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Merge pull request #1296 from LLNL/v0.9.0-rc
v0.9.0 release candidate
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‎.gitlab-ci.yml

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# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
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# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
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# other Axom Project Developers. See the top-level LICENSE file for details.
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#
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# SPDX-License-Identifier: (BSD-3-Clause)
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- ${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} ${EXTRA_OPTIONS}
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- echo -e "\e[0Ksection_end:$(date +%s):src_build_and_test\r\e[0K"
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artifacts:
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expire_in: 2 weeks
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paths:
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- _axom_build_and_test_*/output.log*.txt
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- _axom_build_and_test_*/build-*/output.log*.txt
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- ${ALLOC_COMMAND} python3 scripts/llnl_scripts/build_tpls.py -v --spec="${SPEC} ${EXTRA_SPEC}" --directory=${FULL_BUILD_ROOT}
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- echo -e "\e[0Ksection_end:$(date +%s):full_build_and_test\r\e[0K"
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artifacts:
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expire_in: 2 weeks
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paths:
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- ${FULL_BUILD_ROOT}/${SYS_TYPE}/*/_axom_build_and_test_*/output.log*.txt
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- ${FULL_BUILD_ROOT}/${SYS_TYPE}/*/_axom_build_and_test_*/build-*/output.log*.txt

‎.gitlab/build_lassen.yml

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

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

‎.gitlab/build_rzansel.yml

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# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
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# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
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# other Axom Project Developers. See the top-level LICENSE file for details.
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#
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# SPDX-License-Identifier: (BSD-3-Clause)
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- rzansel
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before_script:
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- module load cuda/11.2.0
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- module load cmake/3.18.0
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- module load cmake/3.21.1
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####
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# Template

‎.gitlab/build_rzgenie.yml

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# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
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# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
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# other Axom Project Developers. See the top-level LICENSE file for details.
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#
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# SPDX-License-Identifier: (BSD-3-Clause)

‎.gitlab/build_tioga.yml

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# Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC and
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# Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC and
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# other Axom Project Developers. See the top-level LICENSE file for details.
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#
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# SPDX-License-Identifier: (BSD-3-Clause)
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.src_build_on_tioga:
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stage: build
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variables:
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ALLOC_COMMAND: "flux mini run --exclusive --time-limit=30m --nodes=1"
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ALLOC_COMMAND: "flux run --queue pci --exclusive --time-limit=30m --nodes=1"
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extends: [.src_build_script, .on_tioga, .src_workflow]
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needs: []
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.full_build_on_tioga:
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stage: build
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variables:
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ALLOC_COMMAND: "flux mini run --exclusive --time-limit=60m --nodes=1"
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ALLOC_COMMAND: "flux run --queue pci --exclusive --time-limit=60m --nodes=1"
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extends: [.full_build_script, .on_tioga, .full_workflow]
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needs: []
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COMPILER: "[email protected]_hip"
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HOST_CONFIG: "tioga-toss_4_x86_64_ib_cray-${COMPILER}.cmake"
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extends: .src_build_on_tioga
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allow_failure: true
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tioga-cce_15_0_1_hip_5_4_3-src:
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variables:
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COMPILER: "[email protected]_hip"
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HOST_CONFIG: "tioga-toss_4_x86_64_ib_cray-${COMPILER}.cmake"
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extends: .src_build_on_tioga
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allow_failure: true
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####
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# Full Build jobs
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SPEC: "%${COMPILER}~openmp+rocm+mfem+c2c"
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EXTRASPEC: "amdgpu_target=gfx90a ^[email protected] ^[email protected] ^[email protected] ^raja~openmp+rocm ^umpire~openmp+rocm ^hdf5 cflags=-Wno-int-conversion"
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allow_failure: true
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tioga-cce_15_0_1_hip_5_4_3-full:
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variables:
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COMPILER: "[email protected]_hip"
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SPEC: "%${COMPILER}~openmp+rocm+mfem+c2c"
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EXTRASPEC: "amdgpu_target=gfx90a ^[email protected] ^[email protected] ^[email protected] ^raja~openmp+rocm ^umpire~openmp+rocm ^hdf5 cflags=-Wno-int-conversion"
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allow_failure: true

