Merge pull request #1296 from LLNL/v0.9.0-rc

v0.9.0 release candidate
LLNL · Mar 20, 2024 · 5f53159 · 5f53159
2 parents 0da8a5b + 1dda8f1
commit 5f53159
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diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -1,4 +1,4 @@
-# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level LICENSE file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)
@@ -36,6 +36,7 @@ stages:
     - ${ALLOC_COMMAND} ${ASSIGN_ID} python3 scripts/llnl_scripts/build_src.py -v --host-config ${HOST_CONFIG} --extra-cmake-options '-DENABLE_DOCS=OFF ${EXTRA_CMAKE_OPTIONS}' --build-type ${BUILD_TYPE:-Debug} ${EXTRA_OPTIONS}
     - echo -e "\e[0Ksection_end:$(date +%s):src_build_and_test\r\e[0K"
   artifacts:
+    expire_in: 2 weeks
     paths:
       - _axom_build_and_test_*/output.log*.txt
       - _axom_build_and_test_*/build-*/output.log*.txt
@@ -48,6 +49,7 @@ stages:
     - ${ALLOC_COMMAND} python3 scripts/llnl_scripts/build_tpls.py -v --spec="${SPEC} ${EXTRA_SPEC}" --directory=${FULL_BUILD_ROOT}
     - echo -e "\e[0Ksection_end:$(date +%s):full_build_and_test\r\e[0K"
   artifacts:
+    expire_in: 2 weeks
     paths:
       - ${FULL_BUILD_ROOT}/${SYS_TYPE}/*/_axom_build_and_test_*/output.log*.txt
       - ${FULL_BUILD_ROOT}/${SYS_TYPE}/*/_axom_build_and_test_*/build-*/output.log*.txt

diff --git a/.gitlab/build_lassen.yml b/.gitlab/build_lassen.yml
@@ -1,12 +1,11 @@
-# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level LICENSE file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)
 
 ####
 # This is the share configuration of jobs for lassen
 .on_lassen:
-  variables:
   tags:
     - shell
     - lassen
@@ -23,14 +22,14 @@
 .src_build_on_lassen:
   stage: build
   variables:
-    ALLOC_COMMAND: "lalloc 1 -W 25 -q pdebug -alloc_flags atsdisable"
+    ALLOC_COMMAND: "lalloc 1 -W 25 -q pci -alloc_flags atsdisable"
   extends: [.src_build_script, .on_lassen, .src_workflow]
   needs: []
 
 .full_build_on_lassen:
   stage: build
   variables:
-    ALLOC_COMMAND: "lalloc 1 -W 45 -q pdebug -alloc_flags atsdisable"
+    ALLOC_COMMAND: "lalloc 1 -W 45 -q pci -alloc_flags atsdisable"
   extends: [.full_build_script, .on_lassen, .full_workflow]
   needs: []
 

diff --git a/.gitlab/build_quartz.yml b/.gitlab/build_quartz.yml
@@ -1,4 +1,4 @@
-# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level LICENSE file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)
@@ -10,7 +10,7 @@
     - shell
     - quartz
   rules:
-    - if: '$CI_COMMIT_BRANCH =~ /_qnone/ || $ON_RUBY == "OFF"' #run except if ...
+    - if: '$CI_COMMIT_BRANCH =~ /_qnone/ || $ON_QUARTZ == "OFF"' #run except if ...
       when: never
     - if: '$CI_JOB_NAME =~ /quartz_release/'
       when: always
@@ -26,9 +26,7 @@ quartz_allocate:
   extends: [.on_quartz, .src_workflow]
   stage: allocate
   script:
-    # Use when ellastic ci is on quartz or we go back to ruby
-    #- salloc --reservation=ci --qos=ci_ruby -N 1 -c 36 -t 60 --no-shell --job-name=${PROJECT_ALLOC_NAME}
-    - salloc -N 1 -c 36 -t 60 -p pdebug --no-shell --job-name=${PROJECT_ALLOC_NAME}
+    - salloc -N 1 -c 36 -t 60 --res=ci --no-shell --job-name=${PROJECT_ALLOC_NAME}
   needs: []
 
