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add patch for EasyBuild v5.1.2 to fix long-lived bug with toolchain prepare when not using $CPATH #24376

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Merged
bedroge merged 3 commits into from
Oct 28, 2025
Merged

add patch for EasyBuild v5.1.2 to fix long-lived bug with toolchain prepare when not using $CPATH #24376

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d617330
Fix long-lived EasyBuild bug with toolchain prepare when not using CPATH
ocaisa Oct 27, 2025
7fdff44
Tweak name to fix CI
ocaisa Oct 27, 2025
80f0006
Delete easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.1.2_pass_deps_to…
ocaisa Oct 27, 2025
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2 changes: 2 additions & 0 deletions easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.1.2.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -35,10 +35,12 @@ sources = [
'extract_cmd': "tar xfvz %s && mv easybuild_easyconfigs-%(version)s easybuild-easyconfigs-%(version)s",
},
]
patches = ['EasyBuild-5.1.2_pass_deps_to_tc_prep.patch']
checksums = [
{'easybuild_framework-5.1.2.tar.gz': '2505834d46dab4cfde1eacac28b7516c1b92c42001236e890cf056c146341749'},
{'easybuild_easyblocks-5.1.2.tar.gz': '68e8e39371dd4bec32bbc3aa55a053a70c0fc8b931dba0dfec25c68770b24c37'},
{'easybuild_easyconfigs-5.1.2.tar.gz': '3427ff7d4da4291840f48b7732997453e556d9ee807e7d249399bd28c1810d9c'},
{'EasyBuild-5.1.2_pass_deps_to_tc_prep.patch': 'f7c2d5f607af9054d7f8b8d84934bc26ff31f35fa14b50b2efc2ab4275832e26'},
]

# EasyBuild is a (set of) Python packages, so it depends on Python
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232 changes: 232 additions & 0 deletions easybuild/easyconfigs/e/EasyBuild/EasyBuild-5.1.2_pass_deps_to_tc_prep.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,232 @@
From 917ed1ac6521a98bd5debd1219149be0df5f45d3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 9 Oct 2025 14:11:35 +0200
Subject: [PATCH 1/3] pass dependencies to toolchain.prepare when setting up
build environment for extensions

---
easybuild/framework/easyblock.py | 6 ++++--
easybuild/tools/toolchain/toolchain.py | 6 +++---
2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/easybuild/framework/easyblock.py b/easybuild/framework/easyblock.py
index 20d69ac066..55107be6f9 100644
--- a/easybuild/framework/easyblock.py
+++ b/easybuild/framework/easyblock.py
@@ -2126,7 +2126,8 @@ def install_extensions_sequential(self, install=True):
self.log.debug("List of loaded modules: %s", self.modules_tool.list())
# don't reload modules for toolchain, there is no need
# since they will be loaded already by the fake module
- ext.toolchain.prepare(onlymod=self.cfg['onlytcmod'], silent=True, loadmod=False,
+ ext.toolchain.prepare(onlymod=self.cfg['onlytcmod'], deps=self.cfg.dependencies(),
+ silent=True, loadmod=False,
rpath_filter_dirs=self.rpath_filter_dirs,
rpath_include_dirs=self.rpath_include_dirs,
rpath_wrappers_dir=self.rpath_wrappers_dir)
@@ -2288,7 +2289,8 @@ def update_exts_progress_bar_helper(running_exts, progress_size):
with self.fake_module_environment(with_build_deps=True):
# don't reload modules for toolchain, there is no
# need since they will be loaded by the fake module
- ext.toolchain.prepare(onlymod=self.cfg['onlytcmod'], silent=True, loadmod=False,
+ ext.toolchain.prepare(onlymod=self.cfg['onlytcmod'], deps=self.cfg.dependencies(),
+ silent=True, loadmod=False,
rpath_filter_dirs=self.rpath_filter_dirs,
rpath_include_dirs=self.rpath_include_dirs,
rpath_wrappers_dir=self.rpath_wrappers_dir)
diff --git a/easybuild/tools/toolchain/toolchain.py b/easybuild/tools/toolchain/toolchain.py
index d89c10b71a..fd9d618d1f 100644
--- a/easybuild/tools/toolchain/toolchain.py
+++ b/easybuild/tools/toolchain/toolchain.py
@@ -535,7 +535,7 @@ def get_dependency_version(self, dependency):
raise EasyBuildError("No toolchain version for dependency name %s (suffix %s) found",
dependency['name'], toolchain_suffix)

