Proposed changest to add a timeout to run_shell_cmd

easybuild/tools/run.py

@@ -46,6 +46,7 @@
 import subprocess
 import tempfile
 import time
+import threading
 from collections import namedtuple
 from datetime import datetime
 
@@ -356,11 +357,80 @@ def _answer_question(stdout, proc, qa_patterns, qa_wait_patterns):
     return match_found
 
 
+def _read_pipe(pipe, output):
+    """Helper function to read from a pipe and store output in a list.
+    :param pipe: pipe to read from
+    :param output: list to store output in
+    """
+    out = b''
+    for line in iter(pipe.readline, b''):
+        _log.debug(f"Captured: {line.decode(errors='ignore').rstrip()}")
+        out += line
+    output.append(out)
+
+
+def read_process_pipe(proc, pipe_name, start=None, timeout=None):
+    """Read from a pipe form a process using a separate thread to avoid blocking and implement a timeout.
+    :param proc: process to read from
+    :param pipe_name: name of the pipe to read from (stdout or stderr)
+    :param start: time when the process was started (used to calculate timeout)
+    :param timeout: timeout in seconds (default: None = no timeout)
+
+    :return: data read from pipe
+
+    :raises EasyBuildError: when reading from pipe takes longer than specified timeout
+    """
+    pipe = getattr(proc, pipe_name, None)
+    if pipe is None:
+        raise EasyBuildError(f"Pipe '{pipe_name}' not found in process '{proc}'. This is probably a bug.")
+
+    error_msg = "Unexpected timeout error during read_process_pipe"
+    current_timeout = None
+    if start is not None and timeout is not None:
+        current_timeout = timeout - (time.time() - start)
+        error_msg = f"Timeout during `{proc.args}` after {timeout} seconds"
+        if current_timeout <= 0:
+            _log.warning(error_msg)
+            try:
+                terminate_process(proc)
+            except subprocess.TimeoutExpired as exc:
+                _log.warning(f"Failed to terminate process '{proc.args}': {exc}")
+            raise EasyBuildError(error_msg)
+
+    output = []
+    t = threading.Thread(target=_read_pipe, args=(pipe, output))
+    t.start()
+    t.join(current_timeout)
+    if t.is_alive():
+        raise EasyBuildError(error_msg)
+    return output[0]
+
+
+def terminate_process(proc, timeout=20):
+    """
+    Terminate specified process (subprocess.Popen instance).
+    Attempt to terminate the process using proc.terminate(), and if that fails, use proc.kill().
+
+    :param proc: process to terminate
+    :param timeout: timeout in seconds to wait for process to terminate
+
+    :raises subprocess.TimeoutExpired: if process does not terminate within specified timeout
+    """
+    proc.terminate()
+    try:
+        proc.wait(timeout=timeout)
+    except subprocess.TimeoutExpired:
+        _log.warning(f"Process did not terminate after {timeout} seconds, sending SIGKILL")
+
+        proc.kill()
+        proc.wait(timeout=timeout)
+
+
 @run_shell_cmd_cache
 def run_shell_cmd(cmd, fail_on_error=True, split_stderr=False, stdin=None, env=None,
                   hidden=False, in_dry_run=False, verbose_dry_run=False, work_dir=None, use_bash=True,
                   output_file=True, stream_output=None, asynchronous=False, task_id=None, with_hooks=True,
-                  qa_patterns=None, qa_wait_patterns=None, qa_timeout=100):
+                  timeout=None, qa_patterns=None, qa_wait_patterns=None, qa_timeout=100):
     """
     Run specified (interactive) shell command, and capture output + exit code.
 
