Merge pull request #697 from LLNL/v0.6.0-RC

V0.6.0 rc

.gitignore

@@ -16,3 +16,4 @@ tpl_dirs_summary.json
 *.vscode*
 uberenv_libs
 *_build*
+.idea

.gitlab-ci.yml

@@ -8,6 +8,7 @@ variables:
   PROJECT_ALLOC_NAME: ${CI_PROJECT_NAME}_ci_${CI_PIPELINE_ID}
   BUILD_ROOT: ${CI_PROJECT_DIR}
   FULL_BUILD_ROOT: ${CI_BUILDS_DIR}/axom/${CI_JOB_NAME}
+  SLURM_OVERLAP: 1
 
 stages:
   - allocate
@@ -30,10 +31,9 @@ stages:
     - JOBID=$(if [[ "$SYS_TYPE" == "toss_3_x86_64_ib" ]]; then squeue -h --name=${PROJECT_ALLOC_NAME} --format=%A; fi)
     - ASSIGN_ID=$(if [[ -n "${JOBID}" ]]; then echo "--jobid=${JOBID}"; fi)
     # BUILD + TEST
-    - echo -e "section_start:$(date +%s):src_build_and_test\r\e[0K
-      Source Build and Test ${CI_PROJECT_NAME}"
-    - ${ALLOC_COMMAND} python3 scripts/llnl_scripts/build_src.py -v --host-config ${HOST_CONFIG} --extra-cmake-options -DENABLE_DOCS=OFF
-    - echo -e "section_end:$(date +%s):src_build_and_test\r\e[0K"
+    - echo -e "\e[0Ksection_start:$(date +%s):src_build_and_test\r\e[0KSource Build and Test ${CI_PROJECT_NAME}"
+    - ${ALLOC_COMMAND} ${ASSIGN_ID} python3 scripts/llnl_scripts/build_src.py -v --host-config ${HOST_CONFIG} --extra-cmake-options -DENABLE_DOCS=OFF
+    - echo -e "\e[0Ksection_end:$(date +%s):src_build_and_test\r\e[0K"
   artifacts:
     paths:
       - _axom_build_and_test_*/output.log*.txt
@@ -43,10 +43,9 @@ stages:
 
 .full_build_script:
   script:
-    - echo -e "section_start:$(date +%s):full_build_and_test\r\e[0K
-      Full Build and Test ${CI_PROJECT_NAME}"
+    - echo -e "\e[0Ksection_start:$(date +%s):full_build_and_test\r\e[0KFull Build and Test ${CI_PROJECT_NAME}"
     - ${ALLOC_COMMAND} python3 scripts/llnl_scripts/build_tpls.py -v --spec="${SPEC} ${EXTRA_SPEC}" --directory=${FULL_BUILD_ROOT}
-    - echo -e "section_end:$(date +%s):full_build_and_test\r\e[0K"
+    - echo -e "\e[0Ksection_end:$(date +%s):full_build_and_test\r\e[0K"
   artifacts:
     paths:
       - ${FULL_BUILD_ROOT}/${SYS_TYPE}/*/_axom_build_and_test_*/output.log*.txt

.gitlab/build_ruby.yml

@@ -44,14 +44,14 @@ ruby_release:
 .src_build_on_ruby:
   stage: build
   variables:
-    ALLOC_COMMAND: "srun -p pdebug -t 30 -N 1 ${ASSIGN_ID}"
+    ALLOC_COMMAND: "srun -p pdebug -t 60 -N 1 "
   extends: [.src_build_script, .on_ruby, .src_workflow]
   needs: [ruby_allocate]
 
 .full_build_on_ruby:
   stage: build
   variables:
-    ALLOC_COMMAND: "srun -p pdebug -t 60 -N 1"
+    ALLOC_COMMAND: "srun -p pdebug -t 60 -N 1 "
   extends: [.full_build_script, .on_ruby, .full_workflow]
   needs: []
 

