Merge pull request #4119 from casparvl/skip_rpath_check

add support for --filter-rpath-sanity-libs to skip RPATH sanity check for designated libraries

easybuild/framework/easyblock.py

@@ -37,6 +37,7 @@
 :author: Damian Alvarez (Forschungszentrum Juelich GmbH)
 :author: Maxime Boissonneault (Compute Canada)
 :author: Davide Vanzo (Vanderbilt University)
+:author: Caspar van Leeuwen (SURF)
 """
 
 import copy
@@ -3047,9 +3048,16 @@ def sanity_check_rpath(self, rpath_dirs=None):
         self.log.debug("$LD_LIBRARY_PATH during RPATH sanity check: %s", os.getenv('LD_LIBRARY_PATH', '(empty)'))
         self.log.debug("List of loaded modules: %s", self.modules_tool.list())
 
-        not_found_regex = re.compile('not found', re.M)
+        not_found_regex = re.compile(r'(\S+)\s*\=\>\s*not found')
         readelf_rpath_regex = re.compile('(RPATH)', re.M)
 
+        # List of libraries that should be exempt from the RPATH sanity check;
+        # For example, libcuda.so.1 should never be RPATH-ed by design,
+        # see https://github.com/easybuilders/easybuild-framework/issues/4095
+        filter_rpath_sanity_libs = build_option('filter_rpath_sanity_libs')
+        msg = "Ignoring the following libraries if they are not found by RPATH sanity check: %s"
+        self.log.info(msg, filter_rpath_sanity_libs)
+
         if rpath_dirs is None:
             rpath_dirs = self.cfg['bin_lib_subdirs'] or self.bin_lib_subdirs()
 
@@ -3076,10 +3084,18 @@ def sanity_check_rpath(self, rpath_dirs=None):
                         self.log.debug(msg, path)
                     else:
                         # check whether all required libraries are found via 'ldd'
-                        if not_found_regex.search(out):
-                            fail_msg = "One or more required libraries not found for %s: %s" % (path, out)
-                            self.log.warning(fail_msg)
-                            fails.append(fail_msg)
+                        matches = re.findall(not_found_regex, out)
+                        if len(matches) > 0:  # Some libraries are not found via 'ldd'
+                            # For each match, check if the library is in the exception list
+                            for match in matches:
+                                if match in filter_rpath_sanity_libs:
+                                    msg = "Library %s not found for %s, but ignored "
+                                    msg += "since it is on the rpath exception list: %s"
+                                    self.log.info(msg, match, path, filter_rpath_sanity_libs)
+                                else:
+                                    fail_msg = "Library %s not found for %s" % (match, path)
+                                    self.log.warning(fail_msg)
+                                    fails.append(fail_msg)
                         else:
                             self.log.debug("Output of 'ldd %s' checked, looks OK", path)
 

easybuild/tools/config.py

@@ -116,6 +116,16 @@
 DEFAULT_PR_TARGET_ACCOUNT = 'easybuilders'
 DEFAULT_PREFIX = os.path.join(os.path.expanduser('~'), ".local", "easybuild")
 DEFAULT_REPOSITORY = 'FileRepository'
+# Filter these CUDA libraries by default from the RPATH sanity check.
+# These are the only four libraries for which the CUDA toolkit ships stubs. By design, one is supposed to build
+# against the stub versions, but use the libraries that come with the CUDA driver at runtime. That means they should
+# never be RPATH-ed, and thus the sanity check should also accept that they aren't RPATH-ed.
+DEFAULT_FILTER_RPATH_SANITY_LIBS = (
+    'libcuda.so',
+    'libcuda.so.1',
+    'libnvidia-ml.so',
+    'libnvidia-ml.so.1'
+)
 DEFAULT_WAIT_ON_LOCK_INTERVAL = 60
 DEFAULT_WAIT_ON_LOCK_LIMIT = 0
 
