Merge pull request #159 from LLNL/v0.3.3-rc

Release Candidate for v0.3.3

.gitignore

@@ -14,3 +14,4 @@ _axom_build_and_test_*
 tpl_dirs_summary.json
 *.swp
 *.vscode*
+uberenv_libs

LICENSE

@@ -1,49 +1,27 @@
-Copyright (c) 2017-2019, Lawrence Livermore National Security, LLC. All rights reserved.
+Copyright (c) 2017-2020, Lawrence Livermore National Security, LLC.
+All rights reserved.
 
-Redistribution and use in source and binary forms, with or without 
+Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
 
-* Redistributions of source code must retain the above copyright notice, 
-  this list of conditions and the disclaimer below.
-
-* Redistributions in binary form must reproduce the above copyright notice, 
-  this list of conditions and the disclaimer (as noted below) in the 
-  documentation and/or other materials provided with the distribution.
-
-* Neither the name of the LLNS/LLNL nor the names of its contributors may be 
-  used to endorse or promote products derived from this software without 
-  specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
-ARE DISCLAIMED. IN NO EVENT SHALL LAWRENCE LIVERMORE NATIONAL SECURITY, LLC, 
-THE U.S. DEPARTMENT OF ENERGY OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, 
-BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY 
-OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 
-NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, 
-EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-Additional BSD Notice
-
-1. This notice is required to be provided under our contract with the U.S. 
-Department of Energy (DOE). This work was produced at Lawrence Livermore 
-National Laboratory under Contract No. DE-AC52-07NA27344 with the DOE.
-
-2. Neither the United States Government nor Lawrence Livermore National 
-Security, LLC nor any of their employees, makes any warranty, express or 
-implied, or assumes any liability or responsibility for the accuracy, 
-completeness, or usefulness of any information, apparatus, product, or 
-process disclosed, or represents that its use would not infringe 
-privately-owned rights.
-
-3. Also, reference herein to any specific commercial products, process, 
-or services by trade name, trademark, manufacturer or otherwise does not 
-necessarily constitute or imply its endorsement, recommendation, or favoring 
-by the United States Government or Lawrence Livermore National Security, LLC. 
-The views and opinions of authors expressed herein do not necessarily state 
-or reflect those of the United States Government or Lawrence Livermore 
-National Security, LLC, and shall not be used for advertising or product 
-endorsement purposes.
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

NOTICE

@@ -0,0 +1,21 @@
+Additional BSD Notice
+
+1. This notice is required to be provided under our contract with the U.S. 
+Department of Energy (DOE). This work was produced at Lawrence Livermore 
+National Laboratory under Contract No. DE-AC52-07NA27344 with the DOE.
+
+2. Neither the United States Government nor Lawrence Livermore National 
+Security, LLC nor any of their employees, makes any warranty, express or 
+implied, or assumes any liability or responsibility for the accuracy, 
+completeness, or usefulness of any information, apparatus, product, or 
+process disclosed, or represents that its use would not infringe 
+privately-owned rights.
+
+3. Also, reference herein to any specific commercial products, process, 
+or services by trade name, trademark, manufacturer or otherwise does not 
+necessarily constitute or imply its endorsement, recommendation, or favoring 
+by the United States Government or Lawrence Livermore National Security, LLC. 
+The views and opinions of authors expressed herein do not necessarily state 
+or reflect those of the United States Government or Lawrence Livermore 
+National Security, LLC, and shall not be used for advertising or product 
+endorsement purposes.

README.md

@@ -1,10 +1,11 @@
+# <img src="/share/axom/logo/axom_logo.png?raw=true" width="250" valign="middle" alt="Axom"/>
+
 [![Azure Pipelines Build Status](https://dev.azure.com/axom/axom/_apis/build/status/LLNL.axom?branchName=develop)](https://dev.azure.com/axom/axom/_build/latest?definitionId=1&branchName=develop)
 [![Documentation Status](https://readthedocs.org/projects/axom/badge/?version=develop)](https://axom.readthedocs.io/en/develop/?badge=develop)
+[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://github.com/LLNL/axom/blob/develop/LICENSE)
+[![GitHub release](https://img.shields.io/github/release/LLNL/axom.svg)](https://github.com/LLNL/axom/releases/latest)
 
-Axom
-====
-
-Axom provides a robust, flexible software infrastructure for the development of multi-physics applications and computational tools.
+Axom provides robust, flexible software infrastructure for the development of multi-physics applications and computational tools.
 
