Merge pull request #155 from PalNilsson/next

3.9.3.2

PILOTVERSION

@@ -1 +1 @@
-3.9.2.41
+3.9.3.2

pilot/control/payload.py

@@ -271,14 +271,16 @@ def execute_payloads(queues: namedtuple, traces: Any, args: object):  # noqa: C9
             job.t0 = os.times()
             exit_code, diagnostics = payload_executor.run()
             if exit_code and exit_code > 1000:  # pilot error code, add to list
-                logger.debug(f'pilot error code received (code={exit_code}, diagnostics=\n{diagnostics})')
+                logger.warning(f'pilot error code received (code={exit_code}, diagnostics=\n{diagnostics})')
                 job.piloterrorcodes, job.piloterrordiags = errors.add_error_code(exit_code, msg=diagnostics)
 
             logger.debug(f'run() returned exit_code={exit_code}')
             set_cpu_consumption_time(job)
             job.transexitcode = exit_code % 255
-            out.close()
-            err.close()
+            if out:
+                out.close()
+            if err:
+                err.close()
 
             # some HPO jobs will produce new output files (following lfn name pattern), discover those and replace the job.outdata list
             pilot_user = os.environ.get('PILOT_USER', 'generic').lower()

pilot/info/jobdata.py

@@ -1088,7 +1088,8 @@ def collect_zombies(self, depth: int = None):
             for zombie in self.zombies:
                 try:
                     logger.info(f"zombie collector waiting for pid {zombie}")
-                    _id, _ = os.waitpid(zombie, os.WNOHANG if current_depth else 0)
+                    # dangerous, can lead to blocking : _id, _ = os.waitpid(zombie, os.WNOHANG if current_depth else 0)
+                    _id, _ = os.waitpid(zombie, os.WNOHANG)
                 except OSError as exc:
                     logger.info(f"harmless exception when collecting zombies: {exc}")
                     zombies_to_remove.append(zombie)
@@ -1099,7 +1100,6 @@ def collect_zombies(self, depth: int = None):
             # Remove collected zombies from the list
             for zombie in zombies_to_remove:
                 self.zombies.remove(zombie)
-
             if current_depth == 0:
                 break
 

pilot/user/atlas/utilities.py

@@ -324,7 +324,7 @@ def get_memory_monitor_info_path(workdir: str, allowtxtfile: bool = False) -> st
         if os.path.exists(init_path):
             path = init_path
         else:
-            logger.info(f"neither {path}, nor {init_path} exist")
+            logger.debug(f"neither {path}, nor {init_path} exist")
             path = ""
 
         if path == "" and allowtxtfile:

pilot/util/constants.py

@@ -27,8 +27,8 @@
 # Pilot version
 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 = '2'  # revision number should be reset to '0' for every new version release, increased for small updates
-BUILD = '41'     # build number should be reset to '1' for every new development cycle
+REVISION = '3'  # revision number should be reset to '0' for every new version release, increased for small updates
+BUILD = '2'     # build number should be reset to '1' for every new development cycle
 
 SUCCESS = 0
 FAILURE = 1

pilot/util/container.py

@@ -113,6 +113,7 @@ def execute(executable: Any, **kwargs: dict) -> Any:  # noqa: C901
 
     def read_output(stream, queue):
         while True:
+            sleep(0.01)
             try:
                 line = stream.readline()
                 if not line:
@@ -126,8 +127,10 @@ def read_output(stream, queue):
                     break
                 else:
                     raise
-
-            queue.put(line)
+            try:
+                queue.put_nowait(line)
+            except queue.Full:
+                sleep(0.01)  # Sleep for a short interval to avoid busy waiting
 
     stdout_thread = threading.Thread(target=read_output, args=(process.stdout, stdout_queue))
     stderr_thread = threading.Thread(target=read_output, args=(process.stderr, stderr_queue))

pilot/util/monitoring.py

@@ -133,7 +133,7 @@ def job_monitor_tasks(job: JobData, mt: MonitoringTime, args: object) -> tuple[i
             return exit_code, diagnostics
 
         # update the OOM process info to prevent killing processes in the wrong order in case the job is killed (once)
-        update_oom_info(job.pid, job.transformation)
+        # update_oom_info(job.pid, job.transformation)
 
     # should the pilot abort the payload?
     exit_code, diagnostics = should_abort_payload(current_time, mt)