoding of locations of binutils/GCC binaries
for path, dirnames, filenames in os.walk(os.getcwd()):
for filename in filenames:
if filename.startswith('CROSSTOOL'):
full_path = os.path.join(path, filename)
self.log.info("Patching %s", full_path)
apply_regex_substitutions(full_path, regex_subs)
tmpdir = tempfile.mkdtemp(suffix='-bazel-build')
user_root_tmpdir = tempfile.mkdtemp(suffix='-user_root')
# compose "bazel build" command with all its options...
cmd = [
self.cfg['prebuildopts'], 'bazel',
'--output_base=%s' % tmpdir,
'--install_base=%s' % os.path.join(tmpdir, 'inst_base'),
'--output_user_root=%s' % user_root_tmpdir, 'build'
]
# build with optimization enabled
# cfr. https://docs.bazel.build/versions/master/user-manual.html#flag--compilation_mode
cmd.append('--compilation_mode=opt')
# select 'opt' config section (this is *not* the same as --compilation_mode=opt!)
# https://docs.bazel.build/versions/master/user-manual.html#flag--config
cmd.append('--config=opt')
# make Bazel print full command line + make it verbose on failures
# https://docs.bazel.build/versions/master/user-manual.html#flag--subcommands
# https://docs.bazel.build/versions/master/user-manual.html#flag--verbose_failures
cmd.extend(['--subcommands', '--verbose_failures'])
# limit the number of parallel jobs running simultaneously (useful on KNL)...
cmd.append('--jobs=%s' % self.cfg['parallel'])
if self.toolchain.options.get('pic', None):
cmd.append('--copt="-fPIC"')
# include install location of Python packages in $PYTHONPATH,
# and specify that value of $PYTHONPATH should be passed down into Bazel build environment;
# this is required to make sure that Python packages included as extensions are found at build time;
# see also https://github.com/tensorflow/tensorflow/issues/22395
pythonpath = os.getenv('PYTHONPATH', '')
env.setvar(
'PYTHONPATH',
os.pathsep.join(
[os.path.join(self.installdir, self.pylibdir), pythonpath]))
cmd.append('--action_env=PYTHONPATH')
# Also export $EBPYTHONPREFIXES to handle the multi-deps python setup
# See https://github.com/easybuilders/easybuild-easyblocks/pull/1664
if 'EBPYTHONPREFIXES' in os.environ:
cmd.append('--action_env=EBPYTHONPREFIXES')
# use same configuration for both host and target programs, which can speed up the build
# only done when optarch is enabled, since this implicitely assumes that host and target platform are the same
# see https://docs.bazel.build/versions/master/guide.html#configurations
if self.toolchain.options.get('optarch'):
cmd.append('--distinct_host_configuration=false')
cmd.append(self.cfg['buildopts'])
# TF 2 (final) sets this in configure
if LooseVersion(self.version) < LooseVersion('2.0'):
if cuda_root:
cmd.append('--config=cuda')
# if mkl-dnn is listed as a dependency it is used. Otherwise downloaded if with_mkl_dnn is true
mkl_root = get_software_root('mkl-dnn')
if mkl_root:
cmd.extend(['--config=mkl'])
cmd.insert(0, "export TF_MKL_DOWNLOAD=0 &&")
cmd.insert(0, "export TF_MKL_ROOT=%s &&" % mkl_root)
elif self.cfg['with_mkl_dnn']:
# this makes TensorFlow use mkl-dnn (cfr. https://github.com/01org/mkl-dnn)
cmd.extend(['--config=mkl'])
cmd.insert(0, "export TF_MKL_DOWNLOAD=1 && ")
# specify target of the build command as last argument
cmd.append('//tensorflow/tools/pip_package:build_pip_package')
run_cmd(' '.join(cmd), log_all=True, simple=True, log_ok=True)
# run generated 'build_pip_package' script to build the .whl
cmd = "bazel-bin/tensorflow/tools/pip_package/build_pip_package %s" % self.builddir
run_cmd(cmd, log_all=True, simple=True, log_ok=True)
def get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR, robot_path=None):
"""
Return a list of absolute paths where the specified subdir can be found, determined by the PYTHONPATH
"""
paths = []
# primary search path is robot path
path_list = []
if isinstance(robot_path, list):
path_list = robot_path[:]
elif robot_path is not None:
path_list = [robot_path]
# consider Python search path, e.g. setuptools install path for easyconfigs
path_list.extend(sys.path)
# figure out installation prefix, e.g. distutils install path for easyconfigs
# prefer using path specified in $EB_SCRIPT_PATH (if defined), which is set by 'eb' wrapper script
eb_path = os.getenv('EB_SCRIPT_PATH')
if eb_path is None:
# try to determine location of 'eb' script via $PATH, as fallback mechanism
eb_path = which('eb')
_log.info("Location to 'eb' script (found via $PATH): %s", eb_path)
else:
_log.info("Found location to 'eb' script via $EB_SCRIPT_PATH: %s",
eb_path)
if eb_path is None:
warning_msg = "'eb' not found in $PATH, failed to determine installation prefix!"
_log.warning(warning_msg)
print_warning(warning_msg)
else:
# eb_path is location to 'eb' wrapper script, e.g. <install_prefix>/bin/eb
# so installation prefix is usually two levels up
install_prefix = os.path.dirname(os.path.dirname(eb_path))
# only consider resolved path to 'eb' script if desired subdir is not found relative to 'eb' script location
if os.path.exists(os.path.join(install_prefix, 'easybuild', subdir)):
path_list.append(install_prefix)
_log.info(
"Also considering installation prefix %s (determined via path to 'eb' script)...",
install_prefix)
else:
_log.info("Not considering %s (no easybuild/%s subdir found)",
install_prefix, subdir)
# also consider fully resolved location to 'eb' wrapper
# see https://github.com/easybuilders/easybuild-framework/pull/2248
resolved_eb_path = resolve_path(eb_path)
if eb_path != resolved_eb_path:
install_prefix = os.path.dirname(
os.path.dirname(resolved_eb_path))
path_list.append(install_prefix)
_log.info(
"Also considering installation prefix %s (via resolved path to 'eb')...",
install_prefix)
# look for desired subdirs
for path in path_list:
path = os.path.join(path, "easybuild", subdir)
_log.debug("Checking for easybuild/%s at %s" % (subdir, path))
try:
if os.path.exists(path):
paths.append(os.path.abspath(path))
_log.debug("Added %s to list of paths for easybuild/%s" %
(path, subdir))
except OSError as err:
raise EasyBuildError(str(err))
return paths
def prepare_step(self, *args, **kwargs):
"""Do compiler appropriate prepare step, determine system compiler version and prefix."""