 Documentation
 -------------
@@ -29,8 +30,9 @@ Contributions
 
 We welcome all kinds of contributions: new features, bug fixes, documentation edits.
 
-To contribute, make a [pull request](https://github.com/llnl/axom/compare), with `develop` as the destination branch.
-We use CI testing and your branch must pass these tests before being merged.
+To contribute, make a [pull request](https://github.com/llnl/axom/compare), with `develop`
+as the destination branch. We use CI testing and your branch must pass these tests before
+being merged.
 
 For more information, see the [contributing guide](https://github.com/llnl/axom/blob/develop/CONTRIBUTING.md).
 
@@ -40,18 +42,59 @@ Authors
 Thanks to all of Axom's
 [contributors](https://github.com/llnl/axom/graphs/contributors).
 
-Release
+License
 -------
 
-Copyright (c) 2017-2019, Lawrence Livermore National Security, LLC. 
+Copyright (c) 2017-2020, Lawrence Livermore National Security, LLC. 
 Produced at the Lawrence Livermore National Laboratory.
 
-All rights reserved. 
+Copyrights and patents in the Axom project are retained by contributors.
+No copyright assignment is required to contribute to Axom.
+
+See [LICENSE](./LICENSE) for details.
 
 Unlimited Open Source - BSD 3-clause Distribution
 `LLNL-CODE-741217` `OCEC-17-187`
 
-Additional license and copyright information can be found in the following files:
- * [LICENSE](./LICENSE)
- * [COPYRIGHT](./COPYRIGHT)
+SPDX usage
+------------
+
+Individual files contain SPDX tags instead of the full license text.
+This enables machine processing of license information based on the SPDX
+License Identifiers that are available here: https://spdx.org/licenses/
+
+Files that are licensed as BSD 3-Clause contain the following
+text in the license header:
+
+    SPDX-License-Identifier: (BSD-3-Clause)
+
+External Packages
+-----------------
+
+Axom bundles some of its external dependencies in its repository.  These
+packages are covered by various permissive licenses.  A summary listing
+follows.  See the license included with each package for full details.
+
+
+[//]: # (Note: The spaces at the end of each line below add line breaks)
+
+PackageName: BLT  
+PackageHomePage: https://github.com/LLNL/blt  
+PackageLicenseDeclared: BSD-3-Clause  
+
+PackageName: CLI11  
+PackageHomePage: https://github.com/CLIUtils/CLI11  
+PackageLicenseDeclared: BSD-3-Clause  
+
+PackageName: fmt  
+PackageHomePage: https://github.com/fmtlib/fmt  
+PackageLicenseDeclared: BSD-2-Clause  
+
+PackageName: sparsehash  
+PackageHomePage: https://github.com/sparsehash/sparsehash  
+PackageLicenseDeclared: BSD-3-Clause  
+
+PackageName: uberenv  
+PackageHomePage: https://github.com/LLNL/uberenv  
+PackageLicenseDeclared: BSD-3-Clause  
 

RELEASE

@@ -1,8 +1,8 @@
 *******************************************************************************
 
-Axom: ................................, version 0.3.2
+Axom: ................................, version 0.3.3
 
-Copyright (c) 2017-2019, Lawrence Livermore National Security, LLC. 
+Copyright (c) 2017-2020, Lawrence Livermore National Security, LLC. 
 Produced at the Lawrence Livermore National Laboratory.
 All rights reserved. See details in the file axom/LICENSE.
 
@@ -14,8 +14,8 @@ The Axom development team is comprised of:
 
 Rich Hornung (hornung1@llnl.gov)
 Arlie Capps (capps2@llnl.gov)
-Ben Corbett (corbett5@llnl.gov)
 Noah Elliott (elliott22@llnl.gov)
+Brian Han (han12@llnl.gov)
 Cyrus Harrison (harrison37@llnl.gov)
 Lee Taylor (taylor16@llnl.gov)
 Kenny Weiss (kweiss@llnl.gov)

RELEASE-NOTES.md

@@ -7,14 +7,48 @@ The format of this file is based on [Keep a Changelog](http://keepachangelog.com
 
