def extract_step(self):
"""Custom extract step for VMD."""
super(EB_VMD, self).extract_step()
if LooseVersion(self.version) >= LooseVersion("1.9.3"):
change_dir(self.surf_dir)
extract_file('surf.tar.Z', os.getcwd())
def configure_step(self):
"""Add some extra configure options."""
# also build shared libraries (not enabled by default)
self.cfg.update('configopts', "--enable-shared")
if self.toolchain.options['pic']:
# Enforce consistency.
self.cfg.update('configopts', "--with-pic")
if LooseVersion(self.version) >= LooseVersion('2.0') and LooseVersion(self.version) < LooseVersion('2.1'):
# the code in libint is automatically generated and hence it is in some
# parts so complex that -O2 or -O3 compiler optimization takes forever
self.cfg.update('configopts', "--with-cxx-optflags='-O1'")
elif LooseVersion(self.version) >= LooseVersion('2.1'):
# pass down $CXXFLAGS to --with-cxxgen-optflags configure option;
# mainly to avoid warning about it not being set (but $CXXFLAGS is picked up anyway in practice)
self.cfg.update('configopts', "--with-cxxgen-optflags='%s'" % os.getenv('CXXFLAGS'))
if LooseVersion(self.version) >= LooseVersion('2.6.0'):
# Libint 2.6.0 requires first compiling the Libint compiler,
# by running configure with appropriate options, followed by 'make export'
# and unpacking the resulting source tarball;
# see https://github.com/evaleev/libint/wiki#compiling-libint-compiler
# CMake is recommended, but configuring with Fortran support doesn't work correctly yet in Libint 2.6.0
# so stick to traditional configure script for now
print_msg("configuring Libint compiler...")
# first run autogen.sh script to generate initial configure script
run_cmd("./autogen.sh")
cmd = ' '.join([
self.cfg['preconfigopts'],
'./configure',
self.cfg['configopts'],
self.cfg['libint_compiler_configopts'],
])
run_cmd(cmd)
print_msg("generating Libint library...")
run_cmd("make export")
source_fn = 'libint-%s.tgz' % self.version
if os.path.exists(source_fn):
extract_file(source_fn, os.getcwd(), change_into_dir=False)
change_dir('libint-%s' % self.version)
else:
raise EasyBuildError("Could not find generated source tarball after 'make export'!")
# --enable-fortran is only a known configure option for Libint library, not for Libint compiler,
# so only add --enable-fortran *after* configuring & generating Libint compiler
if self.cfg['with_fortran']:
self.cfg.update('configopts', '--enable-fortran')
super(EB_Libint, self).configure_step()
def extract_step(self):
"""Custom extract step for NAMD, we need to extract charm++ so we can patch it."""
super(EB_NAMD, self).extract_step()
change_dir(self.src[0]['finalpath'])
self.charm_tarballs = glob.glob('charm-*.tar')
if len(self.charm_tarballs) != 1:
raise EasyBuildError("Expected to find exactly one tarball for Charm++, found: %s", self.charm_tarballs)
extract_file(self.charm_tarballs[0], os.getcwd())
def extract_step(self):
"""Custom extract step for NAMD, we need to extract charm++ so we can patch it."""
super(EB_NAMD, self).extract_step()
change_dir(self.src[0]['finalpath'])
self.charm_tarballs = glob.glob('charm-*.tar')
if len(self.charm_tarballs) != 1:
raise EasyBuildError("Expected to find exactly one tarball for Charm++, found: %s", self.charm_tarballs)
extract_file(self.charm_tarballs[0], os.getcwd())
def configure_step(self):
"""Custom configure step for NAMD, we build charm++ first (if required)."""
# complete Charm ++ and NAMD architecture string with compiler family
comp_fam = self.toolchain.comp_family()
if self.toolchain.options["usempi"]:
charm_arch_comp = "mpicxx"
else:
charm_arch_comps = {toolchain.GCC: "gcc", toolchain.INTELCOMP: "icc"}
charm_arch_comp = charm_arch_comps.get(comp_fam, None)
namd_comps = {toolchain.GCC: "g++", toolchain.INTELCOMP: "icc"}
namd_comp = namd_comps.get(comp_fam, None)
if charm_arch_comp is None or namd_comp is None:
raise EasyBuildError("Unknown compiler family, can't complete Charm++/NAMD target architecture.")
self.cfg.update("charm_arch", charm_arch_comp)
self.log.info("Updated 'charm_arch': %s" % self.cfg["charm_arch"])
self.namd_arch = "%s-%s" % (self.cfg["namd_basearch"], namd_comp)
self.log.info("Completed NAMD target architecture: %s" % self.namd_arch)
charm_tarballs = glob.glob("charm-*.tar")
if len(charm_tarballs) != 1:
raise EasyBuildError("Expected to find exactly one tarball for Charm++, found: %s", charm_tarballs)
extract_file(charm_tarballs[0], os.getcwd())
tup = (self.cfg["charm_arch"], self.cfg["charm_opts"], self.cfg["parallel"], os.environ["CXXFLAGS"])
cmd = "./build charm++ %s %s -j%s %s -DMPICH_IGNORE_CXX_SEEK" % tup
charm_subdir = ".".join(os.path.basename(charm_tarballs[0]).split(".")[:-1])
self.log.debug("Building Charm++ using cmd '%s' in '%s'" % (cmd, charm_subdir))
run_cmd(cmd, path=charm_subdir)
# compiler (options)
self.cfg.update("namd_cfg_opts", '--cc "%s" --cc-opts "%s"' % (os.environ["CC"], os.environ["CFLAGS"]))
self.cfg.update("namd_cfg_opts", '--cxx "%s" --cxx-opts "%s"' % (os.environ["CXX"], os.environ["CXXFLAGS"]))
# NAMD dependencies: CUDA, FFTW
cuda = get_software_root("CUDA")
if cuda:
self.cfg.update("namd_cfg_opts", "--with-cuda --cuda-prefix %s" % cuda)
fftw = get_software_root("FFTW")
if fftw:
if LooseVersion(get_software_version("FFTW")) >= LooseVersion("3.0"):
if LooseVersion(self.version) >= LooseVersion("2.9"):
self.cfg.update("namd_cfg_opts", "--with-fftw3")
else:
raise EasyBuildError("Using FFTW v3.x only supported in NAMD v2.9 and up.")
else:
self.cfg.update("namd_cfg_opts", "--with-fftw")
self.cfg.update("namd_cfg_opts", "--fftw-prefix %s" % fftw)
namd_charm_arch = "--charm-arch %s" % "-".join(self.cfg["charm_arch"].strip().split(" "))
cmd = "./config %s %s %s " % (self.namd_arch, namd_charm_arch, self.cfg["namd_cfg_opts"])
run_cmd(cmd)
def test_extract_file(self):
"""Test extract_file"""
testdir = os.path.dirname(os.path.abspath(__file__))
toy_tarball = os.path.join(testdir, 'sandbox', 'sources', 'toy',
'toy-0.0.tar.gz')
self.assertFalse(
os.path.exists(
os.path.join(self.test_prefix, 'toy-0.0', 'toy.source')))
path = ft.extract_file(toy_tarball, self.test_prefix)
self.assertTrue(
os.path.exists(
os.path.join(self.test_prefix, 'toy-0.0', 'toy.source')))
self.assertTrue(os.path.samefile(path, self.test_prefix))
shutil.rmtree(os.path.join(path, 'toy-0.0'))
toy_tarball_renamed = os.path.join(self.test_prefix, 'toy_tarball')
shutil.copyfile(toy_tarball, toy_tarball_renamed)
path = ft.extract_file(toy_tarball_renamed,
self.test_prefix,
cmd="tar xfvz %s")
self.assertTrue(
os.path.exists(
os.path.join(self.test_prefix, 'toy-0.0', 'toy.source')))
self.assertTrue(os.path.samefile(path, self.test_prefix))
shutil.rmtree(os.path.join(path, 'toy-0.0'))
# also test behaviour of extract_file under --dry-run
build_options = {
'extended_dry_run': True,
'silent': False,
}
init_config(build_options=build_options)
self.mock_stdout(True)
path = ft.extract_file(toy_tarball, self.test_prefix)
txt = self.get_stdout()
self.mock_stdout(False)
self.assertTrue(os.path.samefile(path, self.test_prefix))
self.assertFalse(
os.path.exists(os.path.join(self.test_prefix, 'toy-0.0')))
self.assertTrue(
re.search('running command "tar xzf .*/toy-0.0.tar.gz"', txt))
path = ft.extract_file(toy_tarball, self.test_prefix, forced=True)
self.assertTrue(
os.path.exists(
os.path.join(self.test_prefix, 'toy-0.0', 'toy.source')))
self.assertTrue(os.path.samefile(path, self.test_prefix))
def extract_step(self):
"""Extract sources, if they haven't been already."""
