take into account alternate sysroot for /bin/bash used by run_cmd

easybuild/tools/options.py

@@ -1969,7 +1969,7 @@ def set_tmpdir(tmpdir=None, raise_error=False):
             os.close(fd)
             os.chmod(tmptest_file, 0o700)
             if not run_cmd(tmptest_file, simple=True, log_ok=False, regexp=False, force_in_dry_run=True, trace=False,
-                           stream_output=False, with_hooks=False):
+                           stream_output=False, with_hooks=False, with_sysroot=False):
                 msg = "The temporary directory (%s) does not allow to execute files. " % tempfile.gettempdir()
                 msg += "This can cause problems in the build process, consider using --tmpdir."
                 if raise_error:

easybuild/tools/run.py

@@ -134,7 +134,7 @@ def get_output_from_process(proc, read_size=None, asynchronous=False):
 @run_cmd_cache
 def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True, log_output=False, path=None,
             force_in_dry_run=False, verbose=True, shell=None, trace=True, stream_output=None, asynchronous=False,
-            with_hooks=True):
+            with_hooks=True, with_sysroot=True):
     """
     Run specified command (in a subshell)
     :param cmd: command to run
@@ -152,6 +152,7 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
     :param stream_output: enable streaming command output to stdout
     :param asynchronous: run command asynchronously (returns subprocess.Popen instance if set to True)
     :param with_hooks: trigger pre/post run_shell_cmd hooks (if defined)
+    :param with_sysroot: prepend sysroot to exec_cmd (if defined)
     """
     cwd = os.getcwd()
 
@@ -228,6 +229,16 @@ def run_cmd(cmd, log_ok=True, log_all=False, simple=False, inp=None, regexp=True
 
     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:
+            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):
             exec_cmd = None
@@ -237,6 +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()})

easybuild/tools/systemtools.py

@@ -275,7 +275,8 @@ def get_avail_core_count():
         core_cnt = int(sum(sched_getaffinity()))
     else:
         # BSD-type systems
-        out, _ = run_cmd('sysctl -n hw.ncpu', force_in_dry_run=True, trace=False, stream_output=False, with_hooks=False)
+        out, _ = run_cmd('sysctl -n hw.ncpu', force_in_dry_run=True, trace=False, stream_output=False,
+                         with_hooks=False, with_sysroot=False)
         try:
             if int(out) > 0:
                 core_cnt = int(out)
@@ -312,7 +313,8 @@ def get_total_memory():
     elif os_type == DARWIN:
         cmd = "sysctl -n hw.memsize"
         _log.debug("Trying to determine total memory size on Darwin via cmd '%s'", cmd)
-        out, ec = run_cmd(cmd, force_in_dry_run=True, trace=False, stream_output=False, with_hooks=False)
+        out, ec = run_cmd(cmd, force_in_dry_run=True, trace=False, stream_output=False, with_hooks=False,
+                          with_sysroot=False)
         if ec == 0:
             memtotal = int(out.strip()) // (1024**2)
 
@@ -394,15 +396,16 @@ def get_cpu_vendor():
 
     elif os_type == DARWIN:
         cmd = "sysctl -n machdep.cpu.vendor"
-        out, ec = run_cmd(cmd, force_in_dry_run=True, trace=False, stream_output=False, log_ok=False, with_hooks=False)
+        out, ec = run_cmd(cmd, force_in_dry_run=True, trace=False, stream_output=False, log_ok=False,
+                          with_hooks=False, with_sysroot=False)
         out = out.strip()
         if ec == 0 and out in VENDOR_IDS:
             vendor = VENDOR_IDS[out]
             _log.debug("Determined CPU vendor on DARWIN as being '%s' via cmd '%s" % (vendor, cmd))
         else:
             cmd = "sysctl -n machdep.cpu.brand_string"
             out, ec = run_cmd(cmd, force_in_dry_run=True, trace=False, stream_output=False, log_ok=False,
-                              with_hooks=False)
+                              with_hooks=False, with_sysroot=False)
             out = out.strip().split(' ')[0]
             if ec == 0 and out in CPU_VENDORS:
                 vendor = out
@@ -505,7 +508,8 @@ def get_cpu_model():
 
