Merge branch 'develop' into issue742/archive-should-contain-submit-co…

…mmand

README.rst

@@ -85,9 +85,8 @@ License can be found `here <https://github.com/lanl/BEE/blob/master/LICENSE>`_
 Publications
 ==========================
 
+- An HPC-Container Based Continuous Integration Tool for Detecting Scaling and Performance Issues in HPC Applications, IEEE Transactions on Services Computing, 2024, `DOI: 10.1109/TSC.2023.3337662 <https://doi.ieeecomputersociety.org/10.1109/TSC.2023.3337662>`_
 - BEE Orchestrator: Running Complex Scientific Workflows on Multiple Systems, HiPC, 2021, `DOI: 10.1109/HiPC53243.2021.00052 <https://doi.org/10.1109/HiPC53243.2021.00052>`_
 - "BeeSwarm: Enabling Parallel Scaling Performance Measurement in Continuous Integration for HPC Applications", ASE, 2021, `DOI: 10.1109/ASE51524.2021.9678805 <https://www.computer.org/csdl/proceedings-article/ase/2021/033700b136/1AjTjgnW2pa#:~:text=10.1109/ASE51524.2021.9678805>`_
 - "BeeFlow: A Workflow Management System for In Situ Processing across HPC and Cloud Systems", ICDCS, 2018, `DOI: 10.1109/ICDCS.2018.00103 <https://ieeexplore.ieee.org/abstract/document/8416366>`_
 - "Build and execution environment (BEE): an encapsulated environment enabling HPC applications running everywhere", IEEE BigData, 2018, `DOI: 10.1109/BigData.2018.8622572 <https://ieeexplore.ieee.org/document/8622572>`_
-
-

beeflow/common/parser/parser.py

@@ -307,7 +307,13 @@ def parse_requirements(self, requirements, as_hints=False):
             return reqs
         if as_hints:
             for req in requirements:
-                items = {k: str(v) for k, v in req.items() if k != "class"}
+                items = {}
+                for k, v in req.items():
+                    if k != 'class':
+                        if isinstance(v, (int, float)):
+                            items[k] = v
+                        else:
+                            items[k] = str(v)
                 # Load in the dockerfile at parse time
                 if 'dockerFile' in items:
                     self._read_requirement_file('dockerFile', items)

beeflow/common/wf_interface.py

@@ -94,6 +94,7 @@ def restart_task(self, task, checkpoint_file):
 
         :param task: the task to restart
         :type task: Task
+        :param checkpoint_file: the task checkpoint file
         :rtype: Task or None
         """
         for hint in task.hints:
@@ -102,8 +103,8 @@ def restart_task(self, task, checkpoint_file):
                     hint.params["num_tries"] -= 1
                     hint.params["bee_checkpoint_file__"] = checkpoint_file
                     break
-                state = self.get_task_state(task)
-                self.set_task_state(task, f"FAILED RESTART: {state}")
+                self.set_task_state(task, "FAILED")
+                self.set_workflow_state("FAILED")
                 return None
         else:
             raise ValueError("invalid task for checkpoint restart")

beeflow/task_manager/background.py

@@ -89,10 +89,14 @@ def update_jobs():
                 log.info(f'state: {new_job_state}')
                 log.info(f'TIMELIMIT/TIMEOUT task_checkpoint: {task_checkpoint}')
                 if task_checkpoint:
-                    checkpoint_file = utils.get_restart_file(task_checkpoint, task.workdir)
-                    task_info = {'checkpoint_file': checkpoint_file, 'restart': True}
-                    update_task_state(task.workflow_id, task.id, new_job_state,
-                                      task_info=task_info)
+                    try:
+                        checkpoint_file = utils.get_restart_file(task_checkpoint, task.workdir)
+                        task_info = {'checkpoint_file': checkpoint_file, 'restart': True}
+                        update_task_state(task.workflow_id, task.id, new_job_state,
+                                          task_info=task_info)
+                    except utils.CheckpointRestartError as err:
+                        log.error(f'Checkpoint restart failed for {task.name} ({task.id}): {err}')
+                        update_task_state(task.workflow_id, task.id, 'FAILED')
                 else:
                     update_task_state(task.workflow_id, task.id, new_job_state)
             else:

beeflow/task_manager/utils.py

@@ -67,22 +67,31 @@ def wfm_conn():
     return Connection(paths.wfm_socket())
 
