Merge pull request #862 from Libensemble/release/v_0.9.2

Release/v 0.9.2

.flake8

@@ -22,22 +22,16 @@ exclude =
 per-file-ignores =
         # init needs to import the logger.
         libensemble/__init__.py:F401
-        libensemble/libensemble/__init__.py:F401
-
-        # worker uses regex with chars that resemble escape sequences
-        libensemble/worker.py:W605
 
         # Need to turn of matching probes (before other imports) on some
         # systems/versions of MPI:
         libensemble/tests/standalone_tests/mpi_launch_test/create_mpi_jobs.py:E402
-        libensemble/libensemble/tests/standalone_tests/mpi_launch_test/create_mpi_jobs.py:E402
-        libensemble/tests/regression_tests/test_uniform_sampling_with_different_resources.py:E402
 
         # Similar reasoning for configuring mpi4py
         libensemble/tests/unit_tests/test_executor.py:E402
 
         # Matplotlib needs something set before import
-        postproc_scripts/*:E402
+        scripts/*:E402
 
         # Ignoring linelength in APOSMM
         libensemble/gen_funcs/*aposmm.py:E501
@@ -48,11 +42,11 @@ per-file-ignores =
         examples/calling_scripts/run_libensemble_on_warpx.py:E402
         libensemble/gen_funcs/persistent_aposmm.py:E402, E501
         libensemble/tests/regression_tests/test_persistent_aposmm*:E402
+        libensemble/tests/regression_tests/dont_run_test_persistent_aposmm*:E402
+        libensemble/tests/regression_tests/test_uniform_sampling_then_persistent_localopt_runs.py:E402
+        libensemble/tests/functionality_tests/test_active_persistent_worker_abort.py:E402
         libensemble/tests/deprecated_tests/test_old_aposmm*:E402
-
-        # Ignoring linelength in test_history.py
-        libensemble/tests/unit_tests/test_history.py:E501
-        libensemble/tests/unit_tests/test_allocation_funcs_and_support.py:E501
+        libensemble/tests/unit_tests/test_persistent_aposmm.py:E402
 
         # Allow undefined name '__version__'
         setup.py:F821

.github/workflows/ci.yml

@@ -111,8 +111,8 @@ jobs:
             conda install superlu_dist
             conda install hypre
             conda install mumps-mpi
-            conda install petsc
-            conda install petsc4py
+            # pip install petsc
+            # pip install petsc4py
             pip install DFO-LS
 
             pip install mpmath
@@ -125,6 +125,18 @@ jobs:
             sudo apt-get install octave
             sudo apt-get install bc
 
+            # begin heffte build and dependencies
+            sudo apt install libfftw3-dev
+            git clone https://bitbucket.org/icl/heffte.git
+            mkdir heffte/build
+            cd heffte/build
+            pwd
+            cmake -D CMAKE_BUILD_TYPE=Release -D BUILD_SHARED_LIBS=ON -D CMAKE_INSTALL_PREFIX=./ -D Heffte_ENABLE_AVX=ON -D Heffte_ENABLE_FFTW=ON ../
+            make
+            make install
+            cp ./benchmarks/speed3d_c2c ../../libensemble/tests/regression_tests/
+            # end heffte build and dependencies
+
             pip install dragonfly-opt
             pip install torch
             pip install gpytorch
@@ -198,7 +210,7 @@ jobs:
               BALSAM_DB_PATH: $HOME/test-balsam
           run: |
            source balsamactivate test-balsam
-           ./libensemble/tests/run-tests.sh -re -y 'test_balsam*' -z -l
+           ./libensemble/tests/run-tests.sh -re -y 'test_balsam_hworld*' -z -l
 
         - name: Merge coverage, run Coveralls
           env:

.gitignore

@@ -9,6 +9,12 @@ code/tests/regression_tests/output/
 libensemble.egg-info
 docs/_build
 x.log
+*.bin
+*.mat
+*.npy
+*.out
+*.err
+*.stat
 
