llnl · dylancliche · May 4, 2023 · May 4, 2023 · May 4, 2023 · May 4, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,17 @@ All notable changes to Merlin will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+### Added
+- Pytest fixtures in the `conftest.py` file of the integration test suite
+  - NOTE: an export command `export LC_ALL='C'` had to be added to fix a bug in the WEAVE CI. This can be removed when we resolve this issue for the `merlin server` command
+- Tests for the `celeryadapter.py` module
+- New example for stopping an ensemble workflow in `merlin/examples/workflows/stop_ensemble/`.
+
+## [1.11.1]
+### Fixed
+- Typo in `batch.py` that caused lsf launches to fail (`ALL_SGPUS` changed to `ALL_GPUS`)
+
 ## [1.11.0]
 ### Added
 - New reserved variable:

diff --git a/Makefile b/Makefile
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/__init__.py b/merlin/__init__.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #
@@ -38,7 +38,7 @@
 import sys
 
 
-__version__ = "1.11.0"
+__version__ = "1.11.1"
 VERSION = __version__
 PATH_TO_PROJ = os.path.join(os.path.dirname(__file__), "")
 

diff --git a/merlin/ascii_art.py b/merlin/ascii_art.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/celery.py b/merlin/celery.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/__init__.py b/merlin/common/__init__.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/abstracts/__init__.py b/merlin/common/abstracts/__init__.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/abstracts/enums/__init__.py b/merlin/common/abstracts/enums/__init__.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/openfilelist.py b/merlin/common/openfilelist.py
@@ -8,7 +8,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/opennpylib.py b/merlin/common/opennpylib.py
@@ -8,7 +8,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/sample_index.py b/merlin/common/sample_index.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/sample_index_factory.py b/merlin/common/sample_index_factory.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/security/__init__.py b/merlin/common/security/__init__.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/security/encrypt.py b/merlin/common/security/encrypt.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/security/encrypt_backend_traffic.py b/merlin/common/security/encrypt_backend_traffic.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/common/tasks.py b/merlin/common/tasks.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #
@@ -480,7 +480,7 @@ def expand_tasks_with_samples(  # pylint: disable=R0913,R0914
             if not found_tasks:
                 for next_index_path, next_index in sample_index.traverse(conditional=condition):
                     LOG.info(
-                        f"generating next step for range {next_index.min}:{next_index.max} {next_index.max-next_index.min}"
+                        f"generating next step for range {next_index.min}:{next_index.max} {next_index.max - next_index.min}"
                     )
                     next_index.name = next_index_path
 

diff --git a/merlin/common/util_sampling.py b/merlin/common/util_sampling.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/config/__init__.py b/merlin/config/__init__.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/config/broker.py b/merlin/config/broker.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/config/celeryconfig.py b/merlin/config/celeryconfig.py
@@ -10,7 +10,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/config/configfile.py b/merlin/config/configfile.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/config/results_backend.py b/merlin/config/results_backend.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/config/utils.py b/merlin/config/utils.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/data/celery/__init__.py b/merlin/data/celery/__init__.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/display.py b/merlin/display.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/examples/__init__.py b/merlin/examples/__init__.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/examples/examples.py b/merlin/examples/examples.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/examples/generator.py b/merlin/examples/generator.py
@@ -6,7 +6,7 @@
 #
 # LLNL-CODE-797170
 # All rights reserved.
-# This file is part of Merlin, Version: 1.11.0.
+# This file is part of Merlin, Version: 1.11.1.
 #
 # For details, see https://github.com/LLNL/merlin.
 #

diff --git a/merlin/examples/workflows/stop_ensemble/README b/merlin/examples/workflows/stop_ensemble/README
@@ -0,0 +1,70 @@
++----------------------------------------------------+
+|                                                    |
+|              Stop Ensemble Example                 |
+|                                                    |
+| Description: Hello World example including a quit  |
+|              script to stop running and dependent  |
+|              jobs running the Merlin workflow.     |
+|                                                    |
+| Important Scripts: -workers.sbatch                 |
+|                    -hello_samples.yaml             |
+|                    -quitScript.sh                  |
+|                                                    |
++----------------------------------------------------+
+
+
+==========================================================
+                   Running the Example                 
+==========================================================
+
+1) merlin run <specification file>
+2) sbatch workers.sbatch <specification file> <true/false>
+
+Notes: -<specification file> is your yaml file including
+        the extension ".yaml".
+       -The second input parameter to workers.sbatch tells
+        slurm to either run a diasy chain of dependency
+	jobs ("true") or no dependency jobs ("false" or
+	no second input parameter at all).
+
+
+==========================================================
+                     What is Going On                  
+==========================================================
+
+When the job is allocated, the typical hello_samples will
+execute via step_1 and step_2 within the yaml file. After,
+a stopWorkers step is executed that will copy the
+quitScript.sh bash file from $(SPECROOT) and obtain the
+specfile and the specRoot.
+
+These two variables are passed into quitSript.sh
+which will find all job IDs of both running and awaiting
+job allocations, loop through them, and cancel every
+single one that deals with the <specification file>
+ran from $(SPECROOT) defined in steps 1 and 2 in the
+"Running the Example" section above.
+
+
+==========================================================
+                      Important Notes                   
+==========================================================
+
+1) quitScript.sh is submitted via sbatch instead of a
+   straight source or bash -c call because otherwise the
+   script will stop the workers immediately and the YAML
+   file then stops, but the task would never obtain a
+   successfull exit. Therefore, it would have to be purged
+   each time before starting a new Merlin run. By
+   submitting it via sbatch, once it is submitted the task
+   can exit successfully before the workers are stopped.
+
+2) Make sure the stopWorkers task is the very last task
+   in your workflow as it will stop any and all jobs
+   that have been allocated for the workflow.
+
+3) The virtual environment name and path are defined
+   in workers.sbatch. Change these to your specific needs
+   prior to running.
+
+