if self.cfg['generate_standalone_module']:
if self.cfg['name'] in ['GCC', 'GCCcore']:
EB_GCC.prepare_step(self, *args, **kwargs)
elif self.cfg['name'] in ['icc']:
EB_icc.prepare_step(self, *args, **kwargs)
elif self.cfg['name'] in ['ifort']:
EB_ifort.prepare_step(self, *args, **kwargs)
else:
raise EasyBuildError("I don't know how to do the prepare_step for %s", self.cfg['name'])
else:
Bundle.prepare_step(self, *args, **kwargs)
# Determine compiler path (real path, with resolved symlinks)
compiler_name = self.cfg['name'].lower()
if compiler_name == 'gcccore':
compiler_name = 'gcc'
path_to_compiler = which(compiler_name)
if path_to_compiler:
path_to_compiler = resolve_path(path_to_compiler)
self.log.info("Found path to compiler '%s' (with symlinks resolved): %s", compiler_name, path_to_compiler)
else:
raise EasyBuildError("%s not found in $PATH", compiler_name)
# Determine compiler version
self.compiler_version = extract_compiler_version(compiler_name)
# Determine installation prefix
if compiler_name == 'gcc':
# strip off 'bin/gcc'
self.compiler_prefix = os.path.dirname(os.path.dirname(path_to_compiler))
elif compiler_name in ['icc', 'ifort']:
intelvars_fn = path_to_compiler + 'vars.sh'
if os.path.isfile(intelvars_fn):
self.log.debug("Trying to determine compiler install prefix from %s", intelvars_fn)
intelvars_txt = read_file(intelvars_fn)
prod_dir_regex = re.compile(r'^PROD_DIR=(.*)$', re.M)
res = prod_dir_regex.search(intelvars_txt)
if res:
self.compiler_prefix = res.group(1)
else:
raise EasyBuildError("Failed to determine %s installation prefix from %s",
compiler_name, intelvars_fn)
else:
# strip off 'bin/intel*/icc'
self.compiler_prefix = os.path.dirname(os.path.dirname(os.path.dirname(path_to_compiler)))
# For versions 2016+ of Intel compilers they changed the installation path so must shave off 2 more
# directories from result of the above
if LooseVersion(self.compiler_version) >= LooseVersion('2016'):
self.compiler_prefix = os.path.dirname(os.path.dirname(self.compiler_prefix))
else:
raise EasyBuildError("Unknown system compiler %s" % self.cfg['name'])
if not os.path.exists(self.compiler_prefix):
raise EasyBuildError("Path derived for system compiler (%s) does not exist: %s!",
compiler_name, self.compiler_prefix)
self.log.debug("Derived version/install prefix for system compiler %s: %s, %s",
compiler_name, self.compiler_version, self.compiler_prefix)
# If EasyConfig specified "real" version (not 'system' which means 'derive automatically'), check it
if self.cfg['version'] == 'system':
self.log.info("Found specified version '%s', going with derived compiler version '%s'",
self.cfg['version'], self.compiler_version)
elif self.cfg['version'] != self.compiler_version:
raise EasyBuildError("Specified version (%s) does not match version reported by compiler (%s)" %
(self.cfg['version'], self.compiler_version))
def prepare_step(self, *args, **kwargs):
"""Do compiler appropriate prepare step, determine system compiler version and prefix."""
if self.cfg['generate_standalone_module']:
if self.cfg['name'] in ['GCC', 'GCCcore']:
EB_GCC.prepare_step(self, *args, **kwargs)
elif self.cfg['name'] in ['icc']:
EB_icc.prepare_step(self, *args, **kwargs)
elif self.cfg['name'] in ['ifort']:
EB_ifort.prepare_step(self, *args, **kwargs)
else:
raise EasyBuildError(
"I don't know how to do the prepare_step for %s",
self.cfg['name'])
else:
Bundle.prepare_step(self, *args, **kwargs)
# Determine compiler path (real path, with resolved symlinks)
compiler_name = self.cfg['name'].lower()
if compiler_name == 'gcccore':
compiler_name = 'gcc'
path_to_compiler = which(compiler_name)
if path_to_compiler:
path_to_compiler = resolve_path(path_to_compiler)
self.log.info(
"Found path to compiler '%s' (with symlinks resolved): %s",
compiler_name, path_to_compiler)
else:
raise EasyBuildError("%s not found in $PATH", compiler_name)
# Determine compiler version
self.compiler_version = extract_compiler_version(compiler_name)
# Determine installation prefix
if compiler_name == 'gcc':
# strip off 'bin/gcc'
self.compiler_prefix = os.path.dirname(
os.path.dirname(path_to_compiler))
elif compiler_name in ['icc', 'ifort']:
intelvars_fn = path_to_compiler + 'vars.sh'
if os.path.isfile(intelvars_fn):
self.log.debug(
"Trying to determine compiler install prefix from %s",
intelvars_fn)
intelvars_txt = read_file(intelvars_fn)
prod_dir_regex = re.compile(r'^PROD_DIR=(.*)$', re.M)
res = prod_dir_regex.search(intelvars_txt)
if res:
self.compiler_prefix = res.group(1)
else:
raise EasyBuildError(
"Failed to determine %s installation prefix from %s",
compiler_name, intelvars_fn)
else:
# strip off 'bin/intel*/icc'
self.compiler_prefix = os.path.dirname(
os.path.dirname(os.path.dirname(path_to_compiler)))
# For versions 2016+ of Intel compilers they changed the installation path so must shave off 2 more
# directories from result of the above
if LooseVersion(self.compiler_version) >= LooseVersion('2016'):
self.compiler_prefix = os.path.dirname(
os.path.dirname(self.compiler_prefix))
else:
raise EasyBuildError("Unknown system compiler %s" %
self.cfg['name'])
if not os.path.exists(self.compiler_prefix):
raise EasyBuildError(
"Path derived for system compiler (%s) does not exist: %s!",
compiler_name, self.compiler_prefix)
self.log.debug(
"Derived version/install prefix for system compiler %s: %s, %s",
compiler_name, self.compiler_version, self.compiler_prefix)
# If EasyConfig specified "real" version (not 'system' which means 'derive automatically'), check it
if self.cfg['version'] == 'system':
self.log.info(
"Found specified version '%s', going with derived compiler version '%s'",
self.cfg['version'], self.compiler_version)
elif self.cfg['version'] != self.compiler_version:
raise EasyBuildError(
"Specified version (%s) does not match version reported by compiler (%s)"
% (self.cfg['version'], self.compiler_version))
def build_step(self):
"""Custom build procedure for TensorFlow."""
