def basic_options(self):
"""basic runtime options"""
all_stops = [x[0] for x in EasyBlock.get_steps()]
strictness_options = [filetools.IGNORE, filetools.WARN, filetools.ERROR]
try:
default_robot_path = get_paths_for("easyconfigs", robot_path=None)[0]
except:
self.log.warning("basic_options: unable to determine default easyconfig path")
default_robot_path = False # False as opposed to None, since None is used for indicating that --robot was not used
descr = ("Basic options", "Basic runtime options for EasyBuild.")
opts = OrderedDict({
"only-blocks":("Only build listed blocks",
None, "extend", None, "b", {'metavar':"BLOCKS"}),
"force":(("Force to rebuild software even if it's already installed "
"(i.e. if it can be found as module)"),
None, "store_true", False, "f"),
"job":("Submit the build as a job", None, "store_true", False),
"skip":("Skip existing software (useful for installing additional packages)",
None, "store_true", False, "k"),
"robot":("Path to search for easyconfigs for missing dependencies." ,
None, "store_or_None", default_robot_path, "r", {'metavar':"PATH"}),
"stop":("Stop the installation after certain step",
"choice", "store_or_None", "source", "s", all_stops),
"strict":("Set strictness level",
"choice", "store", filetools.WARN, strictness_options),
"logtostdout":("Redirect main log to stdout", None, "store_true", False, "l"),
})
self.log.debug("basic_options: descr %s opts %s" % (descr, opts))
self.add_group_parser(opts, descr)
def suite():
"""Return all easyblock --module-only tests."""
# initialize configuration (required for e.g. default modules_tool setting)
cleanup()
eb_go = eboptions.parse_options(args=['--prefix=%s' % TMPDIR])
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
# enable --force --module-only
'force': True,
'module_only': True,
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
config.set_tmpdir()
# dynamically generate a separate test for each of the available easyblocks
easyblocks_path = get_paths_for("easyblocks")[0]
all_pys = glob.glob('%s/*/*.py' % easyblocks_path)
easyblocks = [eb for eb in all_pys if os.path.basename(eb) != '__init__.py' and '/test/' not in eb]
# filter out no longer supported easyblocks
easyblocks = [e for e in easyblocks if os.path.basename(e) not in ['versionindependendpythonpackage.py']]
for easyblock in easyblocks:
# dynamically define new inner functions that can be added as class methods to ModuleOnlyTest
exec("def innertest(self): template_module_only_test(self, '%s')" % easyblock)
innertest.__doc__ = "Test for using --module-only with easyblock %s" % easyblock
innertest.__name__ = "test_easyblock_%s" % '_'.join(easyblock.replace('.py', '').split('/'))
setattr(ModuleOnlyTest, innertest.__name__, innertest)
return TestLoader().loadTestsFromTestCase(ModuleOnlyTest)
def basic_options(self):
"""basic runtime options"""
all_stops = [x[0] for x in EasyBlock.get_steps()]
strictness_options = [run.IGNORE, run.WARN, run.ERROR]
try:
default_robot_path = get_paths_for("easyconfigs", robot_path=None)[0]
except:
self.log.warning("basic_options: unable to determine default easyconfig path")
default_robot_path = False # False as opposed to None, since None is used for indicating that --robot was not used
descr = ("Basic options", "Basic runtime options for EasyBuild.")
opts = OrderedDict({
'dry-run': ("Print build overview incl. dependencies (full paths)", None, 'store_true', False),
'dry-run-short': ("Print build overview incl. dependencies (short paths)", None, 'store_true', False, 'D'),
'force': ("Force to rebuild software even if it's already installed (i.e. if it can be found as module)",
None, 'store_true', False, 'f'),
'job': ("Submit the build as a job", None, 'store_true', False),
'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
'robot': ("Path(s) to search for easyconfigs for missing dependencies (colon-separated)" ,
None, 'store_or_None', default_robot_path, 'r', {'metavar': 'PATH'}),
'skip': ("Skip existing software (useful for installing additional packages)",
None, 'store_true', False, 'k'),
'stop': ("Stop the installation after certain step", 'choice', 'store_or_None', 'source', 's', all_stops),
'strict': ("Set strictness level", 'choice', 'store', run.WARN, strictness_options),
})
self.log.debug("basic_options: descr %s opts %s" % (descr, opts))
self.add_group_parser(opts, descr)
def test_path_to_top_of_module_tree_categorized_hmns(self):
"""
Test function to determine path to top of the module tree for a categorized hierarchical module naming
scheme.
"""
ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [ecs_dir],
'valid_stops': all_stops,
'validate': False,
}
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'CategorizedHMNS'
init_config(build_options=build_options)
self.setup_categorized_hmns_modules()
mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
init_modpaths = [os.path.join(mod_prefix, 'Core', 'compiler'), os.path.join(mod_prefix, 'Core', 'toolchain')]
deps = ['GCC/4.7.2', 'OpenMPI/1.6.4', 'FFTW/3.3.3', 'OpenBLAS/0.2.6-LAPACK-3.4.2',
'ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2']
core = os.path.join(mod_prefix, 'Core')
path = self.modtool.path_to_top_of_module_tree(init_modpaths, 'goolf/1.4.10', os.path.join(core, 'toolchain'), deps)
self.assertEqual(path, [])
path = self.modtool.path_to_top_of_module_tree(init_modpaths, 'GCC/4.7.2', os.path.join(core, 'compiler'), [])
self.assertEqual(path, [])
full_mod_subdir = os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'mpi')
deps = ['GCC/4.7.2', 'hwloc/1.6.2']
path = self.modtool.path_to_top_of_module_tree(init_modpaths, 'OpenMPI/1.6.4', full_mod_subdir, deps)
self.assertEqual(path, ['GCC/4.7.2'])
full_mod_subdir = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4', 'numlib')
deps = ['GCC/4.7.2', 'OpenMPI/1.6.4']
path = self.modtool.path_to_top_of_module_tree(init_modpaths, 'FFTW/3.3.3', full_mod_subdir, deps)
self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
def basic_options(self):
"""basic runtime options"""
all_stops = [x[0] for x in EasyBlock.get_steps()]
strictness_options = [run.IGNORE, run.WARN, run.ERROR]
descr = ("Basic options", "Basic runtime options for EasyBuild.")
opts = OrderedDict({
'dry-run': ("Print build overview incl. dependencies (full paths)", None, 'store_true', False),
'dry-run-short': ("Print build overview incl. dependencies (short paths)", None, 'store_true', False, 'D'),
'force': ("Force to rebuild software even if it's already installed (i.e. if it can be found as module)",
None, 'store_true', False, 'f'),
'job': ("Submit the build as a job", None, 'store_true', False),
'logtostdout': ("Redirect main log to stdout", None, 'store_true', False, 'l'),
'only-blocks': ("Only build listed blocks", None, 'extend', None, 'b', {'metavar': 'BLOCKS'}),
'robot': ("Enable dependency resolution, using easyconfigs in specified paths",
'pathlist', 'store_or_None', [], 'r', {'metavar': 'PATH[%sPATH]' % os.pathsep}),
'robot-paths': ("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
'pathlist', 'add_flex', self.default_robot_paths, {'metavar': 'PATH[%sPATH]' % os.pathsep}),
'skip': ("Skip existing software (useful for installing additional packages)",
None, 'store_true', False, 'k'),
'stop': ("Stop the installation after certain step",
'choice', 'store_or_None', SOURCE_STEP, 's', all_stops),
'strict': ("Set strictness level", 'choice', 'store', DEFAULT_STRICT, strictness_options),
})
self.log.debug("basic_options: descr %s opts %s" % (descr, opts))
self.add_group_parser(opts, descr)
def test_path_to_top_of_module_tree_categorized_hmns(self):
"""
Test function to determine path to top of the module tree for a categorized hierarchical module naming
scheme.
"""
ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [ecs_dir],
'valid_stops': all_stops,
'validate': False,
}
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'CategorizedHMNS'
init_config(build_options=build_options)
self.setup_categorized_hmns_modules()
modtool = modules_tool()
mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
init_modpaths = [os.path.join(mod_prefix, 'Core', 'compiler'), os.path.join(mod_prefix, 'Core', 'toolchain')]
deps = ['GCC/4.7.2', 'OpenMPI/1.6.4', 'FFTW/3.3.3', 'OpenBLAS/0.2.6-LAPACK-3.4.2',
'ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2']
path = modtool.path_to_top_of_module_tree(init_modpaths, 'goolf/1.4.10', os.path.join(mod_prefix, 'Core', 'toolchain'), deps)
self.assertEqual(path, [])
path = modtool.path_to_top_of_module_tree(init_modpaths, 'GCC/4.7.2', os.path.join(mod_prefix, 'Core', 'compiler'), [])
self.assertEqual(path, [])
full_mod_subdir = os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2', 'mpi')
deps = ['GCC/4.7.2', 'hwloc/1.6.2']
path = modtool.path_to_top_of_module_tree(init_modpaths, 'OpenMPI/1.6.4', full_mod_subdir, deps)
self.assertEqual(path, ['GCC/4.7.2'])
full_mod_subdir = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4', 'numlib')
deps = ['GCC/4.7.2', 'OpenMPI/1.6.4']
path = modtool.path_to_top_of_module_tree(init_modpaths, 'FFTW/3.3.3', full_mod_subdir, deps)
self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
def init_config(args=None, build_options=None, with_include=True):
"""(re)initialize configuration"""
cleanup()
# initialize configuration so config.get_modules_tool function works
eb_go = eboptions.parse_options(args=args, with_include=with_include)
config.init(eb_go.options, eb_go.get_options_by_section('config'))
# initialize build options
if build_options is None:
build_options = {}
default_build_options = {
'extended_dry_run': False,
'external_modules_metadata': ConfigObj(),
'local_var_naming_check': 'error',
'silence_deprecation_warnings': eb_go.options.silence_deprecation_warnings,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
for key in default_build_options:
if key not in build_options:
build_options[key] = default_build_options[key]
config.init_build_options(build_options=build_options)
return eb_go.options
def basic_options(self):
"""basic runtime options"""
all_stops = [x[0] for x in EasyBlock.get_steps()]
strictness_options = [filetools.IGNORE, filetools.WARN, filetools.ERROR]
try:
default_robot_path = get_paths_for("easyconfigs", robot_path=None)[0]
except:
self.log.warning("basic_options: unable to determine default easyconfig path")
default_robot_path = False # False as opposed to None, since None is used for indicating that --robot was not used
descr = ("Basic options", "Basic runtime options for EasyBuild.")
opts = OrderedDict({
"only-blocks":("Only build listed blocks",
None, "extend", None, "b", {'metavar':"BLOCKS"}),
"force":(("Force to rebuild software even if it's already installed "
"(i.e. if it can be found as module)"),
None, "store_true", False, "f"),
"job":("Submit the build as a job", None, "store_true", False),
"skip":("Skip existing software (useful for installing additional packages)",
None, "store_true", False, "k"),
"robot":("Path to search for easyconfigs for missing dependencies." ,
None, "store_or_None", default_robot_path, "r", {'metavar':"PATH"}),
"stop":("Stop the installation after certain step",
"choice", "store_or_None", "source", "s", all_stops),
"strict":("Set strictness level",
"choice", "store", filetools.WARN, strictness_options),
"logtostdout":("Redirect main log to stdout", None, "store_true", False, "l"),
"dry-run":("Resolve dependencies and print build list, then stop",
None, "store_true", False),
})
self.log.debug("basic_options: descr %s opts %s" % (descr, opts))
self.add_group_parser(opts, descr)
class EasyConfigTest(TestCase):
"""Baseclass for easyconfig testcases."""
if LooseVersion(sys.version) >= LooseVersion('2.6'):
os.environ['EASYBUILD_DEPRECATED'] = '2.0'
# initialize configuration (required for e.g. default modules_tool setting)
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'check_osdeps': False,
'force': True,
'robot_path': get_paths_for("easyconfigs")[0],
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
config.set_tmpdir()
del eb_go
log = fancylogger.getLogger("EasyConfigTest", fname=False)
# make sure a logger is present for main
main._log = log
ordered_specs = None
parsed_easyconfigs = []
def process_all_easyconfigs(self):
"""Process all easyconfigs and resolve inter-easyconfig dependencies."""
# all available easyconfig files
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path)
# parse all easyconfigs if they haven't been already
if not self.parsed_easyconfigs:
for spec in specs:
self.parsed_easyconfigs.extend(process_easyconfig(spec))
self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs)
def test_dep_graph(self):
"""Unit test that builds a full dependency graph."""
# pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6
if LooseVersion(
sys.version) >= LooseVersion('2.6') and single_tests_ok:
# temporary file for dep graph
(hn, fn) = tempfile.mkstemp(suffix='.dot')
os.close(hn)
if self.ordered_specs is None:
self.process_all_easyconfigs()
dep_graph(fn, self.ordered_specs, silent=True)
try:
os.remove(fn)
except OSError, err:
log.error("Failed to remove %s: %s" % (fn, err))
else:
def suite():
"""Return all easyblock --module-only tests."""
# initialize configuration (required for e.g. default modules_tool setting)
cleanup()
eb_go = eboptions.parse_options(args=['--prefix=%s' % TMPDIR])
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'external_modules_metadata': {},
# enable --force --module-only
'force': True,
'module_only': True,
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
# dynamically generate a separate test for each of the available easyblocks
easyblocks_path = get_paths_for("easyblocks")[0]
all_pys = glob.glob('%s/*/*.py' % easyblocks_path)
easyblocks = [
eb for eb in all_pys
if os.path.basename(eb) != '__init__.py' and '/test/' not in eb
]
# filter out no longer supported easyblocks, or easyblocks that are tested in a different way
excluded_easyblocks = ['versionindependendpythonpackage.py']
easyblocks = [
e for e in easyblocks if os.path.basename(e) not in excluded_easyblocks
]
# add dummy PrgEnv-gnu/1.2.3 module, required for testing CrayToolchain easyblock
write_file(os.path.join(TMPDIR, 'modules', 'all', 'PrgEnv-gnu', '1.2.3'),
"#%Module")
for easyblock in easyblocks:
# dynamically define new inner functions that can be added as class methods to ModuleOnlyTest
if os.path.basename(easyblock) == 'systemcompiler.py':
# use GCC as name when testing SystemCompiler easyblock
exec(
"def innertest(self): template_module_only_test(self, '%s', name='GCC', version='system')"
% easyblock)
elif os.path.basename(easyblock) == 'craytoolchain.py':
# make sure that a (known) PrgEnv is included as a dependency
extra_txt = 'dependencies = [("PrgEnv-gnu/1.2.3", EXTERNAL_MODULE)]'
exec(
"def innertest(self): template_module_only_test(self, '%s', extra_txt='%s')"
% (easyblock, extra_txt))
else:
exec("def innertest(self): template_module_only_test(self, '%s')" %
easyblock)
innertest.__doc__ = "Test for using --module-only with easyblock %s" % easyblock
innertest.__name__ = "test_easyblock_%s" % '_'.join(
easyblock.replace('.py', '').split('/'))
setattr(ModuleOnlyTest, innertest.__name__, innertest)
return TestLoader().loadTestsFromTestCase(ModuleOnlyTest)
def setUp(self):
"""Set up everything for running a unit test."""
super(EasyConfigTest, self).setUp()
self.cwd = os.getcwd()
self.all_stops = [x[0] for x in EasyBlock.get_steps()]
if os.path.exists(self.eb_file):
os.remove(self.eb_file)
def setUp(self):
""" create temporary easyconfig file """
self.log = fancylogger.getLogger("EasyConfigTest", fname=False)
self.cwd = os.getcwd()
self.all_stops = [x[0] for x in EasyBlock.get_steps()]
if os.path.exists(self.eb_file):
os.remove(self.eb_file)
config.variables['source_path'] = os.path.join(os.path.dirname(__file__), 'easyconfigs')
def setUp(self):
"""Set up everything for running a unit test."""
super(EasyConfigTest, self).setUp()
self.cwd = os.getcwd()
self.all_stops = [x[0] for x in EasyBlock.get_steps()]
if os.path.exists(self.eb_file):
os.remove(self.eb_file)
def test_hierarchical_mns(self):
"""Test hierarchical module naming scheme."""
ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [ecs_dir],
'valid_stops': all_stops,
'validate': False,
}
def test_ec(ecfile, short_modname, mod_subdir, modpath_exts, init_modpaths):
"""Test whether active module naming scheme returns expected values."""
ec = EasyConfig(os.path.join(ecs_dir, ecfile))
self.assertEqual(ActiveMNS().det_full_module_name(ec), os.path.join(mod_subdir, short_modname))
self.assertEqual(ActiveMNS().det_short_module_name(ec), short_modname)
self.assertEqual(ActiveMNS().det_module_subdir(ec), mod_subdir)
self.assertEqual(ActiveMNS().det_modpath_extensions(ec), modpath_exts)
self.assertEqual(ActiveMNS().det_init_modulepaths(ec), init_modpaths)
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
init_config(build_options=build_options)
# format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions)
iccver = '2013.5.192-GCC-4.8.3'
impi_ec = 'impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb'
imkl_ec = 'imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb'
test_ecs = {
'GCC-4.7.2.eb': ('GCC/4.7.2', 'Core', ['Compiler/GCC/4.7.2'], ['Core']),
'OpenMPI-1.6.4-GCC-4.7.2.eb': ('OpenMPI/1.6.4', 'Compiler/GCC/4.7.2', ['MPI/GCC/4.7.2/OpenMPI/1.6.4'], ['Core']),
'gzip-1.5-goolf-1.4.10.eb': ('gzip/1.5', 'MPI/GCC/4.7.2/OpenMPI/1.6.4', [], ['Core']),
'goolf-1.4.10.eb': ('goolf/1.4.10', 'Core', [], ['Core']),
'icc-2013.5.192-GCC-4.8.3.eb': ('icc/%s' % iccver, 'Core', ['Compiler/intel/%s' % iccver], ['Core']),
'ifort-2013.3.163.eb': ('ifort/2013.3.163', 'Core', ['Compiler/intel/2013.3.163'], ['Core']),
'CUDA-5.5.22-GCC-4.8.2.eb': ('CUDA/5.5.22', 'Compiler/GCC/4.8.2', ['Compiler/GCC-CUDA/4.8.2-5.5.22'], ['Core']),
impi_ec: ('impi/4.1.3.049', 'Compiler/intel/%s' % iccver, ['MPI/intel/%s/impi/4.1.3.049' % iccver], ['Core']),
imkl_ec: ('imkl/11.1.2.144', 'MPI/intel/%s/impi/4.1.3.049' % iccver, [], ['Core']),
}
for ecfile, mns_vals in test_ecs.items():
test_ec(ecfile, *mns_vals)
# impi with dummy toolchain, which doesn't make sense in a hierarchical context
ec = EasyConfig(os.path.join(ecs_dir, 'impi-4.1.3.049.eb'))
self.assertErrorRegex(EasyBuildError, 'No compiler available.*MPI lib', ActiveMNS().det_modpath_extensions, ec)
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
init_config(build_options=build_options)
test_ecs = {
'GCC-4.7.2.eb': ('GCC/4.7.2', '', [], []),
'OpenMPI-1.6.4-GCC-4.7.2.eb': ('OpenMPI/1.6.4-GCC-4.7.2', '', [], []),
'gzip-1.5-goolf-1.4.10.eb': ('gzip/1.5-goolf-1.4.10', '', [], []),
'goolf-1.4.10.eb': ('goolf/1.4.10', '', [], []),
'impi-4.1.3.049.eb': ('impi/4.1.3.049', '', [], []),
}
for ecfile, mns_vals in test_ecs.items():
test_ec(ecfile, *mns_vals)
def setUp(self):
""" create temporary easyconfig file """
self.log = fancylogger.getLogger("EasyConfigTest", fname=False)
self.cwd = os.getcwd()
self.all_stops = [x[0] for x in EasyBlock.get_steps()]
if os.path.exists(self.eb_file):
os.remove(self.eb_file)
config.variables['source_path'] = os.path.join(
os.path.dirname(__file__), 'easyconfigs')
def process_easyconfig(path, onlyBlocks=None, regtest_online=False, validate=True):
"""
Process easyconfig, returning some information for each block
"""
blocks = retrieve_blocks_in_spec(path, onlyBlocks)
easyconfigs = []
for spec in blocks:
# process for dependencies and real installversionname
# - use mod? __init__ and importCfg are ignored.
_log.debug("Processing easyconfig %s" % spec)
# create easyconfig
try:
all_stops = [x[0] for x in EasyBlock.get_steps()]
ec = EasyConfig(spec, validate=validate, valid_module_classes=module_classes(), valid_stops=all_stops)
except EasyBuildError, err:
msg = "Failed to process easyconfig %s:\n%s" % (spec, err.msg)
_log.exception(msg)
name = ec["name"]
# this app will appear as following module in the list
easyconfig = {
"spec": spec,
"module": (ec.name, ec.get_installversion()),
"dependencies": [],
"builddependencies": [],
}
if len(blocks) > 1:
easyconfig["originalSpec"] = path
# add build dependencies
for dep in ec.builddependencies():
deptup = (dep["name"], dep["tc"])
_log.debug("Adding build dependency %s for app %s." % (deptup, name))
easyconfig["builddependencies"].append(deptup)
# add dependencies (including build dependencies)
for dep in ec.dependencies():
deptup = (dep["name"], dep["tc"])
_log.debug("Adding dependency %s for app %s." % (deptup, name))
easyconfig["dependencies"].append(deptup)
# add toolchain as dependency too
if ec.toolchain.name != "dummy":
dep = (ec.toolchain.name, ec.toolchain.version)
_log.debug("Adding toolchain %s as dependency for app %s." % (dep, name))
easyconfig["dependencies"].append(dep)
del ec
# this is used by the parallel builder
easyconfig["unresolvedDependencies"] = copy.copy(easyconfig["dependencies"])
easyconfigs.append(easyconfig)
def process_easyconfig(path, onlyBlocks=None, regtest_online=False, validate=True):
"""
Process easyconfig, returning some information for each block
"""
blocks = retrieve_blocks_in_spec(path, onlyBlocks)
easyconfigs = []
for spec in blocks:
# process for dependencies and real installversionname
# - use mod? __init__ and importCfg are ignored.
_log.debug("Processing easyconfig %s" % spec)
# create easyconfig
try:
all_stops = [x[0] for x in EasyBlock.get_steps()]
ec = EasyConfig(spec, validate=validate, valid_module_classes=module_classes(), valid_stops=all_stops)
except EasyBuildError, err:
msg = "Failed to process easyconfig %s:\n%s" % (spec, err.msg)
_log.exception(msg)
name = ec['name']
# this app will appear as following module in the list
easyconfig = {
'spec': spec,
'module': (ec.name, ec.get_installversion()),
'dependencies': [],
'builddependencies': [],
}
if len(blocks) > 1:
easyconfig['originalSpec'] = path
# add build dependencies
for dep in ec.builddependencies():
deptup = (dep['name'], dep['tc'])
_log.debug("Adding build dependency %s for app %s." % (deptup, name))
easyconfig['builddependencies'].append(deptup)
# add dependencies (including build dependencies)
for dep in ec.dependencies():
deptup = (dep['name'], dep['tc'])
_log.debug("Adding dependency %s for app %s." % (deptup, name))
easyconfig['dependencies'].append(deptup)
# add toolchain as dependency too
if ec.toolchain.name != 'dummy':
dep = (ec.toolchain.name, ec.toolchain.version)
_log.debug("Adding toolchain %s as dependency for app %s." % (dep, name))
easyconfig['dependencies'].append(dep)
del ec
# this is used by the parallel builder
easyconfig['unresolvedDependencies'] = copy.copy(easyconfig['dependencies'])
easyconfigs.append(easyconfig)
def setUp(self):
""" create temporary easyconfig file """
self.log = fancylogger.getLogger("EasyConfigTest", fname=False)
if self.contents is not None:
fd, self.eb_file = tempfile.mkstemp(prefix='easyconfig_test_file_', suffix='.eb')
os.close(fd)
write_file(self.eb_file, self.contents)
self.cwd = os.getcwd()
self.all_stops = [x[0] for x in EasyBlock.get_steps()]
def setUp(self):
"""Set up everything for running a unit test."""