@@ -205,6 +215,7 @@ def mk_full_default_path(name, prefix=DEFAULT_PREFIX):
         'filter_deps',
         'filter_ecs',
         'filter_env_vars',
+        'filter_rpath_sanity_libs',
         'force_download',
         'git_working_dirs_path',
         'github_user',

easybuild/tools/options.py

@@ -68,6 +68,7 @@
 from easybuild.tools.config import DEFAULT_MODULECLASSES, DEFAULT_PATH_SUBDIRS, DEFAULT_PKG_RELEASE, DEFAULT_PKG_TOOL
 from easybuild.tools.config import DEFAULT_PKG_TYPE, DEFAULT_PNS, DEFAULT_PREFIX, DEFAULT_PR_TARGET_ACCOUNT
 from easybuild.tools.config import DEFAULT_REPOSITORY, DEFAULT_WAIT_ON_LOCK_INTERVAL, DEFAULT_WAIT_ON_LOCK_LIMIT
+from easybuild.tools.config import DEFAULT_FILTER_RPATH_SANITY_LIBS
 from easybuild.tools.config import EBROOT_ENV_VAR_ACTIONS, ERROR, FORCE_DOWNLOAD_CHOICES, GENERAL_CLASS, IGNORE
 from easybuild.tools.config import JOB_DEPS_TYPE_ABORT_ON_ERROR, JOB_DEPS_TYPE_ALWAYS_RUN, LOADED_MODULES_ACTIONS
 from easybuild.tools.config import LOCAL_VAR_NAMING_CHECK_WARN, LOCAL_VAR_NAMING_CHECKS
@@ -409,6 +410,11 @@ def override_options(self):
                            'strlist', 'extend', None),
             'filter-env-vars': ("List of names of environment variables that should *not* be defined/updated by "
                                 "module files generated by EasyBuild", 'strlist', 'extend', None),
+            'filter-rpath-sanity-libs': ("List of libraries that should be ignored by the RPATH sanity check. "
+                                         "I.e. if these libraries are not RPATH-ed, that will be accepted "
+                                         "by the RPATH sanity check. Note that you'll need to provide the exact "
+                                         "library name, as it is returned by 'ldd', including any version ",
+                                         'strlist', 'store', DEFAULT_FILTER_RPATH_SANITY_LIBS),
             'fixed-installdir-naming-scheme': ("Use fixed naming scheme for installation directories", None,
                                                'store_true', True),
             'force-download': ("Force re-downloading of sources and/or patches, "

test/framework/easyconfigs/test_ecs/t/toy-app/toy-app-0.0.eb

@@ -0,0 +1,30 @@
+easyblock = 'EB_toy'
+
+name = 'toy-app'
+version = '0.0'
+
+homepage = 'https://easybuilders.github.io/easybuild'
+description = "Toy C program, 100% toy. This toy has a main function that depends on libtoy."
+
+toolchain = SYSTEM
+
+sources = [SOURCE_TAR_GZ]
+checksums = [
+    '9559393c0d747a4940a79be54e82fa8f14dbb0c32979a3e61e9db305f32dad49',  # default (SHA256)
+]
+
+dependencies = [
+    ('libtoy', '0.0')
+]
+
+buildopts = '-ltoy'
+
+sanity_check_paths = {
+    'files': [('bin/toy-app')],
+    'dirs': ['bin'],
+}
+
+postinstallcmds = ["echo TOY > %(installdir)s/README"]
+
+moduleclass = 'tools'
+# trailing comment, leave this here, it may trigger bugs with extract_comments()

test/framework/filetools.py

@@ -2387,7 +2387,7 @@ def test_index_functions(self):
         # test with specified path with and without trailing '/'s
         for path in [test_ecs, test_ecs + '/', test_ecs + '//']:
             index = ft.create_index(path)
-            self.assertEqual(len(index), 90)
+            self.assertEqual(len(index), 91)
 
             expected = [
                 os.path.join('b', 'bzip2', 'bzip2-1.0.6-GCC-4.9.2.eb'),

test/framework/toy_build.py

@@ -106,7 +106,7 @@ def tearDown(self):
         if os.path.exists(self.dummylogfn):
             os.remove(self.dummylogfn)
 