.gitlab/build_rzansel.yml

@@ -0,0 +1,103 @@
+# Copyright (c) 2017-2021, 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 rzansel
+.on_rzansel:
+  variables:
+  tags:
+    - shell
+    - rzansel
+  before_script:
+    - module load cmake/3.14.5
+
+####
+# Load required CUDA module
+.with_cuda:
+  before_script:
+    - module load cuda/10.1.243
+
+####
+# Template
+.src_build_on_rzansel:
+  stage: build
+  variables:
+    ALLOC_COMMAND: "lalloc 1 -W 25 -q pdebug"
+  extends: [.src_build_script, .on_rzansel, .src_workflow]
+  needs: []
+
+.full_build_on_rzansel:
+  stage: build
+  variables:
+    ALLOC_COMMAND: "lalloc 1 -W 45 -q pdebug"
+  extends: [.full_build_script, .on_rzansel, .full_workflow]
+  needs: []
+
+####
+# PR Build jobs
+rzansel-clang_8_0_1_nvcc_xlf-src:
+  variables:
+    COMPILER: "clang@8.0.1_nvcc_xlf"
+    HOST_CONFIG: "rzansel-klee-${COMPILER}.cmake"
+  extends: [.src_build_on_rzansel, .with_cuda]
+
+rzansel-clang_9_0_0_upstream_xlf-src:
+  variables:
+    COMPILER: "clang@9.0.0_upstream_xlf"
+    HOST_CONFIG: "rzansel-blueos_3_ppc64le_ib_p9-${COMPILER}.cmake"
+  extends: [.src_build_on_rzansel]
+
+rzansel-gcc_7_3_1-src:
+  variables:
+    COMPILER: "gcc@7.3.1"
+    HOST_CONFIG: "rzansel-blueos_3_ppc64le_ib_p9-${COMPILER}.cmake"
+  extends: [.src_build_on_rzansel]
+
+rzansel-xl_16_1_1-src:
+  variables:
+    COMPILER: "xl@16.1.1_coral"
+    HOST_CONFIG: "rzansel-blueos_3_ppc64le_ib_p9-${COMPILER}.cmake"
+  extends: [.src_build_on_rzansel]
+
+rzansel-xl_16_1_1_nvcc-src:
+  variables:
+    COMPILER: "xl@16.1.1_nvcc"
+    HOST_CONFIG: "rzansel-blueos_3_ppc64le_ib_p9-${COMPILER}.cmake"
+  extends: [.src_build_on_rzansel, .with_cuda]
+
+
+####
+# Full Build jobs
+rzansel-clang_8_0_1_nvcc_xlf-full:
+  variables:
+    COMPILER: "clang@8.0.1_nvcc_xlf"
+    SPEC: "%${COMPILER}+mfem+cuda~openmp"
+    EXTRA_SPEC: "cuda_arch=70"
+  extends: [.full_build_on_rzansel, .with_cuda]
+
+rzansel-clang_9_0_0_upstream_xlf-full:
+  variables:
+    COMPILER: "clang@9.0.0_upstream_xlf"
+    SPEC: "%${COMPILER}+mfem~openmp"
+  extends: [.full_build_on_rzansel]
+
+rzansel-gcc_7_3_1-full:
+  variables:
+    COMPILER: "gcc@7.3.1"
+    SPEC: "%${COMPILER}+mfem"
+  extends: [.full_build_on_rzansel]
+
+rzansel-xl_16_1_1_coral-full:
+  variables:
+    COMPILER: "xl@16.1.1_coral"
+    SPEC: "%${COMPILER}+mfem~openmp~cpp14"
+  extends: [.full_build_on_rzansel]
+
+rzansel-xl_16_1_1_nvcc-full:
+  variables:
+    COMPILER: "xl@16.1.1_nvcc"
+    SPEC: "%${COMPILER}+mfem+cuda~openmp~cpp14"
+    EXTRA_SPEC: "cuda_arch=70"
+  extends: [.full_build_on_rzansel, .with_cuda]