- def _check_dependencies(self, dependencies):
+ def _check_dependencies(self, dependencies, check_modules=True):
""" Verify if the given dependencies exist and return them """
self.log.debug("_check_dependencies: adding toolchain dependencies %s", dependencies)

@@ -548,7 +548,7 @@ def _check_dependencies(self, dependencies):

# check whether modules exist
self.log.debug("_check_dependencies: MODULEPATH: %s", os.environ['MODULEPATH'])
- if self.dry_run:
+ if self.dry_run or not check_modules:
deps_exist = [True] * len(dep_mod_names)
else:
deps_exist = self.modules_tool.exist(dep_mod_names)
@@ -862,7 +862,7 @@ def prepare(self, onlymod=None, deps=None, silent=False, loadmod=True,
# do all dependencies have a toolchain version?
if deps is None:
deps = []
- self.dependencies = self._check_dependencies(deps)
+ self.dependencies = self._check_dependencies(deps, check_modules=loadmod)
if not len(deps) == len(self.dependencies):
self.log.debug("dep %s (%s)" % (len(deps), deps))
self.log.debug("tc.dep %s (%s)" % (len(self.dependencies), self.dependencies))

From e69babaefc7ed3ccb93413a474c1b1d720ce04ac Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 22 Oct 2025 15:01:01 +0200
Subject: [PATCH 2/3] add test to verify fix w.r.t. passing down dependencies
to set up build environment for extensions

---
test/framework/easyblock.py | 67 +++++++++++++++++++++++++++++++++++++
1 file changed, 67 insertions(+)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 35af52cbcc..6be8873fb0 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -37,6 +37,7 @@
import shutil
import sys
import tempfile
+import textwrap
from inspect import cleandoc
from test.framework.github import requires_github_access
from test.framework.utilities import EnhancedTestCase, TestLoaderFiltered, init_config
@@ -3670,6 +3671,9 @@ def test_create_easyblock_without_logfile(self):
os.remove(eb.logfile)

def test_report_current_step_method(self):
+ """
+ Check whether name of methods in installation steps are correctly reported
+ """
testdir = os.path.abspath(os.path.dirname(__file__))
toy_ec = os.path.join(testdir, 'easyconfigs', 'test_ecs', 't', 'toy', 'toy-0.0.eb')

@@ -3706,6 +3710,69 @@ def custom_step(self):
self.assertRegex(logtxt, f'Running method {method_name} .* {step_name}')
self.assertIn('Ran custom', logtxt)

+ def test_exts_deps_build_env(self):
+ """
+ Test whether dependencies are loaded in build environment for extensions.
+ """
+ # to verify fix made in https://github.com/easybuilders/easybuild-framework/pull/5023
+ testdir = os.path.abspath(os.path.dirname(__file__))
+ toy_ec = os.path.join(testdir, 'easyconfigs', 'test_ecs', 't', 'toy', 'toy-0.0.eb')
+ test_ec = os.path.join(self.test_prefix, 'test.eb')
+ test_ec_txt = read_file(toy_ec)
+ test_ec_txt += textwrap.dedent("""
+ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+ dependencies = [
+ ('zlib', '1.2.13'),
+ ]
+
+ exts_list = [
+ ('bar', '0.0', {
+ 'prebuildopts': "(env | sort) && ",
+ })
+ ]
+
+ sanity_check_paths = {
+ 'files': ['bin/bar', 'bin/toy'],
+ 'dirs': ['bin'],
+ }
+ """)
+ write_file(test_ec, test_ec_txt)
+
+ # put dummy zlib module in place where we can control $EBROOTZLIB value
+ zlib_mod_file = os.path.join(testdir, 'modules', 'zlib', '1.2.13-GCCcore-12.3.0')
+ zlib_fn = os.path.basename(zlib_mod_file)
+
+ zlib_root = os.path.join(self.test_prefix, 'software', 'zlib', zlib_fn)
+ write_file(os.path.join(zlib_root, 'include', 'zlib.h'), '')
+
+ zlib_mod_txt = read_file(zlib_mod_file)
+ zlib_mod_txt = re.sub("set root.*", f"set root {zlib_root}", zlib_mod_txt)
+
+ test_mods = os.path.join(self.test_prefix, 'modules')
+ test_zlib_mod_file = os.path.join(test_mods, 'zlib', zlib_fn)
+ write_file(test_zlib_mod_file, zlib_mod_txt)
+ self.modtool.use(test_mods)
+
+ args = [
+ test_ec,
+ '--rebuild',
+ '--search-path-cpp-headers=include_paths',
+ ]
+ with self.mocked_stdout_stderr():
+ with self.log_to_testlogfile():
+ self.eb_main(args, raise_error=True, do_build=True, verbose=True)
+
+ log_txt = read_file(self.logfile)
+
+ # check whether $EBROOTZLIB is correctly set in build environment of 'bar' extension
+ regex = re.compile(f"^EBROOTZLIB=.*/software/zlib/{zlib_fn}$", re.M)
+ self.assertTrue(regex.search(log_txt), f"Pattern '{regex.pattern}' not found in log output")
+
+ # check whether $C_INCLUDE_PATH is correctly set in build environment of 'bar' extension
+ regex = re.compile(f"^C_INCLUDE_PATH=.*/software/zlib/{zlib_fn}/include$", re.M)
+ self.assertTrue(regex.search(log_txt), f"Pattern '{regex.pattern}' not found in log output")
+