super(EasyConfigTest, self).setUp()
self.cwd = os.getcwd()
self.all_stops = [x[0] for x in EasyBlock.get_steps()]
if os.path.exists(self.eb_file):
os.remove(self.eb_file)
self.orig_current_version = easybuild.tools.build_log.CURRENT_VERSION
def process_easyconfig(path, onlyBlocks=None, regtest_online=False, validate=True):
"""
Process easyconfig, returning some information for each block
"""
blocks = retrieve_blocks_in_spec(path, onlyBlocks)
easyconfigs = []
for spec in blocks:
# process for dependencies and real installversionname
# - use mod? __init__ and importCfg are ignored.
_log.debug("Processing easyconfig %s" % spec)
# create easyconfig
try:
all_stops = [x[0] for x in EasyBlock.get_steps()]
ec = EasyConfig(spec, validate=validate, valid_module_classes=module_classes(), valid_stops=all_stops)
except EasyBuildError, err:
msg = "Failed to process easyconfig %s:\n%s" % (spec, err.msg)
_log.exception(msg)
name = ec['name']
# this app will appear as following module in the list
easyconfig = {
'ec': ec,
'spec': spec,
'module': det_full_module_name(ec),
'dependencies': [],
'builddependencies': [],
}
if len(blocks) > 1:
easyconfig['originalSpec'] = path
# add build dependencies
for dep in ec.builddependencies():
_log.debug("Adding build dependency %s for app %s." % (dep, name))
easyconfig['builddependencies'].append(dep)
# add dependencies (including build dependencies)
for dep in ec.dependencies():
_log.debug("Adding dependency %s for app %s." % (dep, name))
easyconfig['dependencies'].append(dep)
# add toolchain as dependency too
if ec.toolchain.name != DUMMY_TOOLCHAIN_NAME:
dep = ec.toolchain.as_dict()
_log.debug("Adding toolchain %s as dependency for app %s." % (dep, name))
easyconfig['dependencies'].append(dep)
del ec
# this is used by the parallel builder
easyconfig['unresolved_deps'] = copy.deepcopy(easyconfig['dependencies'])
easyconfigs.append(easyconfig)
def test_exclude_path_to_top_of_module_tree(self):
"""
Make sure that modules under the HierarchicalMNS are correct,
w.r.t. not including any load statements for modules that build up the path to the top of the module tree.
"""
self.orig_module_naming_scheme = config.get_module_naming_scheme()
test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [test_ecs_path],
'valid_stops': all_stops,
'validate': False,
}
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
init_config(build_options=build_options)
self.setup_hierarchical_modules()
modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all')
mkdir(os.path.join(modfile_prefix, 'Compiler', 'GCC', '4.8.3'), parents=True)
mkdir(os.path.join(modfile_prefix, 'MPI', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049'), parents=True)
impi_modfile_path = os.path.join('Compiler', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049')
imkl_modfile_path = os.path.join('MPI', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
if get_module_syntax() == 'Lua':
impi_modfile_path += '.lua'
imkl_modfile_path += '.lua'
# example: for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included
# not for the toolchain or any of the toolchain components,
# since both icc/ifort and impi form the path to the top of the module tree
tests = [
('impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb', impi_modfile_path, ['icc', 'ifort', 'iccifort']),
('imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb', imkl_modfile_path, ['icc', 'ifort', 'impi', 'iccifort', 'iimpi']),
]
for ec_file, modfile_path, excluded_deps in tests:
ec = EasyConfig(os.path.join(test_ecs_path, ec_file))
eb = EasyBlock(ec)
eb.toolchain.prepare()
modpath = eb.make_module_step()
modfile_path = os.path.join(modpath, modfile_path)
modtxt = read_file(modfile_path)
for dep in excluded_deps:
tup = (dep, modfile_path, modtxt)
failmsg = "No 'module load' statement found for '%s' not found in module %s: %s" % tup
if get_module_syntax() == 'Tcl':
self.assertFalse(re.search('module load %s' % dep, modtxt), failmsg)
elif get_module_syntax() == 'Lua':
self.assertFalse(re.search('load("%s")' % dep, modtxt), failmsg)
else:
self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
init_config(build_options=build_options)
def test_exclude_path_to_top_of_module_tree(self):
"""
Make sure that modules under the HierarchicalMNS are correct,
w.r.t. not including any load statements for modules that build up the path to the top of the module tree.
"""
self.orig_module_naming_scheme = config.get_module_naming_scheme()
test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [test_ecs_path],
'valid_stops': all_stops,
'validate': False,
}
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
init_config(build_options=build_options)
self.setup_hierarchical_modules()
modfile_prefix = os.path.join(self.test_installpath, 'modules', 'all')
mkdir(os.path.join(modfile_prefix, 'Compiler', 'GCC', '4.8.3'), parents=True)
mkdir(os.path.join(modfile_prefix, 'MPI', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049'), parents=True)
impi_modfile_path = os.path.join('Compiler', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049')
imkl_modfile_path = os.path.join('MPI', 'intel', '2013.5.192-GCC-4.8.3', 'impi', '4.1.3.049', 'imkl', '11.1.2.144')
if get_module_syntax() == 'Lua':
impi_modfile_path += '.lua'
imkl_modfile_path += '.lua'
# example: for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included
# not for the toolchain or any of the toolchain components,
# since both icc/ifort and impi form the path to the top of the module tree
tests = [
('impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb', impi_modfile_path, ['icc', 'ifort', 'iccifort']),
('imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb', imkl_modfile_path, ['icc', 'ifort', 'impi', 'iccifort', 'iimpi']),
]
for ec_file, modfile_path, excluded_deps in tests:
ec = EasyConfig(os.path.join(test_ecs_path, ec_file))
eb = EasyBlock(ec)
eb.toolchain.prepare()
modpath = eb.make_module_step()
modfile_path = os.path.join(modpath, modfile_path)
modtxt = read_file(modfile_path)
for dep in excluded_deps:
tup = (dep, modfile_path, modtxt)
failmsg = "No 'module load' statement found for '%s' not found in module %s: %s" % tup
if get_module_syntax() == 'Tcl':
self.assertFalse(re.search('module load %s' % dep, modtxt), failmsg)
elif get_module_syntax() == 'Lua':
self.assertFalse(re.search('load("%s")' % dep, modtxt), failmsg)
else:
self.assertTrue(False, "Unknown module syntax: %s" % get_module_syntax())
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
init_config(build_options=build_options)
def test_exclude_path_to_top_of_module_tree(self):
"""
Make sure that modules under the HierarchicalMNS are correct,
w.r.t. not including any load statements for modules that build up the path to the top of the module tree.
"""
self.orig_module_naming_scheme = config.get_module_naming_scheme()
test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "easyconfigs")
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
"check_osdeps": False,
"robot_path": [test_ecs_path],
"valid_stops": all_stops,
"validate": False,
}
os.environ["EASYBUILD_MODULE_NAMING_SCHEME"] = "HierarchicalMNS"
init_config(build_options=build_options)
self.setup_hierarchical_modules()
modtool = modules_tool()
modfile_prefix = os.path.join(self.test_installpath, "modules", "all")
mkdir(os.path.join(modfile_prefix, "Compiler", "GCC", "4.8.3"), parents=True)
mkdir(os.path.join(modfile_prefix, "MPI", "intel", "2013.5.192-GCC-4.8.3", "impi", "4.1.3.049"), parents=True)
impi_modfile_path = os.path.join("Compiler", "intel", "2013.5.192-GCC-4.8.3", "impi", "4.1.3.049")
imkl_modfile_path = os.path.join(
"MPI", "intel", "2013.5.192-GCC-4.8.3", "impi", "4.1.3.049", "imkl", "11.1.2.144"
)
# example: for imkl on top of iimpi toolchain with HierarchicalMNS, no module load statements should be included
# not for the toolchain or any of the toolchain components,
# since both icc/ifort and impi form the path to the top of the module tree
tests = [
("impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb", impi_modfile_path, ["icc", "ifort", "iccifort"]),
(
"imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb",
imkl_modfile_path,
["icc", "ifort", "impi", "iccifort", "iimpi"],
),
]
for ec_file, modfile_path, excluded_deps in tests:
ec = EasyConfig(os.path.join(test_ecs_path, ec_file))
eb = EasyBlock(ec)
eb.toolchain.prepare()
modpath = eb.make_module_step()
modfile_path = os.path.join(modpath, modfile_path)
modtxt = read_file(modfile_path)
for imkl_dep in excluded_deps:
tup = (imkl_dep, modfile_path, modtxt)
failmsg = "No 'module load' statement found for '%s' not found in module %s: %s" % tup
self.assertFalse(re.search("module load %s" % imkl_dep, modtxt), failmsg)
os.environ["EASYBUILD_MODULE_NAMING_SCHEME"] = self.orig_module_naming_scheme
init_config(build_options=build_options)
def setUp(self):
""" create temporary easyconfig file """
self.log = get_log("EasyConfigTest")
if self.contents is not None:
fd, self.eb_file = tempfile.mkstemp(prefix='easyconfig_test_file_', suffix='.eb')
os.close(fd)
f = open(self.eb_file, "w")
f.write(self.contents)
f.close()
self.cwd = os.getcwd()
self.all_stops = [x[0] for x in EasyBlock.get_steps()]
def suite():
"""Return all easyblock --module-only tests."""
# initialize configuration (required for e.g. default modules_tool setting)
cleanup()
eb_go = eboptions.parse_options(args=['--prefix=%s' % TMPDIR])
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'external_modules_metadata': {},
# enable --force --module-only
'force': True,
'module_only': True,
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
# dynamically generate a separate test for each of the available easyblocks
easyblocks_path = get_paths_for("easyblocks")[0]
all_pys = glob.glob('%s/*/*.py' % easyblocks_path)
easyblocks = [eb for eb in all_pys if os.path.basename(eb) != '__init__.py' and '/test/' not in eb]
# filter out no longer supported easyblocks, or easyblocks that are tested in a different way
excluded_easyblocks = ['versionindependendpythonpackage.py']
easyblocks = [e for e in easyblocks if os.path.basename(e) not in excluded_easyblocks]
# add dummy PrgEnv-* modules, required for testing CrayToolchain easyblock
for prgenv in ['PrgEnv-cray', 'PrgEnv-gnu', 'PrgEnv-intel', 'PrgEnv-pgi']:
write_file(os.path.join(TMPDIR, 'modules', 'all', prgenv, '1.2.3'), "#%Module")
for easyblock in easyblocks:
# dynamically define new inner functions that can be added as class methods to ModuleOnlyTest
if os.path.basename(easyblock) == 'systemcompiler.py':
# use GCC as name when testing SystemCompiler easyblock
exec("def innertest(self): template_module_only_test(self, '%s', name='GCC', version='system')" % easyblock)
elif os.path.basename(easyblock) == 'systemmpi.py':
# use OpenMPI as name when testing SystemMPI easyblock
exec("def innertest(self): template_module_only_test(self, '%s', name='OpenMPI', version='system')" %
easyblock)
elif os.path.basename(easyblock) == 'craytoolchain.py':
# make sure that a (known) PrgEnv is included as a dependency
extra_txt = 'dependencies = [("PrgEnv-gnu/1.2.3", EXTERNAL_MODULE)]'
exec("def innertest(self): template_module_only_test(self, '%s', extra_txt='%s')" % (easyblock, extra_txt))
else:
exec("def innertest(self): template_module_only_test(self, '%s')" % easyblock)
innertest.__doc__ = "Test for using --module-only with easyblock %s" % easyblock
innertest.__name__ = "test_easyblock_%s" % '_'.join(easyblock.replace('.py', '').split('/'))
setattr(ModuleOnlyTest, innertest.__name__, innertest)
return TestLoader().loadTestsFromTestCase(ModuleOnlyTest)
def setUp(self):
"""Set up everything for running a unit test."""
# initialize configuration so config.get_modules_tool function works
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
self.log = fancylogger.getLogger("EasyConfigTest", fname=False)
self.cwd = os.getcwd()
self.all_stops = [x[0] for x in EasyBlock.get_steps()]
if os.path.exists(self.eb_file):
os.remove(self.eb_file)
config.variables['source_path'] = os.path.join(os.path.dirname(__file__), 'easyconfigs')
class InitTest(TestCase):
""" Baseclass for easyblock testcases """
# initialize configuration (required for e.g. default modules_tool setting)
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
del eb_go
def write_ec(self,
easyblock,
name='foo',
version='1.3.2',
toolchain=None,
extratxt=''):
""" create temporary easyconfig file """
if toolchain is None:
toolchain = 'SYSTEM'
txt = '\n'.join([
'easyblock = "%s"',
'name = "%s"' % name,
'version = "%s"' % version,
'homepage = "http://example.com"',
'description = "Dummy easyconfig file."',
'toolchain = %s' % toolchain,
'sources = []',
extratxt,
])
write_file(self.eb_file, txt % easyblock)
def setUp(self):
"""Setup test."""
self.log = fancylogger.getLogger("EasyblocksInitTest", fname=False)
fd, self.eb_file = tempfile.mkstemp(prefix='easyblocks_init_test_',
suffix='.eb')
os.close(fd)
def tearDown(self):
"""Cleanup."""
try:
os.remove(self.eb_file)
except OSError as err:
self.log.error("Failed to remove %s: %s" % (self.eb_file, err))
def setUp(self):
"""Set up everything for running a unit test."""
# initialize configuration so config.get_modules_tool function works
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
self.log = fancylogger.getLogger("EasyConfigTest", fname=False)
self.cwd = os.getcwd()
self.all_stops = [x[0] for x in EasyBlock.get_steps()]
if os.path.exists(self.eb_file):
os.remove(self.eb_file)
config.variables['source_path'] = os.path.join(
os.path.dirname(__file__), 'easyconfigs')
def test_make_module_dep_hmns(self):
"""Test for make_module_dep under HMNS"""
test_ecs_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'easyconfigs',
'test_ecs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [test_ecs_path],
'valid_stops': all_stops,
'validate': False,
}
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
init_config(build_options=build_options)
self.setup_hierarchical_modules()
self.contents = '\n'.join([
'easyblock = "ConfigureMake"',
'name = "pi"',
'version = "3.14"',
'homepage = "http://example.com"',
'description = "test easyconfig"',
"toolchain = {'name': 'gompi', 'version': '1.4.10'}",
'dependencies = [',
" ('FFTW', '3.3.3'),",
']',
])
self.writeEC()
eb = EasyBlock(EasyConfig(self.eb_file))
eb.installdir = os.path.join(config.install_path(), 'pi', '3.14')
eb.check_readiness_step()
eb.make_builddir()
eb.prepare_step()
# GCC, OpenMPI and hwloc modules should *not* be included in loads for dependencies
mod_dep_txt = eb.make_module_dep()
for mod in ['GCC/4.7.2', 'OpenMPI/1.6.4']:
regex = re.compile('load.*%s' % mod)
self.assertFalse(
regex.search(mod_dep_txt),
"Pattern '%s' found in: %s" % (regex.pattern, mod_dep_txt))
regex = re.compile('load.*FFTW/3.3.3')
self.assertTrue(
regex.search(mod_dep_txt),
"Pattern '%s' found in: %s" % (regex.pattern, mod_dep_txt))
def process_easyconfig(path, onlyBlocks=None, regtest_online=False, validate=True):
"""
Process easyconfig, returning some information for each block
"""
blocks = retrieve_blocks_in_spec(path, onlyBlocks)
easyconfigs = []
for spec in blocks:
# process for dependencies and real installversionname
# - use mod? __init__ and importCfg are ignored.
log.debug("Processing easyconfig %s" % spec)
# create easyconfig
try:
all_stops = [x[0] for x in EasyBlock.get_steps()]
ec = EasyConfig(spec, validate=validate, valid_module_classes=module_classes(), valid_stops=all_stops)
except EasyBuildError, err:
msg = "Failed to process easyconfig %s:\n%s" % (spec, err.msg)
log.exception(msg)
name = ec['name']
# this app will appear as following module in the list
easyconfig = {
'spec': spec,
'module': (ec.name, ec.get_installversion()),
'dependencies': []
}
if len(blocks) > 1:
easyconfig['originalSpec'] = path
for d in ec.dependencies():
dep = (d['name'], d['tc'])
log.debug("Adding dependency %s for app %s." % (dep, name))
easyconfig['dependencies'].append(dep)
if ec.toolchain.name != 'dummy':
dep = (ec.toolchain.name, ec.toolchain.version)
log.debug("Adding toolchain %s as dependency for app %s." % (dep, name))
easyconfig['dependencies'].append(dep)
del ec
# this is used by the parallel builder
easyconfig['unresolvedDependencies'] = copy.copy(easyconfig['dependencies'])
easyconfigs.append(easyconfig)
def test_hierarchical_mns(self):
"""Test hierarchical module naming scheme."""
ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [ecs_dir],
'valid_stops': all_stops,
'validate': False,
}
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
init_config(build_options=build_options)
ec = EasyConfig(os.path.join(ecs_dir, 'GCC-4.7.2.eb'))
self.assertEqual(ActiveMNS().det_full_module_name(ec),
'Core/GCC/4.7.2')
self.assertEqual(ActiveMNS().det_short_module_name(ec), 'GCC/4.7.2')
self.assertEqual(ActiveMNS().det_module_subdir(ec), 'Core')
self.assertEqual(ActiveMNS().det_modpath_extensions(ec),
['Compiler/GCC/4.7.2'])
self.assertEqual(ActiveMNS().det_init_modulepaths(ec), ['Core'])
ec = EasyConfig(os.path.join(ecs_dir, 'OpenMPI-1.6.4-GCC-4.7.2.eb'))
self.assertEqual(ActiveMNS().det_full_module_name(ec),
'Compiler/GCC/4.7.2/OpenMPI/1.6.4')
self.assertEqual(ActiveMNS().det_short_module_name(ec),
'OpenMPI/1.6.4')
self.assertEqual(ActiveMNS().det_module_subdir(ec),
'Compiler/GCC/4.7.2')
self.assertEqual(ActiveMNS().det_modpath_extensions(ec),
['MPI/GCC/4.7.2/OpenMPI/1.6.4'])
self.assertEqual(ActiveMNS().det_init_modulepaths(ec), ['Core'])
ec = EasyConfig(os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'))
self.assertEqual(ActiveMNS().det_full_module_name(ec),
'MPI/GCC/4.7.2/OpenMPI/1.6.4/gzip/1.5')
self.assertEqual(ActiveMNS().det_short_module_name(ec), 'gzip/1.5')
self.assertEqual(ActiveMNS().det_module_subdir(ec),
'MPI/GCC/4.7.2/OpenMPI/1.6.4')
self.assertEqual(ActiveMNS().det_modpath_extensions(ec), [])
self.assertEqual(ActiveMNS().det_init_modulepaths(ec), ['Core'])
os.environ[
'EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
init_config(build_options=build_options)
class InitTest(TestCase):
""" Baseclass for easyblock testcases """
# initialize configuration (required for e.g. default modules_tool setting)
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
config.set_tmpdir()
del eb_go
def writeEC(self, easyblock, extratxt=''):
""" create temporary easyconfig file """
txt = '\n'.join([
'easyblock = "%s"',
'name = "foo"',
'version = "1.3.2"',
'homepage = "http://example.com"',
'description = "Dummy easyconfig file."',
'toolchain = {"name": "dummy", "version": "dummy"}',
'sources = []',
extratxt,
])
f = open(self.eb_file, "w")
f.write(txt % easyblock)
f.close()
def setUp(self):
"""Setup test."""
self.log = fancylogger.getLogger("EasyblocksInitTest", fname=False)
fd, self.eb_file = tempfile.mkstemp(prefix='easyblocks_init_test_',
suffix='.eb')
os.close(fd)
def tearDown(self):
"""Cleanup."""
try:
os.remove(self.eb_file)
except OSError, err:
self.log.error("Failed to remove %s/%s: %s" % (self.eb_file, err))
def basic_options(self):
"""basic runtime options"""
all_stops = [x[0] for x in EasyBlock.get_steps()]
strictness_options = [run.IGNORE, run.WARN, run.ERROR]
descr = ("Basic options", "Basic runtime options for EasyBuild.")
opts = OrderedDict({
'dry-run': ("Print build overview incl. dependencies (full paths)",
None, 'store_true', False),
'dry-run-short':
("Print build overview incl. dependencies (short paths)", None,
'store_true', False, 'D'),
'force':
("Force to rebuild software even if it's already installed (i.e. if it can be found as module)",
None, 'store_true', False, 'f'),
'job': ("Submit the build as a job", None, 'store_true', False),
'logtostdout': ("Redirect main log to stdout", None, 'store_true',
False, 'l'),
'only-blocks': ("Only build listed blocks", None, 'extend', None,
'b', {
'metavar': 'BLOCKS'
}),
'robot':
("Enable dependency resolution, using easyconfigs in specified paths",
'pathlist', 'store_or_None', [], 'r', {
'metavar': 'PATH[%sPATH]' % os.pathsep
}),
'robot-paths':
("Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
'pathlist', 'store', self.default_robot_paths, {
'metavar': 'PATH[%sPATH]' % os.pathsep
}),
'skip':
("Skip existing software (useful for installing additional packages)",
None, 'store_true', False, 'k'),
'stop': ("Stop the installation after certain step", 'choice',
'store_or_None', 'source', 's', all_stops),
'strict': ("Set strictness level", 'choice', 'store', run.WARN,
strictness_options),
})
self.log.debug("basic_options: descr %s opts %s" % (descr, opts))
self.add_group_parser(opts, descr)
def init_config(args=None, build_options=None):
"""(re)initialize configuration"""
# clean up any instances of BuildOptions and ConfigurationVariables before reinitializing configuration
config.ConfigurationVariables.__metaclass__._instances.pop(config.ConfigurationVariables, None)
config.BuildOptions.__metaclass__._instances.pop(config.BuildOptions, None)
# initialize configuration so config.get_modules_tool function works
eb_go = eboptions.parse_options(args=args)
config.init(eb_go.options, eb_go.get_options_by_section('config'))
if build_options is None:
build_options = {
'valid_module_classes': module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options)
return eb_go.options
def suite():
"""Return all easyblock --module-only tests."""
# initialize configuration (required for e.g. default modules_tool setting)
cleanup()
eb_go = eboptions.parse_options(args=['--prefix=%s' % TMPDIR])
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
# enable --force --module-only
'force': True,
'module_only': True,
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
config.set_tmpdir()
# dynamically generate a separate test for each of the available easyblocks
easyblocks_path = get_paths_for("easyblocks")[0]
all_pys = glob.glob('%s/*/*.py' % easyblocks_path)
easyblocks = [
eb for eb in all_pys
if os.path.basename(eb) != '__init__.py' and '/test/' not in eb
]
# filter out no longer supported easyblocks
easyblocks = [
e for e in easyblocks
if os.path.basename(e) not in ['versionindependendpythonpackage.py']
]
for easyblock in easyblocks:
# dynamically define new inner functions that can be added as class methods to ModuleOnlyTest
exec("def innertest(self): template_module_only_test(self, '%s')" %
easyblock)
innertest.__doc__ = "Test for using --module-only with easyblock %s" % easyblock
innertest.__name__ = "test_easyblock_%s" % '_'.join(
easyblock.replace('.py', '').split('/'))
setattr(ModuleOnlyTest, innertest.__name__, innertest)
return TestLoader().loadTestsFromTestCase(ModuleOnlyTest)
def init_config(args=None, build_options=None):
"""(re)initialize configuration"""
cleanup()
# initialize configuration so config.get_modules_tool function works
eb_go = eboptions.parse_options(args=args)
config.init(eb_go.options, eb_go.get_options_by_section('config'))
# initialize build options
if build_options is None:
build_options = {
'valid_module_classes': module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
if 'suffix_modules_path' not in build_options:
build_options.update({'suffix_modules_path': GENERAL_CLASS})
config.init_build_options(build_options)
return eb_go.options
def init_config(args=None, build_options=None):
"""(re)initialize configuration"""
cleanup()
# initialize configuration so config.get_modules_tool function works
eb_go = eboptions.parse_options(args=args)
config.init(eb_go.options, eb_go.get_options_by_section('config'))
# initialize build options
if build_options is None:
build_options = {
'valid_module_classes': module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
if 'suffix_modules_path' not in build_options:
build_options.update({'suffix_modules_path': GENERAL_CLASS})
config.init_build_options(build_options)
return eb_go.options
def init_config(args=None, build_options=None):
"""(re)initialize configuration"""
# clean up any instances of BuildOptions and ConfigurationVariables before reinitializing configuration
config.ConfigurationVariables.__metaclass__._instances.pop(config.ConfigurationVariables, None)
config.BuildOptions.__metaclass__._instances.pop(config.BuildOptions, None)
# initialize configuration so config.get_modules_tool function works
eb_go = eboptions.parse_options(args=args)
config.init(eb_go.options, eb_go.get_options_by_section('config'))
# initialize build options
if build_options is None:
build_options = {
'valid_module_classes': module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options)
return eb_go.options
def test_make_module_dep_hmns(self):
"""Test for make_module_dep under HMNS"""
test_ecs_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'test_ecs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [test_ecs_path],
'valid_stops': all_stops,
'validate': False,
}
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
init_config(build_options=build_options)
self.setup_hierarchical_modules()
self.contents = '\n'.join([
'easyblock = "ConfigureMake"',
'name = "pi"',
'version = "3.14"',
'homepage = "http://example.com"',
'description = "test easyconfig"',
"toolchain = {'name': 'gompi', 'version': '1.4.10'}",
'dependencies = [',
" ('FFTW', '3.3.3'),",
']',
])
self.writeEC()
eb = EasyBlock(EasyConfig(self.eb_file))
eb.installdir = os.path.join(config.install_path(), 'pi', '3.14')
eb.check_readiness_step()
eb.make_builddir()
eb.prepare_step()
# GCC, OpenMPI and hwloc modules should *not* be included in loads for dependencies
mod_dep_txt = eb.make_module_dep()
for mod in ['GCC/4.7.2', 'OpenMPI/1.6.4']:
regex = re.compile('load.*%s' % mod)
self.assertFalse(regex.search(mod_dep_txt), "Pattern '%s' found in: %s" % (regex.pattern, mod_dep_txt))
regex = re.compile('load.*FFTW/3.3.3')
self.assertTrue(regex.search(mod_dep_txt), "Pattern '%s' found in: %s" % (regex.pattern, mod_dep_txt))
def test_path_to_top_of_module_tree(self):
"""Test function to determine path to top of the module tree."""
modtool = modules_tool()
path = modtool.path_to_top_of_module_tree([], 'gompi/1.3.12', '', ['GCC/4.6.4', 'OpenMPI/1.6.4-GCC-4.6.4'])
self.assertEqual(path, [])
path = modtool.path_to_top_of_module_tree([], 'toy/.0.0-deps', '', ['gompi/1.3.12'])
self.assertEqual(path, [])
path = modtool.path_to_top_of_module_tree([], 'toy/0.0', '', [])
self.assertEqual(path, [])
ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [ecs_dir],
'valid_stops': all_stops,
'validate': False,
}
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
init_config(build_options=build_options)
self.setup_hierarchical_modules()
modtool = modules_tool()
mod_prefix = os.path.join(self.test_installpath, 'modules', 'all')
init_modpaths = [os.path.join(mod_prefix, 'Core')]
deps = ['GCC/4.7.2', 'OpenMPI/1.6.4', 'FFTW/3.3.3', 'OpenBLAS/0.2.6-LAPACK-3.4.2',
'ScaLAPACK/2.0.2-OpenBLAS-0.2.6-LAPACK-3.4.2']
path = modtool.path_to_top_of_module_tree(init_modpaths, 'goolf/1.4.10', os.path.join(mod_prefix, 'Core'), deps)
self.assertEqual(path, [])
path = modtool.path_to_top_of_module_tree(init_modpaths, 'GCC/4.7.2', os.path.join(mod_prefix, 'Core'), [])
self.assertEqual(path, [])
full_mod_subdir = os.path.join(mod_prefix, 'Compiler', 'GCC', '4.7.2')
deps = ['GCC/4.7.2', 'hwloc/1.6.2']
path = modtool.path_to_top_of_module_tree(init_modpaths, 'OpenMPI/1.6.4', full_mod_subdir, deps)
self.assertEqual(path, ['GCC/4.7.2'])
full_mod_subdir = os.path.join(mod_prefix, 'MPI', 'GCC', '4.7.2', 'OpenMPI', '1.6.4')
deps = ['GCC/4.7.2', 'OpenMPI/1.6.4']
path = modtool.path_to_top_of_module_tree(init_modpaths, 'FFTW/3.3.3', full_mod_subdir, deps)
self.assertEqual(path, ['OpenMPI/1.6.4', 'GCC/4.7.2'])
def init_config(args=None, build_options=None, with_include=True):
"""(re)initialize configuration"""
cleanup()
# initialize configuration so config.get_modules_tool function works
eb_go = eboptions.parse_options(args=args, with_include=with_include)
config.init(eb_go.options, eb_go.get_options_by_section('config'))
# initialize build options
if build_options is None:
build_options = {
'extended_dry_run': False,
'external_modules_metadata': ConfigObj(),
'valid_module_classes': module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
if 'suffix_modules_path' not in build_options:
build_options.update({'suffix_modules_path': GENERAL_CLASS})
config.init_build_options(build_options=build_options)
return eb_go.options
def init_config(args=None, build_options=None, with_include=True):
"""(re)initialize configuration"""
cleanup()
# initialize configuration so config.get_modules_tool function works
eb_go = eboptions.parse_options(args=args, with_include=with_include)
config.init(eb_go.options, eb_go.get_options_by_section('config'))
# initialize build options
if build_options is None:
build_options = {
'extended_dry_run': False,
'external_modules_metadata': ConfigObj(),
'valid_module_classes': module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
if 'suffix_modules_path' not in build_options:
build_options.update({'suffix_modules_path': GENERAL_CLASS})
config.init_build_options(build_options=build_options)
return eb_go.options
def suite():
"""Return all easyblock --module-only tests."""
# initialize configuration (required for e.g. default modules_tool setting)
cleanup()
eb_go = eboptions.parse_options(args=["--prefix=%s" % TMPDIR])
config.init(eb_go.options, eb_go.get_options_by_section("config"))
build_options = {
# enable --force --module-only
"force": True,
"module_only": True,
"silent": True,
"suffix_modules_path": GENERAL_CLASS,
"valid_module_classes": config.module_classes(),
"valid_stops": [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
config.set_tmpdir()
# dynamically generate a separate test for each of the available easyblocks
easyblocks_path = get_paths_for("easyblocks")[0]
all_pys = glob.glob("%s/*/*.py" % easyblocks_path)
easyblocks = [eb for eb in all_pys if os.path.basename(eb) != "__init__.py" and "/test/" not in eb]
# filter out no longer supported easyblocks, or easyblocks that are tested in a different way
excluded_easyblocks = ["versionindependendpythonpackage.py"]
easyblocks = [e for e in easyblocks if os.path.basename(e) not in excluded_easyblocks]
for easyblock in easyblocks:
# dynamically define new inner functions that can be added as class methods to ModuleOnlyTest
if os.path.basename(easyblock) == "systemcompiler.py":
# use GCC as name when testing SystemCompiler easyblock
exec("def innertest(self): template_module_only_test(self, '%s', name='GCC', version='system')" % easyblock)
else:
exec("def innertest(self): template_module_only_test(self, '%s')" % easyblock)
innertest.__doc__ = "Test for using --module-only with easyblock %s" % easyblock
innertest.__name__ = "test_easyblock_%s" % "_".join(easyblock.replace(".py", "").split("/"))
setattr(ModuleOnlyTest, innertest.__name__, innertest)
return TestLoader().loadTestsFromTestCase(ModuleOnlyTest)
def test_hierarchical_mns(self):
"""Test hierarchical module naming scheme."""
ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [ecs_dir],
'valid_stops': all_stops,
'validate': False,
}
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
init_config(build_options=build_options)
ec = EasyConfig(os.path.join(ecs_dir, 'GCC-4.7.2.eb'))
self.assertEqual(ActiveMNS().det_full_module_name(ec), 'Core/GCC/4.7.2')
self.assertEqual(ActiveMNS().det_short_module_name(ec), 'GCC/4.7.2')
self.assertEqual(ActiveMNS().det_module_subdir(ec), 'Core')
self.assertEqual(ActiveMNS().det_modpath_extensions(ec), ['Compiler/GCC/4.7.2'])
self.assertEqual(ActiveMNS().det_init_modulepaths(ec), ['Core'])
ec = EasyConfig(os.path.join(ecs_dir, 'OpenMPI-1.6.4-GCC-4.7.2.eb'))
self.assertEqual(ActiveMNS().det_full_module_name(ec), 'Compiler/GCC/4.7.2/OpenMPI/1.6.4')
self.assertEqual(ActiveMNS().det_short_module_name(ec), 'OpenMPI/1.6.4')
self.assertEqual(ActiveMNS().det_module_subdir(ec), 'Compiler/GCC/4.7.2')
self.assertEqual(ActiveMNS().det_modpath_extensions(ec), ['MPI/GCC/4.7.2/OpenMPI/1.6.4'])
self.assertEqual(ActiveMNS().det_init_modulepaths(ec), ['Core'])
ec = EasyConfig(os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'))
self.assertEqual(ActiveMNS().det_full_module_name(ec), 'MPI/GCC/4.7.2/OpenMPI/1.6.4/gzip/1.5')
self.assertEqual(ActiveMNS().det_short_module_name(ec), 'gzip/1.5')
self.assertEqual(ActiveMNS().det_module_subdir(ec), 'MPI/GCC/4.7.2/OpenMPI/1.6.4')
self.assertEqual(ActiveMNS().det_modpath_extensions(ec), [])
self.assertEqual(ActiveMNS().det_init_modulepaths(ec), ['Core'])
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
init_config(build_options=build_options)
def main(args=None, logfile=None, do_build=None, testing=False):
"""
Main function: parse command line options, and act accordingly.
@param args: command line arguments to use
@param logfile: log file to use
@param do_build: whether or not to actually perform the build
@param testing: enable testing mode
"""
# purposely session state very early, to avoid modules loaded by EasyBuild meddling in
init_session_state = session_state()
# initialise options
eb_go = eboptions.parse_options(args=args)
options = eb_go.options
orig_paths = eb_go.args
# set umask (as early as possible)
if options.umask is not None:
new_umask = int(options.umask, 8)
old_umask = os.umask(new_umask)
# set by option parsers via set_tmpdir
eb_tmpdir = tempfile.gettempdir()
# initialise logging for main
global _log
_log, logfile = init_logging(logfile, logtostdout=options.logtostdout, silent=testing or options.last_log)
# disallow running EasyBuild as root
if os.getuid() == 0:
raise EasyBuildError(
"You seem to be running EasyBuild with root privileges which is not wise, " "so let's end this here."
)
# log startup info
eb_cmd_line = eb_go.generate_cmd_line() + eb_go.args
log_start(eb_cmd_line, eb_tmpdir)
if options.umask is not None:
_log.info("umask set to '%s' (used to be '%s')" % (oct(new_umask), oct(old_umask)))
# process software build specifications (if any), i.e.
# software name/version, toolchain name/version, extra patches, ...
(try_to_generate, build_specs) = process_software_build_specs(options)
# determine robot path
# --try-X, --dep-graph, --search use robot path for searching, so enable it with path of installed easyconfigs
tweaked_ecs = try_to_generate and build_specs
tweaked_ecs_path, pr_path = alt_easyconfig_paths(eb_tmpdir, tweaked_ecs=tweaked_ecs, from_pr=options.from_pr)
auto_robot = try_to_generate or options.dep_graph or options.search or options.search_short
robot_path = det_robot_path(options.robot_paths, tweaked_ecs_path, pr_path, auto_robot=auto_robot)
_log.debug("Full robot path: %s" % robot_path)
# configure & initialize build options
config_options_dict = eb_go.get_options_by_section("config")
build_options = {
"build_specs": build_specs,
"command_line": eb_cmd_line,
"pr_path": pr_path,
"robot_path": robot_path,
"silent": testing,
"try_to_generate": try_to_generate,
"valid_stops": [x[0] for x in EasyBlock.get_steps()],
}
# initialise the EasyBuild configuration & build options
config.init(options, config_options_dict)
config.init_build_options(build_options=build_options, cmdline_options=options)
if options.last_log:
# print location to last log file, and exit
last_log = find_last_log(logfile) or "(none)"
print_msg(last_log, log=_log, prefix=False)
cleanup(logfile, eb_tmpdir, testing, silent=True)
sys.exit(0)
# check whether packaging is supported when it's being used
if options.package:
check_pkg_support()
else:
_log.debug("Packaging not enabled, so not checking for packaging support.")
# update session state
eb_config = eb_go.generate_cmd_line(add_default=True)
modlist = session_module_list(testing=testing) # build options must be initialized first before 'module list' works
init_session_state.update({"easybuild_configuration": eb_config})
init_session_state.update({"module_list": modlist})
_log.debug("Initial session state: %s" % init_session_state)
# GitHub integration
if options.review_pr or options.new_pr or options.update_pr:
if options.review_pr:
print review_pr(options.review_pr, colored=options.color)
elif options.new_pr:
new_pr(orig_paths, title=options.pr_title, descr=options.pr_descr, commit_msg=options.pr_commit_msg)
elif options.update_pr:
update_pr(options.update_pr, orig_paths, commit_msg=options.pr_commit_msg)
cleanup(logfile, eb_tmpdir, testing)
sys.exit(0)
# search for easyconfigs, if a query is specified
query = options.search or options.search_short
if query:
search_easyconfigs(query, short=not options.search)
# determine easybuild-easyconfigs package install path
easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR)
if not easyconfigs_pkg_paths:
_log.warning("Failed to determine install path for easybuild-easyconfigs package.")