‎.mailmap

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@@ -2,6 +2,7 @@ Aaron Black <[email protected]> Aaron C. Black <[email protected]
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Adam J. Kunen <[email protected]> Adam J. Kunen <[email protected]>
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Adrien M. Bernede <[email protected]> Adrien Bernede <[email protected]>
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Aesha Parekh <[email protected]> Aesha Parekh <[email protected]>
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Alan Dayton <[email protected]> Alan Dayton <[email protected]>
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Arlie Capps <[email protected]> Arlie Capps <[email protected]>
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Arlie Capps <[email protected]> Arlie Capps <[email protected]>
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Arlie Capps <[email protected]> Arlie Capps <[email protected]>
@@ -13,6 +14,7 @@ Benjamin Curtice Corbett <[email protected]> Benjamin Curtice Corbett <corbet
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Benjamin Curtice Corbett <[email protected]> Ben Corbett <[email protected]>
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Benjamin Curtice Corbett <[email protected]> Benjamin Corbett <[email protected]>
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Benjamin Curtice Corbett <[email protected]> Ben Corbett <[email protected]>
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Brad J. Whitlock <[email protected]> Brad Whitlock <[email protected]>
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Brian Manh Hien Han <[email protected]> Brian Han <[email protected]>
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Brian Manh Hien Han <[email protected]> Brian Manh Hien Han <[email protected]>
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Brian T.N. Gunney <[email protected]> Brian Gunney <[email protected]>
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Esteban Pauli <[email protected]> Esteban Pauli <[email protected]>
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Evan Taylor Desantola <[email protected]> Evan Taylor DeSantola <[email protected]>
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George Zagaris <[email protected]> George Zagaris <[email protected]>
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Jacob Spainhour <[email protected]> jcs15c <[email protected]>
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Jacob Spainhour <[email protected]> jcs15c <[email protected]>
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Jacob Spainhour <[email protected]> Jacob Spainhour <[email protected]>
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Jacob Spainhour <[email protected]> Jacob Spainhour <[email protected]>
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Jamie A. Bramwell <[email protected]> Jamie Bramwell <[email protected]>
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Joe Hennis <[email protected]> Hennis <[email protected]>
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Joe Hennis <[email protected]> hennis1 <[email protected]>
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Josh Essman <[email protected]> Josh Essman <[email protected]>
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Robert Carson <[email protected]> rcarson3 <[email protected]>
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Robert Cohn <[email protected]> rscohn2 <[email protected]>
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Samuel P. Mish <[email protected]> samuelpmishLLNL <[email protected]>
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Brad J. Whitlock <[email protected]> Brad Whitlock <[email protected]>
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Axom Shared User <[email protected]> Asctoolkit Shared User <[email protected]>
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Axom Shared User <[email protected]> Asctoolkit Shared User <[email protected]>

‎.readthedocs.yml

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os: ubuntu-22.04
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tools:
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apt_packages:
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- ghostscript
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- graphviz
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- texlive-full
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sphinx:

‎.uberenv_config.json

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"package_final_phase": "initconfig",
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"package_source_dir": "../..",
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"spack_url": "https://github.com/spack/spack.git",
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"spack_commit": "44f0708af424cb12dd05dd761de1cdae986ea5cf",
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"spack_commit": "0d92b07dbd30b41bc6f50a61f26bc0056dca5e44",
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"spack_configs_path": "scripts/spack/configs",
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"spack_packages_path": ["scripts/spack/radiuss-spack-configs/packages", "scripts/spack/packages"],
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"spack_concretizer": "clingo",
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"vcpkg_url": "https://github.com/microsoft/vcpkg",
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"vcpkg_commit": "6f7ffeb18f99796233b958aaaf14ec7bd4fb64b2",
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"vcpkg_commit": "c8696863d371ab7f46e213d8f5ca923c4aef2a00",
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"vcpkg_triplet": "x64-windows",
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"vcpkg_ports_path": "scripts/vcpkg_ports"
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}

‎LICENSE

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Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC.
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Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC.
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All rights reserved.
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Redistribution and use in source and binary forms, with or without

‎README.md

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[comment]: # (#################################################################)
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[comment]: # (Copyright 2017-2023, Lawrence Livermore National Security, LLC)
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[comment]: # (Copyright 2017-2024, Lawrence Livermore National Security, LLC)
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[comment]: # (and Axom Project Developers. See the top-level LICENSE file)
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[comment]: # (for details.)
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[comment]: #
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[comment]: # (# SPDX-License-Identifier: BSD-3-Clause)
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[comment]: # (#################################################################)
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# <img src="/share/axom/logo/axom_logo.png?raw=true" width="250" valign="middle" alt="Axom"/>
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# <img src="/share/axom/logo/axom_logo_transparent.png?raw=true" width="250" valign="middle" alt="Axom"/>
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[![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)
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[![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
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License
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-------
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Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC.
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Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC.
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Produced at the Lawrence Livermore National Laboratory.
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Copyrights and patents in the Axom project are retained by contributors.

‎RELEASE

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*******************************************************************************
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Axom: ................................, version 0.8.1
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Axom: ................................, version 0.9.0
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Copyright (c) 2017-2023, Lawrence Livermore National Security, LLC.
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Copyright (c) 2017-2024, Lawrence Livermore National Security, LLC.
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Produced at the Lawrence Livermore National Laboratory.
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All rights reserved. See details in the file axom/LICENSE.
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‎RELEASE-NOTES.md