 ####
@@ -48,17 +46,13 @@ quartz_release:
 .src_build_on_quartz:
   stage: build
   variables:
-    # Use when ellastic ci is on quartz or we go back to ruby
-    # ALLOC_COMMAND: "srun --reservation=ci --qos=ci_ruby -t 60 -N 1 "
     ALLOC_COMMAND: "srun -t 60 -N 1 -p pdebug"
   extends: [.src_build_script, .on_quartz, .src_workflow]
   needs: [quartz_allocate]
 
 .full_build_on_quartz:
   stage: build
   variables:
-    # Use when ellastic ci is on quartz or we go back to ruby
-    # ALLOC_COMMAND: "srun --reservation=ci --qos=ci_ruby -t 60 -N 1 "
     ALLOC_COMMAND: "srun -t 60 -N 1 -p pdebug"
   extends: [.full_build_script, .on_quartz, .full_workflow]
   needs: []

diff --git a/.gitlab/build_rzansel.yml b/.gitlab/build_rzansel.yml
@@ -1,4 +1,4 @@
-# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level LICENSE file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)
@@ -12,7 +12,7 @@
     - rzansel
   before_script:
     - module load cuda/11.2.0
-    - module load cmake/3.18.0
+    - module load cmake/3.21.1
 
 ####
 # Template

diff --git a/.gitlab/build_rzgenie.yml b/.gitlab/build_rzgenie.yml
@@ -1,4 +1,4 @@
-# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level LICENSE file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)

diff --git a/.gitlab/build_tioga.yml b/.gitlab/build_tioga.yml
@@ -1,4 +1,4 @@
-# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level LICENSE file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)
@@ -21,14 +21,14 @@
 .src_build_on_tioga:
   stage: build
   variables:
-    ALLOC_COMMAND: "flux mini run --exclusive --time-limit=30m --nodes=1"
+    ALLOC_COMMAND: "flux run --queue pci --exclusive --time-limit=30m --nodes=1"
   extends: [.src_build_script, .on_tioga, .src_workflow]
   needs: []
 
 .full_build_on_tioga:
   stage: build
   variables:
-    ALLOC_COMMAND: "flux mini run --exclusive --time-limit=60m --nodes=1"
+    ALLOC_COMMAND: "flux run --queue pci --exclusive --time-limit=60m --nodes=1"
   extends: [.full_build_script, .on_tioga, .full_workflow]
   needs: []
 
@@ -39,14 +39,6 @@ tioga-clang_16_0_0_hip_5_6_0-src:
     COMPILER: "[email protected]_hip"
     HOST_CONFIG: "tioga-toss_4_x86_64_ib_cray-${COMPILER}.cmake"
   extends: .src_build_on_tioga
-  allow_failure: true
-
-tioga-cce_15_0_1_hip_5_4_3-src:
-  variables:
-    COMPILER: "[email protected]_hip"
-    HOST_CONFIG: "tioga-toss_4_x86_64_ib_cray-${COMPILER}.cmake"
-  extends: .src_build_on_tioga
-  allow_failure: true
 
