Added additional exception handling to execute(), to handle "Poll: ba…

…d file descriptor reading from request pipe" in stderr (harmless)

PILOTVERSION

@@ -1 +1 @@
-3.9.1.12
+3.9.1.13

pilot/util/constants.py

@@ -28,7 +28,7 @@
 RELEASE = '3'   # released number should be fixed at 3 for Pilot 3
 VERSION = '9'   # version number is '1' for first release, '0' until then, increased for bigger updates
 REVISION = '1'  # revision number should be reset to '0' for every new version release, increased for small updates
-BUILD = '12'     # build number should be reset to '1' for every new development cycle
+BUILD = '13'     # build number should be reset to '1' for every new development cycle
 
 SUCCESS = 0
 FAILURE = 1

pilot/util/container.py

@@ -21,6 +21,7 @@
 
 """Functions for executing commands."""
 
+import errno
 import os
 import subprocess
 import logging
@@ -118,6 +119,12 @@ def read_output(stream, queue):
             except (AttributeError, ValueError):
                 # Handle the case where stream is None (AttributeError) or closed (ValueError)
                 break
+            except OSError as e:
+                if e.errno == errno.EBADF:
+                    # Handle the case where the file descriptor is bad
+                    break
+                else:
+                    raise
 
             queue.put(line)
 
@@ -145,8 +152,11 @@ def read_output(stream, queue):
         exit_code = process.poll()
 
     # Wait for the threads to finish reading
-    stdout_thread.join()
-    stderr_thread.join()
+    try:
+        stdout_thread.join()
+        stderr_thread.join()
+    except Exception as e:
+        logger.warning(f'exception caught in execute: {e}')
 
     # Read the remaining output from the queues
     while not stdout_queue.empty():