# command line options that do not require any easyconfigs to be specified
no_ec_opts = [
options.aggregate_regtest,
options.new_pr,
options.review_pr,
options.search,
options.search_short,
options.regtest,
options.update_pr,
]
# determine paths to easyconfigs
paths = det_easyconfig_paths(orig_paths)
if paths:
# transform paths into tuples, use 'False' to indicate the corresponding easyconfig files were not generated
paths = [(p, False) for p in paths]
else:
if "name" in build_specs:
# try to obtain or generate an easyconfig file via build specifications if a software name is provided
paths = find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=testing)
elif not any(no_ec_opts):
print_error(
(
"Please provide one or multiple easyconfig files, or use software build "
"options to make EasyBuild search for easyconfigs"
),
log=_log,
opt_parser=eb_go.parser,
exit_on_error=not testing,
)
_log.debug("Paths: %s" % paths)
# run regtest
if options.regtest or options.aggregate_regtest:
_log.info("Running regression test")
# fallback: easybuild-easyconfigs install path
regtest_ok = regtest([path[0] for path in paths] or easyconfigs_pkg_paths)
if not regtest_ok:
_log.info("Regression test failed (partially)!")
sys.exit(31) # exit -> 3x1t -> 31
# read easyconfig files
easyconfigs, generated_ecs = parse_easyconfigs(paths)
# tweak obtained easyconfig files, if requested
# don't try and tweak anything if easyconfigs were generated, since building a full dep graph will fail
# if easyconfig files for the dependencies are not available
if try_to_generate and build_specs and not generated_ecs:
easyconfigs = tweak(easyconfigs, build_specs, targetdir=tweaked_ecs_path)
# dry_run: print all easyconfigs and dependencies, and whether they are already built
if options.dry_run or options.dry_run_short:
txt = dry_run(easyconfigs, short=not options.dry_run)
print_msg(txt, log=_log, silent=testing, prefix=False)
# cleanup and exit after dry run, searching easyconfigs or submitting regression test
if any(no_ec_opts + [options.dry_run, options.dry_run_short]):
cleanup(logfile, eb_tmpdir, testing)
sys.exit(0)
# skip modules that are already installed unless forced
if not (options.force or options.rebuild or options.extended_dry_run):
retained_ecs = skip_available(easyconfigs)
if not testing:
for skipped_ec in [ec for ec in easyconfigs if ec not in retained_ecs]:
print_msg("%s is already installed (module found), skipping" % skipped_ec["full_mod_name"])
easyconfigs = retained_ecs
# determine an order that will allow all specs in the set to build
if len(easyconfigs) > 0:
if options.robot:
print_msg("resolving dependencies ...", log=_log, silent=testing)
ordered_ecs = resolve_dependencies(
easyconfigs,
minimal_toolchains=build_option("minimal_toolchains"),
use_existing_modules=build_option("use_existing_modules"),
)
else:
ordered_ecs = easyconfigs
else:
print_msg("No easyconfigs left to be built.", log=_log, silent=testing)
ordered_ecs = []
# create dependency graph and exit
if options.dep_graph:
_log.info("Creating dependency graph %s" % options.dep_graph)
dep_graph(options.dep_graph, ordered_ecs)
sys.exit(0)
# submit build as job(s), clean up and exit
if options.job:
submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
if not testing:
print_msg("Submitted parallel build jobs, exiting now")
cleanup(logfile, eb_tmpdir, testing)
sys.exit(0)
# build software, will exit when errors occurs (except when testing)
exit_on_failure = not options.dump_test_report and not options.upload_test_report
if not testing or (testing and do_build):
ecs_with_res = build_and_install_software(ordered_ecs, init_session_state, exit_on_failure=exit_on_failure)
else:
ecs_with_res = [(ec, {}) for ec in ordered_ecs]
correct_builds_cnt = len([ec_res for (_, ec_res) in ecs_with_res if ec_res.get("success", False)])
overall_success = correct_builds_cnt == len(ordered_ecs)
success_msg = "Build succeeded for %s out of %s" % (correct_builds_cnt, len(ordered_ecs))
repo = init_repository(get_repository(), get_repositorypath())
repo.cleanup()
# dump/upload overall test report
test_report_msg = overall_test_report(ecs_with_res, len(paths), overall_success, success_msg, init_session_state)
if test_report_msg is not None:
print_msg(test_report_msg)
print_msg(success_msg, log=_log, silent=testing)
# cleanup and spec files
for ec in easyconfigs:
if "original_spec" in ec and os.path.isfile(ec["spec"]):
os.remove(ec["spec"])
# stop logging and cleanup tmp log file, unless one build failed (individual logs are located in eb_tmpdir)
stop_logging(logfile, logtostdout=options.logtostdout)
if overall_success:
cleanup(logfile, eb_tmpdir, testing)
def main(testing_data=(None, None, None)):
"""
Main function:
@arg options: a tuple: (options, paths, logger, logfile, hn) as defined in parse_options
This function will:
- read easyconfig
- build software
"""
# disallow running EasyBuild as root
if os.getuid() == 0:
sys.stderr.write("ERROR: You seem to be running EasyBuild with root privileges.\n"
"That's not wise, so let's end this here.\n"
"Exiting.\n")
sys.exit(1)
# steer behavior when testing main
testing = testing_data[0] is not None
args, logfile, do_build = testing_data
# initialise options
eb_go = eboptions.parse_options(args=args)
options = eb_go.options
orig_paths = eb_go.args
# set umask (as early as possible)
if options.umask is not None:
new_umask = int(options.umask, 8)
old_umask = os.umask(new_umask)
# set temporary directory to use
eb_tmpdir = set_tmpdir(options.tmpdir)
# initialise logging for main
if options.logtostdout:
fancylogger.logToScreen(enable=True, stdout=True)
else:
if logfile is None:
# mkstemp returns (fd,filename), fd is from os.open, not regular open!
fd, logfile = tempfile.mkstemp(suffix='.log', prefix='easybuild-')
os.close(fd)
fancylogger.logToFile(logfile)
print_msg('temporary log file in case of crash %s' % (logfile), log=None, silent=testing)
global _log
_log = fancylogger.getLogger(fname=False)
if options.umask is not None:
_log.info("umask set to '%s' (used to be '%s')" % (oct(new_umask), oct(old_umask)))
# hello world!
_log.info(this_is_easybuild())
# how was EB called?
eb_command_line = eb_go.generate_cmd_line() + eb_go.args
_log.info("Command line: %s" % (" ".join(eb_command_line)))
_log.info("Using %s as temporary directory" % eb_tmpdir)
if not options.robot is None:
if options.robot:
_log.info("Using robot path(s): %s" % options.robot)
else:
_log.error("No robot paths specified, and unable to determine easybuild-easyconfigs install path.")
# do not pass options.robot, it's not a list instance (and it shouldn't be modified)
robot_path = None
if options.robot:
robot_path = list(options.robot)
# determine easybuild-easyconfigs package install path
easyconfigs_paths = get_paths_for("easyconfigs", robot_path=robot_path)
# keep track of paths for install easyconfigs, so we can obtain find specified easyconfigs
easyconfigs_pkg_full_paths = easyconfigs_paths[:]
if not easyconfigs_paths:
_log.warning("Failed to determine install path for easybuild-easyconfigs package.")
# specified robot paths are preferred over installed easyconfig files
if robot_path:
robot_path.extend(easyconfigs_paths)
easyconfigs_paths = robot_path[:]
_log.info("Extended list of robot paths with paths for installed easyconfigs: %s" % robot_path)
# initialise the easybuild configuration
config.init(options, eb_go.get_options_by_section('config'))
# building a dependency graph implies force, so that all dependencies are retained
# and also skips validation of easyconfigs (e.g. checking os dependencies)
retain_all_deps = False
if options.dep_graph:
_log.info("Enabling force to generate dependency graph.")
options.force = True
retain_all_deps = True
config.init_build_options({
'aggregate_regtest': options.aggregate_regtest,
'allow_modules_tool_mismatch': options.allow_modules_tool_mismatch,
'check_osdeps': not options.ignore_osdeps,
'command_line': eb_command_line,
'debug': options.debug,
'dry_run': options.dry_run,
'easyblock': options.easyblock,
'experimental': options.experimental,
'force': options.force,
'group': options.group,
'ignore_dirs': options.ignore_dirs,
'modules_footer': options.modules_footer,
'only_blocks': options.only_blocks,
'recursive_mod_unload': options.recursive_module_unload,
'regtest_online': options.regtest_online,
'regtest_output_dir': options.regtest_output_dir,
'retain_all_deps': retain_all_deps,
'robot_path': robot_path,
'sequential': options.sequential,
'silent': testing,
'set_gid_bit': options.set_gid_bit,
'skip': options.skip,
'skip_test_cases': options.skip_test_cases,
'sticky_bit': options.sticky_bit,
'stop': options.stop,
'umask': options.umask,
'valid_module_classes': module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
'validate': not options.force,
})
# search for easyconfigs
if options.search or options.search_short:
search_path = [os.getcwd()]
if easyconfigs_paths:
search_path = easyconfigs_paths
query = options.search or options.search_short
ignore_dirs = config.build_option('ignore_dirs')
silent = config.build_option('silent')
search_file(search_path, query, short=not options.search, ignore_dirs=ignore_dirs, silent=silent)
# process software build specifications (if any), i.e.
# software name/version, toolchain name/version, extra patches, ...
(try_to_generate, build_specs) = process_software_build_specs(options)
paths = []
if len(orig_paths) == 0:
if 'name' in build_specs:
paths = [obtain_path(build_specs, easyconfigs_paths, try_to_generate=try_to_generate,
exit_on_error=not testing)]
elif not any([options.aggregate_regtest, options.search, options.search_short, options.regtest]):
print_error(("Please provide one or multiple easyconfig files, or use software build "
"options to make EasyBuild search for easyconfigs"),
log=_log, opt_parser=eb_go.parser, exit_on_error=not testing)
else:
# look for easyconfigs with relative paths in easybuild-easyconfigs package,
# unless they were found at the given relative paths
if easyconfigs_pkg_full_paths:
# determine which easyconfigs files need to be found, if any
ecs_to_find = []
for idx, orig_path in enumerate(orig_paths):
if orig_path == os.path.basename(orig_path) and not os.path.exists(orig_path):
ecs_to_find.append((idx, orig_path))
_log.debug("List of easyconfig files to find: %s" % ecs_to_find)
# find missing easyconfigs by walking paths with installed easyconfig files
for path in easyconfigs_pkg_full_paths:
_log.debug("Looking for missing easyconfig files (%d left) in %s..." % (len(ecs_to_find), path))
for (subpath, dirnames, filenames) in os.walk(path, topdown=True):
for idx, orig_path in ecs_to_find[:]:
if orig_path in filenames:
full_path = os.path.join(subpath, orig_path)
_log.info("Found %s in %s: %s" % (orig_path, path, full_path))
orig_paths[idx] = full_path
# if file was found, stop looking for it (first hit wins)
ecs_to_find.remove((idx, orig_path))
# stop os.walk insanity as soon as we have all we need (os.walk loop)
if len(ecs_to_find) == 0:
break
# ignore subdirs specified to be ignored by replacing items in dirnames list used by os.walk
dirnames[:] = [d for d in dirnames if not d in options.ignore_dirs]
# stop os.walk insanity as soon as we have all we need (paths loop)
if len(ecs_to_find) == 0:
break
# indicate that specified paths do not contain generated easyconfig files
paths = [(path, False) for path in orig_paths]
_log.debug("Paths: %s" % paths)
# run regtest
if options.regtest or options.aggregate_regtest:
_log.info("Running regression test")
if paths:
ec_paths = [path[0] for path in paths]
else: # fallback: easybuild-easyconfigs install path
ec_paths = easyconfigs_pkg_full_paths
regtest_ok = regtest(ec_paths)
if not regtest_ok:
_log.info("Regression test failed (partially)!")
sys.exit(31) # exit -> 3x1t -> 31
# read easyconfig files
easyconfigs = []
for (path, generated) in paths:
path = os.path.abspath(path)
if not os.path.exists(path):
print_error("Can't find path %s" % path)
try:
files = find_easyconfigs(path, ignore_dirs=options.ignore_dirs)
for f in files:
if not generated and try_to_generate and build_specs:
ec_file = tweak(f, None, build_specs)
else:
ec_file = f
ecs = process_easyconfig(ec_file, build_specs=build_specs)
easyconfigs.extend(ecs)
except IOError, err:
_log.error("Processing easyconfigs in path %s failed: %s" % (path, err))
def main(args=None, logfile=None, do_build=None, testing=False, modtool=None):
"""
Main function: parse command line options, and act accordingly.
:param args: command line arguments to use
:param logfile: log file to use
:param do_build: whether or not to actually perform the build
:param testing: enable testing mode
"""
# purposely session state very early, to avoid modules loaded by EasyBuild meddling in
init_session_state = session_state()
# initialise options
eb_go = eboptions.parse_options(args=args)
options = eb_go.options
orig_paths = eb_go.args
# set umask (as early as possible)
if options.umask is not None:
new_umask = int(options.umask, 8)
old_umask = os.umask(new_umask)
# set by option parsers via set_tmpdir
eb_tmpdir = tempfile.gettempdir()
search_query = options.search or options.search_filename or options.search_short
# initialise logging for main
global _log
_log, logfile = init_logging(logfile, logtostdout=options.logtostdout,
silent=(testing or options.terse or search_query), colorize=options.color)
# disallow running EasyBuild as root
if os.getuid() == 0:
raise EasyBuildError("You seem to be running EasyBuild with root privileges which is not wise, "
"so let's end this here.")
# log startup info
eb_cmd_line = eb_go.generate_cmd_line() + eb_go.args
log_start(eb_cmd_line, eb_tmpdir)
if options.umask is not None:
_log.info("umask set to '%s' (used to be '%s')" % (oct(new_umask), oct(old_umask)))
# process software build specifications (if any), i.e.
# software name/version, toolchain name/version, extra patches, ...
(try_to_generate, build_specs) = process_software_build_specs(options)
# determine robot path
# --try-X, --dep-graph, --search use robot path for searching, so enable it with path of installed easyconfigs
tweaked_ecs = try_to_generate and build_specs
tweaked_ecs_paths, pr_path = alt_easyconfig_paths(eb_tmpdir, tweaked_ecs=tweaked_ecs, from_pr=options.from_pr)
auto_robot = try_to_generate or options.check_conflicts or options.dep_graph or search_query
robot_path = det_robot_path(options.robot_paths, tweaked_ecs_paths, pr_path, auto_robot=auto_robot)
_log.debug("Full robot path: %s" % robot_path)
# configure & initialize build options
config_options_dict = eb_go.get_options_by_section('config')
build_options = {
'build_specs': build_specs,
'command_line': eb_cmd_line,
'external_modules_metadata': parse_external_modules_metadata(options.external_modules_metadata),
'pr_path': pr_path,
'robot_path': robot_path,
'silent': testing,
'try_to_generate': try_to_generate,
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
# initialise the EasyBuild configuration & build options
config.init(options, config_options_dict)
config.init_build_options(build_options=build_options, cmdline_options=options)
if modtool is None:
modtool = modules_tool(testing=testing)
if options.last_log:
# print location to last log file, and exit
last_log = find_last_log(logfile) or '(none)'
print_msg(last_log, log=_log, prefix=False)
# check whether packaging is supported when it's being used
if options.package:
check_pkg_support()
else:
_log.debug("Packaging not enabled, so not checking for packaging support.")
# search for easyconfigs, if a query is specified
if search_query:
search_easyconfigs(search_query, short=options.search_short, filename_only=options.search_filename,
terse=options.terse)
# GitHub options that warrant a silent cleanup & exit
if options.check_github:
check_github()
elif options.install_github_token:
install_github_token(options.github_user, silent=build_option('silent'))
elif options.review_pr:
print review_pr(options.review_pr, colored=use_color(options.color))
elif options.list_installed_software:
detailed = options.list_installed_software == 'detailed'
print list_software(output_format=options.output_format, detailed=detailed, only_installed=True)
elif options.list_software:
print list_software(output_format=options.output_format, detailed=options.list_software == 'detailed')
# non-verbose cleanup after handling GitHub integration stuff or printing terse info
early_stop_options = [
options.check_github,
options.install_github_token,
options.list_installed_software,
options.list_software,
options.review_pr,
options.terse,
search_query,
]
if any(early_stop_options):
cleanup(logfile, eb_tmpdir, testing, silent=True)
sys.exit(0)
# update session state
eb_config = eb_go.generate_cmd_line(add_default=True)
modlist = modtool.list() # build options must be initialized first before 'module list' works
init_session_state.update({'easybuild_configuration': eb_config})
init_session_state.update({'module_list': modlist})
_log.debug("Initial session state: %s" % init_session_state)
# determine easybuild-easyconfigs package install path
easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR)
if not easyconfigs_pkg_paths:
_log.warning("Failed to determine install path for easybuild-easyconfigs package.")
if options.install_latest_eb_release:
if orig_paths:
raise EasyBuildError("Installing the latest EasyBuild release can not be combined with installing "
"other easyconfigs")
else:
eb_file = find_easybuild_easyconfig()
orig_paths.append(eb_file)
categorized_paths = categorize_files_by_type(orig_paths)
# command line options that do not require any easyconfigs to be specified
no_ec_opts = [options.aggregate_regtest, options.new_pr, options.regtest, options.update_pr, search_query]
# determine paths to easyconfigs
paths = det_easyconfig_paths(categorized_paths['easyconfigs'])
if paths:
# transform paths into tuples, use 'False' to indicate the corresponding easyconfig files were not generated
paths = [(p, False) for p in paths]
else:
if 'name' in build_specs:
# try to obtain or generate an easyconfig file via build specifications if a software name is provided
paths = find_easyconfigs_by_specs(build_specs, robot_path, try_to_generate, testing=testing)
elif not any(no_ec_opts):
print_error(("Please provide one or multiple easyconfig files, or use software build "
"options to make EasyBuild search for easyconfigs"),
log=_log, opt_parser=eb_go.parser, exit_on_error=not testing)
_log.debug("Paths: %s" % paths)
# run regtest
if options.regtest or options.aggregate_regtest:
_log.info("Running regression test")
# fallback: easybuild-easyconfigs install path
regtest_ok = regtest([path[0] for path in paths] or easyconfigs_pkg_paths, modtool)
if not regtest_ok:
_log.info("Regression test failed (partially)!")
sys.exit(31) # exit -> 3x1t -> 31
if options.check_style:
_log.debug("Running style check...")
if cmdline_easyconfigs_style_check([path[0] for path in paths]):
print_msg("All style checks passed!", prefix=False)
cleanup(logfile, eb_tmpdir, testing)
sys.exit(0)
else:
raise EasyBuildError("One or more style checks FAILED!")
# read easyconfig files
easyconfigs, generated_ecs = parse_easyconfigs(paths)
# tweak obtained easyconfig files, if requested
# don't try and tweak anything if easyconfigs were generated, since building a full dep graph will fail
# if easyconfig files for the dependencies are not available
if try_to_generate and build_specs and not generated_ecs:
easyconfigs = tweak(easyconfigs, build_specs, modtool, targetdirs=tweaked_ecs_paths)
dry_run_mode = options.dry_run or options.dry_run_short
new_update_pr = options.new_pr or options.update_pr
# skip modules that are already installed unless forced
if not (options.force or options.rebuild or dry_run_mode or options.extended_dry_run or new_update_pr):
retained_ecs = skip_available(easyconfigs, modtool)
if not testing:
for skipped_ec in [ec for ec in easyconfigs if ec not in retained_ecs]:
print_msg("%s is already installed (module found), skipping" % skipped_ec['full_mod_name'])
easyconfigs = retained_ecs
# determine an order that will allow all specs in the set to build
if len(easyconfigs) > 0:
# resolve dependencies if robot is enabled, except in dry run mode
# one exception: deps *are* resolved with --new-pr or --update-pr when dry run mode is enabled
if options.robot and (not dry_run_mode or new_update_pr):
print_msg("resolving dependencies ...", log=_log, silent=testing)
ordered_ecs = resolve_dependencies(easyconfigs, modtool)
else:
ordered_ecs = easyconfigs
elif new_update_pr:
ordered_ecs = None
else:
print_msg("No easyconfigs left to be built.", log=_log, silent=testing)
ordered_ecs = []
# creating/updating PRs
if new_update_pr:
if options.new_pr:
new_pr(categorized_paths, ordered_ecs, title=options.pr_title, descr=options.pr_descr,
commit_msg=options.pr_commit_msg)
else:
update_pr(options.update_pr, categorized_paths, ordered_ecs, commit_msg=options.pr_commit_msg)
cleanup(logfile, eb_tmpdir, testing, silent=True)
sys.exit(0)
# dry_run: print all easyconfigs and dependencies, and whether they are already built
elif dry_run_mode:
txt = dry_run(easyconfigs, modtool, short=not options.dry_run)
print_msg(txt, log=_log, silent=testing, prefix=False)
elif options.check_conflicts:
if check_conflicts(easyconfigs, modtool):
print_error("One or more conflicts detected!")
sys.exit(1)
else:
print_msg("\nNo conflicts detected!\n", prefix=False)
# dump source script to set up build environment
elif options.dump_env_script:
dump_env_script(easyconfigs)
# cleanup and exit after dry run, searching easyconfigs or submitting regression test
if any(no_ec_opts + [options.check_conflicts, dry_run_mode, options.dump_env_script]):
cleanup(logfile, eb_tmpdir, testing)
sys.exit(0)
# create dependency graph and exit
if options.dep_graph:
_log.info("Creating dependency graph %s" % options.dep_graph)
dep_graph(options.dep_graph, ordered_ecs)
cleanup(logfile, eb_tmpdir, testing, silent=True)
sys.exit(0)
# submit build as job(s), clean up and exit
if options.job:
submit_jobs(ordered_ecs, eb_go.generate_cmd_line(), testing=testing)
if not testing:
print_msg("Submitted parallel build jobs, exiting now")
cleanup(logfile, eb_tmpdir, testing)
sys.exit(0)
# build software, will exit when errors occurs (except when testing)
exit_on_failure = not options.dump_test_report and not options.upload_test_report
if not testing or (testing and do_build):
ecs_with_res = build_and_install_software(ordered_ecs, init_session_state, exit_on_failure=exit_on_failure)
else:
ecs_with_res = [(ec, {}) for ec in ordered_ecs]
correct_builds_cnt = len([ec_res for (_, ec_res) in ecs_with_res if ec_res.get('success', False)])
overall_success = correct_builds_cnt == len(ordered_ecs)
success_msg = "Build succeeded for %s out of %s" % (correct_builds_cnt, len(ordered_ecs))
repo = init_repository(get_repository(), get_repositorypath())
repo.cleanup()
# dump/upload overall test report
test_report_msg = overall_test_report(ecs_with_res, len(paths), overall_success, success_msg, init_session_state)
if test_report_msg is not None:
print_msg(test_report_msg)
print_msg(success_msg, log=_log, silent=testing)
# cleanup and spec files
for ec in easyconfigs:
if 'original_spec' in ec and os.path.isfile(ec['spec']):
os.remove(ec['spec'])
# stop logging and cleanup tmp log file, unless one build failed (individual logs are located in eb_tmpdir)
stop_logging(logfile, logtostdout=options.logtostdout)
if overall_success:
cleanup(logfile, eb_tmpdir, testing)
class EasyConfigTest(TestCase):
"""Baseclass for easyconfig testcases."""