@@ -378,6 +448,7 @@ def run_shell_cmd(cmd, fail_on_error=True, split_stderr=False, stdin=None, env=N
     :param asynchronous: indicate that command is being run asynchronously
     :param task_id: task ID for specified shell command (included in return value)
     :param with_hooks: trigger pre/post run_shell_cmd hooks (if defined)
+    :param timeout: timeout in seconds for command execution
     :param qa_patterns: list of 2-tuples with patterns for questions + corresponding answers
     :param qa_wait_patterns: list of strings with patterns for non-questions
     :param qa_timeout: amount of seconds to wait until more output is produced when there is no matching question
@@ -524,16 +595,14 @@ def to_cmd_str(cmd):
         time_no_match = 0
         prev_stdout = ''
 
+        # collect output piece-wise, while checking for questions to answer (if qa_patterns is provided)
+        start = time.time()
         while exit_code is None:
-            # collect output line by line, while checking for questions to answer (if qa_patterns is provided)
-            for line in iter(proc.stdout.readline, b''):
-                _log.debug(f"Captured stdout: {line.decode(errors='ignore').rstrip()}")
-                stdout += line
+            stdout += read_process_pipe(proc, 'stdout', start=start, timeout=timeout)
 
             # note: we assume that there won't be any questions in stderr output
             if split_stderr:
-                for line in iter(proc.stderr.readline, b''):
-                    stderr += line
+                stderr += read_process_pipe(proc, 'stderr', start=start, timeout=timeout)
 
             if qa_patterns:
                 # only check for question patterns if additional output is available
@@ -565,7 +634,13 @@ def to_cmd_str(cmd):
         if split_stderr:
             stderr += proc.stderr.read() or b''
     else:
-        (stdout, stderr) = proc.communicate(input=stdin)
+        try:
+            (stdout, stderr) = proc.communicate(input=stdin, timeout=timeout)
+        except subprocess.TimeoutExpired:
+            error_msg = f"Timeout during `{cmd}` after {timeout} seconds"
+            _log.warning(error_msg)
+            terminate_process(proc)
+            raise EasyBuildError(error_msg)
 
     # return output as a regular string rather than a byte sequence (and non-UTF-8 characters get stripped out)
     # getpreferredencoding normally gives 'utf-8' but can be ASCII (ANSI_X3.4-1968)

test/framework/run.py

@@ -1726,6 +1726,41 @@ def test_run_shell_cmd_eof_stdin(self):
         self.assertEqual(res.exit_code, 0, "Non-streaming output: Command timed out")
         self.assertEqual(res.output, inp)
 
+    def test_run_shell_cmd_timeout(self):
+        """Test use of run_shell_cmd with a timeout."""
+        cmd = 'sleep 1; echo hello'
+        # Failure on process timeout
+        with self.mocked_stdout_stderr():
+            self.assertErrorRegex(
+                EasyBuildError, "Timeout during `.*` after .* seconds",
+                run_shell_cmd, cmd, timeout=.5
+                )
+
+        # Success
+        with self.mocked_stdout_stderr():
+            res = run_shell_cmd(cmd, timeout=3)
+        self.assertEqual(res.exit_code, 0)
+        self.assertEqual(res.output, "hello\n")
+
+    def test_run_shell_cmd_timeout_stream(self):
+        """Test use of run_shell_cmd with a timeout."""
+        data = '0'*128
+        # Failure on process timeout
+        cmd = f'for i in {{1..20}}; do echo {data} && sleep 0.1; done'
+        with self.mocked_stdout_stderr():
+            self.assertErrorRegex(
+                EasyBuildError, "Timeout during `.*` after .* seconds",
+                run_shell_cmd, cmd, timeout=.5, stream_output=True
+                )
+
+        # Success
+        cmd = 'sleep .5 && echo hello'
+        with self.mocked_stdout_stderr():
+            res = run_shell_cmd(cmd, timeout=1.5, stream_output=True)
+
+        self.assertEqual(res.exit_code, 0)
+        self.assertEqual(res.output, "hello\n")
+
     def test_run_cmd_async(self):
         """Test asynchronously running of a shell command via run_cmd + complete_cmd."""