super(EB_Rosetta, self).extract_step()
# locate sources, and unpack if necessary
# old 'bundles' tarballs contain a gzipped tarball for source, recent ones contain unpacked source
try:
subdirs = os.listdir(self.builddir)
if len(subdirs) == 1:
prefix = os.path.join(self.builddir, subdirs[0])
else:
raise EasyBuildError(
"Found no or multiple subdirectories, expected exactly one: %s",
subdirs)
self.srcdir = os.path.join(prefix, 'rosetta_source')
if not os.path.exists(self.srcdir):
self.srcdir = os.path.join(prefix, 'main', 'source')
if not os.path.exists(self.srcdir):
src_tarball = os.path.join(
prefix, 'rosetta%s_source.tgz' % self.version)
if os.path.isfile(src_tarball):
self.srcdir = extract_file(src_tarball,
prefix,
change_into_dir=False)
change_dir(self.srcdir)
else:
raise EasyBuildError(
"Neither source directory '%s', nor source tarball '%s' found.",
self.srcdir, src_tarball)
except OSError as err:
raise EasyBuildError(
"Getting Rosetta sources dir ready failed: %s", err)
def extract_and_copy(dirname_tmpl, optional=False, symlinks=False):
"""Copy specified directory, after extracting it (if required)."""
try:
srcdir = os.path.join(self.cfg['start_dir'], dirname_tmpl % '')
if not os.path.exists(srcdir):
# try to extract if directory is not there yet
src_tarball = os.path.join(self.cfg['start_dir'],
(dirname_tmpl % self.version) +
'.tgz')
if os.path.isfile(src_tarball):
srcdir = extract_file(src_tarball,
self.cfg['start_dir'])
if os.path.exists(srcdir):
shutil.copytree(srcdir,
os.path.join(self.installdir,
os.path.basename(srcdir)),
symlinks=symlinks)
elif not optional:
raise EasyBuildError(
"Neither source directory '%s', nor source tarball '%s' found.",
srcdir, src_tarball)
except OSError as err:
raise EasyBuildError("Getting Rosetta %s dir ready failed: %s",
dirname_tmpl, err)
def download_repo(repo=GITHUB_EASYCONFIGS_REPO,
branch='master',
account=GITHUB_EB_MAIN,
path=None):
"""
Download entire GitHub repo as a tar.gz archive, and extract it into specified path.
@param repo: repo to download
@param branch: branch to download
@param account: GitHub account to download repo from
@param path: path to extract to
"""
# make sure path exists, create it if necessary
if path is None:
path = tempfile.mkdtemp()
# add account subdir
path = os.path.join(path, account)
mkdir(path, parents=True)
extracted_dir_name = '%s-%s' % (repo, branch)
base_name = '%s.tar.gz' % branch
latest_commit_sha = fetch_latest_commit_sha(repo, account, branch)
expected_path = os.path.join(path, extracted_dir_name)
latest_sha_path = os.path.join(expected_path, 'latest-sha')
# check if directory already exists, don't download if 'latest-sha' file indicates that it's up to date
if os.path.exists(latest_sha_path):
sha = read_file(latest_sha_path).split('\n')[0].rstrip()
if latest_commit_sha == sha:
_log.debug("Not redownloading %s/%s as it already exists: %s" %
(account, repo, expected_path))
return expected_path
url = URL_SEPARATOR.join([GITHUB_URL, account, repo, 'archive', base_name])
target_path = os.path.join(path, base_name)
_log.debug("downloading repo %s/%s as archive from %s to %s" %
(account, repo, url, target_path))
download_file(base_name, url, target_path)
_log.debug("%s downloaded to %s, extracting now" % (base_name, path))
extracted_path = os.path.join(extract_file(target_path, path),
extracted_dir_name)
# check if extracted_path exists
if not os.path.isdir(extracted_path):
raise EasyBuildError(
"%s should exist and contain the repo %s at branch %s",
extracted_path, repo, branch)
write_file(latest_sha_path, latest_commit_sha)
_log.debug("Repo %s at branch %s extracted into %s" %
(repo, branch, extracted_path))
return extracted_path
def run(self, *args, **kwargs):
"""Install as extension: unpack sources and copy (via install step)."""
if self.cfg['install_type'] is None:
self.log.info(
"Auto-enabled install_type=merge because Tarball is being used to install an extension"
)
self.cfg['install_type'] = 'merge'
# unpack sources and call install_step to copy unpacked sources to install directory
srcdir = extract_file(self.src, self.builddir, change_into_dir=False)
kwargs['src'] = srcdir
self.install_step(*args, **kwargs)
def run(self, unpack_src=False):
"""Common operations for extensions: unpacking sources, patching, ..."""
# unpack file if desired
if unpack_src:
targetdir = os.path.join(self.master.builddir, remove_unwanted_chars(self.name))
self.ext_dir = extract_file("%s" % self.src, targetdir, extra_options=self.unpack_options)
# patch if needed
if self.patches:
for patchfile in self.patches:
if not apply_patch(patchfile, self.ext_dir):
raise EasyBuildError("Applying patch %s failed", patchfile)
def run(self, unpack_src=False):
"""Common operations for extensions: unpacking sources, patching, ..."""
# unpack file if desired
if unpack_src:
targetdir = os.path.join(self.master.builddir, remove_unwanted_chars(self.name))
self.ext_dir = extract_file("%s" % self.src, targetdir, extra_options=self.unpack_options)
# patch if needed
if self.patches:
for patchfile in self.patches:
if not apply_patch(patchfile, self.ext_dir):
self.log.error("Applying patch %s failed" % patchfile)
def test_extract_file(self):
"""Test extract_file"""
testdir = os.path.dirname(os.path.abspath(__file__))
toy_tarball = os.path.join(testdir, 'sandbox', 'sources', 'toy', 'toy-0.0.tar.gz')
self.assertFalse(os.path.exists(os.path.join(self.test_prefix, 'toy-0.0', 'toy.source')))
path = ft.extract_file(toy_tarball, self.test_prefix)
self.assertTrue(os.path.exists(os.path.join(self.test_prefix, 'toy-0.0', 'toy.source')))
self.assertTrue(os.path.samefile(path, self.test_prefix))
shutil.rmtree(os.path.join(path, 'toy-0.0'))
toy_tarball_renamed = os.path.join(self.test_prefix, 'toy_tarball')
shutil.copyfile(toy_tarball, toy_tarball_renamed)
path = ft.extract_file(toy_tarball_renamed, self.test_prefix, cmd="tar xfvz %s")
self.assertTrue(os.path.exists(os.path.join(self.test_prefix, 'toy-0.0', 'toy.source')))
self.assertTrue(os.path.samefile(path, self.test_prefix))
shutil.rmtree(os.path.join(path, 'toy-0.0'))
# also test behaviour of extract_file under --dry-run
build_options = {
'extended_dry_run': True,
'silent': False,
}
init_config(build_options=build_options)
self.mock_stdout(True)
path = ft.extract_file(toy_tarball, self.test_prefix)
txt = self.get_stdout()
self.mock_stdout(False)
self.assertTrue(os.path.samefile(path, self.test_prefix))
self.assertFalse(os.path.exists(os.path.join(self.test_prefix, 'toy-0.0')))
self.assertTrue(re.search('running command "tar xzf .*/toy-0.0.tar.gz"', txt))
path = ft.extract_file(toy_tarball, self.test_prefix, forced=True)
self.assertTrue(os.path.exists(os.path.join(self.test_prefix, 'toy-0.0', 'toy.source')))
self.assertTrue(os.path.samefile(path, self.test_prefix))
def test_apply_patch(self):
""" Test apply_patch """
testdir = os.path.dirname(os.path.abspath(__file__))
tmpdir = self.test_prefix
path = ft.extract_file(os.path.join(testdir, 'sandbox', 'sources', 'toy', 'toy-0.0.tar.gz'), tmpdir)
toy_patch = os.path.join(testdir, 'sandbox', 'sources', 'toy', 'toy-0.0_typo.patch')
self.assertTrue(ft.apply_patch(toy_patch, path))
patched = ft.read_file(os.path.join(path, 'toy-0.0', 'toy.source'))
pattern = "I'm a toy, and very proud of it"
self.assertTrue(pattern in patched)
# trying the patch again should fail
self.assertErrorRegex(EasyBuildError, "Couldn't apply patch file", ft.apply_patch, toy_patch, path)
def run(self, unpack_src=False):
"""Common operations for extensions: unpacking sources, patching, ..."""