 The Axom project release numbers follow [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [Version 0.3.3] - Release date 2020-01-31
+
+### Added
+- Define different execution spaces. This refines and consolidates
+  the execution policy concepts from mint and spin, which are now defined in
+  Axom core, such that they can be used by other components.
+- Added a generic axom::for_all(), which can be used to write simple parallel
+  loops.
+- Added [CLI11](https://github.com/CLIUtils/CLI11) command line parser as a built-in third party library.
+
+### Removed
+
+### Deprecated
+
+### Changed
+- Updated Conduit to v0.5.1
+- Updated RAJA to v0.11.0
+- Updated Umpire to v2.1.0, which, natively handles zero byte re-allocations consistently. Workaround
+  for older releases of Umpire is in place for backwards compatibility. 
+- Updated BLT to develop (f0ab9a4) as of Jan 15, 2020
+- Set CUDA_SEPARABLE_COMPILATION globally instead of just in a few components.
+- Reduced verbosity of quest's InOutOctree in cases where query point lies on surface.
+- Changed semantics of ``axom::reallocate(_, 0)`` to always return a valid pointer.
+  This matches the semantics of Umpire's ``reallocate(_, 0)``.
+  Note: Umpire's PR-292 fixed a bug in its handling of this case and Axom
+  includes a workaround to get the new behavior until we upgrade to Umpire v2.0+.
+
+### Fixed
+- Fixed a bug in ``convert_sidre_protocol`` example. Data truncation functionality now
+  works properly when multiple Views point to the same data.
+
+### Known Bugs
+
+
 ## [Version 0.3.2] - Release date 2019-09-22
 
 ### Added
 - Added support in Mint for reading and writing an unstructured mesh in the [SU2 Mesh file format].
-  This includes support for both single and mixed cell type topology unstructured mesh types.   
+  This includes support for both single and mixed cell type topology unstructured mesh types.
 - Added a new option to enable/disable use of CUB, AXOM_USE_CUB, which is disabled by default. This
   allows to disable CUB to circumvent issues encountered with the device linker.
-- Added a BezierCurve primitive type to primal. A new ``intersect`` operator was also added to 
+- Added a BezierCurve primitive type to primal. A new ``intersect`` operator was also added to
   compute the intersection points between a pair of Bezier curves of arbitrary order.
 
 ### Removed
@@ -27,7 +61,7 @@ The Axom project release numbers follow [Semantic Versioning](http://semver.org/
 - AXOM_USE_OPENMP is now being set at configure time accordingly instead of
   auto-detected based on whether "_OPENMP" is passed by the compiler. This
   fixes issues where a host code would compile Axom w/out OpenMP, but, use
-  Axom in parts of the code where OpenMP is enabled. 
+  Axom in parts of the code where OpenMP is enabled.
 
 ### Fixed
 - Fixed usage of Umpire's MemoryResourceType enum in Axom. Axom was assuming that
@@ -248,7 +282,8 @@ The Axom project release numbers follow [Semantic Versioning](http://semver.org/
 ### Known Bugs
 -
 
-[Unreleased]:    https://github.com/LLNL/axom/compare/v0.3.2...develop
+[Unreleased]:    https://github.com/LLNL/axom/compare/v0.3.3...develop
+[Version 0.3.3]: https://github.com/LLNL/axom/compare/v0.3.2...v0.3.3
 [Version 0.3.2]: https://github.com/LLNL/axom/compare/v0.3.1...v0.3.2
 [Version 0.3.1]: https://github.com/LLNL/axom/compare/v0.3.0...v0.3.1
 [Version 0.3.0]: https://github.com/LLNL/axom/compare/v0.2.9...v0.3.0

azure-pipelines.yml

@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2017-2019, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2020, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)

config-build.py

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-# Copyright (c) 2017-2019, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2020, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)

host-configs/other/Darwin.cmake

@@ -1,16 +1,13 @@
-# Copyright (c) 2017-2019, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2020, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level COPYRIGHT file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)
-
-###############################################################################
-#
+#------------------------------------------------------------------------------
 # CMake Cache Seed file for OSX machines.
-#
-###############################################################################
+#------------------------------------------------------------------------------
 
-###############################################################################
+#------------------------------------------------------------------------------
 # use clang compilers
-###############################################################################
+#------------------------------------------------------------------------------
 set(CMAKE_C_COMPILER "clang" CACHE PATH "")
 set(CMAKE_CXX_COMPILER "clang++" CACHE PATH "")