Merge pull request #518 from Libensemble/release/v_0.7.1

Release/v 0.7.1
Libensemble · Oct 16, 2020 · 0d699f4 · 0d699f4
2 parents a870bd4 + 5447d3f
commit 0d699f4
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diff --git a/.flake8 b/.flake8
@@ -22,6 +22,9 @@ per-file-ignores =
         libensemble/__init__.py:F401
         libensemble/libensemble/__init__.py:F401
 
+        # worker uses regex with chars that resemble escape sequences
+        libensemble/libE_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

diff --git a/.travis.yml b/.travis.yml
@@ -36,15 +36,30 @@ jobs:
       env: MPI=mpich PY=3.7 COMMS_TYPE=t  # tcp
       language: generic
       python: 3.7
-
-# Below will update the OSX octave used on Travis.  This was so slow that we
-# were hitting the 50 minute limit on Travis. We no longer update octave in
-# homebrew, and can no longer run regression # tests using octave on OSX.
-# addons:
-#   homebrew:
-#     packages:
-#     - octave
-#     update: true
+    - os: osx
+      osx_image: xcode11.3
+      env: MPI=mpich PY=3.8 COMMS_TYPE=m  # mpi
+      language: generic
+      python: 3.8
+    - os: osx
+      osx_image: xcode11.3
+      env: MPI=mpich PY=3.8 COMMS_TYPE=l  # local
+      language: generic
+      python: 3.8
+    - os: osx
+      osx_image: xcode11.3
+      env: MPI=mpich PY=3.8 COMMS_TYPE=t  # tcp
+      language: generic
+      python: 3.8
+  fast_finish: true
+  allow_failures:
+      - python: 3.8
+      - os: osx
+        env: MPI=mpich PY=3.8 COMMS_TYPE=m  # mpi
+      - os: osx
+        env: MPI=mpich PY=3.8 COMMS_TYPE=l  # mpi
+      - os: osx
+        env: MPI=mpich PY=3.8 COMMS_TYPE=t  # mpi
 
 services:
     - postgresql
@@ -66,7 +81,7 @@ before_install:
   - conda info -a # For debugging conda issues
   - conda config --add channels conda-forge
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-      conda create --yes --name condaenv python=3.7;
+      conda create --yes --name condaenv python=$PY;
     else
       conda create --yes --name condaenv python=$TRAVIS_PYTHON_VERSION;
     fi
@@ -90,14 +105,16 @@ install:
   - if [[ "$TRAVIS_PYTHON_VERSION" == "3.8" ]]; then
       conda install nlopt mpi4py scipy mpich;
       export PETSC_CONFIGURE_OPTIONS='--with-batch';
-      pip install petsc petsc4py;
+      conda install petsc4py;
     else
       conda install nlopt petsc4py petsc $MUMPS mpi4py scipy $MPI;
     fi
 
     # Begin: Dependencies only for regression tests
   - pip install DFO-LS
   - pip install deap
+  - conda install psutil
+  - pip install mpmath
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
         pip install scikit-build packaging Tasmanian --user;
     fi
@@ -125,7 +142,7 @@ before_script:
 
 # Run test (-z show output)
 script:
-  - ./libensemble/tests/run-tests.sh -z -$COMMS_TYPE
+  - ./libensemble/tests/run-tests.sh -A "-W error" -z -$COMMS_TYPE
 
 # Track code coverage
 after_success:

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -4,6 +4,54 @@ Release Notes
 
 Below are the notes from all libEnsemble releases.
 
+Release 0.7.1
+-------------
+
+:Date: Oct 15, 2020
+
+Dependencies:
+
+* ``psutils`` is now a required dependency. (#478 #491)
+
+API additions:
+
+* Executor updates:
+
+ * Addition of a zero-resource worker option for persistent gens (does not allocate nodes to gen). (#500)
+ * Multiple applications can be registered to the Executor (and submitted) by name. (#498)
+ * Wait function added to Tasks. (#499)
+
+* Gen directories can now be created with options analogous to those for sim dirs. (#349 / #489)
+
+Other changes:
+
+* Improve comms efficiency (Repack fields when NumPy version 1.15+). (#511)
+* Fix multiprocessing error on macOS/Python3.8 (Use 'fork' instead of 'spawn'). (#502 / #503)
+
+Updates to example functions:
+
+* Allow APOSMM to trigger ensemble exit when condition reached. (#507)
+* Improvement in how persistent APOSMM shuts down subprocesses (preventing PETSc MPI-abort). (#478)
+
+Documentation:
+
+* APOSMM Tutorial added. (#468)
+* Writing guide for user functions added to docs (e.g., creating sim_f, gen_f, alloc_f). (#510)
+* Addition of posters and presentations section to docs (inc. Jupyter notebooks/binder links). (#492 #497)
+
+:Note:
+
+* Tested platforms include Linux, MacOS, Theta (Cray XC40/Cobalt), Summit (IBM Power9/LSF), Bebop (Cray CS400/Slurm), and Bridges (HPE system at PSC).
+* Cori (Cray XC40/Slurm) was not tested with release code due to system issues.
+* Tested Python versions: (Cpython) 3.5, 3.6, 3.7, 3.8.
+
+:Known issues:
+
+* We currently recommended running in Central mode on Bridges as distributed runs are experiencing hangs.
+* OpenMPI does not work with direct MPI job launches in mpi4py comms mode, since it does not support nested MPI launches
+  (Either use local mode or Balsam job controller).
+* See known issues section in the documentation for more issues.
+
 Release 0.7.0
 -------------
 