# unpack file if desired
if unpack_src:
targetdir = os.path.join(self.master.builddir, remove_unwanted_chars(self.name))
self.ext_dir = extract_file("%s" % self.src, targetdir, extra_options=self.unpack_options)
if self.start_dir and os.path.isdir(self.start_dir):
self.log.debug("Using start_dir: %s", self.start_dir)
change_dir(self.start_dir)
# patch if needed
EasyBlock.patch_step(self, beginpath=self.ext_dir)
def extract_step(self):
"""Extract sources, if they haven't been already."""
super(EB_Rosetta, self).extract_step()
# locate sources, and unpack if necessary
# old 'bundles' tarballs contain a gzipped tarball for source, recent ones contain unpacked source
try:
prefix = os.path.join(self.builddir, '%s-%s' % (self.name.lower(), self.version))
self.srcdir = os.path.join(prefix, 'rosetta_source')
if not os.path.exists(self.srcdir):
src_tarball = os.path.join(prefix, 'rosetta%s_source.tgz' % self.version)
if os.path.isfile(src_tarball):
self.srcdir = extract_file(src_tarball, prefix)
else:
self.log.error("Neither source directory '%s', nor source tarball '%s' found." % (self.srcdir, src_tarball))
except OSError, err:
self.log.error("Getting Rosetta sources dir ready failed: %s" % err)
def extract_and_copy(dirname_tmpl, optional=False):
"""Copy specified directory, after extracting it (if required)."""
try:
srcdir = os.path.join(self.cfg['start_dir'], dirname_tmpl % '')
if not os.path.exists(srcdir):
# try to extract if directory is not there yet
src_tarball = os.path.join(self.cfg['start_dir'], (dirname_tmpl % self.version) + '.tgz')
if os.path.isfile(src_tarball):
srcdir = extract_file(src_tarball, self.cfg['start_dir'])
if os.path.exists(srcdir):
shutil.copytree(srcdir, os.path.join(self.installdir, os.path.basename(srcdir)))
elif not optional:
self.log.error("Neither source directory '%s', nor source tarball '%s' found." % srcdir, src_tarball)
except OSError, err:
self.log.error("Getting Rosetta %s dir ready failed: %s" % (dirname_tmpl, err))
def install_step(self):
"""
Install by unpacking tarball in dist directory,
and copying site-packages dir to installdir.
"""
# locate tarball
tarball = None
shortver = '.'.join(self.version.split('.')[0:2])
fn_pattern = os.path.join(self.cfg['start_dir'], 'dist',
"%s-%s.*.tar.gz" % (self.name, shortver))
matches = glob.glob(fn_pattern)
if not matches:
raise EasyBuildError("No tarball found at %s", fn_pattern)
elif len(matches) > 1:
raise EasyBuildError("Multiple matches found for tarball: %s",
matches)
else:
tarball = matches[0]
self.log.info("Tarball found at %s" % tarball)
# unpack tarball to temporary directory
tmpdir = tempfile.mkdtemp()
srcdir = extract_file(tarball, tmpdir, change_into_dir=False)
if srcdir:
change_dir(srcdir)
else:
raise EasyBuildError("Unpacking tarball %s failed?", tarball)
# locate site-packages dir to copy by diving into unpacked tarball
src = srcdir
while len(os.listdir(src)) == 1:
src = os.path.join(src, os.listdir(src)[0])
if not os.path.basename(src) == 'site-packages':
raise EasyBuildError(
"Expected to find a site-packages path, but found something else: %s",
src)
# copy contents of site-packages dir
dest = os.path.join(self.installdir, 'site-packages')
try:
shutil.copytree(src, dest)
remove_dir(tmpdir)
os.chdir(self.installdir)
except OSError as err:
raise EasyBuildError("Failed to copy directory %s to %s: %s", src,
dest, err)
def download_repo(repo=GITHUB_EASYCONFIGS_REPO, branch='master', account=GITHUB_EB_MAIN, path=None):
"""
Download entire GitHub repo as a tar.gz archive, and extract it into specified path.
@param repo: repo to download
@param branch: branch to download
@param account: GitHub account to download repo from
@param path: path to extract to
"""
# make sure path exists, create it if necessary
if path is None:
path = tempfile.mkdtemp()
# add account subdir
path = os.path.join(path, account)
mkdir(path, parents=True)
extracted_dir_name = '%s-%s' % (repo, branch)
base_name = '%s.tar.gz' % branch
latest_commit_sha = fetch_latest_commit_sha(repo, account, branch)
expected_path = os.path.join(path, extracted_dir_name)
latest_sha_path = os.path.join(expected_path, 'latest-sha')
# check if directory already exists, don't download if 'latest-sha' file indicates that it's up to date
if os.path.exists(latest_sha_path):
sha = read_file(latest_sha_path).split('\n')[0].rstrip()
if latest_commit_sha == sha:
_log.debug("Not redownloading %s/%s as it already exists: %s" % (account, repo, expected_path))
return expected_path
url = URL_SEPARATOR.join([GITHUB_URL, account, repo, 'archive', base_name])
target_path = os.path.join(path, base_name)
_log.debug("downloading repo %s/%s as archive from %s to %s" % (account, repo, url, target_path))
download_file(base_name, url, target_path)
_log.debug("%s downloaded to %s, extracting now" % (base_name, path))
extracted_path = os.path.join(extract_file(target_path, path), extracted_dir_name)
# check if extracted_path exists
if not os.path.isdir(extracted_path):
raise EasyBuildError("%s should exist and contain the repo %s at branch %s", extracted_path, repo, branch)
write_file(latest_sha_path, latest_commit_sha)
_log.debug("Repo %s at branch %s extracted into %s" % (repo, branch, extracted_path))
return extracted_path
def test_apply_patch(self):
""" Test apply_patch """
testdir = os.path.dirname(os.path.abspath(__file__))
tmpdir = self.test_prefix
path = ft.extract_file(
os.path.join(testdir, 'sandbox', 'sources', 'toy',
'toy-0.0.tar.gz'), tmpdir)
toy_patch = os.path.join(testdir, 'sandbox', 'sources', 'toy',
'toy-0.0_typo.patch')
self.assertTrue(ft.apply_patch(toy_patch, path))
patched = ft.read_file(os.path.join(path, 'toy-0.0', 'toy.source'))
pattern = "I'm a toy, and very proud of it"
self.assertTrue(pattern in patched)
# trying the patch again should fail
self.assertErrorRegex(EasyBuildError, "Couldn't apply patch file",
ft.apply_patch, toy_patch, path)
def install_step(self):
"""
Install by unpacking tarball in dist directory,
and copying site-packages dir to installdir.