# initialize configuration (required for e.g. default modules_tool setting)
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'check_osdeps': False,
'external_modules_metadata': {},
'force': True,
'optarch': 'test',
'robot_path': get_paths_for("easyconfigs")[0],
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
del eb_go
# put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains
TMPDIR = tempfile.mkdtemp()
os.environ['MODULEPATH'] = TMPDIR
write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n')
log = fancylogger.getLogger("EasyConfigTest", fname=False)
# make sure a logger is present for main
main._log = log
ordered_specs = None
parsed_easyconfigs = []
def process_all_easyconfigs(self):
"""Process all easyconfigs and resolve inter-easyconfig dependencies."""
# all available easyconfig files
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path)
# parse all easyconfigs if they haven't been already
if not self.parsed_easyconfigs:
for spec in specs:
self.parsed_easyconfigs.extend(process_easyconfig(spec))
# filter out external modules
for ec in self.parsed_easyconfigs:
for dep in ec['dependencies'][:]:
if dep.get('external_module', False):
ec['dependencies'].remove(dep)
self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs,
retain_all_deps=True)
def test_dep_graph(self):
"""Unit test that builds a full dependency graph."""
# pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6
if LooseVersion(
sys.version) >= LooseVersion('2.6') and single_tests_ok:
# temporary file for dep graph
(hn, fn) = tempfile.mkstemp(suffix='.dot')
os.close(hn)
if self.ordered_specs is None:
self.process_all_easyconfigs()
dep_graph(fn, self.ordered_specs)
try:
os.remove(fn)
except OSError, err:
log.error("Failed to remove %s: %s" % (fn, err))
else:
class EasyConfigTest(TestCase):
"""Baseclass for easyconfig testcases."""
# initialize configuration (required for e.g. default modules_tool setting)
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'check_osdeps': False,
'external_modules_metadata': {},
'force': True,
'local_var_naming_check': 'error',
'optarch': 'test',
'robot_path': get_paths_for("easyconfigs")[0],
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
del eb_go
# put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains
TMPDIR = tempfile.mkdtemp()
os.environ['MODULEPATH'] = TMPDIR
write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n')
log = fancylogger.getLogger("EasyConfigTest", fname=False)
# make sure a logger is present for main
eb_main._log = log
ordered_specs = None
parsed_easyconfigs = []
def process_all_easyconfigs(self):
"""Process all easyconfigs and resolve inter-easyconfig dependencies."""
# all available easyconfig files
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path)
# parse all easyconfigs if they haven't been already
if not EasyConfigTest.parsed_easyconfigs:
for spec in specs:
EasyConfigTest.parsed_easyconfigs.extend(process_easyconfig(spec))
# filter out external modules
for ec in EasyConfigTest.parsed_easyconfigs:
for dep in ec['dependencies'][:]:
if dep.get('external_module', False):
ec['dependencies'].remove(dep)
EasyConfigTest.ordered_specs = resolve_dependencies(EasyConfigTest.parsed_easyconfigs, modules_tool(), retain_all_deps=True)
def test_dep_graph(self):
"""Unit test that builds a full dependency graph."""
# pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6
if LooseVersion(sys.version) >= LooseVersion('2.6') and single_tests_ok:
# temporary file for dep graph
(hn, fn) = tempfile.mkstemp(suffix='.dot')
os.close(hn)
if EasyConfigTest.ordered_specs is None:
self.process_all_easyconfigs()
dep_graph(fn, EasyConfigTest.ordered_specs)
remove_file(fn)
else:
print("(skipped dep graph test)")
def test_conflicts(self):
"""Check whether any conflicts occur in software dependency graphs."""
if not single_tests_ok:
print("(skipped conflicts test)")
return
if EasyConfigTest.ordered_specs is None:
self.process_all_easyconfigs()
self.assertFalse(check_conflicts(EasyConfigTest.ordered_specs, modules_tool(), check_inter_ec_conflicts=False),
"No conflicts detected")
def check_dep_vars(self, dep, dep_vars):
"""Check whether available variants of a particular dependency are acceptable or not."""
# 'guilty' until proven 'innocent'
res = False
# filter out wrapped Java versions
# i.e. if the version of one is a prefix of the version of the other one (e.g. 1.8 & 1.8.0_181)
if dep == 'Java':
dep_vars_to_check = sorted(dep_vars.keys())
retained_dep_vars = []
while dep_vars_to_check:
dep_var = dep_vars_to_check.pop()
dep_var_version = dep_var.split(';')[0]
# remove dep vars wrapped by current dep var
dep_vars_to_check = [x for x in dep_vars_to_check if not x.startswith(dep_var_version + '.')]
retained_dep_vars = [x for x in retained_dep_vars if not x.startswith(dep_var_version + '.')]
retained_dep_vars.append(dep_var)
for key in list(dep_vars.keys()):
if key not in retained_dep_vars:
del dep_vars[key]
# filter out binutils with empty versionsuffix which is used to build toolchain compiler
if dep == 'binutils' and len(dep_vars) > 1:
empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')]
if len(empty_vsuff_vars) == 1:
dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0])
# multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools;
# same goes for WRF and WPS
for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS')]:
if dep == dep_name and len(dep_vars) > 1:
for key in list(dep_vars):
ecs = dep_vars[key]
# filter out dep variants that are only used as dependency for parent with same version
dep_ver = re.search('^version: (?P<ver>[^;]+);', key).group('ver')
if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1:
dep_vars.pop(key)
# multiple versions of Boost is OK as long as they are deps for a matching Boost.Python
if dep == 'Boost' and len(dep_vars) > 1:
for key in list(dep_vars):
ecs = dep_vars[key]
# filter out Boost variants that are only used as dependency for Boost.Python with same version
boost_ver = re.search('^version: (?P<ver>[^;]+);', key).group('ver')
if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs):
dep_vars.pop(key)
# filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains
if dep in ['FFTW', 'imkl']:
serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')]
if len(serial_vsuff_vars) == 1:
dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0])
# for some dependencies, we allow exceptions for software that depends on a particular version,
# as long as that's indicated by the versionsuffix
if dep in ['ASE', 'Boost', 'Java', 'Lua', 'PLUMED', 'R', 'TensorFlow'] and len(dep_vars) > 1:
for key in list(dep_vars):
dep_ver = re.search('^version: (?P<ver>[^;]+);', key).group('ver')
# use version of Java wrapper rather than full Java version
if dep == 'Java':
dep_ver = '.'.join(dep_ver.split('.')[:2])
# filter out dep version if all easyconfig filenames using it include specific dep version
if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]):
dep_vars.pop(key)
# always retain at least one dep variant
if len(dep_vars) == 1:
break
# filter R dep for a specific version of Python 2.x
if dep == 'R' and len(dep_vars) > 1:
for key in list(dep_vars):
if '; versionsuffix: -Python-2' in key:
dep_vars.pop(key)
# always retain at least one variant
if len(dep_vars) == 1:
break
# filter out variants that are specific to a particular version of CUDA
cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v]
if len(dep_vars) > len(cuda_dep_vars):
for key in list(dep_vars):
if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key):
dep_vars.pop(key)
# some software packages require an old version of a particular dependency
old_dep_versions = {
# libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k
# (Qiskit depends on PySCF)
'libxc': (r'[23]\.', ['ABINIT-', 'AtomPAW-', 'CP2K-', 'GPAW-', 'horton-', 'PySCF-', 'Qiskit-', 'WIEN2k-']),
# OPERA requires SAMtools 0.x
'SAMtools': (r'0\.', ['ChimPipe-0.9.5', 'Cufflinks-2.2.1', 'OPERA-2.0.6']),
# Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x)
'Jellyfish': (r'1\.', ['Kraken-1.', 'Roary-3.12.0', 'metaWRAP-1.2']),
# EMAN2 2.3 requires Boost(.Python) 1.64.0
'Boost': ('1.64.0;', ['Boost.Python-1.64.0-', 'EMAN2-2.3-']),
'Boost.Python': ('1.64.0;', ['EMAN2-2.3-']),
}
if dep in old_dep_versions and len(dep_vars) > 1:
for key in list(dep_vars):
version_pattern, parents = old_dep_versions[dep]
# filter out known old dependency versions
if re.search('^version: %s' % version_pattern, key):
# only filter if the easyconfig using this dep variants is known
if all(any(x.startswith(p) for p in parents) for x in dep_vars[key]):
dep_vars.pop(key)
# only single variant is always OK
if len(dep_vars) == 1:
res = True
elif len(dep_vars) == 2 and dep in ['Python', 'Tkinter']:
# for Python & Tkinter, it's OK to have on 2.x and one 3.x version
v2_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 2.')]
v3_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 3.')]
if len(v2_dep_vars) == 1 and len(v3_dep_vars) == 1:
res = True
# two variants is OK if one is for Python 2.x and the other is for Python 3.x (based on versionsuffix)
elif len(dep_vars) == 2:
py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x]
py3_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-3.' in x]
if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1:
res = True
return res
def test_check_dep_vars(self):
"""Test check_dep_vars utility method."""
# one single dep version: OK
self.assertTrue(self.check_dep_vars('testdep', {
'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb', 'bar-4.5.6.eb'],
}))
self.assertTrue(self.check_dep_vars('testdep', {
'version: 1.2.3; versionsuffix: -test': ['foo-1.2.3.eb', 'bar-4.5.6.eb'],
}))
# two or more dep versions (no special case: not OK)
self.assertFalse(self.check_dep_vars('testdep', {
'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'],
'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'],
}))
self.assertFalse(self.check_dep_vars('testdep', {
'version: 0.0; versionsuffix:': ['foobar-0.0.eb'],
'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'],
'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'],
}))
# Java is a special case, with wrapped Java versions
self.assertTrue(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
}))
# two Java wrappers is not OK
self.assertFalse(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6.eb'],
}))
# OK to have two or more wrappers if versionsuffix is used to indicate exception
self.assertTrue(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
}))
# versionsuffix must be there for all easyconfigs to indicate exception
self.assertFalse(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'],
}))
self.assertTrue(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
'version: 12.1.6; versionsuffix:': ['foobar-0.0-Java-12.eb'],
'version: 12; versionsuffix:': ['foobar-0.0-Java-12.eb'],
}))
# strange situation: odd number of Java versions
# not OK: two Java wrappers (and no versionsuffix to indicate exception)
self.assertFalse(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6.eb'],
}))
# OK because of -Java-11 versionsuffix
self.assertTrue(self.check_dep_vars('Java', {
'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
}))
# not OK: two Java wrappers (and no versionsuffix to indicate exception)
self.assertFalse(self.check_dep_vars('Java', {
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6.eb'],
}))
# OK because of -Java-11 versionsuffix
self.assertTrue(self.check_dep_vars('Java', {
'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'],
'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'],
}))
# two different versions of Boost is not OK
self.assertFalse(self.check_dep_vars('Boost', {
'version: 1.64.0; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'],
}))
# a different Boost version that is only used as dependency for a matching Boost.Python is fine
self.assertTrue(self.check_dep_vars('Boost', {
'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'],
'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'],
}))
self.assertTrue(self.check_dep_vars('Boost', {
'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2018b.eb'],
'version: 1.66.0; versionsuffix:': ['Boost.Python-1.66.0-gompi-2019a.eb'],
'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'],
}))
self.assertFalse(self.check_dep_vars('Boost', {
'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'],
'version: 1.66.0; versionsuffix:': ['foo-1.2.3.eb'],
'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'],
}))
self.assertTrue(self.check_dep_vars('Boost', {
'version: 1.63.0; versionsuffix: -Python-2.7.14': ['EMAN2-2.21a-foss-2018a-Python-2.7.14-Boost-1.63.0.eb'],
'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2018a.eb'],
'version: 1.66.0; versionsuffix:': ['BLAST+-2.7.1-foss-2018a.eb'],
}))
self.assertTrue(self.check_dep_vars('Boost', {
'version: 1.64.0; versionsuffix:': [
'Boost.Python-1.64.0-gompi-2019a.eb',
'EMAN2-2.3-foss-2019a-Python-2.7.15.eb',
],
'version: 1.70.0; versionsuffix:': [
'BLAST+-2.9.0-gompi-2019a.eb',
'Boost.Python-1.70.0-gompi-2019a.eb',
],
}))
def test_dep_versions_per_toolchain_generation(self):
"""
Check whether there's only one dependency version per toolchain generation actively used.
This is enforced to try and limit the chance of running into conflicts when multiple modules built with
the same toolchain are loaded together.
"""
if EasyConfigTest.ordered_specs is None:
self.process_all_easyconfigs()
def get_deps_for(ec):
"""Get list of (direct) dependencies for specified easyconfig."""
deps = []
for dep in ec['ec']['dependencies']:
dep_mod_name = dep['full_mod_name']
deps.append((dep['name'], dep['version'], dep['versionsuffix'], dep_mod_name))
res = [x for x in EasyConfigTest.ordered_specs if x['full_mod_name'] == dep_mod_name]
if len(res) == 1:
deps.extend(get_deps_for(res[0]))
else:
raise EasyBuildError("Failed to find %s in ordered list of easyconfigs", dep_mod_name)
return deps
# some software also follows <year>{a,b} versioning scheme,
# which throws off the pattern matching done below for toolchain versions
false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]')
# restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a)
# and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x
for pattern in ['201[89][ab]', '20[2-9][0-9][ab]', 'GCCcore-[7-9]\.[0-9]']:
all_deps = {}
regex = re.compile('^.*-(?P<tc_gen>%s).*\.eb$' % pattern)
# collect variants for all dependencies of easyconfigs that use a toolchain that matches
for ec in EasyConfigTest.ordered_specs:
ec_file = os.path.basename(ec['spec'])
# take into account software which also follows a <year>{a,b} versioning scheme
ec_file = false_positives_regex.sub('', ec_file)
res = regex.match(ec_file)
if res:
tc_gen = res.group('tc_gen')
all_deps_tc_gen = all_deps.setdefault(tc_gen, {})
for dep_name, dep_ver, dep_versuff, dep_mod_name in get_deps_for(ec):
dep_variants = all_deps_tc_gen.setdefault(dep_name, {})
# a variant is defined by version + versionsuffix
variant = "version: %s; versionsuffix: %s" % (dep_ver, dep_versuff)
# keep track of which easyconfig this is a dependency
dep_variants.setdefault(variant, set()).add(ec_file)
# check which dependencies have more than 1 variant
multi_dep_vars, multi_dep_vars_msg = [], ''
for tc_gen in sorted(all_deps.keys()):
for dep in sorted(all_deps[tc_gen].keys()):
dep_vars = all_deps[tc_gen][dep]
if not self.check_dep_vars(dep, dep_vars):
multi_dep_vars.append(dep)
multi_dep_vars_msg += "\nfound %s variants of '%s' dependency " % (len(dep_vars), dep)
multi_dep_vars_msg += "in easyconfigs using '%s' toolchain generation\n* " % tc_gen
multi_dep_vars_msg += '\n* '.join("%s as dep for %s" % v for v in sorted(dep_vars.items()))
multi_dep_vars_msg += '\n'
error_msg = "No multi-variant deps found for '%s' easyconfigs:\n%s" % (regex.pattern, multi_dep_vars_msg)
self.assertFalse(multi_dep_vars, error_msg)
def test_sanity_check_paths(self):
"""Make sure specified sanity check paths adher to the requirements."""
if EasyConfigTest.ordered_specs is None:
self.process_all_easyconfigs()
for ec in EasyConfigTest.parsed_easyconfigs:
ec_scp = ec['ec']['sanity_check_paths']
if ec_scp != {}:
# if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements
# both 'files' and 'dirs' keys, both with list values and with at least one a non-empty list
error_msg = "sanity_check_paths for %s does not meet requirements: %s" % (ec['spec'], ec_scp)
self.assertEqual(sorted(ec_scp.keys()), ['dirs', 'files'], error_msg)
self.assertTrue(isinstance(ec_scp['dirs'], list), error_msg)
self.assertTrue(isinstance(ec_scp['files'], list), error_msg)
self.assertTrue(ec_scp['dirs'] or ec_scp['files'], error_msg)
def test_easyconfig_locations(self):
"""Make sure all easyconfigs files are in the right location."""
easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$')
topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
for (dirpath, _, filenames) in os.walk(topdir):
# ignore git/svn dirs & archived easyconfigs
if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath:
continue
# check whether list of .eb files is non-empty
easyconfig_files = [fn for fn in filenames if fn.endswith('eb')]
if easyconfig_files:
# check whether path matches required pattern
if not easyconfig_dirs_regex.search(dirpath):
# only exception: TEMPLATE.eb
if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']):
self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames))
def check_sha256_checksums(self, changed_ecs):
"""Make sure changed easyconfigs have SHA256 checksums in place."""
# list of software for which checksums can not be required,
# e.g. because 'source' files need to be constructed manually
whitelist = ['Kent_tools-*', 'MATLAB-*', 'OCaml-*']
# the check_sha256_checksums function (again) creates an EasyBlock instance
# for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter
# is updated in place (sources for components are added the 'parent' sources) in Bundle's __init__;
# therefore, we need to reset 'sources' to an empty list here if Bundle is used...
# likewise for 'patches' and 'checksums'
for ec in changed_ecs:
if ec['easyblock'] == 'Bundle':
ec['sources'] = []
ec['patches'] = []
ec['checksums'] = []
# filter out deprecated easyconfigs
retained_changed_ecs = []
for ec in changed_ecs:
if not ec['deprecated']:
retained_changed_ecs.append(ec)
checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist)
self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues))
def check_python_packages(self, changed_ecs, added_ecs_filenames):
"""Several checks for easyconfigs that install (bundles of) Python packages."""
# These packages do not support installation with 'pip'
whitelist_pip = [r'MATLAB-Engine-.*', r'PyTorch-.*', r'Meld-.*']
failing_checks = []
for ec in changed_ecs:
ec_fn = os.path.basename(ec.path)
easyblock = ec.get('easyblock')
exts_defaultclass = ec.get('exts_defaultclass')
exts_default_options = ec.get('exts_default_options', {})
download_dep_fail = ec.get('download_dep_fail')
exts_download_dep_fail = ec.get('exts_download_dep_fail')
use_pip = ec.get('use_pip')
# download_dep_fail should be set when using PythonPackage
if easyblock == 'PythonPackage':
if download_dep_fail is None:
failing_checks.append("'download_dep_fail' set in %s" % ec_fn)
# use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs)
if easyblock in ['PythonBundle', 'PythonPackage']:
if use_pip is None and not any(re.match(regex, ec_fn) for regex in whitelist_pip):
failing_checks.append("'use_pip' set in %s" % ec_fn)
# download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set
if easyblock == 'PythonBundle':
if download_dep_fail or exts_download_dep_fail:
fail = "'*download_dep_fail' set in %s (shouldn't, since PythonBundle easyblock is used)" % ec_fn
failing_checks.append(fail)
elif exts_defaultclass == 'PythonPackage':
# bundle of Python packages should use PythonBundle
if easyblock == 'Bundle':
fail = "'PythonBundle' easyblock is used for bundle of Python packages in %s" % ec_fn
failing_checks.append(fail)
else:
# both download_dep_fail and use_pip should be set via exts_default_options
# when installing Python packages as extensions
for key in ['download_dep_fail', 'use_pip']:
if exts_default_options.get(key) is None:
failing_checks.append("'%s' set in exts_default_options in %s" % (key, ec_fn))
# if Python is a dependency, that should be reflected in the versionsuffix
# Tkinter is an exception, since its version always matches the Python version anyway
if any(dep['name'] == 'Python' for dep in ec['dependencies']) and ec.name != 'Tkinter':
if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']):
msg = "'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn
# This is only a failure for newly added ECs, not for existing ECS
# As that would probably break many ECs
if ec_fn in added_ecs_filenames:
failing_checks.append(msg)
else:
print('\nNote: Failed non-critical check: ' + msg)
# require that running of "pip check" during sanity check is enabled via sanity_pip_check
if use_pip and easyblock in ['PythonBundle', 'PythonPackage']:
sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check')
if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip):
failing_checks.append("sanity_pip_check is enabled in %s" % ec_fn)
self.assertFalse(failing_checks, '\n'.join(failing_checks))
def check_sanity_check_paths(self, changed_ecs):
"""Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock."""