@@ -20,34 +68,34 @@ Breaking API changes:
 
 API additions:
 
-* Added gen_funcs.rc configuration framework with option to select APOSMM Optimizers for import (#444)
-* Provide ``alloc_specs`` defaults via `alloc_funcs.defaults` module (#325)
-* Added ``extra_args`` option to the Executor submit function to allow addition of arbitrary MPI runner options (#445)
-* Added ``custom_info`` argument to MPI Executor to allow overriding of detected settings (#448)
-* Added ``libE_specs`` option to disable log files (#368)
+* Added gen_funcs.rc configuration framework with option to select APOSMM Optimizers for import. (#444)
+* Provide ``alloc_specs`` defaults via `alloc_funcs.defaults` module. (#325)
+* Added ``extra_args`` option to the Executor submit function to allow addition of arbitrary MPI runner options. (#445)
+* Added ``custom_info`` argument to MPI Executor to allow overriding of detected settings. (#448)
+* Added ``libE_specs`` option to disable log files. (#368)
 
 Other changes:
 
 * Added libEnsemble Conda package, hosted on conda-forge.
-* Bugfix: Intermittent failures with repeated libE calls under `mpi4py` comms
+* Bugfix: Intermittent failures with repeated libE calls under `mpi4py` comms.
   Every libE call now uses its own duplicate of provided communicator and closes out. (#373/#387)
 * More accurate timing in `libE_stats.txt`. (#318)
 * Addition of new post-processing scripts.
 
 Updates to example functions:
 
-* Persistent APOSMM is now the recommended APOSMM (`aposmm.py` renamed to `old_aposmm.py`) (#435)
+* Persistent APOSMM is now the recommended APOSMM (`aposmm.py` renamed to `old_aposmm.py`). (#435)
 * New alloc/gen func: Finite difference parameters with noise estimation.  (#350)
 * New example gen func: Tasmanian UQ generator.  (#351)
 * New example gen func: Deap/NSGA2 generator.  (#407)
 * New example gen func to interface with VTMOP.
-* New example sim func: Borehole (#367)
-* New example use-case: WarpX/APOSMM (#425)
+* New example sim func: Borehole. (#367)
+* New example use-case: WarpX/APOSMM. (#425)
 
 :Note:
 
 * Tested platforms include Linux, MacOS, Theta (Cray XC40/Cobalt), Summit (IBM Power9/LSF), Bebop (Cray CS400/Slurm), Cori (Cray XC40/Slurm), and Bridges (HPE system at PSC).
-* Tested Python versions: (Cpython) 3.5, 3.6, 3.7, 3.8
+* Tested Python versions: (Cpython) 3.5, 3.6, 3.7, 3.8.
 
 :Known issues:
 
@@ -61,21 +109,21 @@ Release 0.6.0
 
 API changes:
 
-* sim/gen/alloc_specs options that do not directly involve these routines are moved to libE_specs (see docs) (#266, #269)
-* sim/gen/alloc_specs now require user-defined attributes to be added under the ``'user'`` field (see docs and examples) (#266, #269).
-* Addition of a utils module to help users create calling scripts. Includes an argument parser and utility functions (#308).
-* check_inputs() function is moved to the utils module (#308).
-* The libE_specs option ``nprocesses`` has been changed to ``nworkers`` (#235)
+* sim/gen/alloc_specs options that do not directly involve these routines are moved to libE_specs (see docs). (#266, #269)
+* sim/gen/alloc_specs now require user-defined attributes to be added under the ``'user'`` field (see docs and examples). (#266, #269)
+* Addition of a utils module to help users create calling scripts. Includes an argument parser and utility functions. (#308)
+* check_inputs() function is moved to the utils module. (#308)
+* The libE_specs option ``nprocesses`` has been changed to ``nworkers``. (#235)
 
 New example functions:
 
-* Addition of a persistent APOSMM generator function (#217).
+* Addition of a persistent APOSMM generator function. (#217)
 
 Other changes:
 