"""
# locate tarball
tarball = None
shortver = '.'.join(self.version.split('.')[0:2])
fn_pattern = os.path.join(self.cfg['start_dir'],
'dist',
"%s-%s.*.tar.gz" % (self.name, shortver))
matches = glob.glob(fn_pattern)
if not matches:
raise EasyBuildError("No tarball found at %s", fn_pattern)
elif len(matches) > 1:
raise EasyBuildError("Multiple matches found for tarball: %s", matches)
else:
tarball = matches[0]
self.log.info("Tarball found at %s" % tarball)
# unpack tarball to temporary directory
tmpdir = tempfile.mkdtemp()
srcdir = extract_file(tarball, tmpdir)
if not srcdir:
raise EasyBuildError("Unpacking tarball %s failed?", tarball)
# locate site-packages dir to copy by diving into unpacked tarball
src = srcdir
while len(os.listdir(src)) == 1:
src = os.path.join(src, os.listdir(src)[0])
if not os.path.basename(src) =='site-packages':
raise EasyBuildError("Expected to find a site-packages path, but found something else: %s", src)
# copy contents of site-packages dir
dest = os.path.join(self.installdir, 'site-packages')
try:
shutil.copytree(src, dest)
rmtree2(tmpdir)
os.chdir(self.installdir)
except OSError, err:
raise EasyBuildError("Failed to copy directory %s to %s: %s", src, dest, err)
def run(self, unpack_src=False):
"""Common operations for extensions: unpacking sources, patching, ..."""
# unpack file if desired
if unpack_src:
targetdir = os.path.join(self.master.builddir, remove_unwanted_chars(self.name))
self.ext_dir = extract_file(self.src, targetdir, extra_options=self.unpack_options,
change_into_dir=False, cmd=self.src_extract_cmd)
# setting start dir must be done from unpacked source directory for extension,
# because start_dir value is usually a relative path (if it is set)
change_dir(self.ext_dir)
self._set_start_dir()
change_dir(self.start_dir)
else:
self._set_start_dir()
# patch if needed
EasyBlock.patch_step(self, beginpath=self.ext_dir)
def run(self):
"""Perform the actual Python package build/installation procedure"""
# extract_file
if not self.src:
self.log.error("No source found for Python package %s, required for installation. (src: %s)" % \
(self.name, self.src))
self.ext_dir = extract_file("%s" % self.src, "%s/%s" % (self.builddir, self.name), extra_options=self.unpack_options)
# patch if needed
if self.patches:
for patchfile in self.patches:
if not apply_patch(patchfile, self.ext_dir):
self.log.error("Applying patch %s failed" % patchfile)
# configure, build_step, test, make install
self.configure_step()
self.build_step()
self.test_step()
self.install_step()
def extract_step(self):
"""Extract sources, if they haven't been already."""
super(EB_Rosetta, self).extract_step()
# locate sources, and unpack if necessary
# old 'bundles' tarballs contain a gzipped tarball for source, recent ones contain unpacked source
try:
subdirs = os.listdir(self.builddir)
if len(subdirs) == 1:
prefix = os.path.join(self.builddir, subdirs[0])
else:
raise EasyBuildError("Found multiple subdirectories, don't know which one to pick: %s", subdirs)
self.srcdir = os.path.join(prefix, 'rosetta_source')
if not os.path.exists(self.srcdir):
self.srcdir = os.path.join(prefix, 'main', 'source')
if not os.path.exists(self.srcdir):
src_tarball = os.path.join(prefix, 'rosetta%s_source.tgz' % self.version)
if os.path.isfile(src_tarball):
self.srcdir = extract_file(src_tarball, prefix)
else:
raise EasyBuildError("Neither source directory '%s', nor source tarball '%s' found.",
self.srcdir, src_tarball)
except OSError, err:
raise EasyBuildError("Getting Rosetta sources dir ready failed: %s", err)
def configure_step(self):
"""Custom configure step for NAMD, we build charm++ first (if required)."""
# complete Charm ++ and NAMD architecture string with compiler family
comp_fam = self.toolchain.comp_family()
if self.toolchain.options['usempi']:
charm_arch_comp = 'mpicxx'
else:
charm_arch_comps = {
toolchain.GCC: 'gcc',
toolchain.INTELCOMP: 'icc',
}
charm_arch_comp = charm_arch_comps.get(comp_fam, None)
namd_comps = {
toolchain.GCC: 'g++',
toolchain.INTELCOMP: 'icc',
}
namd_comp = namd_comps.get(comp_fam, None)
if charm_arch_comp is None or namd_comp is None:
raise EasyBuildError(
"Unknown compiler family, can't complete Charm++/NAMD target architecture."
)
self.cfg.update('charm_arch', charm_arch_comp)
self.log.info("Updated 'charm_arch': %s" % self.cfg['charm_arch'])
self.namd_arch = '%s-%s' % (self.cfg['namd_basearch'], namd_comp)
self.log.info("Completed NAMD target architecture: %s" %
self.namd_arch)
charm_tarballs = glob.glob('charm-*.tar')
if len(charm_tarballs) != 1:
raise EasyBuildError(
"Expected to find exactly one tarball for Charm++, found: %s",
charm_tarballs)
extract_file(charm_tarballs[0], os.getcwd())
tup = (self.cfg['charm_arch'], self.cfg['charm_opts'],
self.cfg['parallel'], os.environ['CXXFLAGS'])
cmd = "./build charm++ %s %s -j%s %s -DMPICH_IGNORE_CXX_SEEK" % tup
charm_subdir = '.'.join(
os.path.basename(charm_tarballs[0]).split('.')[:-1])
self.log.debug("Building Charm++ using cmd '%s' in '%s'" %
(cmd, charm_subdir))
run_cmd(cmd, path=charm_subdir)
# compiler (options)
self.cfg.update(
'namd_cfg_opts', '--cc "%s" --cc-opts "%s"' %
(os.environ['CC'], os.environ['CFLAGS']))
self.cfg.update(
'namd_cfg_opts', '--cxx "%s" --cxx-opts "%s"' %
(os.environ['CXX'], os.environ['CXXFLAGS']))
# NAMD dependencies: CUDA, FFTW
cuda = get_software_root('CUDA')
if cuda:
self.cfg.update('namd_cfg_opts',
"--with-cuda --cuda-prefix %s" % cuda)
fftw = get_software_root('FFTW')
if fftw:
if LooseVersion(
get_software_version('FFTW')) >= LooseVersion('3.0'):
if LooseVersion(self.version) >= LooseVersion('2.9'):
self.cfg.update('namd_cfg_opts', "--with-fftw3")
else:
raise EasyBuildError(
"Using FFTW v3.x only supported in NAMD v2.9 and up.")
else:
self.cfg.update('namd_cfg_opts', "--with-fftw")
self.cfg.update('namd_cfg_opts', "--fftw-prefix %s" % fftw)
namd_charm_arch = "--charm-arch %s" % '-'.join(
self.cfg['charm_arch'].strip().split(' '))
cmd = "./config %s %s %s " % (self.namd_arch, namd_charm_arch,
self.cfg["namd_cfg_opts"])
run_cmd(cmd)
def configure_step(self):
"""Configure Xmipp build via a provided wrapper around scons."""