# pre-create target installation directory
mkdir(os.path.join(self.installdir, self.pylibdir), parents=True)
binutils_root = get_software_root('binutils')
if binutils_root:
binutils_bin = os.path.join(binutils_root, 'bin')
else:
raise EasyBuildError("Failed to determine installation prefix for binutils")
gcc_root = get_software_root('GCCcore') or get_software_root('GCC')
if gcc_root:
gcc_lib64 = os.path.join(gcc_root, 'lib64')
gcc_ver = get_software_version('GCCcore') or get_software_version('GCC')
# figure out location of GCC include files
res = glob.glob(os.path.join(gcc_root, 'lib', 'gcc', '*', gcc_ver, 'include'))
if res and len(res) == 1:
gcc_lib_inc = res[0]
else:
raise EasyBuildError("Failed to pinpoint location of GCC include files: %s", res)
# make sure include-fixed directory is where we expect it to be
gcc_lib_inc_fixed = os.path.join(os.path.dirname(gcc_lib_inc), 'include-fixed')
if not os.path.exists(gcc_lib_inc_fixed):
raise EasyBuildError("Derived directory %s does not exist", gcc_lib_inc_fixed)
# also check on location of include/c++/<gcc version> directory
gcc_cplusplus_inc = os.path.join(gcc_root, 'include', 'c++', gcc_ver)
if not os.path.exists(gcc_cplusplus_inc):
raise EasyBuildError("Derived directory %s does not exist", gcc_cplusplus_inc)
else:
raise EasyBuildError("Failed to determine installation prefix for GCC")
inc_paths = [gcc_lib_inc, gcc_lib_inc_fixed, gcc_cplusplus_inc]
lib_paths = [gcc_lib64]
cuda_root = get_software_root('CUDA')
if cuda_root:
inc_paths.append(os.path.join(cuda_root, 'include'))
lib_paths.append(os.path.join(cuda_root, 'lib64'))
# fix hardcoded locations of compilers & tools
cxx_inc_dir_lines = '\n'.join(r'cxx_builtin_include_directory: "%s"' % resolve_path(p) for p in inc_paths)
cxx_inc_dir_lines_no_resolv_path = '\n'.join(r'cxx_builtin_include_directory: "%s"' % p for p in inc_paths)
regex_subs = [
(r'-B/usr/bin/', '-B%s/ %s' % (binutils_bin, ' '.join('-L%s/' % p for p in lib_paths))),
(r'(cxx_builtin_include_directory:).*', ''),
(r'^toolchain {', 'toolchain {\n' + cxx_inc_dir_lines + '\n' + cxx_inc_dir_lines_no_resolv_path),
]
for tool in ['ar', 'cpp', 'dwp', 'gcc', 'gcov', 'ld', 'nm', 'objcopy', 'objdump', 'strip']:
path = which(tool)
if path:
regex_subs.append((os.path.join('/usr', 'bin', tool), path))
else:
raise EasyBuildError("Failed to determine path to '%s'", tool)
# -fPIE/-pie and -fPIC are not compatible, so patch out hardcoded occurences of -fPIE/-pie if -fPIC is used
if self.toolchain.options.get('pic', None):
regex_subs.extend([('-fPIE', '-fPIC'), ('"-pie"', '"-fPIC"')])
# patch all CROSSTOOL* scripts to fix hardcoding of locations of binutils/GCC binaries
for path, dirnames, filenames in os.walk(self.start_dir):
for filename in filenames:
if filename.startswith('CROSSTOOL'):
full_path = os.path.join(path, filename)
self.log.info("Patching %s", full_path)
apply_regex_substitutions(full_path, regex_subs)
tmpdir = tempfile.mkdtemp(suffix='-bazel-build')
# compose "bazel build" command with all its options...
cmd = [self.cfg['prebuildopts'], 'bazel', '--output_base=%s' % tmpdir, 'build']
# build with optimization enabled
# cfr. https://docs.bazel.build/versions/master/user-manual.html#flag--compilation_mode
cmd.append('--compilation_mode=opt')
# select 'opt' config section (this is *not* the same as --compilation_mode=opt!)
# https://docs.bazel.build/versions/master/user-manual.html#flag--config
cmd.append('--config=opt')
# make Bazel print full command line + make it verbose on failures
# https://docs.bazel.build/versions/master/user-manual.html#flag--subcommands
# https://docs.bazel.build/versions/master/user-manual.html#flag--verbose_failures
cmd.extend(['--subcommands', '--verbose_failures'])
# limit the number of parallel jobs running simultaneously (useful on KNL)...
cmd.append('--jobs=%s' % self.cfg['parallel'])
if self.toolchain.options.get('pic', None):
cmd.append('--copt="-fPIC"')
cmd.append(self.cfg['buildopts'])
if cuda_root:
cmd.append('--config=cuda')
# enable mkl-dnn by default, but only if cuDNN is not listed as dependency
if self.cfg['with_mkl_dnn'] is None and get_software_root('cuDNN') is None:
self.log.info("Enabling use of mkl-dnn since cuDNN is not listed as dependency")
self.cfg['with_mkl_dnn'] = True
# if mkl-dnn is listed as a dependency it is used. Otherwise downloaded if with_mkl_dnn is true
mkl_root = get_software_root('mkl-dnn')
if mkl_root:
cmd.extend(['--config=mkl'])
cmd.insert(0, 'export TF_MKL_DOWNLOAD=0 &&' )
cmd.insert(0, 'export TF_MKL_ROOT=%s &&' % mkl_root)
elif self.cfg['with_mkl_dnn']:
# this makes TensorFlow use mkl-dnn (cfr. https://github.com/01org/mkl-dnn)
cmd.extend(['--config=mkl'])
cmd.insert(0, 'export TF_MKL_DOWNLOAD=1 &&' )
# specify target of the build command as last argument
cmd.append('//tensorflow/tools/pip_package:build_pip_package')
run_cmd(' '.join(cmd), log_all=True, simple=True, log_ok=True)
# run generated 'build_pip_package' script to build the .whl
cmd = "bazel-bin/tensorflow/tools/pip_package/build_pip_package %s" % self.builddir
run_cmd(cmd, log_all=True, simple=True, log_ok=True)
def make_module_step(self, fake=False):
"""Install .modulerc file."""