# PythonBundle & PythonPackage already have a decent customised sanity_check_paths
# BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check.
whitelist = ['CrayToolchain', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain', 'BuildEnv']
# Autotools & (recent) GCC are just bundles (Autotools: Autoconf+Automake+libtool, GCC: GCCcore+binutils)
bundles_whitelist = ['Autotools', 'GCC']
failing_checks = []
for ec in changed_ecs:
easyblock = ec.get('easyblock')
if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'):
if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist):
pass
else:
ec_fn = os.path.basename(ec.path)
failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn)
self.assertFalse(failing_checks, '\n'.join(failing_checks))
def check_https(self, changed_ecs):
"""Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://)."""
whitelist = [
'Kaiju', # invalid certificate at https://kaiju.binf.ku.dk
'libxml2', # https://xmlsoft.org works, but invalid certificate
'p4vasp', # https://www.p4vasp.at doesn't work
'ITSTool', # https://itstool.org/ doesn't work
'UCX-', # bad certificate for https://www.openucx.org
]
http_regex = re.compile('http://[^"\'\n]+', re.M)
failing_checks = []
for ec in changed_ecs:
ec_fn = os.path.basename(ec.path)
# skip whitelisted easyconfigs
if any(ec_fn.startswith(x) for x in whitelist):
continue
# ignore commented out lines in easyconfig files when checking for http:// URLs
ec_txt = '\n'.join(l for l in ec.rawtxt.split('\n') if not l.startswith('#'))
for http_url in http_regex.findall(ec_txt):
https_url = http_url.replace('http://', 'https://')
try:
https_url_works = bool(urlopen(https_url, timeout=5))
except Exception:
https_url_works = False
if https_url_works:
failing_checks.append("Found http:// URL in %s, should be https:// : %s" % (ec_fn, http_url))
self.assertFalse(failing_checks, '\n'.join(failing_checks))
def test_changed_files_pull_request(self):
"""Specific checks only done for the (easyconfig) files that were changed in a pull request."""
def get_eb_files_from_diff(diff_filter):
cmd = "git diff --name-only --diff-filter=%s %s...HEAD" % (diff_filter, target_branch)
out, ec = run_cmd(cmd, simple=False)
return [os.path.basename(f) for f in out.strip().split('\n') if f.endswith('.eb')]
# $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR
travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '(none)'))
# when testing a PR in GitHub Actions, $GITHUB_EVENT_NAME will be set to 'pull_request'
github_pr_test = os.environ.get('GITHUB_EVENT_NAME') == 'pull_request'
if travis_pr_test or github_pr_test:
# target branch should be anything other than 'master';
# usually is 'develop', but could also be a release branch like '3.7.x'
if travis_pr_test:
target_branch = os.environ.get('TRAVIS_BRANCH', None)
else:
target_branch = os.environ.get('GITHUB_BASE_REF', None)
if target_branch is None:
self.assertTrue(False, "Failed to determine target branch for current pull request.")
if target_branch != 'master':
if not EasyConfigTest.parsed_easyconfigs:
self.process_all_easyconfigs()
# relocate to top-level directory of repository to run 'git diff' command
top_dir = os.path.dirname(os.path.dirname(get_paths_for('easyconfigs')[0]))
cwd = change_dir(top_dir)
# get list of changed easyconfigs
changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M')
added_ecs_filenames = get_eb_files_from_diff(diff_filter='A')
if changed_ecs_filenames:
print("\nList of changed easyconfig files in this PR: %s" % '\n'.join(changed_ecs_filenames))
if added_ecs_filenames:
print("\nList of added easyconfig files in this PR: %s" % '\n'.join(added_ecs_filenames))
change_dir(cwd)
# grab parsed easyconfigs for changed easyconfig files
changed_ecs = []
for ec_fn in changed_ecs_filenames + added_ecs_filenames:
match = None
for ec in EasyConfigTest.parsed_easyconfigs:
if os.path.basename(ec['spec']) == ec_fn:
match = ec['ec']
break
if match:
changed_ecs.append(match)
else:
# if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR...
# so as a last resort, try to find the easyconfig file in __archive__
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn))
if len(specs) == 1:
ec = process_easyconfig(specs[0])[0]
changed_ecs.append(ec['ec'])
else:
error_msg = "Failed to find parsed easyconfig for %s" % ec_fn
error_msg += " (and could not isolate it in easyconfigs archive either)"
self.assertTrue(False, error_msg)
# run checks on changed easyconfigs
self.check_sha256_checksums(changed_ecs)
self.check_python_packages(changed_ecs, added_ecs_filenames)
self.check_sanity_check_paths(changed_ecs)
self.check_https(changed_ecs)
def test_zzz_cleanup(self):
"""Dummy test to clean up global temporary directory."""
shutil.rmtree(self.TMPDIR)
class EasyConfigTest(TestCase):
"""Baseclass for easyconfig testcases."""
# initialize configuration (required for e.g. default modules_tool setting)
eb_go = eboptions.parse_options()
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'check_osdeps': False,
'external_modules_metadata': {},
'force': True,
'optarch': 'test',
'robot_path': get_paths_for("easyconfigs")[0],
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
del eb_go
# put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains
TMPDIR = tempfile.mkdtemp()
os.environ['MODULEPATH'] = TMPDIR
write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n')
log = fancylogger.getLogger("EasyConfigTest", fname=False)
# make sure a logger is present for main
eb_main._log = log
ordered_specs = None
parsed_easyconfigs = []
def process_all_easyconfigs(self):
"""Process all easyconfigs and resolve inter-easyconfig dependencies."""
# all available easyconfig files
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path)
# parse all easyconfigs if they haven't been already
if not self.parsed_easyconfigs:
for spec in specs:
self.parsed_easyconfigs.extend(process_easyconfig(spec))
# filter out external modules
for ec in self.parsed_easyconfigs:
for dep in ec['dependencies'][:]:
if dep.get('external_module', False):
ec['dependencies'].remove(dep)
self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs,
modules_tool(),
retain_all_deps=True)
def test_dep_graph(self):
"""Unit test that builds a full dependency graph."""
# pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6
if LooseVersion(
sys.version) >= LooseVersion('2.6') and single_tests_ok:
# temporary file for dep graph
(hn, fn) = tempfile.mkstemp(suffix='.dot')
os.close(hn)
if self.ordered_specs is None:
self.process_all_easyconfigs()
dep_graph(fn, self.ordered_specs)
remove_file(fn)
else:
print "(skipped dep graph test)"
def test_conflicts(self):
"""Check whether any conflicts occur in software dependency graphs."""
if not single_tests_ok:
print "(skipped conflicts test)"
return
if self.ordered_specs is None:
self.process_all_easyconfigs()
self.assertFalse(
check_conflicts(self.ordered_specs,
modules_tool(),
check_inter_ec_conflicts=False),
"No conflicts detected")
def test_dep_versions_per_toolchain_generation(self):
"""
Check whether there's only one dependency version per toolchain generation actively used.
This is enforced to try and limit the chance of running into conflicts when multiple modules built with
the same toolchain are loaded together.
"""
if self.ordered_specs is None:
self.process_all_easyconfigs()
def get_deps_for(ec):
"""Get list of (direct) dependencies for specified easyconfig."""
deps = []
for dep in ec['ec']['dependencies']:
dep_mod_name = dep['full_mod_name']
deps.append((dep['name'], dep['version'], dep['versionsuffix'],
dep_mod_name))
res = [
x for x in self.ordered_specs
if x['full_mod_name'] == dep_mod_name
]
if len(res) == 1:
deps.extend(get_deps_for(res[0]))
else:
raise EasyBuildError(
"Failed to find %s in ordered list of easyconfigs",
dep_mod_name)
return deps
def check_dep_vars(dep, dep_vars):
"""Check whether available variants of a particular dependency are acceptable or not."""
# 'guilty' until proven 'innocent'
res = False
# filter out binutils with empty versionsuffix which is used to build toolchain compiler
if dep == 'binutils' and len(dep_vars) > 1:
empty_vsuff_vars = [
v for v in dep_vars.keys() if v.endswith('versionsuffix: ')
]
if len(empty_vsuff_vars) == 1:
dep_vars = dict((k, v) for (k, v) in dep_vars.items()
if k != empty_vsuff_vars[0])
# multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools
elif dep == 'HTSlib' and len(dep_vars) > 1:
for key, ecs in dep_vars.items():
# filter out HTSlib variants that are only used as dependency for BCFtools with same version
htslib_ver = re.search('^version: (?P<ver>[^;]+);',
key).group('ver')
if all(
ec.startswith('BCFtools-%s-' % htslib_ver)
for ec in ecs):
dep_vars.pop(key)
# filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains
elif dep in ['FFTW', 'imkl']:
serial_vsuff_vars = [
v for v in dep_vars.keys()
if v.endswith('versionsuffix: -serial')
]
if len(serial_vsuff_vars) == 1:
dep_vars = dict((k, v) for (k, v) in dep_vars.items()
if k != serial_vsuff_vars[0])
# for some dependencies, we allow exceptions for software that depends on a particular version,
# as long as that's indicated by the versionsuffix
elif dep in ['Boost', 'R', 'PLUMED'] and len(dep_vars) > 1:
for key in dep_vars.keys():
dep_ver = re.search('^version: (?P<ver>[^;]+);',
key).group('ver')
# filter out dep version if all easyconfig filenames using it include specific dep version
if all(
re.search('-%s-%s' % (dep, dep_ver), v)
for v in dep_vars[key]):
dep_vars.pop(key)
# always retain at least one dep variant
if len(dep_vars) == 1:
break
# filter R dep for a specific version of Python 2.x
if dep == 'R' and len(dep_vars) > 1:
for key in dep_vars.keys():
if '; versionsuffix: -Python-2' in key:
dep_vars.pop(key)
# always retain at least one variant
if len(dep_vars) == 1:
break
# filter out Java 'wrapper'
# i.e. if the version of one is a prefix of the version of the other one (e.g. 1.8 & 1.8.0_181)
elif dep == 'Java' and len(dep_vars) == 2:
key1, key2 = sorted(dep_vars.keys())
ver1, ver2 = [k.split(';')[0] for k in [key1, key2]]
if ver1.startswith(ver2):
dep_vars.pop(key2)
elif ver2.startswith(ver1):
dep_vars.pop(key1)
# filter out variants that are specific to a particular version of CUDA
cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v]
if len(dep_vars) > len(cuda_dep_vars):
for key in dep_vars.keys():
if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key):
dep_vars.pop(key)
# some software packages require an old version of a particular dependency
old_dep_versions = {
# libxc (CP2K & ABINIT require libxc 2.x or 3.x)
'libxc': r'[23]\.',
# OPERA requires SAMtools 0.x
'SAMtools': r'0\.',
# Kraken 1.0 requires Jellyfish 1.x
'Jellyfish': r'1\.',
}
if dep in old_dep_versions and len(dep_vars) > 1:
for key in dep_vars.keys():
# filter out known old dependency versions
if re.search('^version: %s' % old_dep_versions[dep], key):
dep_vars.pop(key)
# only single variant is always OK
if len(dep_vars) == 1:
res = True
elif len(dep_vars) == 2 and dep in ['Python', 'Tkinter']:
# for Python & Tkinter, it's OK to have on 2.x and one 3.x version
v2_dep_vars = [
x for x in dep_vars.keys() if x.startswith('version: 2.')
]
v3_dep_vars = [
x for x in dep_vars.keys() if x.startswith('version: 3.')
]
if len(v2_dep_vars) == 1 and len(v3_dep_vars) == 1:
res = True
# two variants is OK if one is for Python 2.x and the other is for Python 3.x (based on versionsuffix)
elif len(dep_vars) == 2:
py2_dep_vars = [
x for x in dep_vars.keys()
if '; versionsuffix: -Python-2.' in x
]
py3_dep_vars = [
x for x in dep_vars.keys()
if '; versionsuffix: -Python-3.' in x
]
if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1:
res = True
return res
# some software also follows <year>{a,b} versioning scheme,
# which throws off the pattern matching done below for toolchain versions
false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]')
# restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a)
# and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x
for pattern in [
'201[89][ab]', '20[2-9][0-9][ab]', 'GCCcore-[7-9]\.[0-9]'
]:
all_deps = {}
regex = re.compile('^.*-(?P<tc_gen>%s).*\.eb$' % pattern)
# collect variants for all dependencies of easyconfigs that use a toolchain that matches
for ec in self.ordered_specs:
ec_file = os.path.basename(ec['spec'])
# take into account software which also follows a <year>{a,b} versioning scheme
ec_file = false_positives_regex.sub('', ec_file)
res = regex.match(ec_file)
if res:
tc_gen = res.group('tc_gen')
all_deps_tc_gen = all_deps.setdefault(tc_gen, {})
for dep_name, dep_ver, dep_versuff, dep_mod_name in get_deps_for(
ec):
dep_variants = all_deps_tc_gen.setdefault(dep_name, {})
# a variant is defined by version + versionsuffix
variant = "version: %s; versionsuffix: %s" % (
dep_ver, dep_versuff)
# keep track of which easyconfig this is a dependency
dep_variants.setdefault(variant, set()).add(ec_file)
# check which dependencies have more than 1 variant
multi_dep_vars, multi_dep_vars_msg = [], ''
for tc_gen in sorted(all_deps.keys()):
for dep in sorted(all_deps[tc_gen].keys()):
dep_vars = all_deps[tc_gen][dep]
if not check_dep_vars(dep, dep_vars):
multi_dep_vars.append(dep)
multi_dep_vars_msg += "\nfound %s variants of '%s' dependency " % (
len(dep_vars), dep)
multi_dep_vars_msg += "in easyconfigs using '%s' toolchain generation\n* " % tc_gen
multi_dep_vars_msg += '\n* '.join(
"%s as dep for %s" % v
for v in sorted(dep_vars.items()))
multi_dep_vars_msg += '\n'
error_msg = "No multi-variant deps found for '%s' easyconfigs:\n%s" % (
regex.pattern, multi_dep_vars_msg)
self.assertFalse(multi_dep_vars, error_msg)
def test_sanity_check_paths(self):
"""Make sure specified sanity check paths adher to the requirements."""
if self.ordered_specs is None:
self.process_all_easyconfigs()
for ec in self.parsed_easyconfigs:
ec_scp = ec['ec']['sanity_check_paths']
if ec_scp != {}:
# if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements
# both 'files' and 'dirs' keys, both with list values and with at least one a non-empty list
error_msg = "sanity_check_paths for %s does not meet requirements: %s" % (
ec['spec'], ec_scp)
self.assertEqual(sorted(ec_scp.keys()), ['dirs', 'files'],
error_msg)
self.assertTrue(isinstance(ec_scp['dirs'], list), error_msg)
self.assertTrue(isinstance(ec_scp['files'], list), error_msg)
self.assertTrue(ec_scp['dirs'] or ec_scp['files'], error_msg)
def test_easyconfig_locations(self):
"""Make sure all easyconfigs files are in the right location."""
easyconfig_dirs_regex = re.compile(
r'/easybuild/easyconfigs/[0a-z]/[^/]+$')
topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
for (dirpath, _, filenames) in os.walk(topdir):
# ignore git/svn dirs & archived easyconfigs
if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath:
continue
# check whether list of .eb files is non-empty
easyconfig_files = [fn for fn in filenames if fn.endswith('eb')]
if easyconfig_files:
# check whether path matches required pattern
if not easyconfig_dirs_regex.search(dirpath):
# only exception: TEMPLATE.eb
if not (dirpath.endswith('/easybuild/easyconfigs')
and filenames == ['TEMPLATE.eb']):
self.assertTrue(
False,
"List of easyconfig files in %s is empty: %s" %
(dirpath, filenames))
def check_sha256_checksums(self, changed_ecs):
"""Make sure changed easyconfigs have SHA256 checksums in place."""
# list of software for which checksums can not be required,
# e.g. because 'source' files need to be constructed manually
whitelist = ['Kent_tools-*', 'MATLAB-*', 'OCaml-*']
# the check_sha256_checksums function (again) creates an EasyBlock instance
# for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter
# is updated in place (sources for components are added the 'parent' sources) in Bundle's __init__;
# therefore, we need to reset 'sources' to an empty list here if Bundle is used...
for ec in changed_ecs:
if ec['easyblock'] == 'Bundle':
ec['sources'] = []
# filter out deprecated easyconfigs
retained_changed_ecs = []
for ec in changed_ecs:
if not ec['deprecated']:
retained_changed_ecs.append(ec)
checksum_issues = check_sha256_checksums(retained_changed_ecs,
whitelist=whitelist)
self.assertTrue(
len(checksum_issues) == 0,
"No checksum issues:\n%s" % '\n'.join(checksum_issues))
def check_python_packages(self, changed_ecs):
"""Several checks for easyconfigs that install (bundles of) Python packages."""
# MATLAB-Engine, PyTorch do not support installation with 'pip'
whitelist_pip = ['MATLAB-Engine-*', 'PyTorch-*']
failing_checks = []
for ec in changed_ecs:
ec_fn = os.path.basename(ec.path)
easyblock = ec.get('easyblock')
exts_defaultclass = ec.get('exts_defaultclass')
download_dep_fail = ec.get('download_dep_fail')
exts_download_dep_fail = ec.get('exts_download_dep_fail')
use_pip = ec.get('use_pip')
# download_dep_fail should be set when using PythonPackage
if easyblock == 'PythonPackage':
if not download_dep_fail:
failing_checks.append("'download_dep_fail' set in %s" %
ec_fn)
# use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs)
if easyblock in ['PythonBundle', 'PythonPackage']:
if not use_pip and not any(
re.match(regex, ec_fn) for regex in whitelist_pip):
failing_checks.append("'use_pip' set in %s" % ec_fn)
# download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set
if easyblock == 'PythonBundle':
if download_dep_fail or exts_download_dep_fail:
fail = "'*download_dep_fail' set in %s (shouldn't, since PythonBundle easyblock is used)" % ec_fn
failing_checks.append(fail)
elif exts_defaultclass == 'PythonPackage':
# bundle of Python packages should use PythonBundle
if easyblock == 'Bundle':
fail = "'PythonBundle' easyblock is used for bundle of Python packages in %s" % ec_fn
failing_checks.append(fail)
else:
# both download_dep_fail and use_pip should be set via exts_default_options
# when installing Python packages as extensions
exts_default_options = ec.get('exts_default_options', {})
for key in ['download_dep_fail', 'use_pip']:
if not exts_default_options.get(key):
failing_checks.append(
"'%s' set in exts_default_options in %s" %
(key, ec_fn))
# if Python is a dependency, that should be reflected in the versionsuffix
if any(dep['name'] == 'Python' for dep in ec['dependencies']):
if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+',
ec['versionsuffix']):
failing_checks.append(
"'-Python-%%(pyver)s' included in versionsuffix in %s"
% ec_fn)
self.assertFalse(failing_checks, '\n'.join(failing_checks))
def test_changed_files_pull_request(self):
"""Specific checks only done for the (easyconfig) files that were changed in a pull request."""
# $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR
if re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST',
'(none)')):
# target branch should be anything other than 'master';
# usually is 'develop', but could also be a release branch like '3.7.x'
travis_branch = os.environ.get('TRAVIS_BRANCH', None)
if travis_branch and travis_branch != 'master':
if not self.parsed_easyconfigs:
self.process_all_easyconfigs()
# relocate to top-level directory of repository to run 'git diff' command
top_dir = os.path.dirname(
os.path.dirname(get_paths_for('easyconfigs')[0]))
cwd = change_dir(top_dir)
# get list of changed easyconfigs
cmd = "git diff --name-only --diff-filter=AM %s...HEAD" % travis_branch
out, ec = run_cmd(cmd, simple=False)
changed_ecs_filenames = [
os.path.basename(f) for f in out.strip().split('\n')
if f.endswith('.eb')
]
print("\nList of changed easyconfig files in this PR: %s" %
'\n'.join(changed_ecs_filenames))
change_dir(cwd)
# grab parsed easyconfigs for changed easyconfig files
changed_ecs = []
for ec_fn in changed_ecs_filenames:
match = None
for ec in self.parsed_easyconfigs:
if os.path.basename(ec['spec']) == ec_fn:
match = ec['ec']
break
if match:
changed_ecs.append(match)
else:
# if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR...
# so as a last resort, try to find the easyconfig file in __archive__
easyconfigs_path = get_paths_for("easyconfigs")[0]
specs = glob.glob('%s/__archive__/*/*/%s' %
(easyconfigs_path, ec_fn))
if len(specs) == 1:
ec = process_easyconfig(specs[0])[0]
changed_ecs.append(ec['ec'])
else:
error_msg = "Failed to find parsed easyconfig for %s" % ec_fn
error_msg += " (and could not isolate it in easyconfigs archive either)"
self.assertTrue(False, error_msg)
# run checks on changed easyconfigs
self.check_sha256_checksums(changed_ecs)
self.check_python_packages(changed_ecs)
def test_zzz_cleanup(self):
"""Dummy test to clean up global temporary directory."""
shutil.rmtree(self.TMPDIR)
def basic_options(self):
"""basic runtime options"""
all_stops = [x[0] for x in EasyBlock.get_steps()]
strictness_options = [run.IGNORE, run.WARN, run.ERROR]
descr = ("Basic options", "Basic runtime options for EasyBuild.")
opts = OrderedDict(
{
"dry-run": ("Print build overview incl. dependencies (full paths)", None, "store_true", False),
"dry-run-short": (
"Print build overview incl. dependencies (short paths)",
None,
"store_true",
False,
"D",
),
"force": (
"Force to rebuild software even if it's already installed (i.e. if it can be found as module)",
None,
"store_true",
False,
"f",
),
"job": ("Submit the build as a job", None, "store_true", False),
"logtostdout": ("Redirect main log to stdout", None, "store_true", False, "l"),
"only-blocks": ("Only build listed blocks", None, "extend", None, "b", {"metavar": "BLOCKS"}),
"robot": (
"Enable dependency resolution, using easyconfigs in specified paths",
"pathlist",
"store_or_None",
[],
"r",
{"metavar": "PATH[%sPATH]" % os.pathsep},
),
"robot-paths": (
"Additional paths to consider by robot for easyconfigs (--robot paths get priority)",
"pathlist",
"add_flex",
self.default_robot_paths,
{"metavar": "PATH[%sPATH]" % os.pathsep},
),
"skip": (
"Skip existing software (useful for installing additional packages)",
None,
"store_true",
False,
"k",
),
"stop": (
"Stop the installation after certain step",
"choice",
"store_or_None",
SOURCE_STEP,
"s",
all_stops,
),
"strict": ("Set strictness level", "choice", "store", run.WARN, strictness_options),
}
)
self.log.debug("basic_options: descr %s opts %s" % (descr, opts))
self.add_group_parser(opts, descr)
def main(testing_data=(None, None, None)):
"""
Main function:
@arg options: a tuple: (options, paths, logger, logfile, hn) as defined in parse_options
This function will:
- read easyconfig
- build software
"""
# purposely session state very early, to avoid modules loaded by EasyBuild meddling in
init_session_state = session_state()
# disallow running EasyBuild as root
if os.getuid() == 0:
sys.stderr.write(
"ERROR: You seem to be running EasyBuild with root privileges.\n"
"That's not wise, so let's end this here.\n"
"Exiting.\n")
sys.exit(1)
# steer behavior when testing main
testing = testing_data[0] is not None
args, logfile, do_build = testing_data
# initialise options
eb_go = eboptions.parse_options(args=args)
options = eb_go.options
orig_paths = eb_go.args
eb_config = eb_go.generate_cmd_line(add_default=True)
init_session_state.update({'easybuild_configuration': eb_config})
# set umask (as early as possible)
if options.umask is not None:
new_umask = int(options.umask, 8)
old_umask = os.umask(new_umask)
# set temporary directory to use
eb_tmpdir = set_tmpdir(options.tmpdir)
# initialise logging for main
if options.logtostdout:
fancylogger.logToScreen(enable=True, stdout=True)
else:
if logfile is None:
# mkstemp returns (fd,filename), fd is from os.open, not regular open!
fd, logfile = tempfile.mkstemp(suffix='.log', prefix='easybuild-')
os.close(fd)
fancylogger.logToFile(logfile)
print_msg('temporary log file in case of crash %s' % (logfile),
log=None,
silent=testing)
global _log
_log = fancylogger.getLogger(fname=False)
if options.umask is not None:
_log.info("umask set to '%s' (used to be '%s')" %
(oct(new_umask), oct(old_umask)))
# hello world!
_log.info(this_is_easybuild())
# how was EB called?
eb_command_line = eb_go.generate_cmd_line() + eb_go.args
_log.info("Command line: %s" % (" ".join(eb_command_line)))
_log.info("Using %s as temporary directory" % eb_tmpdir)
if not options.robot is None:
if options.robot:
_log.info("Using robot path(s): %s" % options.robot)
else:
_log.error(
"No robot paths specified, and unable to determine easybuild-easyconfigs install path."