-    def check_toy(self, installpath, outtxt, version='0.0', versionprefix='', versionsuffix='', error=None):
+    def check_toy(self, installpath, outtxt, name='toy', version='0.0', versionprefix='', versionsuffix='', error=None):
         """Check whether toy build succeeded."""
 
         full_version = ''.join([versionprefix, version, versionsuffix])
@@ -121,38 +121,39 @@ def check_toy(self, installpath, outtxt, version='0.0', versionprefix='', versio
         self.assertTrue(success.search(outtxt), "COMPLETED message found in '%s'%s" % (outtxt, error_msg))
 
         # if the module exists, it should be fine
-        toy_module = os.path.join(installpath, 'modules', 'all', 'toy', full_version)
+        toy_module = os.path.join(installpath, 'modules', 'all', name, full_version)
         msg = "module for toy build toy/%s found (path %s)" % (full_version, toy_module)
         if get_module_syntax() == 'Lua':
             toy_module += '.lua'
         self.assertTrue(os.path.exists(toy_module), msg + error_msg)
 
         # module file is symlinked according to moduleclass
-        toy_module_symlink = os.path.join(installpath, 'modules', 'tools', 'toy', full_version)
+        toy_module_symlink = os.path.join(installpath, 'modules', 'tools', name, full_version)
         if get_module_syntax() == 'Lua':
             toy_module_symlink += '.lua'
         self.assertTrue(os.path.islink(toy_module_symlink))
         self.assertTrue(os.path.exists(toy_module_symlink))
 
         # make sure installation log file and easyconfig file are copied to install dir
-        software_path = os.path.join(installpath, 'software', 'toy', full_version)
-        install_log_path_pattern = os.path.join(software_path, 'easybuild', 'easybuild-toy-%s*.log' % version)
+        software_path = os.path.join(installpath, 'software', name, full_version)
+        install_log_path_pattern = os.path.join(software_path, 'easybuild', 'easybuild-%s-%s*.log' % (name, version))
         self.assertTrue(len(glob.glob(install_log_path_pattern)) >= 1,
                         "Found  at least 1 file at %s" % install_log_path_pattern)
 
         # make sure test report is available
-        test_report_path_pattern = os.path.join(software_path, 'easybuild', 'easybuild-toy-%s*test_report.md' % version)
+        report_name = 'easybuild-%s-%s*test_report.md' % (name, version)
+        test_report_path_pattern = os.path.join(software_path, 'easybuild', report_name)
         self.assertTrue(len(glob.glob(test_report_path_pattern)) >= 1,
                         "Found  at least 1 file at %s" % test_report_path_pattern)
 
-        ec_file_path = os.path.join(software_path, 'easybuild', 'toy-%s.eb' % full_version)
+        ec_file_path = os.path.join(software_path, 'easybuild', '%s-%s.eb' % (name, full_version))
         self.assertTrue(os.path.exists(ec_file_path))
 
-        devel_module_path = os.path.join(software_path, 'easybuild', 'toy-%s-easybuild-devel' % full_version)
+        devel_module_path = os.path.join(software_path, 'easybuild', '%s-%s-easybuild-devel' % (name, full_version))
         self.assertTrue(os.path.exists(devel_module_path))
 
     def test_toy_build(self, extra_args=None, ec_file=None, tmpdir=None, verify=True, fails=False, verbose=True,
-                       raise_error=False, test_report=None, versionsuffix='', testing=True,
+                       raise_error=False, test_report=None, name='toy', versionsuffix='', testing=True,
                        raise_systemexit=False, force=True, test_report_regexs=None):
         """Perform a toy build."""
         if extra_args is None:
@@ -188,7 +189,7 @@ def test_toy_build(self, extra_args=None, ec_file=None, tmpdir=None, verify=True
                 raise myerr
 
         if verify:
-            self.check_toy(self.test_installpath, outtxt, versionsuffix=versionsuffix, error=myerr)
+            self.check_toy(self.test_installpath, outtxt, name=name, versionsuffix=versionsuffix, error=myerr)
 
         if test_readme:
             # make sure postinstallcmds were used
@@ -2660,7 +2661,7 @@ def grab_gcc_rpath_wrapper_args():
 
             return {'filter_paths': res_filter.group(1), 'include_paths': res_include.group(1)}
 