def suite(loader=None):
""" return all the tests in this file """

From f9e1af19dbc436a8a47eeb147a1c4b60044a9596 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 22 Oct 2025 19:29:47 +0200
Subject: [PATCH 3/3] parameterize test_exts_deps_build_env over different
valid values for --search-path-cpp-headers

---
test/framework/easyblock.py | 38 ++++++++++++++++++++++---------------
1 file changed, 23 insertions(+), 15 deletions(-)

diff --git a/test/framework/easyblock.py b/test/framework/easyblock.py
index 6be8873fb0..085a6c947f 100644
--- a/test/framework/easyblock.py
+++ b/test/framework/easyblock.py
@@ -3754,24 +3754,32 @@ def test_exts_deps_build_env(self):
write_file(test_zlib_mod_file, zlib_mod_txt)
self.modtool.use(test_mods)

- args = [
- test_ec,
- '--rebuild',
- '--search-path-cpp-headers=include_paths',
- ]
- with self.mocked_stdout_stderr():
- with self.log_to_testlogfile():
- self.eb_main(args, raise_error=True, do_build=True, verbose=True)
+ env_vars = {
+ 'cpath': ['CPATH'],
+ 'flags': ['CPPFLAGS'],
+ 'include_paths': ['C_INCLUDE_PATH', 'CPLUS_INCLUDE_PATH', 'OBJC_INCLUDE_PATH'],
+ }
+
+ for search_path_cpp_headers in ('cpath', 'flags', 'include_paths'):
+ args = [
+ test_ec,
+ '--rebuild',
+ f'--search-path-cpp-headers={search_path_cpp_headers}',
+ ]
+ with self.mocked_stdout_stderr():
+ with self.log_to_testlogfile():
+ self.eb_main(args, raise_error=True, do_build=True, verbose=True)

- log_txt = read_file(self.logfile)
+ log_txt = read_file(self.logfile)

- # check whether $EBROOTZLIB is correctly set in build environment of 'bar' extension
- regex = re.compile(f"^EBROOTZLIB=.*/software/zlib/{zlib_fn}$", re.M)
- self.assertTrue(regex.search(log_txt), f"Pattern '{regex.pattern}' not found in log output")
+ # check whether $EBROOTZLIB is correctly set in build environment of 'bar' extension
+ regex = re.compile(f"^EBROOTZLIB=.*/software/zlib/{zlib_fn}$", re.M)
+ self.assertTrue(regex.search(log_txt), f"Pattern '{regex.pattern}' not found in log output")

- # check whether $C_INCLUDE_PATH is correctly set in build environment of 'bar' extension
- regex = re.compile(f"^C_INCLUDE_PATH=.*/software/zlib/{zlib_fn}/include$", re.M)
- self.assertTrue(regex.search(log_txt), f"Pattern '{regex.pattern}' not found in log output")
+ # check whether $C_INCLUDE_PATH is correctly set in build environment of 'bar' extension
+ for env_var in env_vars[search_path_cpp_headers]:
+ regex = re.compile(f"^{env_var}=.*/software/zlib/{zlib_fn}/include$", re.M)
+ self.assertTrue(regex.search(log_txt), f"Pattern '{regex.pattern}' not found in log output")


def suite(loader=None):