 
+class CheckpointRestartError(Exception):
+    """Exception to be thrown on checkpoint-restart failure."""
+
+
 def get_restart_file(task_checkpoint, task_workdir):
     """Find latest checkpoint file."""
     if 'file_regex' not in task_checkpoint:
-        raise RuntimeError('file_regex is required for checkpointing')
+        raise CheckpointRestartError('file_regex is required for checkpointing')
     if 'file_path' not in task_checkpoint:
-        raise RuntimeError('file_path is required for checkpointing')
+        raise CheckpointRestartError('file_path is required for checkpointing')
     file_regex = task_checkpoint['file_regex']
     file_path = Path(task_workdir, task_checkpoint['file_path'])
     regex = re.compile(file_regex)
-    checkpoint_files = [
-        Path(file_path, fname) for fname in os.listdir(file_path)
-        if regex.match(fname)
-    ]
+    try:
+        checkpoint_files = [
+            Path(file_path, fname) for fname in os.listdir(file_path)
+            if regex.match(fname)
+        ]
+    except FileNotFoundError:
+        raise CheckpointRestartError(
+            f'Checkpoint file_path ("{file_path}") not found'
+        ) from None
     checkpoint_files.sort(key=os.path.getmtime)
     try:
         checkpoint_file = checkpoint_files[-1]
         return str(checkpoint_file)
     except IndexError:
-        raise RuntimeError('Missing checkpoint file for task') from None
+        raise CheckpointRestartError('Missing checkpoint file for task') from None

beeflow/wf_manager/resources/wf_update.py

@@ -96,11 +96,13 @@ def put(self):
             task_info = jsonpickle.decode(data['task_info'])
             checkpoint_file = task_info['checkpoint_file']
             new_task = wfi.restart_task(task, checkpoint_file)
-            db.workflows.add_task(new_task.id, wf_id, new_task.name, "WAITING")
             if new_task is None:
                 log.info('No more restarts')
-                wf_state = wfi.get_task_state(task)
+                wf_state = wfi.get_workflow_state()
+                wf_utils.update_wf_status(wf_id, 'Failed')
+                db.workflows.update_workflow_state(wf_id, 'Failed')
                 return make_response(jsonify(status=f'Task {task_id} set to {job_state}'))
+            db.workflows.add_task(new_task.id, wf_id, new_task.name, "WAITING")
             # Submit the restart task
             tasks = [new_task]
             wf_utils.schedule_submit_tasks(wf_id, tasks)

ci/test_workflows/checkpoint-too-long/workflow.cwl

@@ -20,8 +20,8 @@ steps:
     hints:
       beeflow:CheckpointRequirement:
         enabled: true
-        file_path: checkpoint_output
-        container_path: checkpoint_output
+        file_path: .
+        container_path: .
         file_regex: backup[0-9]*.crx
         restart_parameters: -R
         num_tries: 1

ci/test_workflows/clamr-wf-checkpoint/clamr_job_long.yml

@@ -1,7 +1,7 @@
 {
   "grid_resolution": 32,
   "max_levels": 3,
-  "time_steps": 80000,
+  "time_steps": 150000,
   "steps_between_outputs": 10,
   "steps_between_graphics": 25,
   "graphics_type": "png",

pyproject.toml

@@ -47,8 +47,8 @@ beeflow = 'beeflow.client.bee_client:main'
 beecloud = 'beeflow.cloud_launcher:main'
 
 [tool.poetry.dependencies]
-# Python version (>=3.8.3, <3.11)
-python = ">=3.8.3,<=3.11"
+# Python version (>=3.8.3, <=3.12.2)
+python = ">=3.8.3,<=3.12.2"
 
 # Package dependencies
 Flask = { version = "^2.0" }