Merge pull request #310 from Libensemble/develop

Release v0.6.0
Libensemble · Dec 4, 2019 · f226891 · f226891
2 parents f06bdd3 + 9a3d36a
commit f226891
Show file tree

Hide file tree

Showing 234 changed files with 7,413 additions and 2,784 deletions.
diff --git a/.flake8 b/.flake8
@@ -1,5 +1,5 @@
 [flake8]
-ignore = 
+ignore =
         # Not worrying about line length for now
         E501,
         # Not worrying about spaces around arithmetic operations
@@ -12,20 +12,16 @@ ignore =
         W504
         # Lambda expressions are okay
         E731
-exclude = 
+exclude =
         # Don't need to check .git
         .git,
         # Largely autogenerated
         docs/conf.py
-        # Keeping bad python format to match PETSc source code 
+        # Keeping bad python format to match PETSc source code
         libensemble/sim_funcs/chwirut1.py
         examples/sim_funcs/chwirut1.py
-        # This is not implemented yet
-        controller_tests/test_jobcontroller_manager_poll.py
         # Not checking these scripts yet
         postproc_scripts
-        # Do not check these experimental tests
-        balsam_tests
 
 # Note that you can use wildcard exceptions with something such as
 # libensemble/libensemble/tests/regression_tests/*:F401
@@ -35,5 +31,5 @@ per-file-ignores =
         libensemble/libensemble/__init__.py:F401
         # 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/standalone_tests/mpi_launch_test/create_mpi_jobs.py:E402
+        libensemble/libensemble/tests/standalone_tests/mpi_launch_test/create_mpi_jobs.py:E402
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,4 @@ code/tests/regression_tests/output/
 .cache
 libensemble.egg-info
 docs/_build
+x.log
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,7 +1,20 @@
+version: 2
+
 conda:
-    file: conda/environment.yml
-
+    environment: conda/environment.yml
+
+sphinx:
+    configuration: docs/conf.py
+
+build:
+    image: latest
+
+formats:
+  - pdf
+
 python:
-    version: 3.6
-    pip_install: true
-    setup_py_install: true
+    install:
+      - method: pip
+        path: .
+        extra_requirements:
+         - docs
diff --git a/.style.yapf b/.style.yapf
@@ -6,7 +6,7 @@ SPLIT_BEFORE_DOT = True
 COLUMN_LIMIT = 79
 SPLIT_BEFORE_NAMED_ASSIGNS = False
 SPACE_BETWEEN_ENDING_COMMA_AND_CLOSING_BRACKET = False
-ALLOW_SPLIT_BEFORE_DEFAULT_OR_NAMED_ASSIGNS = False 
+ALLOW_SPLIT_BEFORE_DEFAULT_OR_NAMED_ASSIGNS = False
 ALLOW_SPLIT_BEFORE_DICT_VALUE = False
 DEDENT_CLOSING_BRACKETS = False
 EACH_DICT_ENTRY_ON_SEPARATE_LINE = True

diff --git a/.travis.yml b/.travis.yml
@@ -14,87 +14,77 @@ env:
     - OMPI_MCA_rmaps_base_oversubscribe=yes
   matrix:
     - MPI=mpich
-    #- MPI=openmpi
 
 matrix:
   include:
     - os: osx
-      osx_image: xcode11
-      env: MPI=mpich PY=3
+      osx_image: xcode10.1
+      env: MPI=mpich PY=3.7
       language: generic
-      python: 3
+      python: 3.7
 
-# matrix:
-#  allow_failures:
-#    - env: MPI=openmpi
-
-# addons:
-#   apt:
-#     packages:
-#       - gfortran
-#       - libblas-dev
-#       - liblapack-dev
+services:
+    - postgresql
 
 cache:
   pip: true
   apt: true
 
-# Setup Miniconda
 before_install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-      wget https://repo.continuum.io/miniconda/Miniconda3-4.6.14-MacOSX-x86_64.sh -O miniconda.sh;
+      wget https://repo.continuum.io/miniconda/Miniconda3-4.7.10-MacOSX-x86_64.sh -O miniconda.sh;
     else
-      wget https://repo.continuum.io/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh -O miniconda.sh;
+      wget https://repo.continuum.io/miniconda/Miniconda3-4.7.10-Linux-x86_64.sh -O miniconda.sh;
     fi
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
-  #- conda update -q -y conda
-  - conda info -a # For debugging any issues with conda
+  - conda info -a # For debugging conda issues
   - conda config --add channels conda-forge
-  - conda create --yes --name condaenv python=$TRAVIS_PYTHON_VERSION
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+      conda create --yes --name condaenv python=3.7;
+    else
+      conda create --yes --name condaenv python=$TRAVIS_PYTHON_VERSION;
+    fi
   - source activate condaenv
 
