Merge pull request #3333 from boegel/sanity_LD_LIBRARY_PATH

avoid empty entries in $LD_LIBRARY_PATH and other path-like environment variables

easybuild/tools/environment.py

@@ -189,18 +189,39 @@ def sanitize_env():
     """
     Sanitize environment.
 
-    This function undefines all $PYTHON* environment variables,
-    since they may affect the build/install procedure of Python packages.
+    This function:
 
-    cfr. https://docs.python.org/2/using/cmdline.html#environment-variables
+    * Filters out empty entries from environment variables like $PATH, $LD_LIBRARY_PATH, etc.
+      Empty entries make no sense, and can cause problems,
+      see for example https://github.com/easybuilders/easybuild-easyconfigs/issues/9843 .
 
-    While the $PYTHON* environment variables may be relevant/required for EasyBuild itself,
-    and for any non-stdlib Python packages it uses,
-    they are irrelevant (and potentially harmful) when installing Python packages.
+    * Undefines all $PYTHON* environment variables,
+      since they may affect the build/install procedure of Python packages.
 
-    Note that this is not an airtight protection against the Python being used in the build/install procedure
-    picking up non-stdlib Python packages (e.g., setuptools, vsc-base, ...), thanks to the magic of .pth files,
-    cfr. https://docs.python.org/2/library/site.html .
+      cfr. https://docs.python.org/2/using/cmdline.html#environment-variables
+
+      While the $PYTHON* environment variables may be relevant/required for EasyBuild itself,
+      and for any non-stdlib Python packages it uses,
+      they are irrelevant (and potentially harmful) when installing Python packages.
+
+      Note that this is not an airtight protection against the Python being used in the build/install procedure
+      picking up non-stdlib Python packages (e.g., setuptools, vsc-base, ...), thanks to the magic of .pth files,
+      cfr. https://docs.python.org/2/library/site.html .
     """
+
+    # remove empty entries from $*PATH variables
+    for key in ['CPATH', 'LD_LIBRARY_PATH', 'LIBRARY_PATH', 'LD_PRELOAD', 'PATH']:
+        val = os.getenv(key)
+        if val:
+            entries = val.split(os.pathsep)
+            if '' in entries:
+                _log.info("Found %d empty entries in $%s, filtering them out...", entries.count(''), key)
+                newval = os.pathsep.join(x for x in entries if x)
+                if newval:
+                    setvar(key, newval)
+                else:
+                    unset_env_vars([key], verbose=False)
+
+    # unset all $PYTHON* environment variables
     keys_to_unset = [key for key in os.environ if key.startswith('PYTHON')]
     unset_env_vars(keys_to_unset, verbose=False)

test/framework/environment.py

@@ -131,6 +131,37 @@ def test_unset_env_vars(self):
         }
         self.assertEqual(res, expected)
 
+    def test_sanitize_env(self):
+        """Test sanitize_env function."""
+
+        # define $*PATH variable that include empty entries, those should get filtered out
+        os.environ['PATH'] = '/bar::/foo:' + self.test_prefix  # middle empty entry
+        os.environ['LD_LIBRARY_PATH'] = '/apps/slurm/default/lib:/usr/lib:'  # trailing empty entry
+        os.environ['LIBRARY_PATH'] = self.test_prefix + ':' + os.environ['HOME']  # no empty entries here
+        os.environ['CPATH'] = ':' + self.test_prefix  # leading empty entry
+        os.environ['LD_PRELOAD'] = ':::'  # only empty entries (should get unset!)
+
+        # define $PYTHON* environment variables, these should be unset by sanitize_env
+        os.environ['PYTHONNOUSERSITE'] = '1'
+        os.environ['PYTHONPATH'] = self.test_prefix
+        os.environ['PYTHONOPTIMIZE'] = '1'
+
+        env.sanitize_env()
+
+        self.assertFalse(any(x for x in os.environ.keys() if x.startswith('PYTHON')))
+
+        expected = {
+            'CPATH': self.test_prefix,
+            'LD_LIBRARY_PATH': '/apps/slurm/default/lib:/usr/lib',
+            'LIBRARY_PATH': self.test_prefix + ':' + os.environ['HOME'],
+            'PATH': '/bar:/foo:' + self.test_prefix,
+        }
+        for key in sorted(expected):
+            self.assertEqual(os.getenv(key), expected[key])
+            self.assertEqual(os.environ[key], expected[key])
+
+        self.assertEqual(os.getenv('LD_PRELOAD'), None)
+
 
 def suite():
     """ returns all the testcases in this module """