# check if all our dependencies are in place
self.python_root = get_software_root('Python')
if not self.python_root:
raise EasyBuildError(
"Python not loaded as a dependency, which is required for %s",
self.name)
python_libdir = det_pylibdir()
self.python_short_ver = '.'.join(
get_software_version('Python').split('.')[:2])
java_root = get_software_root('Java')
if not java_root:
raise EasyBuildError(
"Java not loaded as a dependency, which is required for %s",
self.name)
# extract some dependencies that we really need and can't find anywhere else
# alglib tarball has version in name, so lets find it with a glob
# we can't do this in extract step before these are in the original sources tarball, so we need to know
# startdir first
external_path = os.path.join(self.cfg['start_dir'], 'external')
alglib_tar = glob.glob(os.path.join(external_path, 'alglib*.tgz'))[0]
for src in [
'bilib.tgz', 'bilib.tgz', 'condor.tgz', alglib_tar, 'scons.tgz'
]:
extract_file(os.path.join(external_path, src), external_path)
# make sure we are back in the start dir
os.chdir(self.cfg['start_dir'])
# build step expects these to exist
mkdir(os.path.join(self.cfg['start_dir'], 'bin'))
mkdir(os.path.join(self.cfg['start_dir'], 'lib'))
python_inc_dir = os.path.join(self.python_root, 'include',
'python%s' % self.python_short_ver)
numpy_inc_dir = os.path.join(self.python_root, python_libdir, 'numpy',
'core', 'include')
if self.toolchain.mpi_family() == toolchain.INTELMPI:
mpi_bindir = os.path.join(get_software_root('impi'), 'intel64',
'bin')
else:
mpi_bindir = os.path.join(
get_software_root(self.toolchain.MPI_MODULE_NAME[0]), 'bin')
if not os.path.exists(numpy_inc_dir):
raise EasyBuildError("numpy 'include' directory %s not found",
numpy_inc_dir)
if not os.path.exists(mpi_bindir):
raise EasyBuildError("MPI 'bin' subdir %s does not exist",
mpi_bindir)
cmd = ' '.join([
self.cfg['preconfigopts'],
'python external/scons/scons.py',
'mode=configure',
'-j %s' % self.cfg['parallel'],
'--config=force',
'profile=no',
'fast=yes',
'warn=no',
'release=yes',
'gtest=no',
'cuda=no',
'debug=no',
'matlab=no',
'java=no',
'LINKERFORPROGRAMS="$CXX"',
'MPI_BINDIR=%s' % mpi_bindir,
'JAVA_HOME=%s' % java_root,
'JAVAC=javac',
'CC="$CC"',
'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK -I%s -I%s"' %
(python_inc_dir, numpy_inc_dir),
'CXX="$CXX"',
'MPI_CC="$MPICC"',
'MPI_CXX="$MPICXX"',
'MPI_INCLUDE="$MPI_INC_DIR"',
'MPI_LIBDIR="$MPI_LIB_DIR"',
'MPI_LINKERFORPROGRAMS="$MPICC"',
'LIBPATH="$LD_LIBRARY_PATH"',
self.cfg['configopts'],
])
run_cmd(cmd, log_all=True, simple=True)
def test_step(self):
"""Run WPS test (requires large dataset to be downloaded). """
wpsdir = None
def run_wps_cmd(cmdname, mpi_cmd=True):
"""Run a WPS command, and check for success."""
cmd = os.path.join(wpsdir, "%s.exe" % cmdname)
if mpi_cmd:
cmd = self.toolchain.mpi_cmd_for(cmd, 1)
(out, _) = run_cmd(cmd, log_all=True, simple=False)
re_success = re.compile("Successful completion of %s" % cmdname)
if not re_success.search(out):
self.log.error("%s.exe failed (pattern '%s' not found)?" % (cmdname, re_success.pattern))
if self.cfg['runtest']:
if not self.cfg['testdata']:
self.log.error("List of URLs for testdata not provided.")
wpsdir = os.path.join(self.builddir, "WPS")
try:
# create temporary directory
tmpdir = tempfile.mkdtemp()
os.chdir(tmpdir)
# download data
testdata_paths = []
for testdata in self.cfg['testdata']:
path = self.obtain_file(testdata)
if not path:
self.log.error("Downloading file from %s failed?" % testdata)
testdata_paths.append(path)
# unpack data
for path in testdata_paths:
extract_file(path, tmpdir)
# copy namelist.wps file
fn = "namelist.wps"
shutil.copy2(os.path.join(wpsdir, fn), tmpdir)
namelist_file = os.path.join(tmpdir, fn)
# GEOGRID
# setup directories and files
for d in os.listdir(os.path.join(tmpdir, "geog")):
os.symlink(os.path.join(tmpdir, "geog", d), os.path.join(tmpdir, d))
# patch namelist.wps file for geogrib
for line in fileinput.input(namelist_file, inplace=1, backup='.orig.geogrid'):
line = re.sub(r"^(\s*geog_data_path\s*=\s*).*$", r"\1 '%s'" % tmpdir, line)
sys.stdout.write(line)
# GEOGRID.TBL
geogrid_dir = os.path.join(tmpdir, "geogrid")
os.mkdir(geogrid_dir)
os.symlink(os.path.join(wpsdir, "geogrid", "GEOGRID.TBL.ARW"),
os.path.join(geogrid_dir, "GEOGRID.TBL"))
# run geogrid.exe
run_wps_cmd("geogrid")
# UNGRIB
# determine start and end time stamps of grib files
grib_file_prefix = "fnl_"
k = len(grib_file_prefix)
fs = [f for f in sorted(os.listdir('.')) if f.startswith(grib_file_prefix)]
start = "%s:00:00" % fs[0][k:]
end = "%s:00:00" % fs[-1][k:]
# patch namelist.wps file for ungrib
shutil.copy2(os.path.join(wpsdir, "namelist.wps"), tmpdir)
for line in fileinput.input(namelist_file, inplace=1, backup='.orig.ungrib'):
line = re.sub(r"^(\s*start_date\s*=\s*).*$", r"\1 '%s','%s'," % (start, start), line)
line = re.sub(r"^(\s*end_date\s*=\s*).*$", r"\1 '%s','%s'," % (end, end), line)
sys.stdout.write(line)
# copy correct Vtable
shutil.copy2(os.path.join(wpsdir, "ungrib", "Variable_Tables", "Vtable.ARW"),
os.path.join(tmpdir, "Vtable"))
# run link_grib.csh script
cmd = "%s %s*" % (os.path.join(wpsdir, "link_grib.csh"), grib_file_prefix)
run_cmd(cmd, log_all=True, simple=True)
# run ungrib.exe
run_wps_cmd("ungrib", mpi_cmd=False)
# METGRID.TBL
metgrid_dir = os.path.join(tmpdir, "metgrid")
os.mkdir(metgrid_dir)
os.symlink(os.path.join(wpsdir, "metgrid", "METGRID.TBL.ARW"),
os.path.join(metgrid_dir, "METGRID.TBL"))
# run metgrid.exe
run_wps_cmd('metgrid')
# clean up
rmtree2(tmpdir)
os.chdir(self.builddir)
except OSError, err:
self.log.error("Failed to run WPS test: %s" % err)
def install_step(self):
"""
Actual installation
- create silent cfg file
- execute command
"""
impiver = LooseVersion(self.version)
if impiver >= LooseVersion('4.0.1'):
# impi starting from version 4.0.1.x uses standard installation procedure.
silent_cfg_names_map = {}
if impiver < LooseVersion('4.1.1'):
# since impi v4.1.1, silent.cfg has been slightly changed to be 'more standard'
silent_cfg_names_map.update({
'activation_name': ACTIVATION_NAME_2012,
'license_file_name': LICENSE_FILE_NAME_2012,
})
super(EB_impi, self).install_step(silent_cfg_names_map=silent_cfg_names_map)
# impi v4.1.1 and v5.0.1 installers create impi/<version> subdir, so stuff needs to be moved afterwards
if impiver == LooseVersion('4.1.1.036') or impiver >= LooseVersion('5.0.1.035'):
super(EB_impi, self).move_after_install()
else:
# impi up until version 4.0.0.x uses custom installation procedure.
silent = """[mpi]
INSTALLDIR=%(ins)s
LICENSEPATH=%(lic)s
INSTALLMODE=NONRPM
INSTALLUSER=NONROOT
UPDATE_LD_SO_CONF=NO
PROCEED_WITHOUT_PYTHON=yes
AUTOMOUNTED_CLUSTER=yes
EULA=accept
[mpi-rt]
INSTALLDIR=%(ins)s
LICENSEPATH=%(lic)s
INSTALLMODE=NONRPM
INSTALLUSER=NONROOT
UPDATE_LD_SO_CONF=NO
PROCEED_WITHOUT_PYTHON=yes
AUTOMOUNTED_CLUSTER=yes
EULA=accept
""" % {'lic': self.license_file, 'ins': self.installdir}
# already in correct directory
silentcfg = os.path.join(os.getcwd(), "silent.cfg")
write_file(silentcfg, silent)
self.log.debug("Contents of %s: %s", silentcfg, silent)
tmpdir = os.path.join(os.getcwd(), self.version, 'mytmpdir')
mkdir(tmpdir, parents=True)
cmd = "./install.sh --tmp-dir=%s --silent=%s" % (tmpdir, silentcfg)
run_cmd(cmd, log_all=True, simple=True)
# recompile libfabric (if requested)
# some Intel MPI versions (like 2019 update 6) no longer ship libfabric sources
libfabric_path = os.path.join(self.installdir, 'libfabric')
if impiver >= LooseVersion('2019') and self.cfg['libfabric_rebuild']:
if self.cfg['ofi_internal']:
libfabric_src_tgz_fn = 'src.tgz'
if os.path.exists(os.path.join(libfabric_path, libfabric_src_tgz_fn)):
change_dir(libfabric_path)
srcdir = extract_file(libfabric_src_tgz_fn, os.getcwd(), change_into_dir=False)
change_dir(srcdir)
libfabric_installpath = os.path.join(self.installdir, 'intel64', 'libfabric')
make = 'make'
if self.cfg['parallel']:
make += ' -j %d' % self.cfg['parallel']
cmds = [
'./configure --prefix=%s %s' % (libfabric_installpath, self.cfg['libfabric_configopts']),
make,
'make install'
]
for cmd in cmds:
run_cmd(cmd, log_all=True, simple=True)
else:
self.log.info("Rebuild of libfabric is requested, but %s does not exist, so skipping...",
libfabric_src_tgz_fn)
else:
raise EasyBuildError("Rebuild of libfabric is requested, but ofi_internal is set to False.")
def configure_step(self):
"""Custom configure step for NAMD, we build charm++ first (if required)."""
# complete Charm ++ and NAMD architecture string with compiler family
comp_fam = self.toolchain.comp_family()
if self.toolchain.options['usempi']:
charm_arch_comp = 'mpicxx'
else:
charm_arch_comps = {
toolchain.GCC: 'gcc',
toolchain.INTELCOMP: 'icc',
}
charm_arch_comp = charm_arch_comps.get(comp_fam, None)
namd_comps = {
toolchain.GCC: 'g++',
toolchain.INTELCOMP: 'icc',
}
namd_comp = namd_comps.get(comp_fam, None)
if charm_arch_comp is None or namd_comp is None:
self.log.error("Unknown compiler family, can't complete Charm++/NAMD target architecture.")
self.cfg.update('charm_arch', charm_arch_comp)
self.log.info("Updated 'charm_arch': %s" % self.cfg['charm_arch'])
self.namd_arch = '%s-%s' % (self.cfg['namd_basearch'], namd_comp)
self.log.info("Completed NAMD target architecture: %s" % self.namd_arch)
charm_tarballs = glob.glob('charm-*.tar')
if len(charm_tarballs) != 1:
self.log.error("Expected to find exactly one tarball for Charm++, found: %s" % charm_tarballs)
extract_file(charm_tarballs[0], os.getcwd())
tup = (self.cfg['charm_arch'], self.cfg['charm_opts'], self.cfg['parallel'], os.environ['CXXFLAGS'])
cmd = "./build charm++ %s %s -j%s %s -DMPICH_IGNORE_CXX_SEEK" % tup
charm_subdir = '.'.join(os.path.basename(charm_tarballs[0]).split('.')[:-1])
self.log.debug("Building Charm++ using cmd '%s' in '%s'" % (cmd, charm_subdir))
run_cmd(cmd, path=charm_subdir)
# compiler (options)
self.cfg.update('namd_cfg_opts', '--cc "%s" --cc-opts "%s"' % (os.environ['CC'], os.environ['CFLAGS']))
self.cfg.update('namd_cfg_opts', '--cxx "%s" --cxx-opts "%s"' % (os.environ['CXX'], os.environ['CXXFLAGS']))
# NAMD dependencies: CUDA, FFTW
cuda = get_software_root('CUDA')
if cuda:
self.cfg.update('namd_cfg_opts', "--with-cuda --cuda-prefix %s" % cuda)
fftw = get_software_root('FFTW')
if fftw:
if LooseVersion(get_software_version('FFTW')) >= LooseVersion('3.0'):
if LooseVersion(self.version) >= LooseVersion('2.9'):
self.cfg.update('namd_cfg_opts', "--with-fftw3")
else:
self.log.error("Using FFTW v3.x only supported in NAMD v2.9 and up.")
else:
self.cfg.update('namd_cfg_opts', "--with-fftw")
self.cfg.update('namd_cfg_opts', "--fftw-prefix %s" % fftw)
namd_charm_arch = "--charm-arch %s" % '-'.join(self.cfg['charm_arch'].strip().split(' '))
cmd = "./config %s %s %s " % (self.namd_arch, namd_charm_arch, self.cfg["namd_cfg_opts"])
run_cmd(cmd)
def test_step(self):
"""Run WIEN2k test benchmarks. """
def run_wien2k_test(cmd_arg):
"""Run a WPS command, and check for success."""
cmd = "x_lapw lapw1 %s" % cmd_arg
(out, _) = run_cmd(cmd, log_all=True, simple=False)
re_success = re.compile("LAPW1\s+END")
if not re_success.search(out):
self.log.error(
"Test '%s' in %s failed (pattern '%s' not found)?" % (cmd, os.getcwd(), re_success.pattern)
)
else:
self.log.info("Test '%s' seems to have run successfully: %s" % (cmd, out))
if self.cfg["runtest"]:
if not self.cfg["testdata"]:
self.log.error("List of URLs for testdata not provided.")
path = os.getenv("PATH")
env.setvar("PATH", "%s:%s" % (self.installdir, path))
try:
cwd = os.getcwd()
# create temporary directory
tmpdir = tempfile.mkdtemp()
os.chdir(tmpdir)
# download data
testdata_paths = {}
for testdata in self.cfg["testdata"]:
td_path = self.obtain_file(testdata)
if not td_path:
self.log.error("Downloading file from %s failed?" % testdata)
testdata_paths.update({os.path.basename(testdata): td_path})
self.log.debug("testdata_paths: %s" % testdata_paths)
# unpack serial benchmark
serial_test_name = "test_case"
extract_file(testdata_paths["%s.tar.gz" % serial_test_name], tmpdir)
# run serial benchmark
os.chdir(os.path.join(tmpdir, serial_test_name))
run_wien2k_test("-c")
# unpack parallel benchmark (in serial benchmark dir)
parallel_test_name = "mpi-benchmark"
extract_file(testdata_paths["%s.tar.gz" % parallel_test_name], tmpdir)
# run parallel benchmark
os.chdir(os.path.join(tmpdir, serial_test_name))
run_wien2k_test("-p")
os.chdir(cwd)
shutil.rmtree(tmpdir)
except OSError, err:
self.log.error("Failed to run WIEN2k benchmark tests: %s" % err)
# reset original path
env.setvar("PATH", path)
self.log.debug("Current dir: %s" % os.getcwd())
def test_step(self):
"""Run WIEN2k test benchmarks. """
def run_wien2k_test(cmd_arg):
"""Run a WPS command, and check for success."""
cmd = "x_lapw lapw1 %s" % cmd_arg
(out, _) = run_cmd(cmd, log_all=True, simple=False)
re_success = re.compile("LAPW1\s+END")
if not re_success.search(out):
self.log.error(
"Test '%s' in %s failed (pattern '%s' not found)?" %
(cmd, os.getcwd(), re_success.pattern))
else:
self.log.info("Test '%s' seems to have run successfully: %s" %
(cmd, out))
if self.cfg['runtest']:
if not self.cfg['testdata']:
self.log.error("List of URLs for testdata not provided.")