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[comment]: # (#################################################################)
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[comment]: # (Copyright 2017-2023, Lawrence Livermore National Security, LLC)
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[comment]: # (Copyright 2017-2024, Lawrence Livermore National Security, LLC)
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[comment]: # (and Axom Project Developers. See the top-level LICENSE file)
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[comment]: # (for details.)
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[comment]: #
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2020
## [Unreleased] - Release date yyyy-mm-dd
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## [v0.8.1] - Release date 2023-08-16
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## [Version 0.9.0] - Release date 2024-03-19
23+
24+
### Added
25+
- Primal: Adds a `Quadrilateral` primitive
26+
- Primal: Adds a `compute_bounding_box()` operator for computing the bounding
27+
box of a `Quadrilateral`
28+
- Primal: Adds a `clip()` operator for clipping a tetrahedron against the
29+
half-space defined by a plane
30+
- Primal: Adds a `checkAndFixOrientation()` function to `primal::Tetrahedron`
31+
that swaps the order of vertices if the signed volume of the Tetrahedron is
32+
negative, resulting in the signed volume becoming positive.
33+
- Adds `FlatMap`, a generic key-value store which aims for drop-in compatibility
34+
with `std::unordered_map`, but utilizes an open-addressing design.
35+
- Adds support for device-side use of `Array::push_back()` and `Array::emplace_back()`.
36+
- Adds initial support for using Slic streams with tags
37+
- Adds an example that finds intersection candidate pairs between two Silo
38+
hexahedral meshes using either a BVH or Implicit Grid spatial index
39+
- Quest: Adds `setTetPredFromBoundingBox()` and `setTetPred()` functions to
40+
`quest::ProEReader` and `PProEReader` that set a tet predicate, allowing
41+
user code to read in a subset of a Pro/E ASCII tetrahedron mesh file.
42+
43+
### Changed
44+
- `MarchingCubes` has optimizations to improve GPU performance, particularly for
45+
repeated computations. The constructor has changed and a new `setMesh` method
46+
is added to set (or change) the mesh. New accessors present output data
47+
without moving them from device to host. These accessors are an interim
48+
solution and likely to be updated in the future.
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- `DistributedClosestPoint` outputs are now controlled by the `setOutput` method.
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- `MarchingCubes` allows user to select the underlying data-parallel implementation
51+
- `fullParallel` works best on GPUs.
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- `hybridParallel` reduces the amount of data processed and works best with
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`MarchingCubesRuntimePolicy::seq`.
54+
- `byPolicy` (the default) selects the implementation based on the runtime policy.
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- `MarchingCubes` and `DistributedClosestPoint` classes identify domains by their
56+
`state/domain_id` parameters if provided, or the local iteration index if not.
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- `MarchingCubes` and `DistributedClosestPoint` classes changed from requiring the Blueprint
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coordset name to requiring the Blueprint topology name. The changed interface methods are:
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- `DistributedClosestPoint::setObjectMesh`
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- `DistributedClosestPoint::computeClosestPoints`
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- `MarchingCubes::MarchingCubes`
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- `MarchingCubesSingleDomain::MarchingCubesSingleDomain`
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- Primal: `Polyhedron::volume()` function changed from returning a signed
64+
volume to an unsigned volume. The added `Polyhedron::signedVolume()` function
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returns the signed volume.
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- Primal: `intersection_volume()` operators changed from returning a signed
67+
volume to an unsigned volume.
68+
- Primal's `BoundingBox::contains(BoundingBox)` now returns `true` when the input is empty
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- Renamed axom's bit utility functions to conform to `C++20` standard: `popCount() -> popcount()`,
70+
`trailingZeros() -> countr_zero()` and `leadingZeros() -> countl_zero()`
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- Renamed `axom::utilities::swapEndian() -> byteswap()` to conform to `C++23` standard
72+
73+
### Fixed
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- quest's `SamplingShaper` now properly handles material names containing underscores
75+
- quest's `SamplingShaper` can now be used with an mfem that is configured for (GPU) devices
76+
- 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.
77+
- 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)
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- Fixed a bug in the bounds checks for `primal::clip(Triangle, BoundingBox)`
79+
- Fixed a bug when loading Sidre groups with attributes that already exist
80+
- Fixed `std::locale` error when when compiling `src/axom/core/utilities/System.cpp` using nvcc
81+
- Include `cstdint` for higher gcc version support (e.g. gcc-13)
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- Fixed several memory leaks in `axom::Array`, `quest::Shaping` and `sidre::MFEMSidreDataCollection`
83+
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## [Version 0.8.1] - Release date 2023-08-16
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### Changed
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- 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/
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- Fixed MFEMSidreDataCollection finite element space bug
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- Various fixes to CMake machinery
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## [v0.8.0] - Release date 2023-07-26
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## [Version 0.8.0] - Release date 2023-07-26
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### Added
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- 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.
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- Use this section in case of vulnerabilities
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[Unreleased]: https://github.com/LLNL/axom/compare/v0.8.1...develop
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[Unreleased]: https://github.com/LLNL/axom/compare/v0.9.0...develop
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[Version 0.9.0]: https://github.com/LLNL/axom/compare/v0.8.1...v0.9.0
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[Version 0.8.1]: https://github.com/LLNL/axom/compare/v0.8.0...v0.8.1
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[Version 0.8.0]: https://github.com/LLNL/axom/compare/v0.7.0...v0.8.0
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[Version 0.7.0]: https://github.com/LLNL/axom/compare/v0.6.1...v0.7.0

‎azure-pipelines.yml

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

‎config-build.py

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

‎data

Submodule data updated 29 files

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