-        args = ['--rpath', '--experimental']
+        args = ['--rpath']
         self.test_toy_build(extra_args=args, raise_error=True)
 
         # by default, /lib and /usr are included in RPATH filter,
@@ -2672,23 +2673,23 @@ def grab_gcc_rpath_wrapper_args():
         self.assertTrue(any(p.startswith(self.test_buildpath) for p in rpath_filter_paths))
 
         # Check that we can use --rpath-override-dirs
-        args = ['--rpath', '--experimental', '--rpath-override-dirs=/opt/eessi/2021.03/lib:/opt/eessi/lib']
+        args = ['--rpath', '--rpath-override-dirs=/opt/eessi/2021.03/lib:/opt/eessi/lib']
         self.test_toy_build(extra_args=args, raise_error=True)
         rpath_include_paths = grab_gcc_rpath_wrapper_args()['include_paths'].split(',')
         # Make sure our directories appear in dirs to be included in the rpath (and in the right order)
         self.assertEqual(rpath_include_paths[0], '/opt/eessi/2021.03/lib')
         self.assertEqual(rpath_include_paths[1], '/opt/eessi/lib')
 
         # Check that when we use --rpath-override-dirs empty values are filtered
-        args = ['--rpath', '--experimental', '--rpath-override-dirs=/opt/eessi/2021.03/lib::/opt/eessi/lib']
+        args = ['--rpath', '--rpath-override-dirs=/opt/eessi/2021.03/lib::/opt/eessi/lib']
         self.test_toy_build(extra_args=args, raise_error=True)
         rpath_include_paths = grab_gcc_rpath_wrapper_args()['include_paths'].split(',')
         # Make sure our directories appear in dirs to be included in the rpath (and in the right order)
         self.assertEqual(rpath_include_paths[0], '/opt/eessi/2021.03/lib')
         self.assertEqual(rpath_include_paths[1], '/opt/eessi/lib')
 