path = os.getenv('PATH')
env.setvar('PATH', "%s:%s" % (self.installdir, path))
try:
cwd = os.getcwd()
# create temporary directory
tmpdir = tempfile.mkdtemp()
os.chdir(tmpdir)
# download data
testdata_paths = {}
for testdata in self.cfg['testdata']:
td_path = self.obtain_file(testdata)
if not td_path:
self.log.error("Downloading file from %s failed?" %
testdata)
testdata_paths.update(
{os.path.basename(testdata): td_path})
self.log.debug('testdata_paths: %s' % testdata_paths)
# unpack serial benchmark
serial_test_name = "test_case"
extract_file(testdata_paths['%s.tar.gz' % serial_test_name],
tmpdir)
# run serial benchmark
os.chdir(os.path.join(tmpdir, serial_test_name))
run_wien2k_test("-c")
# unpack parallel benchmark (in serial benchmark dir)
parallel_test_name = "mpi-benchmark"
extract_file(testdata_paths['%s.tar.gz' % parallel_test_name],
tmpdir)
# run parallel benchmark
os.chdir(os.path.join(tmpdir, serial_test_name))
run_wien2k_test("-p")
os.chdir(cwd)
rmtree2(tmpdir)
except OSError, err:
self.log.error("Failed to run WIEN2k benchmark tests: %s" %
err)
# reset original path
env.setvar('PATH', path)
self.log.debug("Current dir: %s" % os.getcwd())
def test_step(self):
"""Run WPS test (requires large dataset to be downloaded). """
wpsdir = None
def run_wps_cmd(cmdname, mpi_cmd=True):
"""Run a WPS command, and check for success."""
cmd = os.path.join(wpsdir, "%s.exe" % cmdname)
if mpi_cmd:
if build_option('mpi_tests'):
cmd = self.toolchain.mpi_cmd_for(cmd, 1)
else:
self.log.info("Skipping MPI test for %s, since MPI tests are disabled", cmd)
return
(out, _) = run_cmd(cmd, log_all=True, simple=False)
re_success = re.compile("Successful completion of %s" % cmdname)
if not re_success.search(out):
raise EasyBuildError("%s.exe failed (pattern '%s' not found)?", cmdname, re_success.pattern)
if self.cfg['runtest']:
if not self.cfg['testdata']:
raise EasyBuildError("List of URLs for testdata not provided.")
wpsdir = os.path.join(self.builddir, self.wps_subdir)
try:
# create temporary directory
tmpdir = tempfile.mkdtemp()
change_dir(tmpdir)
# download data
testdata_paths = []
for testdata in self.cfg['testdata']:
path = self.obtain_file(testdata)
if not path:
raise EasyBuildError("Downloading file from %s failed?", testdata)
testdata_paths.append(path)
# unpack data
for path in testdata_paths:
extract_file(path, tmpdir)
namelist_file = os.path.join(tmpdir, 'namelist.wps')
# GEOGRID
# setup directories and files
if LooseVersion(self.version) < LooseVersion("4.0"):
geog_data_dir = "geog"
else:
geog_data_dir = "WPS_GEOG"
for dir_name in os.listdir(os.path.join(tmpdir, geog_data_dir)):
symlink(os.path.join(tmpdir, geog_data_dir, dir_name), os.path.join(tmpdir, dir_name))
# copy namelist.wps file and patch it for geogrid
copy_file(os.path.join(wpsdir, 'namelist.wps'), namelist_file)
regex_subs = [(r"^(\s*geog_data_path\s*=\s*).*$", r"\1 '%s'" % tmpdir)]
apply_regex_substitutions(namelist_file, regex_subs)
# GEOGRID.TBL
geogrid_dir = os.path.join(tmpdir, 'geogrid')
mkdir(geogrid_dir)
symlink(os.path.join(wpsdir, 'geogrid', 'GEOGRID.TBL.ARW'),
os.path.join(geogrid_dir, 'GEOGRID.TBL'))
# run geogrid.exe
run_wps_cmd("geogrid")
# UNGRIB
# determine start and end time stamps of grib files
grib_file_prefix = "fnl_"
k = len(grib_file_prefix)
fs = [f for f in sorted(os.listdir('.')) if f.startswith(grib_file_prefix)]
start = "%s:00:00" % fs[0][k:]
end = "%s:00:00" % fs[-1][k:]
# copy namelist.wps file and patch it for ungrib
copy_file(os.path.join(wpsdir, 'namelist.wps'), namelist_file)
regex_subs = [
(r"^(\s*start_date\s*=\s*).*$", r"\1 '%s','%s'," % (start, start)),
(r"^(\s*end_date\s*=\s*).*$", r"\1 '%s','%s'," % (end, end)),
]
apply_regex_substitutions(namelist_file, regex_subs)
# copy correct Vtable
vtable_dir = os.path.join(wpsdir, 'ungrib', 'Variable_Tables')
if os.path.exists(os.path.join(vtable_dir, 'Vtable.ARW')):
copy_file(os.path.join(vtable_dir, 'Vtable.ARW'), os.path.join(tmpdir, 'Vtable'))
elif os.path.exists(os.path.join(vtable_dir, 'Vtable.ARW.UPP')):
copy_file(os.path.join(vtable_dir, 'Vtable.ARW.UPP'), os.path.join(tmpdir, 'Vtable'))
else:
raise EasyBuildError("Could not find Vtable file to use for testing ungrib")
# run link_grib.csh script
cmd = "%s %s*" % (os.path.join(wpsdir, "link_grib.csh"), grib_file_prefix)
run_cmd(cmd, log_all=True, simple=True)
# run ungrib.exe
run_wps_cmd("ungrib", mpi_cmd=False)
# METGRID.TBL
metgrid_dir = os.path.join(tmpdir, 'metgrid')
mkdir(metgrid_dir)
symlink(os.path.join(wpsdir, 'metgrid', 'METGRID.TBL.ARW'),
os.path.join(metgrid_dir, 'METGRID.TBL'))
# run metgrid.exe
run_wps_cmd('metgrid')
# clean up
change_dir(self.builddir)
remove_dir(tmpdir)
except OSError as err:
raise EasyBuildError("Failed to run WPS test: %s", err)
def test_step(self):
"""Run WPS test (requires large dataset to be downloaded). """
wpsdir = None
def run_wps_cmd(cmdname, mpi_cmd=True):
"""Run a WPS command, and check for success."""
cmd = os.path.join(wpsdir, "%s.exe" % cmdname)
if mpi_cmd:
if build_option('mpi_tests'):
cmd = self.toolchain.mpi_cmd_for(cmd, 1)
else:
self.log.info(
"Skipping MPI test for %s, since MPI tests are disabled",
cmd)
return
(out, _) = run_cmd(cmd, log_all=True, simple=False)
re_success = re.compile("Successful completion of %s" % cmdname)
if not re_success.search(out):
raise EasyBuildError("%s.exe failed (pattern '%s' not found)?",
cmdname, re_success.pattern)
if self.cfg['runtest']:
if not self.cfg['testdata']:
raise EasyBuildError("List of URLs for testdata not provided.")
