be a bit more careful with sysroot in run_cmd, add logging + add dedi…

…cated test for run_cmd using with_sysroot=True

easybuild/tools/run.py

@@ -227,14 +227,17 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
     if cmd_log:
         cmd_log.write("# output for command: %s\n\n" % cmd_msg)
 
+    exec_cmd = "/bin/bash"
+
+    # if EasyBuild is configured to use an alternate sysroot,
+    # we should also run shell commands using the bash shell provided in there,
+    # since /bin/bash may not be compatible with the alternate sysroot
     if with_sysroot:
         sysroot = build_option('sysroot')
         if sysroot:
-            exec_cmd = "%s/bin/bash" % sysroot
-        else:
-            exec_cmd = "/bin/bash"
-    else:
-        exec_cmd = "/bin/bash"
+            sysroot_bin_bash = os.path.join(sysroot, 'bin', 'bash')
+            if os.path.exists(sysroot_bin_bash):
+                exec_cmd = sysroot_bin_bash
 
     if not shell:
         if isinstance(cmd, list):
@@ -245,6 +248,8 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
         else:
             raise EasyBuildError("Don't know how to prefix with /usr/bin/env for commands of type %s", type(cmd))
 
+    _log.info("Using %s as shell for running cmd: %s", exec_cmd, cmd)
+
     if with_hooks:
         hooks = load_hooks(build_option('hooks'))
         hook_res = run_hook(RUN_SHELL_CMD, hooks, pre_step_hook=True, args=[cmd], kwargs={'work_dir': os.getcwd()})

test/framework/run.py

@@ -796,6 +796,31 @@ def post_run_shell_cmd_hook(cmd, *args, **kwargs):
         ])
         self.assertEqual(stdout, expected_stdout)
 
+    def test_run_cmd_sysroot(self):
+        """Test with_sysroot option of run_cmd function."""
+
+        # put fake /bin/bash in place that will be picked up when using run_cmd with with_sysroot=True
+        bin_bash = os.path.join(self.test_prefix, 'bin', 'bash')
+        bin_bash_txt = '\n'.join([
+            "#!/bin/bash",
+            "echo 'Hi there I am a fake /bin/bash in %s'" % self.test_prefix,
+            '/bin/bash "$@"',
+        ])
+        write_file(bin_bash, bin_bash_txt)
+        adjust_permissions(bin_bash, stat.S_IXUSR)
+
+        update_build_option('sysroot', self.test_prefix)
+
+        (out, ec) = run_cmd("echo hello")
+        self.assertEqual(ec, 0)
+        self.assertTrue(out.startswith("Hi there I am a fake /bin/bash in"))
+        self.assertTrue(out.endswith("\nhello\n"))
+
+        # picking up on alternate sysroot is enabled by default, but can be disabled via with_sysroot=False
+        (out, ec) = run_cmd("echo hello", with_sysroot=False)
+        self.assertEqual(ec, 0)
+        self.assertEqual(out, "hello\n")
+
 
 def suite():
     """ returns all the testcases in this module """