 ####
 # Full Build jobs
@@ -56,12 +48,3 @@ tioga-clang_16_0_0_hip_5_6_0-full:
     SPEC: "%${COMPILER}~openmp+rocm+mfem+c2c"
     EXTRASPEC: "amdgpu_target=gfx90a ^[email protected] ^[email protected] ^[email protected] ^raja~openmp+rocm ^umpire~openmp+rocm ^hdf5 cflags=-Wno-int-conversion"
   extends: .full_build_on_tioga
-  allow_failure: true
-
-tioga-cce_15_0_1_hip_5_4_3-full:
-  variables:
-    COMPILER: "[email protected]_hip"
-    SPEC: "%${COMPILER}~openmp+rocm+mfem+c2c"
-    EXTRASPEC: "amdgpu_target=gfx90a ^[email protected] ^[email protected] ^[email protected] ^raja~openmp+rocm ^umpire~openmp+rocm ^hdf5 cflags=-Wno-int-conversion"
-  extends: .full_build_on_tioga
-  allow_failure: true
diff --git a/.mailmap b/.mailmap
@@ -2,6 +2,7 @@ Aaron Black <[email protected]>                  Aaron C. Black <[email protected]
 Adam J. Kunen <[email protected]>                 Adam J. Kunen <[email protected]>
 Adrien M. Bernede <[email protected]>           Adrien Bernede <[email protected]>
 Aesha Parekh <[email protected]>           Aesha Parekh <[email protected]>
+Alan Dayton <[email protected]>                  Alan Dayton <[email protected]>
 Arlie Capps <[email protected]>                   Arlie Capps <[email protected]>
 Arlie Capps <[email protected]>                   Arlie Capps <[email protected]>
 Arlie Capps <[email protected]>                   Arlie Capps <[email protected]>
@@ -13,6 +14,7 @@ Benjamin Curtice Corbett <[email protected]>    Benjamin Curtice Corbett <corbet
 Benjamin Curtice Corbett <[email protected]>    Ben Corbett <[email protected]>
 Benjamin Curtice Corbett <[email protected]>    Benjamin Corbett <[email protected]>
 Benjamin Curtice Corbett <[email protected]>    Ben Corbett <[email protected]>
+Brad J. Whitlock <[email protected]>           Brad Whitlock <[email protected]>
 Brian Manh Hien Han <[email protected]>            Brian Han <[email protected]>          
 Brian Manh Hien Han <[email protected]>            Brian Manh Hien Han <[email protected]>
 Brian T.N. Gunney <[email protected]>            Brian Gunney <[email protected]>
@@ -24,7 +26,10 @@ Daniel Taller <[email protected]>                Danny Taller <66029857+dtaller@u
 Esteban Pauli <[email protected]>                 Esteban Pauli <[email protected]>
 Evan Taylor Desantola <[email protected]>     Evan Taylor DeSantola <[email protected]>
 George Zagaris <[email protected]>              George Zagaris <[email protected]>
-Jacob Spainhour <[email protected]>           jcs15c <[email protected]>
+Jacob Spainhour <[email protected]>  jcs15c <[email protected]>
+Jacob Spainhour <[email protected]>  Jacob Spainhour <[email protected]>
+Jacob Spainhour <[email protected]>  Jacob Spainhour <[email protected]>
+Jamie A. Bramwell <[email protected]>          Jamie Bramwell <[email protected]>
 Joe Hennis <[email protected]>                   Hennis <[email protected]>
 Joe Hennis <[email protected]>                   hennis1 <[email protected]>
 Josh Essman <[email protected]>                  Josh Essman <[email protected]>
@@ -59,7 +64,6 @@ Robert Carson <[email protected]>              Robert <[email protected]>
 Robert Carson <[email protected]>              rcarson3 <[email protected]>
 Robert Cohn <[email protected]>           rscohn2 <[email protected]>
 Samuel P. Mish <[email protected]>                 samuelpmishLLNL <[email protected]>
-Brad J. Whitlock <[email protected]>           Brad Whitlock <[email protected]>
 
 Axom Shared User <[email protected]>            Asctoolkit Shared User <[email protected]>
 Axom Shared User <[email protected]>            Asctoolkit Shared User <[email protected]>

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -10,6 +10,10 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
+  apt_packages:
+    - ghostscript
+    - graphviz
+    - texlive-full
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

diff --git a/.uberenv_config.json b/.uberenv_config.json
@@ -4,12 +4,12 @@
 "package_final_phase": "initconfig",
 "package_source_dir": "../..",
 "spack_url": "https://github.com/spack/spack.git",
-"spack_commit": "44f0708af424cb12dd05dd761de1cdae986ea5cf",
+"spack_commit": "0d92b07dbd30b41bc6f50a61f26bc0056dca5e44",
 "spack_configs_path": "scripts/spack/configs",
 "spack_packages_path": ["scripts/spack/radiuss-spack-configs/packages", "scripts/spack/packages"],
 "spack_concretizer": "clingo",
 "vcpkg_url": "https://github.com/microsoft/vcpkg",
-"vcpkg_commit": "6f7ffeb18f99796233b958aaaf14ec7bd4fb64b2",
+"vcpkg_commit": "c8696863d371ab7f46e213d8f5ca923c4aef2a00",
 "vcpkg_triplet": "x64-windows",
 "vcpkg_ports_path": "scripts/vcpkg_ports"
 }
diff --git a/LICENSE b/LICENSE
@@ -1,4 +1,4 @@
-Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC.
+Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/README.md b/README.md
@@ -1,13 +1,13 @@
 [comment]: # (#################################################################)
-[comment]: # (Copyright 2017-2023, Lawrence Livermore National Security, LLC)
+[comment]: # (Copyright 2017-2024, Lawrence Livermore National Security, LLC)
 [comment]: # (and Axom Project Developers. See the top-level LICENSE file)
 [comment]: # (for details.)
 [comment]: #
 [comment]: # (# SPDX-License-Identifier: BSD-3-Clause)
 [comment]: # (#################################################################)
 