         # Check that when we use --rpath-override-dirs we can only provide absolute paths
-        eb_args = ['--rpath', '--experimental', '--rpath-override-dirs=/opt/eessi/2021.03/lib:eessi/lib']
+        eb_args = ['--rpath', '--rpath-override-dirs=/opt/eessi/2021.03/lib:eessi/lib']
         error_pattern = r"Path used in rpath_override_dirs is not an absolute path: eessi/lib"
         self.assertErrorRegex(EasyBuildError, error_pattern, self.test_toy_build, extra_args=eb_args, raise_error=True,
                               verbose=False)
@@ -2710,7 +2711,67 @@ def grab_gcc_rpath_wrapper_args():
         toy_ec_txt += "\ntoolchainopts = {'rpath': False}\n"
         toy_ec = os.path.join(self.test_prefix, 'toy.eb')
         write_file(toy_ec, toy_ec_txt)
-        self.test_toy_build(ec_file=toy_ec, extra_args=['--rpath', '--experimental'], raise_error=True)
+        self.test_toy_build(ec_file=toy_ec, extra_args=['--rpath'], raise_error=True)
+
+    def test_toy_filter_rpath_sanity_libs(self):
+        """Test use of --filter-rpath-sanity-libs."""
+
+        test_ecs = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'easyconfigs', 'test_ecs')
+        toy_ec = os.path.join(test_ecs, 't', 'toy-app', 'toy-app-0.0.eb')
+
+        # This should just build succesfully
+        args = ['--rpath']
+        self.test_toy_build(ec_file=toy_ec, name='toy-app', extra_args=args, raise_error=True)
+
+        libtoy_libdir = os.path.join(self.test_installpath, 'software', 'libtoy', '0.0', 'lib')
+        toyapp_bin = os.path.join(self.test_installpath, 'software', 'toy-app', '0.0', 'bin', 'toy-app')
+        rpath_regex = re.compile(r"RPATH.*%s" % libtoy_libdir, re.M)
+        out, ec = run_cmd("readelf -d %s" % toyapp_bin, simple=False)
+        self.assertTrue(rpath_regex.search(out), "Pattern '%s' should be found in: %s" % (rpath_regex.pattern, out))
+
+        out, ec = run_cmd("ldd %s" % toyapp_bin, simple=False)
+        libtoy_regex = re.compile(r"libtoy.so => /.*/libtoy.so", re.M)
+        notfound = re.compile(r"libtoy\.so\s*=>\s*not found", re.M)
+        self.assertTrue(libtoy_regex.search(out), "Pattern '%s' should be found in: %s" % (libtoy_regex.pattern, out))
+        self.assertFalse(notfound.search(out), "Pattern '%s' should not be found in: %s" % (notfound.pattern, out))
+
+        # test sanity error when --rpath-filter is used to filter a required library
+        # In this test, libtoy.so will be linked, but not RPATH-ed due to the --rpath-filter
+        # Thus, the RPATH sanity check is expected to fail with libtoy.so not being found
+        error_pattern = r"Sanity check failed\: Library libtoy\.so not found"
+        self.assertErrorRegex(EasyBuildError, error_pattern, self.test_toy_build, ec_file=toy_ec,
+                              extra_args=['--rpath', '--rpath-filter=.*libtoy.*'],
+                              name='toy-app', raise_error=True, verbose=False)
+
+        # test use of --filter-rpath-sanity-libs option. In this test, we use --rpath-filter to make sure libtoy.so is
+        # not rpath-ed. Then, we use --filter-rpath-sanity-libs to make sure the RPATH sanity checks ignores
+        # the fact that libtoy.so is not found. Thus, this build should complete succesfully
+        args = ['--rpath', '--rpath-filter=.*libtoy.*', '--filter-rpath-sanity-libs=libtoy.so']
+        self.test_toy_build(ec_file=toy_ec, name='toy-app', extra_args=args, raise_error=True)
+
+        out, ec = run_cmd("readelf -d %s" % toyapp_bin, simple=False)
+        self.assertFalse(rpath_regex.search(out),
+                         "Pattern '%s' should not be found in: %s" % (rpath_regex.pattern, out))
+
+        out, ec = run_cmd("ldd %s" % toyapp_bin, simple=False)
+        self.assertFalse(libtoy_regex.search(out),
+                         "Pattern '%s' should not be found in: %s" % (libtoy_regex.pattern, out))
+        self.assertTrue(notfound.search(out),
+                        "Pattern '%s' should be found in: %s" % (notfound.pattern, out))
+
+        # test again with list of library names passed to --filter-rpath-sanity-libs
+        args = ['--rpath', '--rpath-filter=.*libtoy.*', '--filter-rpath-sanity-libs=libfoo.so,libtoy.so,libbar.so']
+        self.test_toy_build(ec_file=toy_ec, name='toy-app', extra_args=args, raise_error=True)
+
+        out, ec = run_cmd("readelf -d %s" % toyapp_bin, simple=False)
+        self.assertFalse(rpath_regex.search(out),
+                         "Pattern '%s' should not be found in: %s" % (rpath_regex.pattern, out))
+
+        out, ec = run_cmd("ldd %s" % toyapp_bin, simple=False)
+        self.assertFalse(libtoy_regex.search(out),
+                         "Pattern '%s' should not be found in: %s" % (libtoy_regex.pattern, out))
+        self.assertTrue(notfound.search(out),
+                        "Pattern '%s' should be found in: %s" % (notfound.pattern, out))
 
     def test_toy_modaltsoftname(self):
         """Build two dependent toys as in test_toy_toy but using modaltsoftname"""
@@ -2780,7 +2841,7 @@ def test_toy_build_trace(self):
 
         self.mock_stderr(True)
         self.mock_stdout(True)
-        self.test_toy_build(ec_file=test_ec, extra_args=['--trace', '--experimental'], verify=False, testing=False)
+        self.test_toy_build(ec_file=test_ec, extra_args=['--trace'], verify=False, testing=False)
         stderr = self.get_stderr()
         stdout = self.get_stdout()
         self.mock_stderr(False)