From e225f3b95df311a6c94e926475189df8c6602eeb Mon Sep 17 00:00:00 2001 From: Sare Beste Zeytun - 407210 Date: Wed, 19 Aug 2026 10:56:19 -0600 Subject: [PATCH 1/3] Archive sbatch script --- beeflow/common/worker/slurm_worker.py | 1 + beeflow/common/worker/worker.py | 16 ++++++++++++++++ beeflow/wf_manager/resources/wf_utils.py | 4 ++-- 3 files changed, 19 insertions(+), 2 deletions(-) diff --git a/beeflow/common/worker/slurm_worker.py b/beeflow/common/worker/slurm_worker.py index d3a3507bf..31d14d87e 100644 --- a/beeflow/common/worker/slurm_worker.py +++ b/beeflow/common/worker/slurm_worker.py @@ -217,6 +217,7 @@ def submit_task(self, task): task.stdout = stdout task.stderr = stderr task_script = sbatch_script + self.save_script(task,task_script) else: task_script = self.write_script(task) diff --git a/beeflow/common/worker/worker.py b/beeflow/common/worker/worker.py index 8460dd3b1..c7c352a3a 100644 --- a/beeflow/common/worker/worker.py +++ b/beeflow/common/worker/worker.py @@ -5,6 +5,7 @@ from abc import ABC, abstractmethod import os +import shutil from beeflow.common import log as bee_logging from beeflow.common.crt_interface import ContainerRuntimeInterface @@ -73,6 +74,21 @@ def task_save_path(self, task): """Return the task save path used for storing submission scripts output logs.""" return f'{self.workdir}/workflows/{task.workflow_id}/{task.name}-{task.id[:4]}' + def save_script(self,task,sbatch_script): + """Save provided sbatch script into the appropriate archive and workflow directories""" + sbatch_script_name = os.path.basename(sbatch_script) + + sbatch_archive_dir = self.task_save_path(task) + os.makedirs(sbatch_archive_dir,exist_ok=True) + sbatch_script_archive = f"{sbatch_archive_dir}/{sbatch_script_name}" + + sbatch_script_dir = f"{task.workdir}/{task.name}-{task.id[:4]}" + os.makedirs(sbatch_script_dir, exist_ok=True) + sbatch_script_workdir = f"{sbatch_script_dir}/{sbatch_script_name}" + + shutil.copy(sbatch_script, sbatch_script_archive) + shutil.copy(sbatch_script, sbatch_script_workdir) + def write_script(self, task): """Build task script; returns filename of script.""" # If the user has provided an sbatch script this will just return diff --git a/beeflow/wf_manager/resources/wf_utils.py b/beeflow/wf_manager/resources/wf_utils.py index 2db37a535..da8def3ac 100644 --- a/beeflow/wf_manager/resources/wf_utils.py +++ b/beeflow/wf_manager/resources/wf_utils.py @@ -271,7 +271,7 @@ def copy_task_output(task): # Need to get this from the worker task_save_path = pathlib.Path(bee_workdir) / "workflows" / task.workflow_id / task_name_id task_workdir = pathlib.Path(task.workdir) - task_metadata_path = task_workdir / task_name_id / "metadata.txt" + task_metadata_path = task_workdir / task_name_id / "metadata.yaml" if task.stdout is not None: stdout_path = _resolve_output_path(task_workdir, task.stdout) else: @@ -286,7 +286,7 @@ def copy_task_output(task): shutil.copy(stderr_path, task_save_path / f"{task_name_id}.err") if task_metadata_path.exists(): - shutil.copy(task_metadata_path, task_save_path / "metadata.txt") + shutil.copy(task_metadata_path, task_save_path / "metadata.yaml") else: log.warning("Task metadata file not found: %s", task_metadata_path) From 6d94b319d22e5f180088608fea74e22f7084ceea Mon Sep 17 00:00:00 2001 From: Sare Beste Zeytun - 407210 Date: Tue, 25 Aug 2026 16:16:21 -0600 Subject: [PATCH 2/3] Test PR and remove debug logging from last PR --- beeflow/common/worker/utils.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/beeflow/common/worker/utils.py b/beeflow/common/worker/utils.py index b064f987f..4e173df38 100644 --- a/beeflow/common/worker/utils.py +++ b/beeflow/common/worker/utils.py @@ -63,9 +63,7 @@ def format_runtime(runtime): def calc_runtime(job_state,job_info): """Calculate the runtime of a task when using slurmrestd.""" start_time = job_info['start_time']['number'] - log.info(f"Start time: {start_time}") end_time = job_info['end_time']['number'] - log.info(f"End time: {end_time}") cur_time = dt.now() cur_unix_time = int(cur_time.timestamp()) From a6730e697f23e6d409f75d5fb3af5a19ecbedb35 Mon Sep 17 00:00:00 2001 From: Patricia Grubel Date: Wed, 9 Sep 2026 13:53:28 -0600 Subject: [PATCH 3/3] Correct the stable release version, documentation. --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index f913639dc..26b34c078 100644 --- a/README.rst +++ b/README.rst @@ -47,7 +47,7 @@ BEE Sites - Documentation * - Stable release - - ``0.1.14`` + - ``0.1.13`` - `https://lanl.github.io/BEE/ `__ * - Pre-release - ``0.1.14dev1``