)
# do not pass options.robot, it's not a list instance (and it shouldn't be modified)
robot_path = None
if options.robot:
robot_path = list(options.robot)
# determine easybuild-easyconfigs package install path
easyconfigs_paths = get_paths_for("easyconfigs", robot_path=robot_path)
# keep track of paths for install easyconfigs, so we can obtain find specified easyconfigs
easyconfigs_pkg_full_paths = easyconfigs_paths[:]
if not easyconfigs_paths:
_log.warning(
"Failed to determine install path for easybuild-easyconfigs package."
)
# process software build specifications (if any), i.e.
# software name/version, toolchain name/version, extra patches, ...
(try_to_generate, build_specs) = process_software_build_specs(options)
# specified robot paths are preferred over installed easyconfig files
# --try-X and --dep-graph both require --robot, so enable it with path of installed easyconfigs
if robot_path or try_to_generate or options.dep_graph:
if robot_path is None:
robot_path = []
robot_path.extend(easyconfigs_paths)
easyconfigs_paths = robot_path[:]
_log.info(
"Extended list of robot paths with paths for installed easyconfigs: %s"
% robot_path)
# initialise the easybuild configuration
config.init(options, eb_go.get_options_by_section('config'))
# building a dependency graph implies force, so that all dependencies are retained
# and also skips validation of easyconfigs (e.g. checking os dependencies)
retain_all_deps = False
if options.dep_graph:
_log.info("Enabling force to generate dependency graph.")
options.force = True
retain_all_deps = True
config.init_build_options({
'aggregate_regtest':
options.aggregate_regtest,
'allow_modules_tool_mismatch':
options.allow_modules_tool_mismatch,
'check_osdeps':
not options.ignore_osdeps,
'cleanup_builddir':
options.cleanup_builddir,
'command_line':
eb_command_line,
'debug':
options.debug,
'dry_run':
options.dry_run,
'easyblock':
options.easyblock,
'experimental':
options.experimental,
'force':
options.force,
'github_user':
options.github_user,
'group':
options.group,
'ignore_dirs':
options.ignore_dirs,
'modules_footer':
options.modules_footer,
'only_blocks':
options.only_blocks,
'recursive_mod_unload':
options.recursive_module_unload,
'regtest_output_dir':
options.regtest_output_dir,
'retain_all_deps':
retain_all_deps,
'robot_path':
robot_path,
'sequential':
options.sequential,
'silent':
testing,
'set_gid_bit':
options.set_gid_bit,
'skip':
options.skip,
'skip_test_cases':
options.skip_test_cases,
'sticky_bit':
options.sticky_bit,
'stop':
options.stop,
'umask':
options.umask,
'valid_module_classes':
module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
'validate':
not options.force,
})
# obtain list of loaded modules, build options must be initialized first
modlist = session_module_list()
init_session_state.update({'module_list': modlist})
_log.debug("Initial session state: %s" % init_session_state)
# search for easyconfigs
if options.search or options.search_short:
search_path = [os.getcwd()]
if easyconfigs_paths:
search_path = easyconfigs_paths
query = options.search or options.search_short
ignore_dirs = config.build_option('ignore_dirs')
silent = config.build_option('silent')
search_file(search_path,
query,
short=not options.search,
ignore_dirs=ignore_dirs,
silent=silent)
paths = []
if len(orig_paths) == 0:
if options.from_pr:
pr_path = os.path.join(eb_tmpdir, "files_pr%s" % options.from_pr)
pr_files = fetch_easyconfigs_from_pr(
options.from_pr, path=pr_path, github_user=options.github_user)
paths = [(path, False) for path in pr_files
if path.endswith('.eb')]
elif 'name' in build_specs:
paths = [
obtain_path(build_specs,
easyconfigs_paths,
try_to_generate=try_to_generate,
exit_on_error=not testing)
]
elif not any([
options.aggregate_regtest, options.search,
options.search_short, options.regtest
]):
print_error((
"Please provide one or multiple easyconfig files, or use software build "
"options to make EasyBuild search for easyconfigs"),
log=_log,
opt_parser=eb_go.parser,
exit_on_error=not testing)
else:
# look for easyconfigs with relative paths in easybuild-easyconfigs package,
# unless they were found at the given relative paths
if easyconfigs_pkg_full_paths:
# determine which easyconfigs files need to be found, if any
ecs_to_find = []
for idx, orig_path in enumerate(orig_paths):
if orig_path == os.path.basename(
orig_path) and not os.path.exists(orig_path):
ecs_to_find.append((idx, orig_path))
_log.debug("List of easyconfig files to find: %s" % ecs_to_find)
# find missing easyconfigs by walking paths with installed easyconfig files
for path in easyconfigs_pkg_full_paths:
_log.debug(
"Looking for missing easyconfig files (%d left) in %s..." %
(len(ecs_to_find), path))
for (subpath, dirnames, filenames) in os.walk(path,
topdown=True):
for idx, orig_path in ecs_to_find[:]:
if orig_path in filenames:
full_path = os.path.join(subpath, orig_path)
_log.info("Found %s in %s: %s" %
(orig_path, path, full_path))
orig_paths[idx] = full_path
# if file was found, stop looking for it (first hit wins)
ecs_to_find.remove((idx, orig_path))
# stop os.walk insanity as soon as we have all we need (os.walk loop)
if len(ecs_to_find) == 0:
break
# ignore subdirs specified to be ignored by replacing items in dirnames list used by os.walk
dirnames[:] = [
d for d in dirnames if not d in options.ignore_dirs
]
# stop os.walk insanity as soon as we have all we need (paths loop)
if len(ecs_to_find) == 0:
break
# indicate that specified paths do not contain generated easyconfig files
paths = [(path, False) for path in orig_paths]
_log.debug("Paths: %s" % paths)
# run regtest
if options.regtest or options.aggregate_regtest:
_log.info("Running regression test")
if paths:
ec_paths = [path[0] for path in paths]
else: # fallback: easybuild-easyconfigs install path
ec_paths = easyconfigs_pkg_full_paths
regtest_ok = regtest(ec_paths)
if not regtest_ok:
_log.info("Regression test failed (partially)!")
sys.exit(31) # exit -> 3x1t -> 31
# read easyconfig files
easyconfigs = []
for (path, generated) in paths:
path = os.path.abspath(path)
if not os.path.exists(path):
print_error("Can't find path %s" % path)
try:
ec_files = find_easyconfigs(path, ignore_dirs=options.ignore_dirs)
for ec_file in ec_files:
# only pass build specs when not generating easyconfig files
if try_to_generate:
ecs = process_easyconfig(ec_file)
else:
ecs = process_easyconfig(ec_file, build_specs=build_specs)
easyconfigs.extend(ecs)
except IOError, err:
_log.error("Processing easyconfigs in path %s failed: %s" %
(path, err))
def test_module_naming_scheme(self):
"""Test using default module naming scheme."""
all_stops = [x[0] for x in EasyBlock.get_steps()]
init_config(build_options={'valid_stops': all_stops})
ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
ec_files = [os.path.join(subdir, fil) for (subdir, _, files) in os.walk(ecs_dir) for fil in files]
# TODO FIXME: drop this once 2.0/.yeb support works
ec_files = [fil for fil in ec_files if not ('v2.0/' in fil or 'yeb/' in fil)]
build_options = {
'check_osdeps': False,
'external_modules_metadata': {},
'robot_path': [ecs_dir],
'valid_stops': all_stops,
'validate': False,
}
init_config(build_options=build_options)
def test_mns():
"""Test default module naming scheme."""
# test default naming scheme
for ec_file in [f for f in ec_files if not 'broken' in os.path.basename(f)]:
ec_path = os.path.abspath(ec_file)
ecs = process_easyconfig(ec_path, validate=False)
# derive module name directly from easyconfig file name
ec_fn = os.path.basename(ec_file)
if ec_fn in ec2mod_map:
# only check first, ignore any others (occurs when blocks are used (format v1.0 only))
self.assertEqual(ec2mod_map[ec_fn], ActiveMNS().det_full_module_name(ecs[0]['ec']))
# test default module naming scheme
default_ec2mod_map = {
'GCC-4.6.3.eb': 'GCC/4.6.3',
'gzip-1.4.eb': 'gzip/1.4',
'gzip-1.4-GCC-4.6.3.eb': 'gzip/1.4-GCC-4.6.3',
'gzip-1.5-goolf-1.4.10.eb': 'gzip/1.5-goolf-1.4.10',
'gzip-1.5-ictce-4.1.13.eb': 'gzip/1.5-ictce-4.1.13',
'toy-0.0.eb': 'toy/0.0',
'toy-0.0-multiple.eb': 'toy/0.0-somesuffix', # first block sets versionsuffix to '-somesuffix'
}
ec2mod_map = default_ec2mod_map
test_mns()
# generating module name from non-parsed easyconfig works fine
non_parsed = {
'name': 'foo',
'version': '1.2.3',
'versionsuffix': '-bar',
'toolchain': {
'name': 't00ls',
'version': '6.6.6',
},
}
self.assertEqual('foo/1.2.3-t00ls-6.6.6-bar', ActiveMNS().det_full_module_name(non_parsed))
# install custom module naming scheme dynamically
test_mns_parent_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'sandbox')
sys.path.append(test_mns_parent_dir)
reload(easybuild)
reload(easybuild.tools)
reload(easybuild.tools.module_naming_scheme)
# make sure test module naming schemes are available
mns_mods = ['broken_module_naming_scheme', 'test_module_naming_scheme', 'test_module_naming_scheme_more']
for test_mns_mod in mns_mods:
mns_path = "easybuild.tools.module_naming_scheme.%s" % test_mns_mod
__import__(mns_path, globals(), locals(), [''])
init_config(build_options=build_options)
# verify that key errors in module naming scheme are reported properly
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'BrokenModuleNamingScheme'
init_config(build_options=build_options)
err_pattern = 'nosucheasyconfigparameteravailable'
self.assertErrorRegex(EasyBuildError, err_pattern, EasyConfig, os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'))
# test simple custom module naming scheme
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'TestModuleNamingScheme'
init_config(build_options=build_options)
ec2mod_map = {
'GCC-4.6.3.eb': 'GCC/4.6.3',
'gzip-1.4.eb': 'gzip/1.4',
'gzip-1.4-GCC-4.6.3.eb': 'gnu/gzip/1.4',
'gzip-1.5-goolf-1.4.10.eb': 'gnu/openmpi/gzip/1.5',
'gzip-1.5-ictce-4.1.13.eb': 'intel/intelmpi/gzip/1.5',
'toy-0.0.eb': 'toy/0.0',
'toy-0.0-multiple.eb': 'toy/0.0', # test module naming scheme ignores version suffixes
}
test_mns()
ec = EasyConfig(os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'))
self.assertEqual(ec.toolchain.det_short_module_name(), 'goolf/1.4.10')
# test module naming scheme using all available easyconfig parameters
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'TestModuleNamingSchemeMore'
init_config(build_options=build_options)
# note: these checksums will change if another easyconfig parameter is added
ec2mod_map = {
'GCC-4.6.3.eb': 'GCC/9e9ab5a1e978f0843b5aedb63ac4f14c51efb859',
'gzip-1.4.eb': 'gzip/53d5c13e85cb6945bd43a58d1c8d4a4c02f3462d',
'gzip-1.4-GCC-4.6.3.eb': 'gzip/585eba598f33c64ef01c6fa47af0fc37f3751311',
'gzip-1.5-goolf-1.4.10.eb': 'gzip/fceb41e04c26b540b7276c4246d1ecdd1e8251c9',
'gzip-1.5-ictce-4.1.13.eb': 'gzip/ae16b3a0a330d4323987b360c0d024f244ac4498',
'toy-0.0.eb': 'toy/44a206d9e8c14130cc9f79e061468303c6e91b53',
'toy-0.0-multiple.eb': 'toy/44a206d9e8c14130cc9f79e061468303c6e91b53',
}
test_mns()
# test determining module name for dependencies (i.e. non-parsed easyconfigs)
# using a module naming scheme that requires all easyconfig parameters
ec2mod_map['gzip-1.5-goolf-1.4.10.eb'] = 'gzip/.fceb41e04c26b540b7276c4246d1ecdd1e8251c9'
for dep_ec, dep_spec in [
('GCC-4.6.3.eb', {
'name': 'GCC',
'version': '4.6.3',
'versionsuffix': '',
'toolchain': {'name': 'dummy', 'version': 'dummy'},
'hidden': False,
}),
('gzip-1.5-goolf-1.4.10.eb', {
'name': 'gzip',
'version': '1.5',
'versionsuffix': '',
'toolchain': {'name': 'goolf', 'version': '1.4.10'},
'hidden': True,
}),
('toy-0.0-multiple.eb', {
'name': 'toy',
'version': '0.0',
'versionsuffix': '-multiple',
'toolchain': {'name': 'dummy', 'version': 'dummy'},
'hidden': False,
}),
]:
# determine full module name
self.assertEqual(ActiveMNS().det_full_module_name(dep_spec), ec2mod_map[dep_ec])
ec = EasyConfig(os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'), hidden=True)
self.assertEqual(ec.full_mod_name, ec2mod_map['gzip-1.5-goolf-1.4.10.eb'])
self.assertEqual(ec.toolchain.det_short_module_name(), 'goolf/a86eb41d8f9c1d6f2d3d61cdb8f420cc2a21cada')
# restore default module naming scheme, and retest
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
init_config(build_options=build_options)
ec2mod_map = default_ec2mod_map
test_mns()
def test_module_naming_scheme(self):
"""Test using default module naming scheme."""
all_stops = [x[0] for x in EasyBlock.get_steps()]
init_config(build_options={'valid_stops': all_stops})
ecs_dir = os.path.join(os.path.dirname(__file__), 'easyconfigs')
ec_files = [
os.path.join(subdir, fil)
for (subdir, _, files) in os.walk(ecs_dir) for fil in files
]
# TODO FIXME: drop this once 2.0/.yeb support works
ec_files = [
fil for fil in ec_files if not ('v2.0/' in fil or 'yeb/' in fil)
]
build_options = {
'check_osdeps': False,
'external_modules_metadata': {},
'robot_path': [ecs_dir],
'valid_stops': all_stops,
'validate': False,
}
init_config(build_options=build_options)
def test_mns():
"""Test default module naming scheme."""
# test default naming scheme
for ec_file in [
f for f in ec_files if not 'broken' in os.path.basename(f)
]:
ec_path = os.path.abspath(ec_file)
ecs = process_easyconfig(ec_path, validate=False)
# derive module name directly from easyconfig file name
ec_fn = os.path.basename(ec_file)
if ec_fn in ec2mod_map:
# only check first, ignore any others (occurs when blocks are used (format v1.0 only))
self.assertEqual(
ec2mod_map[ec_fn],
ActiveMNS().det_full_module_name(ecs[0]['ec']))
# test default module naming scheme
default_ec2mod_map = {
'GCC-4.6.3.eb': 'GCC/4.6.3',
'gzip-1.4.eb': 'gzip/1.4',
'gzip-1.4-GCC-4.6.3.eb': 'gzip/1.4-GCC-4.6.3',
'gzip-1.5-goolf-1.4.10.eb': 'gzip/1.5-goolf-1.4.10',
'gzip-1.5-ictce-4.1.13.eb': 'gzip/1.5-ictce-4.1.13',
'toy-0.0.eb': 'toy/0.0',
'toy-0.0-multiple.eb':
'toy/0.0-somesuffix', # first block sets versionsuffix to '-somesuffix'
}
ec2mod_map = default_ec2mod_map
test_mns()
# generating module name from non-parsed easyconfig works fine
non_parsed = {
'name': 'foo',
'version': '1.2.3',
'versionsuffix': '-bar',
'toolchain': {
'name': 't00ls',
'version': '6.6.6',
},
}
self.assertEqual('foo/1.2.3-t00ls-6.6.6-bar',
ActiveMNS().det_full_module_name(non_parsed))
# install custom module naming scheme dynamically
test_mns_parent_dir = os.path.join(
os.path.dirname(os.path.abspath(__file__)), 'sandbox')
sys.path.append(test_mns_parent_dir)
reload(easybuild)
reload(easybuild.tools)
reload(easybuild.tools.module_naming_scheme)
# make sure test module naming schemes are available
mns_mods = [
'broken_module_naming_scheme', 'test_module_naming_scheme',
'test_module_naming_scheme_more'
]
for test_mns_mod in mns_mods:
mns_path = "easybuild.tools.module_naming_scheme.%s" % test_mns_mod
__import__(mns_path, globals(), locals(), [''])
init_config(build_options=build_options)
# verify that key errors in module naming scheme are reported properly
os.environ[
'EASYBUILD_MODULE_NAMING_SCHEME'] = 'BrokenModuleNamingScheme'
init_config(build_options=build_options)
err_pattern = 'nosucheasyconfigparameteravailable'
self.assertErrorRegex(
EasyBuildError, err_pattern, EasyConfig,
os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'))
# test simple custom module naming scheme
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'TestModuleNamingScheme'
init_config(build_options=build_options)
ec2mod_map = {
'GCC-4.6.3.eb': 'GCC/4.6.3',
'gzip-1.4.eb': 'gzip/1.4',
'gzip-1.4-GCC-4.6.3.eb': 'gnu/gzip/1.4',
'gzip-1.5-goolf-1.4.10.eb': 'gnu/openmpi/gzip/1.5',
'gzip-1.5-ictce-4.1.13.eb': 'intel/intelmpi/gzip/1.5',
'toy-0.0.eb': 'toy/0.0',
'toy-0.0-multiple.eb':
'toy/0.0', # test module naming scheme ignores version suffixes
}
test_mns()
ec = EasyConfig(os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'))
self.assertEqual(ec.toolchain.det_short_module_name(), 'goolf/1.4.10')
# test module naming scheme using all available easyconfig parameters
os.environ[
'EASYBUILD_MODULE_NAMING_SCHEME'] = 'TestModuleNamingSchemeMore'
init_config(build_options=build_options)
# note: these checksums will change if another easyconfig parameter is added
ec2mod_map = {
'GCC-4.6.3.eb': 'GCC/9e9ab5a1e978f0843b5aedb63ac4f14c51efb859',
'gzip-1.4.eb': 'gzip/53d5c13e85cb6945bd43a58d1c8d4a4c02f3462d',
'gzip-1.4-GCC-4.6.3.eb':
'gzip/585eba598f33c64ef01c6fa47af0fc37f3751311',
'gzip-1.5-goolf-1.4.10.eb':
'gzip/fceb41e04c26b540b7276c4246d1ecdd1e8251c9',
'gzip-1.5-ictce-4.1.13.eb':
'gzip/ae16b3a0a330d4323987b360c0d024f244ac4498',
'toy-0.0.eb': 'toy/44a206d9e8c14130cc9f79e061468303c6e91b53',
'toy-0.0-multiple.eb':
'toy/44a206d9e8c14130cc9f79e061468303c6e91b53',
}
test_mns()
# test determining module name for dependencies (i.e. non-parsed easyconfigs)
# using a module naming scheme that requires all easyconfig parameters
ec2mod_map[
'gzip-1.5-goolf-1.4.10.eb'] = 'gzip/.fceb41e04c26b540b7276c4246d1ecdd1e8251c9'
for dep_ec, dep_spec in [
('GCC-4.6.3.eb', {
'name': 'GCC',
'version': '4.6.3',
'versionsuffix': '',
'toolchain': {
'name': 'dummy',
'version': 'dummy'
},
'hidden': False,
}),
('gzip-1.5-goolf-1.4.10.eb', {
'name': 'gzip',
'version': '1.5',
'versionsuffix': '',
'toolchain': {
'name': 'goolf',
'version': '1.4.10'
},
'hidden': True,
}),
('toy-0.0-multiple.eb', {
'name': 'toy',
'version': '0.0',
'versionsuffix': '-multiple',
'toolchain': {
'name': 'dummy',
'version': 'dummy'
},
'hidden': False,
}),
]:
# determine full module name
self.assertEqual(ActiveMNS().det_full_module_name(dep_spec),
ec2mod_map[dep_ec])
ec = EasyConfig(os.path.join(ecs_dir, 'gzip-1.5-goolf-1.4.10.eb'),
hidden=True)
self.assertEqual(ec.full_mod_name,
ec2mod_map['gzip-1.5-goolf-1.4.10.eb'])
self.assertEqual(ec.toolchain.det_short_module_name(),
'goolf/a86eb41d8f9c1d6f2d3d61cdb8f420cc2a21cada')
# restore default module naming scheme, and retest
os.environ[
'EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
init_config(build_options=build_options)
ec2mod_map = default_ec2mod_map
test_mns()
succes = []
for app in apps:
# if initialisation step failed, app will be None
if app:
applog = os.path.join(output_dir, "%s-%s.log" % (app.name, app.get_installversion()))
start_time = time.time()
# start with a clean slate
os.chdir(base_dir)
modify_env(os.environ, base_env)
steps = EasyBlock.get_steps(iteration_count=app.det_iter_cnt())
for (step_name, _, step_methods, skippable) in steps:
if skippable and step_name in app.cfg["skipsteps"]:
_log.info("Skipping step %s" % step_name)
else:
for step_method in step_methods:
method_name = "_".join(step_method.func_code.co_names)
perform_step("_".join([step_name, method_name]), app, step_method, applog)
# close log and move it
app.close_log()
try:
# retain old logs
if os.path.exists(applog):
i = 0
def test_hierarchical_mns(self):
"""Test hierarchical module naming scheme."""