-* Overhaul of documentation, including HPC platform guides and a new pdf structure (inc. #232, #282)
-* Addition of OpenMP threading and GPU support to forces test (#250).
-* Balsam job_controller now tested on Travis (#47)
+* Overhaul of documentation, including HPC platform guides and a new pdf structure. (inc. #232, #282)
+* Addition of OpenMP threading and GPU support to forces test. (#250)
+* Balsam job_controller now tested on Travis. (#47)
 
 :Note:
 
@@ -97,7 +145,7 @@ Release 0.5.2
 * All output from libEnsemble goes via logger. MANAGER_WARNING level added. This level and above are echoed to stderr by default. API option to change echo level.
 * Simulation directories are created only during sim_f calls are suffixed by _worker. #146
 * New user function libE.check_inputs() can be used to check valid configuration of inputs. Can be called in serial or under MPI (see libE API). #65
-* Installation option has been added to install dependencies used in tests ``pip install libensemble[extras]``
+* Installation option has been added to install dependencies used in tests ``pip install libensemble[extras]``.
 * A profiling option has been added to sim_specs. #170
 * Results comparison scripts have been included for convenience.
 
@@ -116,14 +164,14 @@ Release 0.5.1
 
 :Date: July 11, 2019
 
-* Fixed LSF resource detection for large jobs on LSF systems (e.g., Summit) #184
-* Added support for macOS #182
-* Improved the documentation (including addition of beginner's tutorial and FAQ)
+* Fixed LSF resource detection for large jobs on LSF systems (e.g., Summit). #184
+* Added support for macOS. #182
+* Improved the documentation (including addition of beginner's tutorial and FAQ).
 
 :Note:
 
 * Tested platforms include Local Linux, Theta (Cray XC40/Cobalt), Summit (IBM Power9/LSF), and Bebop (Cray CS400/Slurm).
-* Tested Python versions: (Cpython) 3.4, 3.5, 3.6, 3.7
+* Tested Python versions: (Cpython) 3.4, 3.5, 3.6, 3.7.
 
 :Known issues:
 
@@ -134,19 +182,19 @@ Release 0.5.0
 
 :Date: May 22, 2019
 
-* Added local (multiprocessing) and TCP options for manager/worker communications, in addition to mpi4py (#42).
+* Added local (multiprocessing) and TCP options for manager/worker communications, in addition to mpi4py. (#42).
 
  * Example: libEnsemble can be run on MOM/launch nodes (e.g., those of ALCF/Theta & OLCF/Summit) and can remotely detect compute resources.
  * Example: libEnsemble can be run on a system without MPI.
  * Example: libEnsemble can be run with a local manager and remote TCP workers.
 
 * Added support for Summit/LSF scheduler in job controller.
-* MPI job controller detects and retries launches on failure; adding resilience (#143).
-* Job controller supports option to extract/print job times in libE_stats.txt (#136).
-* Default logging level changed to INFO (#164).
-* Logging interface added, which allows user to change logging level and file (#110).
+* MPI job controller detects and retries launches on failure; adding resilience. (#143)
+* Job controller supports option to extract/print job times in libE_stats.txt. (#136)
+* Default logging level changed to INFO. (#164)
+* Logging interface added, which allows user to change logging level and file. (#110)
 * All worker logging and calculation stats are routed through manager.
-* libEnsemble can be run without a gen_func, for example, when using a previously computed random sample (#122).
+* libEnsemble can be run without a gen_func, for example, when using a previously computed random sample. (#122)
 * Aborts dump persis_info with the history.
 
 :Note:
@@ -167,22 +215,22 @@ Release 0.4.1
 
 :Date: February 20, 2019
 
-* Logging no longer uses root logger (also added option to change libEnsemble log level) (#105)
-* Added wait_on_run option for job controller launch to block until jobs have started (#111)
-* persis_info can be passed to sim as well as gen functions (#112)
-* Postprocessing scripts added to create performance/utilization graphs (#102)
-* New scaling test added (not part of current CI test suite) (#114)
+* Logging no longer uses root logger (also added option to change libEnsemble log level). (#105)
+* Added wait_on_run option for job controller launch to block until jobs have started. (#111)
+* persis_info can be passed to sim as well as gen functions. (#112)
+* Postprocessing scripts added to create performance/utilization graphs. (#102)
+* New scaling test added (not part of current CI test suite). (#114)
 