modfile_path = self.module_generator.get_module_filepath(fake=fake)
modulerc = os.path.join(os.path.dirname(modfile_path),
self.module_generator.DOT_MODULERC)
deps = self.cfg['dependencies']
if len(deps) != 1:
raise EasyBuildError(
"There should be exactly one dependency specified, found %d",
len(deps))
# names should match
if self.name != deps[0]['name']:
raise EasyBuildError(
"Name does not match dependency name: %s vs %s", self.name,
deps[0]['name'])
# ensure version to alias to is a prefix of the version of the dependency
if not deps[0]['version'].startswith(
self.version) and not self.version == "default":
raise EasyBuildError(
"Version is not 'default' and not a prefix of dependency version: %s vs %s",
self.version, deps[0]['version'])
alias_modname = deps[0]['short_mod_name']
self.log.info("Adding module version alias for %s to %s",
alias_modname, modulerc)
# add symlink to wrapped module file when generating .modulerc in temporary directory (done during sanity check)
# this is strictly required for Lmod 6.x, for which .modulerc and wrapped module file must be in same location
if fake:
wrapped_mod_path = self.modules_tool.modulefile_path(alias_modname)
wrapped_mod_filename = os.path.basename(wrapped_mod_path)
target = os.path.join(os.path.dirname(modulerc),
wrapped_mod_filename)
mkdir(os.path.dirname(target), parents=True)
symlink(wrapped_mod_path, target)
module_version_specs = {
'modname': alias_modname,
'sym_version': self.version,
'version': deps[0]['version'],
}
self.module_generator.modulerc(module_version=module_version_specs,
filepath=modulerc)
if not fake:
print_msg("updated .modulerc file at %s" % modulerc, log=self.log)
# symlink .modulerc in other locations (unless they're already linked)
mod_symlink_dirs = ActiveMNS().det_module_symlink_paths(self.cfg)
mod_subdir = os.path.dirname(ActiveMNS().det_full_module_name(
self.cfg))
mod_install_path = install_path('mod')
modulerc_filename = os.path.basename(modulerc)
for mod_symlink_dir in mod_symlink_dirs:
modulerc_symlink = os.path.join(mod_install_path,
mod_symlink_dir, mod_subdir,
modulerc_filename)
if os.path.islink(modulerc_symlink):
if resolve_path(modulerc_symlink) == resolve_path(
modulerc):
print_msg("symlink %s to %s already exists",
modulerc_symlink, modulerc)
else:
raise EasyBuildError(
"%s exists but is not a symlink to %s",
modulerc_symlink, modulerc)
else:
# Make sure folder exists
mkdir(os.path.dirname(modulerc_symlink), parents=True)
symlink(modulerc, modulerc_symlink)
print_msg("created symlink %s to .modulerc file at %s",
modulerc_symlink,
modulerc,
log=self.log)
modpath = self.module_generator.get_modules_path(fake=fake)
self.invalidate_module_caches(modpath)
return modpath
def prepare_step(self, *args, **kwargs):
"""Load all dependencies, determine system MPI version, prefix and any associated envvars."""
# Do the bundle prepare step to ensure any deps are loaded (no need to worry about licences for Intel MPI)
Bundle.prepare_step(self, *args, **kwargs)
# Prepare additional parameters: determine system MPI version, prefix and any associated envvars.
mpi_name = self.cfg['name'].lower()
# Determine MPI wrapper path (real path, with resolved symlinks) to ensure it exists
if mpi_name == 'impi':
# For impi the version information is only found in *some* of the wrappers it ships, in particular it is
# not in mpicc
mpi_c_wrapper = 'mpiicc'
path_to_mpi_c_wrapper = which(mpi_c_wrapper)
if not path_to_mpi_c_wrapper:
mpi_c_wrapper = 'mpigcc'
path_to_mpi_c_wrapper = which(mpi_c_wrapper)
if not path_to_mpi_c_wrapper:
raise EasyBuildError(
"Could not find suitable MPI wrapper to extract version for impi"
)
else:
mpi_c_wrapper = 'mpicc'
path_to_mpi_c_wrapper = which(mpi_c_wrapper)
if path_to_mpi_c_wrapper:
path_to_mpi_c_wrapper = resolve_path(path_to_mpi_c_wrapper)
self.log.info(
"Found path to MPI implementation '%s' %s compiler (with symlinks resolved): %s",
mpi_name, mpi_c_wrapper, path_to_mpi_c_wrapper)
else:
raise EasyBuildError("%s not found in $PATH", mpi_c_wrapper)
# Determine MPI version, installation prefix and underlying compiler
if mpi_name in ('openmpi', 'spectrummpi'):
# Spectrum MPI is based on Open MPI so is also covered by this logic
output_of_ompi_info, _ = run_cmd("ompi_info", simple=False)
# Extract the version of the MPI implementation
if mpi_name == 'spectrummpi':
mpi_version_string = 'Spectrum MPI'
else:
mpi_version_string = 'Open MPI'
self.mpi_version = self.extract_ompi_setting(
mpi_version_string, output_of_ompi_info)
# Extract the installation prefix
self.mpi_prefix = self.extract_ompi_setting(
"Prefix", output_of_ompi_info)
# Extract any OpenMPI environment variables in the current environment and ensure they are added to the
# final module
self.mpi_env_vars = dict((key, value)
for key, value in os.environ.items()
if key.startswith('OMPI_'))
# Extract the C compiler used underneath the MPI implementation, check for the definition of OMPI_MPICC
self.mpi_c_compiler = self.extract_ompi_setting(
"C compiler", output_of_ompi_info)
elif mpi_name == 'impi':
# Extract the version of IntelMPI
# The prefix in the the mpiicc (or mpigcc) script can be used to extract the explicit version
contents_of_mpixcc = read_file(path_to_mpi_c_wrapper)
prefix_regex = re.compile(
r'(?<=compilers_and_libraries_)(.*)(?=/linux/mpi)', re.M)
self.mpi_version = None
res = prefix_regex.search(contents_of_mpixcc)
if res:
self.mpi_version = res.group(1)
else:
# old iimpi version
prefix_regex = re.compile(r'^prefix=(.*)$', re.M)
res = prefix_regex.search(contents_of_mpixcc)
if res:
self.mpi_version = res.group(1).split('/')[-1]
if self.mpi_version is None:
raise EasyBuildError("No version found for system Intel MPI")
else:
self.log.info("Found Intel MPI version %s for system MPI" %
self.mpi_version)
# Extract the installation prefix, if I_MPI_ROOT is defined, let's use that
i_mpi_root = os.environ.get('I_MPI_ROOT')
if i_mpi_root:
self.mpi_prefix = i_mpi_root
else:
# Else just go up three directories from where mpiicc is found
# (it's 3 because bin64 is a symlink to intel64/bin and we are assuming 64 bit)
self.mpi_prefix = os.path.dirname(
os.path.dirname(os.path.dirname(path_to_mpi_c_wrapper)))
# Extract any IntelMPI environment variables in the current environment and ensure they are added to the
# final module
self.mpi_env_vars = {}
for key, value in os.environ.items():
i_mpi_key = key.startswith('I_MPI_') or key.startswith(
'MPICH_')
mpi_profile_key = key.startswith('MPI') and key.endswith(
'PROFILE')
if i_mpi_key or mpi_profile_key:
self.mpi_env_vars[key] = value
# Extract the C compiler used underneath Intel MPI
compile_info, exit_code = run_cmd("%s -compile-info" %
mpi_c_wrapper,
simple=False)
if exit_code == 0:
self.mpi_c_compiler = compile_info.split(' ', 1)[0]
else:
raise EasyBuildError(
"Could not determine C compiler underneath Intel MPI, '%s -compiler-info' "
"returned %s", mpi_c_wrapper, compile_info)
else:
raise EasyBuildError("Unrecognised system MPI implementation %s",
mpi_name)
# Ensure install path of system MPI actually exists
if not os.path.exists(self.mpi_prefix):
raise EasyBuildError(
"Path derived for system MPI (%s) does not exist: %s!",
mpi_name, self.mpi_prefix)
self.log.debug(
"Derived version/install prefix for system MPI %s: %s, %s",
mpi_name, self.mpi_version, self.mpi_prefix)
# For the version of the underlying C compiler need to explicitly extract (to be certain)
self.c_compiler_version = extract_compiler_version(self.mpi_c_compiler)
self.log.debug(
"Derived compiler/version for C compiler underneath system MPI %s: %s, %s",
mpi_name, self.mpi_c_compiler, self.c_compiler_version)
# If EasyConfig specified "real" version (not 'system' which means 'derive automatically'), check it
if self.cfg['version'] == 'system':
self.log.info(
"Found specified version '%s', going with derived MPI version '%s'",
self.cfg['version'], self.mpi_version)
elif self.cfg['version'] == self.mpi_version:
self.log.info("Specified MPI version %s matches found version" %
self.mpi_version)
else:
raise EasyBuildError(
"Specified version (%s) does not match version reported by MPI (%s)",
self.cfg['version'], self.mpi_version)
def make_module_step(self, fake=False):
"""Install .modulerc file."""
modfile_path = self.module_generator.get_module_filepath(fake=fake)
modulerc = os.path.join(os.path.dirname(modfile_path), self.module_generator.DOT_MODULERC)
deps = self.cfg['dependencies']
if len(deps) != 1:
raise EasyBuildError("There should be exactly one dependency specified, found %d", len(deps))
# names should match
if self.name != deps[0]['name']:
raise EasyBuildError("Name does not match dependency name: %s vs %s", self.name, deps[0]['name'])
# ensure version to alias to is a prefix of the version of the dependency
if not deps[0]['version'].startswith(self.version):
raise EasyBuildError("Version is not a prefix of dependency version: %s vs %s",
self.version, deps[0]['version'])
alias_modname = deps[0]['short_mod_name']
self.log.info("Adding module version alias for %s to %s", alias_modname, modulerc)
# add symlink to wrapped module file when generating .modulerc in temporary directory (done during sanity check)
# this is strictly required for Lmod 6.x, for which .modulerc and wrapped module file must be in same location
if fake:
wrapped_mod_path = self.modules_tool.modulefile_path(alias_modname)
wrapped_mod_filename = os.path.basename(wrapped_mod_path)
target = os.path.join(os.path.dirname(modulerc), wrapped_mod_filename)
mkdir(os.path.dirname(target), parents=True)
symlink(wrapped_mod_path, target)
module_version_specs = {
'modname': alias_modname,
'sym_version': self.version,
'version': deps[0]['version'],
}
self.module_generator.modulerc(module_version=module_version_specs, filepath=modulerc)
if not fake:
print_msg("updated .modulerc file at %s" % modulerc, log=self.log)
# symlink .modulerc in other locations (unless they're already linked)
mod_symlink_dirs = ActiveMNS().det_module_symlink_paths(self.cfg)
mod_subdir = os.path.dirname(ActiveMNS().det_full_module_name(self.cfg))
mod_install_path = install_path('mod')
modulerc_filename = os.path.basename(modulerc)
for mod_symlink_dir in mod_symlink_dirs:
modulerc_symlink = os.path.join(mod_install_path, mod_symlink_dir, mod_subdir, modulerc_filename)
if os.path.islink(modulerc_symlink):
if resolve_path(modulerc_symlink) == resolve_path(modulerc):
print_msg("symlink %s to %s already exists", modulerc_symlink, modulerc)
else:
raise EasyBuildError("%s exists but is not a symlink to %s", modulerc_symlink, modulerc)
else:
symlink(modulerc, modulerc_symlink)
print_msg("created symlink %s to .modulerc file at %s", modulerc_symlink, modulerc, log=self.log)
modpath = self.module_generator.get_modules_path(fake=fake)
self.invalidate_module_caches(modpath)
return modpath
def build_step(self):
"""Custom build procedure for TensorFlow."""