 
-# <img src="/share/axom/logo/axom_logo.png?raw=true" width="250" valign="middle" alt="Axom"/>
+# <img src="/share/axom/logo/axom_logo_transparent.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)
@@ -56,7 +56,7 @@ Thanks to all of Axom's
 License
 -------
 
-Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC. 
+Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC. 
 Produced at the Lawrence Livermore National Laboratory.
 
 Copyrights and patents in the Axom project are retained by contributors.

diff --git a/RELEASE b/RELEASE
@@ -1,8 +1,8 @@
 *******************************************************************************
 
-Axom: ................................, version 0.8.1
+Axom: ................................, version 0.9.0
 
-Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC. 
+Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC. 
 Produced at the Lawrence Livermore National Laboratory.
 All rights reserved. See details in the file axom/LICENSE.
 

diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
@@ -1,6 +1,6 @@
 
 [comment]: # (#################################################################)
-[comment]: # (Copyright 2017-2023, Lawrence Livermore National Security, LLC)
+[comment]: # (Copyright 2017-2024, Lawrence Livermore National Security, LLC)
 [comment]: # (and Axom Project Developers. See the top-level LICENSE file)
 [comment]: # (for details.)
 [comment]: #
@@ -19,7 +19,69 @@ The Axom project release numbers follow [Semantic Versioning](http://semver.org/
 
 ## [Unreleased] - Release date yyyy-mm-dd
 
-## [v0.8.1] - Release date 2023-08-16
+## [Version 0.9.0] - Release date 2024-03-19
+
+### Added
+- Primal: Adds a `Quadrilateral` primitive
+- Primal: Adds a `compute_bounding_box()` operator for computing the bounding
+  box of a `Quadrilateral`
+- Primal: Adds a `clip()` operator for clipping a tetrahedron against the
+  half-space defined by a plane
+- Primal: Adds a `checkAndFixOrientation()` function to `primal::Tetrahedron`
+  that swaps the order of vertices if the signed volume of the Tetrahedron is
+  negative, resulting in the signed volume becoming positive.
+- Adds `FlatMap`, a generic key-value store which aims for drop-in compatibility
+  with `std::unordered_map`, but utilizes an open-addressing design.
+- Adds support for device-side use of `Array::push_back()` and `Array::emplace_back()`.
+- Adds initial support for using Slic streams with tags
+- Adds an example that finds intersection candidate pairs between two Silo
+  hexahedral meshes using either a BVH or Implicit Grid spatial index
+- Quest: Adds `setTetPredFromBoundingBox()` and `setTetPred()` functions to
+  `quest::ProEReader` and `PProEReader` that set a tet predicate, allowing
+  user code to read in a subset of a Pro/E ASCII tetrahedron mesh file.
+
+### Changed
+- `MarchingCubes` has optimizations to improve GPU performance, particularly for
+  repeated computations.  The constructor has changed and a new `setMesh` method
+  is added to set (or change) the mesh.  New accessors present output data
+  without moving them from device to host.  These accessors are an interim
+  solution and likely to be updated in the future.
+- `DistributedClosestPoint` outputs are now controlled by the `setOutput` method.
+- `MarchingCubes` allows user to select the underlying data-parallel implementation
+  - `fullParallel` works best on GPUs.
+  - `hybridParallel` reduces the amount of data processed and works best with
+     `MarchingCubesRuntimePolicy::seq`.
+  - `byPolicy` (the default) selects the implementation based on the runtime policy.
+- `MarchingCubes` and `DistributedClosestPoint` classes identify domains by their
+  `state/domain_id` parameters if provided, or the local iteration index if not.
+- `MarchingCubes` and `DistributedClosestPoint` classes changed from requiring the Blueprint
+  coordset name to requiring the Blueprint topology name.  The changed interface methods are:
+  - `DistributedClosestPoint::setObjectMesh`
+  - `DistributedClosestPoint::computeClosestPoints`
+  - `MarchingCubes::MarchingCubes`
+  - `MarchingCubesSingleDomain::MarchingCubesSingleDomain`
+- Primal: `Polyhedron::volume()` function changed from returning a signed
+  volume to an unsigned volume. The added `Polyhedron::signedVolume()` function
+  returns the signed volume.
+- Primal: `intersection_volume()` operators changed from returning a signed
+  volume to an unsigned volume.
+- Primal's `BoundingBox::contains(BoundingBox)`  now returns `true` when the input is empty
+- Renamed axom's bit utility functions to conform to `C++20` standard: `popCount() -> popcount()`, 
+  `trailingZeros() -> countr_zero()` and `leadingZeros() -> countl_zero()`
+- Renamed `axom::utilities::swapEndian() -> byteswap()` to conform to `C++23` standard
+
+### Fixed
+- quest's `SamplingShaper` now properly handles material names containing underscores
+- quest's `SamplingShaper` can now be used with an mfem that is configured for (GPU) devices
+- primal's `Polygon` area computation in 3D previously only worked when the polygon was aligned with the XY-plane. It now works for arbitrary polygons.
+- Upgrades our `vcpkg` usage for automated Windows builds of our TPLs to its [2023.12.12 release](https://github.com/microsoft/vcpkg/releases/tag/2023.12.12)
+- Fixed a bug in the bounds checks for `primal::clip(Triangle, BoundingBox)`
+- Fixed a bug when loading Sidre groups with attributes that already exist
+- Fixed `std::locale` error when when compiling `src/axom/core/utilities/System.cpp` using nvcc
+- Include `cstdint` for higher gcc version support (e.g. gcc-13)
+- Fixed several memory leaks in `axom::Array`, `quest::Shaping` and `sidre::MFEMSidreDataCollection`
+
+## [Version 0.8.1] - Release date 2023-08-16
 