moduleclasses = [
'base', 'compiler', 'mpi', 'numlib', 'system', 'toolchain'
]
ecs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'easyconfigs')
all_stops = [x[0] for x in EasyBlock.get_steps()]
build_options = {
'check_osdeps': False,
'robot_path': [ecs_dir],
'valid_stops': all_stops,
'validate': False,
'valid_module_classes': moduleclasses,
}
def test_ec(ecfile, short_modname, mod_subdir, modpath_exts,
init_modpaths):
"""Test whether active module naming scheme returns expected values."""
ec = EasyConfig(os.path.join(ecs_dir, ecfile))
self.assertEqual(ActiveMNS().det_full_module_name(ec),
os.path.join(mod_subdir, short_modname))
self.assertEqual(ActiveMNS().det_short_module_name(ec),
short_modname)
self.assertEqual(ActiveMNS().det_module_subdir(ec), mod_subdir)
self.assertEqual(ActiveMNS().det_modpath_extensions(ec),
modpath_exts)
self.assertEqual(ActiveMNS().det_init_modulepaths(ec),
init_modpaths)
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'HierarchicalMNS'
init_config(build_options=build_options)
# format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions, init_modpaths)
iccver = '2013.5.192-GCC-4.8.3'
impi_ec = 'impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb'
imkl_ec = 'imkl-11.1.2.144-iimpi-5.5.3-GCC-4.8.3.eb'
test_ecs = {
'GCC-4.7.2.eb':
('GCC/4.7.2', 'Core', ['Compiler/GCC/4.7.2'], ['Core']),
'OpenMPI-1.6.4-GCC-4.7.2.eb':
('OpenMPI/1.6.4', 'Compiler/GCC/4.7.2',
['MPI/GCC/4.7.2/OpenMPI/1.6.4'], ['Core']),
'gzip-1.5-goolf-1.4.10.eb':
('gzip/1.5', 'MPI/GCC/4.7.2/OpenMPI/1.6.4', [], ['Core']),
'goolf-1.4.10.eb': ('goolf/1.4.10', 'Core', [], ['Core']),
'icc-2013.5.192-GCC-4.8.3.eb':
('icc/%s' % iccver, 'Core', ['Compiler/intel/%s' % iccver],
['Core']),
'ifort-2013.3.163.eb': ('ifort/2013.3.163', 'Core',
['Compiler/intel/2013.3.163'], ['Core']),
'CUDA-5.5.22-GCC-4.8.2.eb': ('CUDA/5.5.22', 'Compiler/GCC/4.8.2',
['Compiler/GCC-CUDA/4.8.2-5.5.22'
], ['Core']),
impi_ec: ('impi/4.1.3.049', 'Compiler/intel/%s' % iccver,
['MPI/intel/%s/impi/4.1.3.049' % iccver], ['Core']),
imkl_ec: ('imkl/11.1.2.144',
'MPI/intel/%s/impi/4.1.3.049' % iccver, [], ['Core']),
}
for ecfile, mns_vals in test_ecs.items():
test_ec(ecfile, *mns_vals)
# impi with dummy toolchain, which doesn't make sense in a hierarchical context
ec = EasyConfig(os.path.join(ecs_dir, 'impi-4.1.3.049.eb'))
self.assertErrorRegex(EasyBuildError, 'No compiler available.*MPI lib',
ActiveMNS().det_modpath_extensions, ec)
os.environ['EASYBUILD_MODULE_NAMING_SCHEME'] = 'CategorizedHMNS'
init_config(build_options=build_options)
# format: easyconfig_file: (short_mod_name, mod_subdir, modpath_extensions)
test_ecs = {
'GCC-4.7.2.eb':
('GCC/4.7.2', 'Core/compiler',
['Compiler/GCC/4.7.2/%s' % c for c in moduleclasses]),
'OpenMPI-1.6.4-GCC-4.7.2.eb':
('OpenMPI/1.6.4', 'Compiler/GCC/4.7.2/mpi',
['MPI/GCC/4.7.2/OpenMPI/1.6.4/%s' % c for c in moduleclasses]),
'gzip-1.5-goolf-1.4.10.eb':
('gzip/1.5', 'MPI/GCC/4.7.2/OpenMPI/1.6.4/tools', []),
'goolf-1.4.10.eb': ('goolf/1.4.10', 'Core/toolchain', []),
'icc-2013.5.192-GCC-4.8.3.eb':
('icc/%s' % iccver, 'Core/compiler',
['Compiler/intel/%s/%s' % (iccver, c) for c in moduleclasses]),
'ifort-2013.3.163.eb':
('ifort/2013.3.163', 'Core/compiler',
['Compiler/intel/2013.3.163/%s' % c for c in moduleclasses]),
'CUDA-5.5.22-GCC-4.8.2.eb':
('CUDA/5.5.22', 'Compiler/GCC/4.8.2/system',
['Compiler/GCC-CUDA/4.8.2-5.5.22/%s' % c for c in moduleclasses]),
impi_ec: ('impi/4.1.3.049', 'Compiler/intel/%s/mpi' % iccver, [
'MPI/intel/%s/impi/4.1.3.049/%s' % (iccver, c)
for c in moduleclasses
]),
imkl_ec: ('imkl/11.1.2.144',
'MPI/intel/%s/impi/4.1.3.049/numlib' % iccver, []),
}
for ecfile, mns_vals in test_ecs.items():
test_ec(ecfile,
*mns_vals,
init_modpaths=['Core/%s' % c for c in moduleclasses])
# impi with dummy toolchain, which doesn't make sense in a hierarchical context
ec = EasyConfig(os.path.join(ecs_dir, 'impi-4.1.3.049.eb'))
self.assertErrorRegex(EasyBuildError, 'No compiler available.*MPI lib',
ActiveMNS().det_modpath_extensions, ec)
os.environ[
'EASYBUILD_MODULE_NAMING_SCHEME'] = self.orig_module_naming_scheme
init_config(build_options=build_options)
test_ecs = {
'GCC-4.7.2.eb': ('GCC/4.7.2', '', [], []),
'OpenMPI-1.6.4-GCC-4.7.2.eb':
('OpenMPI/1.6.4-GCC-4.7.2', '', [], []),
'gzip-1.5-goolf-1.4.10.eb': ('gzip/1.5-goolf-1.4.10', '', [], []),
'goolf-1.4.10.eb': ('goolf/1.4.10', '', [], []),
'impi-4.1.3.049.eb': ('impi/4.1.3.049', '', [], []),
}
for ecfile, mns_vals in test_ecs.items():
test_ec(ecfile, *mns_vals)
def suite():
"""Return all easyblock --module-only tests."""
def make_inner_test(easyblock, **kwargs):
def innertest(self):
template_module_only_test(self, easyblock, **kwargs)
return innertest
# initialize configuration (required for e.g. default modules_tool setting)
cleanup()
eb_go = eboptions.parse_options(args=['--prefix=%s' % TMPDIR])
config.init(eb_go.options, eb_go.get_options_by_section('config'))
build_options = {
'external_modules_metadata': {},
# enable --force --module-only
'force': True,
'module_only': True,
'silent': True,
'suffix_modules_path': GENERAL_CLASS,
'valid_module_classes': config.module_classes(),
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
config.init_build_options(build_options=build_options)
set_tmpdir()
# dynamically generate a separate test for each of the available easyblocks
easyblocks_path = get_paths_for("easyblocks")[0]
all_pys = glob.glob('%s/*/*.py' % easyblocks_path)
easyblocks = [
eb for eb in all_pys
if os.path.basename(eb) != '__init__.py' and '/test/' not in eb
]
# filter out no longer supported easyblocks, or easyblocks that are tested in a different way
excluded_easyblocks = ['versionindependendpythonpackage.py']
easyblocks = [
e for e in easyblocks if os.path.basename(e) not in excluded_easyblocks
]
# add dummy PrgEnv-* modules, required for testing CrayToolchain easyblock
for prgenv in ['PrgEnv-cray', 'PrgEnv-gnu', 'PrgEnv-intel', 'PrgEnv-pgi']:
write_file(os.path.join(TMPDIR, 'modules', 'all', prgenv, '1.2.3'),
"#%Module")
# add foo/1.3.2.1.1 module, required for testing ModuleAlias easyblock
write_file(os.path.join(TMPDIR, 'modules', 'all', 'foo', '1.2.3.4.5'),
"#%Module")
for easyblock in easyblocks:
eb_fn = os.path.basename(easyblock)
# dynamically define new inner functions that can be added as class methods to ModuleOnlyTest
if eb_fn == 'systemcompiler.py':
# use GCC as name when testing SystemCompiler easyblock
innertest = make_inner_test(easyblock,
name='GCC',
version='system')
elif eb_fn == 'systemmpi.py':
# use OpenMPI as name when testing SystemMPI easyblock
innertest = make_inner_test(easyblock,
name='OpenMPI',
version='system')
elif eb_fn == 'craytoolchain.py':
# make sure that a (known) PrgEnv is included as a dependency
extra_txt = 'dependencies = [("PrgEnv-gnu/1.2.3", EXTERNAL_MODULE)]'
innertest = make_inner_test(easyblock,
name='CrayCC',
extra_txt=extra_txt)
elif eb_fn == 'modulerc.py':
# exactly one dependency is included with ModuleRC generic easyblock (and name must match)
extra_txt = 'dependencies = [("foo", "1.2.3.4.5")]'
innertest = make_inner_test(easyblock,
name='foo',
version='1.2.3.4',
extra_txt=extra_txt)
elif eb_fn == 'intel_compilers.py':
# custom easyblock for intel-compilers (oneAPI) requires v2021.x or newer
innertest = make_inner_test(easyblock,
name='intel-compilers',
version='2021.1')
elif eb_fn == 'openssl_wrapper.py':
# easyblock to create OpenSSL wrapper expects an OpenSSL version
innertest = make_inner_test(easyblock,
name='OpenSSL-wrapper',
version='1.1')
elif eb_fn == 'ucx_plugins.py':
# install fake ucx_info command (used in make_module_extra)
tmpdir = tempfile.mkdtemp()
install_fake_command('ucx_info', FAKE_UCX_INFO, tmpdir)
innertest = make_inner_test(easyblock,
name='UCX-CUDA',
tmpdir=tmpdir)
else:
# Make up some unique name
innertest = make_inner_test(easyblock,
name=eb_fn.replace('.', '-') + '-sw')
innertest.__doc__ = "Test for using --module-only with easyblock %s" % easyblock
innertest.__name__ = "test_easyblock_%s" % '_'.join(
easyblock.replace('.py', '').split('/'))
setattr(ModuleOnlyTest, innertest.__name__, innertest)
return TestLoader().loadTestsFromTestCase(ModuleOnlyTest)
def main(testing_data=(None, None, None)):
"""
Main function: parse command line options, and act accordingly.
@param testing_data: tuple with command line arguments, log file and boolean indicating whether or not to build
"""
# purposely session state very early, to avoid modules loaded by EasyBuild meddling in
init_session_state = session_state()
# steer behavior when testing main
testing = testing_data[0] is not None
args, logfile, do_build = testing_data
# initialise options
eb_go = eboptions.parse_options(args=args)
options = eb_go.options
orig_paths = eb_go.args
# set umask (as early as possible)
if options.umask is not None:
new_umask = int(options.umask, 8)
old_umask = os.umask(new_umask)
# set temporary directory to use
eb_tmpdir = set_tmpdir(options.tmpdir)
# initialise logging for main
global _log
_log, logfile = init_logging(logfile,
logtostdout=options.logtostdout,
testing=testing)
# disallow running EasyBuild as root
if os.getuid() == 0:
raise EasyBuildError(
"You seem to be running EasyBuild with root privileges which is not wise, "
"so let's end this here.")
# log startup info
eb_cmd_line = eb_go.generate_cmd_line() + eb_go.args
log_start(eb_cmd_line, eb_tmpdir)
if options.umask is not None:
_log.info("umask set to '%s' (used to be '%s')" %
(oct(new_umask), oct(old_umask)))
# process software build specifications (if any), i.e.
# software name/version, toolchain name/version, extra patches, ...
(try_to_generate, build_specs) = process_software_build_specs(options)
# determine robot path
# --try-X, --dep-graph, --search use robot path for searching, so enable it with path of installed easyconfigs
tweaked_ecs = try_to_generate and build_specs
tweaked_ecs_path, pr_path = alt_easyconfig_paths(eb_tmpdir,
tweaked_ecs=tweaked_ecs,
from_pr=options.from_pr)
auto_robot = try_to_generate or options.dep_graph or options.search or options.search_short
robot_path = det_robot_path(options.robot_paths,
tweaked_ecs_path,
pr_path,
auto_robot=auto_robot)
_log.debug("Full robot path: %s" % robot_path)
# configure & initialize build options
config_options_dict = eb_go.get_options_by_section('config')
build_options = {
'build_specs': build_specs,
'command_line': eb_cmd_line,
'pr_path': pr_path,
'robot_path': robot_path,
'silent': testing,
'try_to_generate': try_to_generate,
'valid_stops': [x[0] for x in EasyBlock.get_steps()],
}
# initialise the EasyBuild configuration & build options
config.init(options, config_options_dict)
config.init_build_options(build_options=build_options,
cmdline_options=options)
# update session state
eb_config = eb_go.generate_cmd_line(add_default=True)
modlist = session_module_list(
testing=testing
) # build options must be initialized first before 'module list' works
init_session_state.update({'easybuild_configuration': eb_config})
init_session_state.update({'module_list': modlist})
_log.debug("Initial session state: %s" % init_session_state)
# search for easyconfigs, if a query is specified
query = options.search or options.search_short
if query:
search_easyconfigs(query, short=not options.search)
# determine easybuild-easyconfigs package install path
easyconfigs_pkg_paths = get_paths_for(subdir=EASYCONFIGS_PKG_SUBDIR)
if not easyconfigs_pkg_paths:
_log.warning(
"Failed to determine install path for easybuild-easyconfigs package."
)
# determine paths to easyconfigs
paths = det_easyconfig_paths(orig_paths)
if paths:
# transform paths into tuples, use 'False' to indicate the corresponding easyconfig files were not generated
paths = [(p, False) for p in paths]
else:
if 'name' in build_specs:
# try to obtain or generate an easyconfig file via build specifications if a software name is provided
paths = find_easyconfigs_by_specs(build_specs,
robot_path,
try_to_generate,
testing=testing)
elif not any([
options.aggregate_regtest, options.search,
options.search_short, options.regtest
]):
print_error((
"Please provide one or multiple easyconfig files, or use software build "
"options to make EasyBuild search for easyconfigs"),
log=_log,
opt_parser=eb_go.parser,
exit_on_error=not testing)
_log.debug("Paths: %s" % paths)
# run regtest
if options.regtest or options.aggregate_regtest:
_log.info("Running regression test")
# fallback: easybuild-easyconfigs install path
regtest_ok = regtest([path[0] for path in paths]
or easyconfigs_pkg_paths)
if not regtest_ok:
_log.info("Regression test failed (partially)!")
sys.exit(31) # exit -> 3x1t -> 31
# read easyconfig files
easyconfigs, generated_ecs = parse_easyconfigs(paths)
# tweak obtained easyconfig files, if requested
# don't try and tweak anything if easyconfigs were generated, since building a full dep graph will fail
# if easyconfig files for the dependencies are not available
if try_to_generate and build_specs and not generated_ecs:
easyconfigs = tweak(easyconfigs,
build_specs,
targetdir=tweaked_ecs_path)
# dry_run: print all easyconfigs and dependencies, and whether they are already built
if options.dry_run or options.dry_run_short:
txt = dry_run(easyconfigs,
short=not options.dry_run,
build_specs=build_specs)
print_msg(txt, log=_log, silent=testing, prefix=False)
# cleanup and exit after dry run, searching easyconfigs or submitting regression test
if any([
options.dry_run, options.dry_run_short, options.regtest,
options.search, options.search_short
]):
cleanup(logfile, eb_tmpdir, testing)
sys.exit(0)
# skip modules that are already installed unless forced
if not options.force:
retained_ecs = skip_available(easyconfigs)
if not testing:
for skipped_ec in [
ec for ec in easyconfigs if ec not in retained_ecs
]:
print_msg("%s is already installed (module found), skipping" %
skipped_ec['full_mod_name'])
easyconfigs = retained_ecs
# determine an order that will allow all specs in the set to build
if len(easyconfigs) > 0:
if options.robot:
print_msg("resolving dependencies ...", log=_log, silent=testing)
ordered_ecs = resolve_dependencies(easyconfigs,
build_specs=build_specs)
else:
ordered_ecs = easyconfigs
else:
print_msg("No easyconfigs left to be built.", log=_log, silent=testing)
ordered_ecs = []
# create dependency graph and exit
if options.dep_graph:
_log.info("Creating dependency graph %s" % options.dep_graph)
dep_graph(options.dep_graph, ordered_ecs)
sys.exit(0)
# submit build as job(s), clean up and exit
if options.job:
job_info_txt = submit_jobs(ordered_ecs,
eb_go.generate_cmd_line(),
testing=testing)
if not testing:
print_msg("Submitted parallel build jobs, exiting now: %s" %
job_info_txt)
cleanup(logfile, eb_tmpdir, testing)
sys.exit(0)
# build software, will exit when errors occurs (except when testing)
exit_on_failure = not options.dump_test_report and not options.upload_test_report
if not testing or (testing and do_build):
ecs_with_res = build_and_install_software(
ordered_ecs, init_session_state, exit_on_failure=exit_on_failure)
else:
ecs_with_res = [(ec, {}) for ec in ordered_ecs]
correct_builds_cnt = len([
ec_res for (_, ec_res) in ecs_with_res if ec_res.get('success', False)
])
overall_success = correct_builds_cnt == len(ordered_ecs)
success_msg = "Build succeeded for %s out of %s" % (correct_builds_cnt,
len(ordered_ecs))
repo = init_repository(get_repository(), get_repositorypath())
repo.cleanup()
# dump/upload overall test report
test_report_msg = overall_test_report(ecs_with_res, len(paths),
overall_success, success_msg,
init_session_state)
if test_report_msg is not None:
print_msg(test_report_msg)
print_msg(success_msg, log=_log, silent=testing)
# cleanup and spec files
for ec in easyconfigs:
if 'original_spec' in ec and os.path.isfile(ec['spec']):
os.remove(ec['spec'])
# stop logging and cleanup tmp log file, unless one build failed (individual logs are located in eb_tmpdir path)
stop_logging(logfile, logtostdout=options.logtostdout)
if overall_success:
cleanup(logfile, eb_tmpdir, testing)