# pre-create target installation directory
mkdir(os.path.join(self.installdir, self.pylibdir), parents=True)
binutils_root = get_software_root('binutils')
if binutils_root:
binutils_bin = os.path.join(binutils_root, 'bin')
else:
raise EasyBuildError("Failed to determine installation prefix for binutils")
gcc_root = get_software_root('GCCcore') or get_software_root('GCC')
if gcc_root:
gcc_lib64 = os.path.join(gcc_root, 'lib64')
gcc_ver = get_software_version('GCCcore') or get_software_version('GCC')
# figure out location of GCC include files
res = glob.glob(os.path.join(gcc_root, 'lib', 'gcc', '*', gcc_ver, 'include'))
if res and len(res) == 1:
gcc_lib_inc = res[0]
else:
raise EasyBuildError("Failed to pinpoint location of GCC include files: %s", res)
# make sure include-fixed directory is where we expect it to be
gcc_lib_inc_fixed = os.path.join(os.path.dirname(gcc_lib_inc), 'include-fixed')
if not os.path.exists(gcc_lib_inc_fixed):
raise EasyBuildError("Derived directory %s does not exist", gcc_lib_inc_fixed)
# also check on location of include/c++/<gcc version> directory
gcc_cplusplus_inc = os.path.join(gcc_root, 'include', 'c++', gcc_ver)
if not os.path.exists(gcc_cplusplus_inc):
raise EasyBuildError("Derived directory %s does not exist", gcc_cplusplus_inc)
else:
raise EasyBuildError("Failed to determine installation prefix for GCC")
inc_paths = [gcc_lib_inc, gcc_lib_inc_fixed, gcc_cplusplus_inc]
lib_paths = [gcc_lib64]
cuda_root = get_software_root('CUDA')
if cuda_root:
inc_paths.append(os.path.join(cuda_root, 'include'))
lib_paths.append(os.path.join(cuda_root, 'lib64'))
# fix hardcoded locations of compilers & tools
cxx_inc_dir_lines = '\n'.join(r'cxx_builtin_include_directory: "%s"' % resolve_path(p) for p in inc_paths)
cxx_inc_dir_lines_no_resolv_path = '\n'.join(r'cxx_builtin_include_directory: "%s"' % p for p in inc_paths)
regex_subs = [
(r'-B/usr/bin/', '-B%s/ %s' % (binutils_bin, ' '.join('-L%s/' % p for p in lib_paths))),
(r'(cxx_builtin_include_directory:).*', ''),
(r'^toolchain {', 'toolchain {\n' + cxx_inc_dir_lines + '\n' + cxx_inc_dir_lines_no_resolv_path),
]
for tool in ['ar', 'cpp', 'dwp', 'gcc', 'gcov', 'ld', 'nm', 'objcopy', 'objdump', 'strip']:
path = which(tool)
if path:
regex_subs.append((os.path.join('/usr', 'bin', tool), path))
else:
raise EasyBuildError("Failed to determine path to '%s'", tool)
# -fPIE/-pie and -fPIC are not compatible, so patch out hardcoded occurences of -fPIE/-pie if -fPIC is used
if self.toolchain.options.get('pic', None):
regex_subs.extend([('-fPIE', '-fPIC'), ('"-pie"', '"-fPIC"')])
# patch all CROSSTOOL* scripts to fix hardcoding of locations of binutils/GCC binaries
for path, dirnames, filenames in os.walk(self.start_dir):
for filename in filenames:
if filename.startswith('CROSSTOOL'):
full_path = os.path.join(path, filename)
self.log.info("Patching %s", full_path)
apply_regex_substitutions(full_path, regex_subs)
tmpdir = tempfile.mkdtemp(suffix='-bazel-build')
# compose "bazel build" command with all its options...
cmd = [self.cfg['prebuildopts'], 'bazel', '--output_base=%s' % tmpdir, 'build']
# build with optimization enabled
# cfr. https://docs.bazel.build/versions/master/user-manual.html#flag--compilation_mode
cmd.append('--compilation_mode=opt')
# select 'opt' config section (this is *not* the same as --compilation_mode=opt!)
# https://docs.bazel.build/versions/master/user-manual.html#flag--config
cmd.append('--config=opt')
# make Bazel print full command line + make it verbose on failures
# https://docs.bazel.build/versions/master/user-manual.html#flag--subcommands
# https://docs.bazel.build/versions/master/user-manual.html#flag--verbose_failures
cmd.extend(['--subcommands', '--verbose_failures'])
# limit the number of parallel jobs running simultaneously (useful on KNL)...
cmd.append('--jobs=%s' % self.cfg['parallel'])
if self.toolchain.options.get('pic', None):
cmd.append('--copt="-fPIC"')
cmd.append(self.cfg['buildopts'])
if cuda_root:
cmd.append('--config=cuda')
# enable mkl-dnn by default, but only if cuDNN is not listed as dependency
if self.cfg['with_mkl_dnn'] is None and get_software_root('cuDNN') is None:
self.log.info("Enabling use of mkl-dnn since cuDNN is not listed as dependency")
self.cfg['with_mkl_dnn'] = True
# if mkl-dnn is listed as a dependency it is used. Otherwise downloaded if with_mkl_dnn is true
mkl_root = get_software_root('mkl-dnn')
if mkl_root:
cmd.extend(['--config=mkl'])
cmd.insert(0, "export TF_MKL_DOWNLOAD=0 &&")
cmd.insert(0, "export TF_MKL_ROOT=%s &&" % mkl_root)
elif self.cfg['with_mkl_dnn']:
# this makes TensorFlow use mkl-dnn (cfr. https://github.com/01org/mkl-dnn)
cmd.extend(['--config=mkl'])
cmd.insert(0, "export TF_MKL_DOWNLOAD=1 && ")
# specify target of the build command as last argument
cmd.append('//tensorflow/tools/pip_package:build_pip_package')
run_cmd(' '.join(cmd), log_all=True, simple=True, log_ok=True)
# run generated 'build_pip_package' script to build the .whl
cmd = "bazel-bin/tensorflow/tools/pip_package/build_pip_package %s" % self.builddir
run_cmd(cmd, log_all=True, simple=True, log_ok=True)
def __init__(self, *args, **kwargs):
"""Extra initialization: determine system compiler version and prefix."""