 Release 0.4.0
 -------------
 
 :Date: November 7, 2018
 
-* Separated job controller classes into different modules including a base class (API change)
-* Added central_mode run option to distributed type (MPI) job_controllers (API addition) (#93)
-* Made poll and kill job methods (API change)
-* In job_controller, set_kill_mode is removed and replaced by a wait argument for a hard kill (API change)
-* Removed register module - incorporated into job_controller (API change)
+* Separated job controller classes into different modules including a base class (API change).
+* Added central_mode run option to distributed type (MPI) job_controllers (API addition). (#93)
+* Made poll and kill job methods (API change).
+* In job_controller, set_kill_mode is removed and replaced by a wait argument for a hard kill (API change).
+* Removed register module - incorporated into job_controller (API change).
 * APOSMM has improved asynchronicity when batch mode is false (with new example). (#96)
 * Manager errors (instead of hangs) when alloc_f or gen_f don't return work when all workers are idle. (#95)
 
@@ -195,17 +243,17 @@ Release 0.3.0
 
 :Date: September 7, 2018
 
-* Issues with killing jobs have been fixed (#21)
-* Fixed job_controller manager_poll to work with multiple jobs (#62)
+* Issues with killing jobs have been fixed. (#21)
+* Fixed job_controller manager_poll to work with multiple jobs. (#62)
 * API change: persis_info now included as an argument to libE and is returned from libE instead of gen_info
 * Gen funcs: aposmm_logic module renamed to aposmm.
 * New example gen and allocation functions.
-* Updated Balsam launch script (with new Balsam workflow)
-* History is dumped to file on manager or worker exception and MPI aborted (with exit code 1) (#46)
-* Default logging level changed to DEBUG and redirected to file ensemble.log
-* Added directory of standalone tests (comms, job kills, and nested MPI launches)
-* Improved and speeded up unit tests (#68)
-* Considerable documentation enhancements
+* Updated Balsam launch script (with new Balsam workflow).
+* History is dumped to file on manager or worker exception and MPI aborted (with exit code 1). (#46)
+* Default logging level changed to DEBUG and redirected to file ensemble.log.
+* Added directory of standalone tests (comms, job kills, and nested MPI launches).
+* Improved and speeded up unit tests. (#68)
+* Considerable documentation enhancements.
 
 :Known issues:
 

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -4,8 +4,10 @@ include *.rst
 include LICENSE
 include CONTRIBUTING
 include install/*
+include .flake8
 
 recursive-include libensemble *
+recursive-include postproc_scripts *
 recursive-include examples *
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
@@ -14,4 +16,4 @@ recursive-exclude * *.o
 recursive-exclude * *.npy
 recursive-exclude * *.gitignore
 
-recursive-include docs *.pdf *.rst conf.py Makefile make.bat
+recursive-include docs *
diff --git a/README.rst b/README.rst
@@ -64,6 +64,7 @@ Required dependencies:
 
 * Python_ 3.5 or above
 * NumPy_
+* psutil_
 
 For libEnsemble running with the mpi4py parallelism:
 
@@ -213,16 +214,16 @@ Resources
                    David Bindel and John-Luke Navarro},
     title       = {{libEnsemble} Users Manual},
     institution = {Argonne National Laboratory},
-    number      = {Revision 0.7.0},
+    number      = {Revision 0.7.1},
     year        = {2020},
     url         = {https://buildmedia.readthedocs.org/media/pdf/libensemble/latest/libensemble.pdf}
   }
 
 .. after_resources_rst_tag
 
 .. _Balsam: https://www.alcf.anl.gov/support-center/theta/balsam
-.. _Coveralls: https://coveralls.io/github/Libensemble/libensemble?branch=master
 .. _Conda: https://docs.conda.io/en/latest/
+.. _Coveralls: https://coveralls.io/github/Libensemble/libensemble?branch=master
 .. _DFO-LS: https://github.com/numericalalgorithmsgroup/dfols
 .. _GitHub: https://github.com/Libensemble/libensemble
 .. _libEnsemble mailing list: https://lists.mcs.anl.gov/mailman/listinfo/libensemble
@@ -235,7 +236,8 @@ Resources
 .. _NumPy: http://www.numpy.org
 .. _petsc4py: https://bitbucket.org/petsc/petsc4py
 .. _PETSc: http://www.mcs.anl.gov/petsc
-.. _poster: https://figshare.com/articles/LibEnsemble_PETSc_TAO-_Sustaining_a_library_for_dynamic_ensemble-based_computations/7765454
+.. _poster: https://figshare.com/articles/libEnsemble_A_Python_Library_for_Dynamic_Ensemble-Based_Computations/12559520
+.. _psutil: https://pypi.org/project/psutil/
 .. _PyPI: https://pypi.org
 .. _pytest-cov: https://pypi.org/project/pytest-cov/
 .. _pytest-timeout: https://pypi.org/project/pytest-timeout/

diff --git a/binder/environment.yml b/binder/environment.yml
@@ -0,0 +1,11 @@
+name: libensemble-python
+
+channels:
+    - conda-forge
+
+dependencies:
+    - numpy
+    - openmpi
+    - openmpi-mpicc
+    - mpi4py
+    - libensemble