 ### Changed
 - Updates to [RAJA version 2023.06.0][https://github.com/LLNL/RAJA/releases/tag/v2023.06.0]
@@ -30,7 +92,7 @@ The Axom project release numbers follow [Semantic Versioning](http://semver.org/
 - Fixed MFEMSidreDataCollection finite element space bug
 - Various fixes to CMake machinery
 
-## [v0.8.0] - Release date 2023-07-26
+## [Version 0.8.0] - Release date 2023-07-26
 
 ### Added
 - Adds MarchingCubes class implementing the marching cubes algorithm for surface detection.
@@ -969,7 +1031,8 @@ fractions for the associated materials must be supplied before shaping.
 - Use this section in case of vulnerabilities
 
 
-[Unreleased]:    https://github.com/LLNL/axom/compare/v0.8.1...develop
+[Unreleased]:    https://github.com/LLNL/axom/compare/v0.9.0...develop
+[Version 0.9.0]: https://github.com/LLNL/axom/compare/v0.8.1...v0.9.0
 [Version 0.8.1]: https://github.com/LLNL/axom/compare/v0.8.0...v0.8.1
 [Version 0.8.0]: https://github.com/LLNL/axom/compare/v0.7.0...v0.8.0
 [Version 0.7.0]: https://github.com/LLNL/axom/compare/v0.6.1...v0.7.0

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level LICENSE file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)
@@ -9,8 +9,8 @@ variables:
   DO_BUILD: 'yes'
   DO_TEST: 'yes'
   DO_CLEAN: 'no'
-  CLANG10_IMAGENAME: 'axom/tpls:clang-10_07-26-23_22h-58m'
-  GCC11_IMAGENAME: 'axom/tpls:gcc-11_07-26-23_22h-58m'
+  CLANG10_IMAGENAME: 'axom/tpls:clang-10_03-07-24_19h-20m'
+  GCC11_IMAGENAME: 'axom/tpls:gcc-11_03-07-24_19h-20m'
   system.debug: false
 
 jobs:

diff --git a/config-build.py b/config-build.py
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
+# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
 # other Axom Project Developers. See the top-level LICENSE file for details.
 #
 # SPDX-License-Identifier: (BSD-3-Clause)

diff --git a/data b/data