super(SystemCompiler, self).__init__(*args, **kwargs)
# Determine compiler path (real path, with resolved symlinks)
compiler_name = self.cfg['name'].lower()
if compiler_name == 'gcccore':
compiler_name = 'gcc'
path_to_compiler = which(compiler_name)
if path_to_compiler:
path_to_compiler = resolve_path(path_to_compiler)
self.log.info(
"Found path to compiler '%s' (with symlinks resolved): %s",
compiler_name, path_to_compiler)
else:
raise EasyBuildError("%s not found in $PATH", compiler_name)
# Determine compiler version
self.compiler_version = extract_compiler_version(compiler_name)
# Determine installation prefix
if compiler_name == 'gcc':
# strip off 'bin/gcc'
self.compiler_prefix = os.path.dirname(
os.path.dirname(path_to_compiler))
elif compiler_name in ['icc', 'ifort']:
intelvars_fn = path_to_compiler + 'vars.sh'
if os.path.isfile(intelvars_fn):
self.log.debug(
"Trying to determine compiler install prefix from %s",
intelvars_fn)
intelvars_txt = read_file(intelvars_fn)
prod_dir_regex = re.compile(r'^PROD_DIR=(.*)$', re.M)
res = prod_dir_regex.search(intelvars_txt)
if res:
self.compiler_prefix = res.group(1)
else:
raise EasyBuildError(
"Failed to determine %s installation prefix from %s",
compiler_name, intelvars_fn)
else:
# strip off 'bin/intel*/icc'
self.compiler_prefix = os.path.dirname(
os.path.dirname(os.path.dirname(path_to_compiler)))
# For versions 2016+ of Intel compilers they changed the installation path so must shave off 2 more
# directories from result of the above
if LooseVersion(self.compiler_version) >= LooseVersion('2016'):
self.compiler_prefix = os.path.dirname(
os.path.dirname(self.compiler_prefix))
else:
raise EasyBuildError("Unknown system compiler %s" %
self.cfg['name'])
if not os.path.exists(self.compiler_prefix):
raise EasyBuildError(
"Path derived for system compiler (%s) does not exist: %s!",
compiler_name, self.compiler_prefix)
self.log.debug(
"Derived version/install prefix for system compiler %s: %s, %s",
compiler_name, self.compiler_version, self.compiler_prefix)
# If EasyConfig specified "real" version (not 'system' which means 'derive automatically'), check it
if self.cfg['version'] == 'system':
self.log.info(
"Found specified version '%s', going with derived compiler version '%s'",
self.cfg['version'], self.compiler_version)
elif self.cfg['version'] != self.compiler_version:
raise EasyBuildError(
"Specified version (%s) does not match version reported by compiler (%s)"
% (self.cfg['version'], self.compiler_version))
# fix installdir and module names (may differ because of changes to version)
mns = ActiveMNS()
self.cfg.full_mod_name = mns.det_full_module_name(self.cfg)
self.cfg.short_mod_name = mns.det_short_module_name(self.cfg)
self.cfg.mod_subdir = mns.det_module_subdir(self.cfg)
# keep track of original values, for restoring later
self.orig_version = self.cfg['version']
self.orig_installdir = self.installdir
def patch_crosstool_files(self):
"""Patches the CROSSTOOL files to include EasyBuild provided compiler paths"""
inc_paths, lib_paths = [], []
gcc_root = get_software_root('GCCcore') or get_software_root('GCC')
if gcc_root:
gcc_lib64 = os.path.join(gcc_root, 'lib64')
lib_paths.append(gcc_lib64)
gcc_ver = get_software_version('GCCcore') or get_software_version(
'GCC')
# figure out location of GCC include files
res = glob.glob(
os.path.join(gcc_root, 'lib', 'gcc', '*', gcc_ver, 'include'))
if res and len(res) == 1:
gcc_lib_inc = res[0]
inc_paths.append(gcc_lib_inc)
else:
raise EasyBuildError(
"Failed to pinpoint location of GCC include files: %s",
res)
# make sure include-fixed directory is where we expect it to be
gcc_lib_inc_fixed = os.path.join(os.path.dirname(gcc_lib_inc),
'include-fixed')
if os.path.exists(gcc_lib_inc_fixed):
inc_paths.append(gcc_lib_inc_fixed)
else:
self.log.info(
"Derived directory %s does not exist, so discarding it",
gcc_lib_inc_fixed)
# also check on location of include/c++/<gcc version> directory
gcc_cplusplus_inc = os.path.join(gcc_root, 'include', 'c++',
gcc_ver)
if os.path.exists(gcc_cplusplus_inc):
inc_paths.append(gcc_cplusplus_inc)
else:
raise EasyBuildError("Derived directory %s does not exist",
gcc_cplusplus_inc)
else:
raise EasyBuildError(
"Failed to determine installation prefix for GCC")
cuda_root = get_software_root('CUDA')
if cuda_root:
inc_paths.append(os.path.join(cuda_root, 'include'))
lib_paths.append(os.path.join(cuda_root, 'lib64'))
# fix hardcoded locations of compilers & tools
cxx_inc_dirs = [
'cxx_builtin_include_directory: "%s"' % resolve_path(p)
for p in inc_paths
]
cxx_inc_dirs += [
'cxx_builtin_include_directory: "%s"' % p for p in inc_paths
]
regex_subs = [
(r'-B/usr/bin/', '-B%s %s' %
(self.binutils_bin_path, ' '.join('-L%s/' % p
for p in lib_paths))),
(r'(cxx_builtin_include_directory:).*', ''),
(r'^toolchain {', 'toolchain {\n' + '\n'.join(cxx_inc_dirs)),
]
for tool in [
'ar', 'cpp', 'dwp', 'gcc', 'gcov', 'ld', 'nm', 'objcopy',
'objdump', 'strip'
]:
path = which(tool)
if path:
regex_subs.append((os.path.join('/usr', 'bin', tool), path))
else:
raise EasyBuildError("Failed to determine path to '%s'", tool)
# -fPIE/-pie and -fPIC are not compatible, so patch out hardcoded occurences of -fPIE/-pie if -fPIC is used
if self.toolchain.options.get('pic', None):
regex_subs.extend([('-fPIE', '-fPIC'), ('"-pie"', '"-fPIC"')])
# patch all CROSSTOOL* scripts to fix hardcoding of locations of binutils/GCC binaries
for path, dirnames, filenames in os.walk(os.getcwd()):
for filename in filenames:
if filename.startswith('CROSSTOOL'):
full_path = os.path.join(path, filename)
self.log.info("Patching %s", full_path)
apply_regex_substitutions(full_path, regex_subs)
def prepare_step(self, *args, **kwargs):
"""Load all dependencies, determine system MPI version, prefix and any associated envvars."""