     elif os_type == DARWIN:
         cmd = "sysctl -n machdep.cpu.brand_string"
-        out, ec = run_cmd(cmd, force_in_dry_run=True, trace=False, stream_output=False, with_hooks=False)
+        out, ec = run_cmd(cmd, force_in_dry_run=True, trace=False, stream_output=False, with_hooks=False,
+                          with_sysroot=False)
         if ec == 0:
             model = out.strip()
             _log.debug("Determined CPU model on Darwin using cmd '%s': %s" % (cmd, model))
@@ -550,7 +554,8 @@ def get_cpu_speed():
     elif os_type == DARWIN:
         cmd = "sysctl -n hw.cpufrequency_max"
         _log.debug("Trying to determine CPU frequency on Darwin via cmd '%s'" % cmd)
-        out, ec = run_cmd(cmd, force_in_dry_run=True, trace=False, stream_output=False, with_hooks=False)
+        out, ec = run_cmd(cmd, force_in_dry_run=True, trace=False, stream_output=False, with_hooks=False,
+                          with_sysroot=False)
         out = out.strip()
         cpu_freq = None
         if ec == 0 and out:
@@ -599,7 +604,7 @@ def get_cpu_features():
             cmd = "sysctl -n machdep.cpu.%s" % feature_set
             _log.debug("Trying to determine CPU features on Darwin via cmd '%s'", cmd)
             out, ec = run_cmd(cmd, force_in_dry_run=True, trace=False, stream_output=False, log_ok=False,
-                              with_hooks=False)
+                              with_hooks=False, with_sysroot=False)
             if ec == 0:
                 cpu_feat.extend(out.strip().lower().split())
 
@@ -626,8 +631,8 @@ def get_gpu_info():
         try:
             cmd = "nvidia-smi --query-gpu=gpu_name,driver_version --format=csv,noheader"
             _log.debug("Trying to determine NVIDIA GPU info on Linux via cmd '%s'", cmd)
-            out, ec = run_cmd(cmd, simple=False, log_ok=False, log_all=False,
-                              force_in_dry_run=True, trace=False, stream_output=False, with_hooks=False)
+            out, ec = run_cmd(cmd, simple=False, log_ok=False, log_all=False, force_in_dry_run=True,
+                              trace=False, stream_output=False, with_hooks=False, with_sysroot=False)
             if ec == 0:
                 for line in out.strip().split('\n'):
                     nvidia_gpu_info = gpu_info.setdefault('NVIDIA', {})
@@ -645,15 +650,15 @@ def get_gpu_info():
         try:
             cmd = "rocm-smi --showdriverversion --csv"
             _log.debug("Trying to determine AMD GPU driver on Linux via cmd '%s'", cmd)
-            out, ec = run_cmd(cmd, simple=False, log_ok=False, log_all=False,
-                              force_in_dry_run=True, trace=False, stream_output=False, with_hooks=False)
+            out, ec = run_cmd(cmd, simple=False, log_ok=False, log_all=False, force_in_dry_run=True,
+                              trace=False, stream_output=False, with_hooks=False, with_sysroot=False)
             if ec == 0:
                 amd_driver = out.strip().split('\n')[1].split(',')[1]
 
             cmd = "rocm-smi --showproductname --csv"
             _log.debug("Trying to determine AMD GPU info on Linux via cmd '%s'", cmd)
-            out, ec = run_cmd(cmd, simple=False, log_ok=False, log_all=False,
-                              force_in_dry_run=True, trace=False, stream_output=False, with_hooks=False)
+            out, ec = run_cmd(cmd, simple=False, log_ok=False, log_all=False, force_in_dry_run=True,
+                              trace=False, stream_output=False, with_hooks=False, with_sysroot=False)
             if ec == 0:
                 for line in out.strip().split('\n')[1:]:
                     amd_card_series = line.split(',')[1]
@@ -900,7 +905,7 @@ def get_tool_version(tool, version_option='--version', ignore_ec=False):
     Output is returned as a single-line string (newlines are replaced by '; ').
     """
     out, ec = run_cmd(' '.join([tool, version_option]), simple=False, log_ok=False, force_in_dry_run=True,
-                      trace=False, stream_output=False, with_hooks=False)
+                      trace=False, stream_output=False, with_hooks=False, with_sysroot=False)
     if not ignore_ec and ec:
         _log.warning("Failed to determine version of %s using '%s %s': %s" % (tool, tool, version_option, out))
         return UNKNOWN

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 """