 .vscode
 build/

.wci.yml

@@ -17,8 +17,8 @@ description: |
 language: Python
 
 release:
-  version: 0.9.1
-  date: 2022-05-11
+  version: 0.9.2
+  date: 2022-07-06
 
 documentation:
   general: https://libensemble.readthedocs.io

CHANGELOG.rst

@@ -8,6 +8,37 @@ GitHub issues are referenced, and can be viewed with hyperlinks on the `github r
 
 .. _`github releases page`: https://github.com/Libensemble/libensemble/releases
 
+Release 0.9.2
+-------------
+
+:Date: July 06, 2022
+
+New capabilities:
+
+* Support auto-detection of PBS node lists. #602
+* Added configuration options for `libE_stats.txt` file. #743
+* Support for `spawn` and `forkserver` multiprocessing start methods. #797
+
+ * Note that macOS no longer switches to using `fork`. macOS (since Python 3.8) and Windows
+ default to using `spawn`. When using `spawn`, we recommend placing calling script code in
+ an ``if __name__ == "__main__":`` block. The multiprocessing interface can be used to switch methods (https://docs.python.org/3/library/multiprocessing.html#multiprocessing.set_start_method).
+
+Updates to example functions:
+
+Added simple dynamic sampling example. #833
+Added heFFTe example. #844
+Regression tests separated into problem examples and functionality tests. #839
+
+:Note:
+
+* Tested platforms include Linux, MacOS, Theta (Cray XC40/Cobalt), Summit (IBM Power9/LSF), Bebop (Cray CS400/Slurm), Swing (A100 GPU system), Perlmutter (HPE Cray EX with A100 NVIDIA GPUs).
+* Tested Python versions: (Cpython) 3.7, 3.8, 3.9, 3.10.
+
+:Known issues:
+
+* The APOSMM generator function has been noted to operate slower than expected with the `spawn` multiprocessing start method. For this reason we recommend using `fork` with APOSMM, when using `local` comms (`fork` is the default method on Linux systems).
+* See known issues section in the documentation.
+
 Release 0.9.1
 -------------
 

CONTRIBUTING.rst

@@ -12,6 +12,10 @@ repository write access.
 
 Code should pass flake8 tests, allowing for the exceptions
 given in the flake8_ file in the project directory.
+Python code should be formatted using the latest version of black_ by running
+the following in the base libensemble directory::
+
+  black --config=.black .
 
 Issues can be raised at
 
@@ -67,4 +71,5 @@ following:
       maintained indefinitely and may be redistributed consistent with
       this project or the open source license(s) involved.
 
+.. _black: https://pypi.org/project/black/
 .. _flake8: https://github.com/Libensemble/libensemble/blob/develop/.flake8

MANIFEST.in

@@ -7,7 +7,7 @@ include install/*
 include .flake8
 
 recursive-include libensemble *
-recursive-include postproc_scripts *
+recursive-include scripts *
 recursive-include examples *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

README.rst

@@ -76,6 +76,7 @@ Required dependencies:
 * Python_ 3.7 or above
 * NumPy_
 * psutil_
+* setuptools_
 
 When using  ``mpi4py`` for libEnsemble communications:
 
@@ -242,7 +243,7 @@ Resources
     author  = {Stephen Hudson and Jeffrey Larson and Stefan M. Wild and
                David Bindel and John-Luke Navarro},
     institution = {Argonne National Laboratory},
-    number  = {Revision 0.9.1},
+    number  = {Revision 0.9.2},
     year    = {2022},
     url     = {https://buildmedia.readthedocs.org/media/pdf/libensemble/latest/libensemble.pdf}
   }
@@ -339,6 +340,7 @@ See a complete list of `example user scripts`_.
 .. _ReadtheDocs: http://libensemble.readthedocs.org/
 .. _SciPy: http://www.scipy.org
 .. _scipy.optimize: https://docs.scipy.org/doc/scipy/reference/optimize.html
+.. _setuptools: https://setuptools.pypa.io/en/latest/
 .. _Spack: https://spack.readthedocs.io/en/latest
 .. _Summit: https://www.olcf.ornl.gov/olcf-resources/compute-systems/summit/
 .. _Surmise: https://surmise.readthedocs.io/en/latest/index.html