# Do the bundle prepare step to ensure any deps are loaded (no need to worry about licences for Intel MPI)
Bundle.prepare_step(self, *args, **kwargs)
# Prepare additional parameters: determine system MPI version, prefix and any associated envvars.
mpi_name = self.cfg['name'].lower()
# Determine MPI wrapper path (real path, with resolved symlinks) to ensure it exists
if mpi_name == 'impi':
# For impi the version information is only found in *some* of the wrappers it ships, in particular it is
# not in mpicc
mpi_c_wrapper = 'mpiicc'
path_to_mpi_c_wrapper = which(mpi_c_wrapper)
if not path_to_mpi_c_wrapper:
mpi_c_wrapper = 'mpigcc'
path_to_mpi_c_wrapper = which(mpi_c_wrapper)
if not path_to_mpi_c_wrapper:
raise EasyBuildError("Could not find suitable MPI wrapper to extract version for impi")
else:
mpi_c_wrapper = 'mpicc'
path_to_mpi_c_wrapper = which(mpi_c_wrapper)
if path_to_mpi_c_wrapper:
path_to_mpi_c_wrapper = resolve_path(path_to_mpi_c_wrapper)
self.log.info("Found path to MPI implementation '%s' %s compiler (with symlinks resolved): %s",
mpi_name, mpi_c_wrapper, path_to_mpi_c_wrapper)
else:
raise EasyBuildError("%s not found in $PATH", mpi_c_wrapper)
# Determine MPI version, installation prefix and underlying compiler
if mpi_name in ('openmpi', 'spectrummpi'):
# Spectrum MPI is based on Open MPI so is also covered by this logic
output_of_ompi_info, _ = run_cmd("ompi_info", simple=False)
# Extract the version of the MPI implementation
if mpi_name == 'spectrummpi':
mpi_version_string = 'Spectrum MPI'
else:
mpi_version_string = 'Open MPI'
self.mpi_version = self.extract_ompi_setting(mpi_version_string, output_of_ompi_info)
# Extract the installation prefix
self.mpi_prefix = self.extract_ompi_setting("Prefix", output_of_ompi_info)
# Extract any OpenMPI environment variables in the current environment and ensure they are added to the
# final module
self.mpi_env_vars = dict((key, value) for key, value in os.environ.iteritems() if key.startswith("OMPI_"))
# Extract the C compiler used underneath the MPI implementation, check for the definition of OMPI_MPICC
self.mpi_c_compiler = self.extract_ompi_setting("C compiler", output_of_ompi_info)
elif mpi_name == 'impi':
# Extract the version of IntelMPI
# The prefix in the the mpiicc (or mpigcc) script can be used to extract the explicit version
contents_of_mpixcc = read_file(path_to_mpi_c_wrapper)
prefix_regex = re.compile(r'(?<=compilers_and_libraries_)(.*)(?=/linux/mpi)', re.M)
self.mpi_version = None
res = prefix_regex.search(contents_of_mpixcc)
if res:
self.mpi_version = res.group(1)
else:
# old iimpi version
prefix_regex = re.compile(r'^prefix=(.*)$', re.M)
res = prefix_regex.search(contents_of_mpixcc)
if res:
self.mpi_version = res.group(1).split('/')[-1]
if self.mpi_version is None:
raise EasyBuildError("No version found for system Intel MPI")
else:
self.log.info("Found Intel MPI version %s for system MPI" % self.mpi_version)
# Extract the installation prefix, if I_MPI_ROOT is defined, let's use that
i_mpi_root = os.environ.get('I_MPI_ROOT')
if i_mpi_root:
self.mpi_prefix = i_mpi_root
else:
# Else just go up three directories from where mpiicc is found
# (it's 3 because bin64 is a symlink to intel64/bin and we are assuming 64 bit)
self.mpi_prefix = os.path.dirname(os.path.dirname(os.path.dirname(path_to_mpi_c_wrapper)))
# Extract any IntelMPI environment variables in the current environment and ensure they are added to the
# final module
self.mpi_env_vars = {}
for key, value in os.environ.iteritems():
i_mpi_key = key.startswith('I_MPI_') or key.startswith('MPICH_')
mpi_profile_key = key.startswith('MPI') and key.endswith('PROFILE')
if i_mpi_key or mpi_profile_key:
self.mpi_env_vars[key] = value
# Extract the C compiler used underneath Intel MPI
compile_info, exit_code = run_cmd("%s -compile-info" % mpi_c_wrapper, simple=False)
if exit_code == 0:
self.mpi_c_compiler = compile_info.split(' ', 1)[0]
else:
raise EasyBuildError("Could not determine C compiler underneath Intel MPI, '%s -compiler-info' "
"returned %s", mpi_c_wrapper, compile_info)
else:
raise EasyBuildError("Unrecognised system MPI implementation %s", mpi_name)
# Ensure install path of system MPI actually exists
if not os.path.exists(self.mpi_prefix):
raise EasyBuildError("Path derived for system MPI (%s) does not exist: %s!", mpi_name, self.mpi_prefix)
self.log.debug("Derived version/install prefix for system MPI %s: %s, %s",
mpi_name, self.mpi_version, self.mpi_prefix)
# For the version of the underlying C compiler need to explicitly extract (to be certain)
self.c_compiler_version = extract_compiler_version(self.mpi_c_compiler)
self.log.debug("Derived compiler/version for C compiler underneath system MPI %s: %s, %s",
mpi_name, self.mpi_c_compiler, self.c_compiler_version)
# If EasyConfig specified "real" version (not 'system' which means 'derive automatically'), check it
if self.cfg['version'] == 'system':
self.log.info("Found specified version '%s', going with derived MPI version '%s'",
self.cfg['version'], self.mpi_version)
elif self.cfg['version'] == self.mpi_version:
self.log.info("Specified MPI version %s matches found version" % self.mpi_version)
else:
raise EasyBuildError("Specified version (%s) does not match version reported by MPI (%s)",
self.cfg['version'], self.mpi_version)