 install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-        wget https://github.com/phracker/MacOSX-SDKs/releases/download/10.13/MacOSX10.13.sdk.tar.xz;
-        mkdir ../sdk; tar xf MacOSX10.13.sdk.tar.xz -C ../sdk;
         COMPILERS=clang_osx-64;
         MUMPS=mumps-mpi=5.1.2=haf446c3_1007;
     else
         COMPILERS=gcc_linux-64;
         MUMPS=mumps-mpi=5.1.2=h5bebb2f_1007;
     fi
+
   - conda install $COMPILERS
-  #S- conda install nlopt petsc4py petsc mpi4py scipy $MPI
+  - conda install libblas libopenblas # Prevent 'File exists' error
   - conda install nlopt petsc4py petsc $MUMPS mpi4py scipy $MPI
-  # pip install these as the conda installs downgrade pytest on python3.4
-  - pip install flake8
+  - pip install flake8       # Conda installs downgrade pytest on python3.4
   - pip install pytest
   - pip install pytest-cov
   - pip install pytest-timeout
   - pip install mock
   - pip install coveralls
-  # For confirmation of MPI library being used.
-  - python conda/find_mpi.py # locate compilers
-  - mpiexec --version # Show MPI library details
-  - pip install -e .
-
+  - python conda/find_mpi.py # Locate compilers. Confirm MPI library
+  - mpiexec --version        # Show MPI library details
+  - pip install -e .         # Installing libEnsemble
+  - wget https://github.com/balsam-alcf/balsam/archive/0.3.5.1.tar.gz
+  - mkdir ../balsam; tar xf 0.3.5.1.tar.gz -C ../balsam;
+  - python conda/install-balsam.py
 
 before_script:
   - flake8 libensemble
-  # Set conda compilers to use new SDK instead of Travis default.
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
-        echo "export CONDA_BUILD_SYSROOT=/Users/travis/build/Libensemble/sdk/MacOSX10.13.sdk" > setenv.sh;
-        source setenv.sh;
-    fi
+  - echo "export BALSAM_DB_PATH=~/test-balsam" > setbalsampath.sh
+  - source setbalsampath.sh # Imperfect method for env var persist after setup
+  - ulimit -Sn 10000   # More concurrent file descriptors (for persis aposmm)
 
 # Run test (-z show output)
 script:
-  - libensemble/tests/run-tests.sh -z
+  - ./libensemble/tests/run-tests.sh -z
 
-# Coverage
+# Track code coverage
 after_success:
   - mv libensemble/tests/.cov* .
   - coveralls

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,6 +2,38 @@
 Release Notes
 =============
 
+Release 0.6.0
+-------------
+
+:Date: December 4, 2019
+
+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)
+
+New example functions:
+
+* 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)
+
+:Note:
+
+* Tested platforms include: Linux, MacOS, Theta (Cray XC40/Cobalt), Summit (IBM Power9/LSF), Bebop (Cray CS400/Slurm), Cori (Cray XC40/Slurm).
+* Tested Python versions: (Cpython) 3.5, 3.6, 3.7
+
+:Known issues:
+
+* These are unchanged from v0.5.0
+* A known issues section has now been added to the documentation.
 
 Release 0.5.2
 -------------
@@ -27,7 +59,6 @@ Release 0.5.2
 
 * These are unchanged from v0.5.0
 
-
 Release 0.5.1
 -------------
 
@@ -46,7 +77,6 @@ Release 0.5.1
 
 * These are unchanged from v0.5.0
 
-
 Release 0.5.0
 -------------
 
@@ -80,20 +110,17 @@ Release 0.5.0
 * Remote detection of logical cores via LSB_HOSTS (e.g., Summit) returns number of physical cores as SMT info not available.
 * TCP mode does not support: 1) more than one libEnsemble call in a given script or 2) the auto-resources option to the job controller.
 
-
 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)
 * Post-processing scripts added to create performance/utilization graphs (#102)
 * New scaling test added (not part of current CI test suite) (#114)
 
-
 Release 0.4.0
 -------------
 
@@ -111,7 +138,6 @@ Release 0.4.0
 
 * OpenMPI is not supported with direct MPI launches as nested MPI launches are not supported.
 
-
 Release 0.3.0
 -------------
 
@@ -133,7 +159,6 @@ Release 0.3.0
 
 * OpenMPI is not supported with direct MPI launches as nested MPI launches are not supported.
 
-
 Release 0.2.0
 -------------
 
@@ -150,7 +175,6 @@ Release 0.2.0
 * Killing MPI jobs does not work correctly on some systems (including Cray XC40 and CS400). In these cases, libEnsemble continues, but processes remain running.
 * OpenMPI does not work correctly with direct launches (and has not been tested with Balsam).
 
-
 Release 0.1.0
 -------------
 

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -1,26 +1,29 @@
-Contributing
-============
+Contributing to libEnsemble
+===========================
 
-Contributions may be made via Github pull request to:
+Contributions may be made via GitHub pull request to:
 
     https://github.com/Libensemble/libensemble
 
 libEnsemble uses the Gitflow model. Contributors should branch from, and
 make pull requests to, the develop branch. The master branch is used only
-for releases. Code should pass flake8 tests, allowing for the exceptions
-given in the ".flake8" configuration file in the project directory.
+for releases. Pull requests may be made from a fork, for those without
+repository write access.
+
+Code should pass flake8 tests, allowing for the exceptions
+given in the flake8_ file in the project directory.
 
 Issues can be raised at:
 
     https://github.com/Libensemble/libensemble/issues
-    
+
 Issues may include reporting bugs or suggested features. Administrators
 will add issues, as appropriate, to the project board at:
 
     https://github.com/Libensemble/libensemble/projects
 
 By convention, user branch names should have a <type>/<name> format, where
-example types are feature, bugfix, testing, docs and experimental.
+example types are feature, bugfix, testing, docs, and experimental.
 Administrators may take a hotfix branch from the the master, which will be
 merged into master (as a patch) and develop. Administrators may also take a
 release branch off develop and merge into master and develop for a release.
@@ -64,3 +67,5 @@ following:
       personal information I submit with it, including my sign-off) is
       maintained indefinitely and may be redistributed consistent with
       this project or the open source license(s) involved.
+
+.. _flake8: https://github.com/Libensemble/libensemble/blob/develop/.flake8