wpsdir = os.path.join(self.builddir, self.wps_subdir)
try:
# create temporary directory
tmpdir = tempfile.mkdtemp()
change_dir(tmpdir)
# download data
testdata_paths = []
for testdata in self.cfg['testdata']:
path = self.obtain_file(testdata)
if not path:
raise EasyBuildError(
"Downloading file from %s failed?", testdata)
testdata_paths.append(path)
# unpack data
for path in testdata_paths:
srcdir = extract_file(path, tmpdir, change_into_dir=False)
change_dir(srcdir)
namelist_file = os.path.join(tmpdir, 'namelist.wps')
# GEOGRID
# setup directories and files
if LooseVersion(self.version) < LooseVersion("4.0"):
geog_data_dir = "geog"
else:
geog_data_dir = "WPS_GEOG"
for dir_name in os.listdir(os.path.join(tmpdir,
geog_data_dir)):
symlink(os.path.join(tmpdir, geog_data_dir, dir_name),
os.path.join(tmpdir, dir_name))
# copy namelist.wps file and patch it for geogrid
copy_file(os.path.join(wpsdir, 'namelist.wps'), namelist_file)
regex_subs = [(r"^(\s*geog_data_path\s*=\s*).*$",
r"\1 '%s'" % tmpdir)]
apply_regex_substitutions(namelist_file, regex_subs)
# GEOGRID.TBL
geogrid_dir = os.path.join(tmpdir, 'geogrid')
mkdir(geogrid_dir)
symlink(os.path.join(wpsdir, 'geogrid', 'GEOGRID.TBL.ARW'),
os.path.join(geogrid_dir, 'GEOGRID.TBL'))
# run geogrid.exe
run_wps_cmd("geogrid")
# UNGRIB
# determine start and end time stamps of grib files
grib_file_prefix = "fnl_"
k = len(grib_file_prefix)
fs = [
f for f in sorted(os.listdir('.'))
if f.startswith(grib_file_prefix)
]
start = "%s:00:00" % fs[0][k:]
end = "%s:00:00" % fs[-1][k:]
# copy namelist.wps file and patch it for ungrib
copy_file(os.path.join(wpsdir, 'namelist.wps'), namelist_file)
regex_subs = [
(r"^(\s*start_date\s*=\s*).*$",
r"\1 '%s','%s'," % (start, start)),
(r"^(\s*end_date\s*=\s*).*$",
r"\1 '%s','%s'," % (end, end)),
]
apply_regex_substitutions(namelist_file, regex_subs)
# copy correct Vtable
vtable_dir = os.path.join(wpsdir, 'ungrib', 'Variable_Tables')
if os.path.exists(os.path.join(vtable_dir, 'Vtable.ARW')):
copy_file(os.path.join(vtable_dir, 'Vtable.ARW'),
os.path.join(tmpdir, 'Vtable'))
elif os.path.exists(os.path.join(vtable_dir,
'Vtable.ARW.UPP')):
copy_file(os.path.join(vtable_dir, 'Vtable.ARW.UPP'),
os.path.join(tmpdir, 'Vtable'))
else:
raise EasyBuildError(
"Could not find Vtable file to use for testing ungrib")
# run link_grib.csh script
cmd = "%s %s*" % (os.path.join(
wpsdir, "link_grib.csh"), grib_file_prefix)
run_cmd(cmd, log_all=True, simple=True)
# run ungrib.exe
run_wps_cmd("ungrib", mpi_cmd=False)
# METGRID.TBL
metgrid_dir = os.path.join(tmpdir, 'metgrid')
mkdir(metgrid_dir)
symlink(os.path.join(wpsdir, 'metgrid', 'METGRID.TBL.ARW'),
os.path.join(metgrid_dir, 'METGRID.TBL'))
# run metgrid.exe
run_wps_cmd('metgrid')
# clean up
change_dir(self.builddir)
remove_dir(tmpdir)
except OSError as err:
raise EasyBuildError("Failed to run WPS test: %s", err)
def test_step(self):
"""Run WIEN2k test benchmarks. """
def run_wien2k_test(cmd_arg):
"""Run a WPS command, and check for success."""
cmd = "x_lapw lapw1 %s" % cmd_arg
(out, _) = run_cmd(cmd, log_all=True, simple=False)
re_success = re.compile("LAPW1\s+END")
if not re_success.search(out):
raise EasyBuildError(
"Test '%s' in %s failed (pattern '%s' not found)?", cmd,
os.getcwd(), re_success.pattern)
else:
self.log.info("Test '%s' seems to have run successfully: %s" %
(cmd, out))
if self.cfg['runtest']:
if not self.cfg['testdata']:
raise EasyBuildError("List of URLs for testdata not provided.")
# prepend $PATH with install directory, define $SCRATCH which is used by the tests
env.setvar('PATH', "%s:%s" % (self.installdir, os.environ['PATH']))
try:
cwd = os.getcwd()
# create temporary directory
tmpdir = tempfile.mkdtemp()
os.chdir(tmpdir)
self.log.info("Running tests in %s" % tmpdir)
scratch = os.path.join(tmpdir, 'scratch')
mkdir(scratch)
env.setvar('SCRATCH', scratch)
# download data
testdata_paths = {}
for testdata in self.cfg['testdata']:
td_path = self.obtain_file(testdata)
if not td_path:
raise EasyBuildError(
"Downloading file from %s failed?", testdata)
testdata_paths.update(
{os.path.basename(testdata): td_path})
self.log.debug('testdata_paths: %s' % testdata_paths)
# unpack serial benchmark
serial_test_name = "test_case"
srcdir = extract_file(testdata_paths['%s.tar.gz' %
serial_test_name],
tmpdir,
change_into_dir=False)
change_dir(srcdir)
# run serial benchmark
os.chdir(os.path.join(tmpdir, serial_test_name))
run_wien2k_test("-c")
# unpack parallel benchmark (in serial benchmark dir)
parallel_test_name = "mpi-benchmark"
srcdir = extract_file(testdata_paths['%s.tar.gz' %
parallel_test_name],
tmpdir,
change_into_dir=False)
change_dir(srcdir)
# run parallel benchmark
os.chdir(os.path.join(tmpdir, serial_test_name))
run_wien2k_test("-p")
os.chdir(cwd)
remove_dir(tmpdir)
except OSError as err:
raise EasyBuildError(
"Failed to run WIEN2k benchmark tests: %s", err)
self.log.debug("Current dir: %s" % os.getcwd())
def test_step(self):
"""Run WIEN2k test benchmarks. """
def run_wien2k_test(cmd_arg):
"""Run a WPS command, and check for success."""
cmd = "x_lapw lapw1 %s" % cmd_arg
(out, _) = run_cmd(cmd, log_all=True, simple=False)
re_success = re.compile("LAPW1\s+END")
if not re_success.search(out):
raise EasyBuildError("Test '%s' in %s failed (pattern '%s' not found)?",
cmd, os.getcwd(), re_success.pattern)
else:
self.log.info("Test '%s' seems to have run successfully: %s" % (cmd, out))
if self.cfg['runtest']:
if not self.cfg['testdata']:
raise EasyBuildError("List of URLs for testdata not provided.")
# prepend $PATH with install directory, define $SCRATCH which is used by the tests
env.setvar('PATH', "%s:%s" % (self.installdir, os.environ['PATH']))
try:
cwd = os.getcwd()
# create temporary directory
tmpdir = tempfile.mkdtemp()
os.chdir(tmpdir)
self.log.info("Running tests in %s" % tmpdir)
scratch = os.path.join(tmpdir, 'scratch')
mkdir(scratch)
env.setvar('SCRATCH', scratch)
# download data
testdata_paths = {}
for testdata in self.cfg['testdata']:
td_path = self.obtain_file(testdata)
if not td_path:
raise EasyBuildError("Downloading file from %s failed?", testdata)
testdata_paths.update({os.path.basename(testdata): td_path})
self.log.debug('testdata_paths: %s' % testdata_paths)
# unpack serial benchmark
serial_test_name = "test_case"
extract_file(testdata_paths['%s.tar.gz' % serial_test_name], tmpdir)
# run serial benchmark
os.chdir(os.path.join(tmpdir, serial_test_name))
run_wien2k_test("-c")
# unpack parallel benchmark (in serial benchmark dir)
parallel_test_name = "mpi-benchmark"
extract_file(testdata_paths['%s.tar.gz' % parallel_test_name], tmpdir)
# run parallel benchmark
os.chdir(os.path.join(tmpdir, serial_test_name))
run_wien2k_test("-p")
os.chdir(cwd)
rmtree2(tmpdir)
except OSError, err:
raise EasyBuildError("Failed to run WIEN2k benchmark tests: %s", err)
self.log.debug("Current dir: %s" % os.getcwd())