.gitlab/build_rzgenie.yml

@@ -0,0 +1,96 @@
+# Copyright (c) 2017-2021, 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 shared configuration of jobs for rzgenie
+.on_rzgenie:
+  tags:
+    - shell
+    - rzgenie
+  before_script:
+    - module load cmake/3.14.5
+
+
+####
+# Template
+.src_build_on_rzgenie:
+  stage: build
+  variables:
+    ALLOC_COMMAND: "salloc -p pdebug -t 30 -N 1 -n36 srun --interactive -n1"
+  extends: [.src_build_script, .on_rzgenie, .src_workflow]
+  needs: []
+
+.full_build_on_rzgenie:
+  stage: build
+  variables:
+    ALLOC_COMMAND: "srun -p pdebug -t 60 -N 1 -n 1"
+  extends: [.full_build_script, .on_rzgenie, .full_workflow]
+  needs: []
+
+####
+# PR Build jobs
+rzgenie-clang_10_0_0-src:
+  variables:
+    COMPILER: "clang@10.0.0"
+    HOST_CONFIG: "rzgenie-klee-clang@10.cmake"
+  extends: .src_build_on_rzgenie
+
+rzgenie-gcc_8_1_0-src:
+  variables:
+    COMPILER: "gcc@8.1.0"
+    HOST_CONFIG: "rzgenie-toss_3_x86_64_ib-${COMPILER}.cmake"
+  extends: .src_build_on_rzgenie
+
+# disabled due to time limit
+# rzgenie-intel_18_0_2-src:
+#   variables:
+#     COMPILER: "intel@18.0.2"
+#     HOST_CONFIG: "rzgenie-toss_3_x86_64_ib-${COMPILER}.cmake"
+#   extends: .src_build_on_rzgenie
+
+rzgenie-intel_19_0_4-src:
+  variables:
+    COMPILER: "intel@19.0.4"
+    HOST_CONFIG: "rzgenie-toss_3_x86_64_ib-${COMPILER}.cmake"
+  extends: .src_build_on_rzgenie
+
+
+####
+# Full Build jobs
+rzgenie-clang_10_0_0-full:
+  variables:
+    COMPILER: "clang@10.0.0"
+    SPEC: "%${COMPILER}+mfem"
+  extends: .full_build_on_rzgenie
+
+rzgenie-clang_9_0_0-full:
+  variables:
+    COMPILER: "clang@9.0.0"
+    SPEC: "%${COMPILER}+mfem"
+  extends: .full_build_on_rzgenie
+
+rzgenie-gcc_8_1_0-full:
+  variables:
+    COMPILER: "gcc@8.1.0"
+    SPEC: "%${COMPILER}+mfem"
+  extends: .full_build_on_rzgenie
+
+rzgenie-gcc_8_1_no_fortran-full:
+  variables:
+    COMPILER: "gcc@8.1_no_fortran"
+    SPEC: "%${COMPILER}~fortran+mfem"
+  extends: .full_build_on_rzgenie
+
+rzgenie-intel_18_0_2-full:
+  variables:
+    COMPILER: "intel@18.0.2"
+    SPEC: "%${COMPILER}+mfem~cpp14"
+  extends: .full_build_on_rzgenie
+
+rzgenie-intel_19_0_4-full:
+  variables:
+    COMPILER: "intel@19.0.4"
+    SPEC: "%${COMPILER}+mfem~cpp14"
+  extends: .full_build_on_rzgenie

.mailmap

@@ -1,5 +1,6 @@
 Aaron Black <black27@llnl.gov>                  Aaron C. Black <black27@llnl.gov>
 Adam J. Kunen <kunen1@llnl.gov>                 Adam J. Kunen <kunen1@sierra1626.llnl.gov>
+Adrien M. Bernede <bernede1@llnl.gov>           Adrien Bernede <51493078+adrienbernede@users.noreply.github.com>
 Aesha Parekh <aeshabparekh@gmail.com>           Aesha Parekh <29237123+aeshapar@users.noreply.github.com>
 Arlie Capps <capps2@llnl.gov>                   Arlie Capps <capps2@cab669.llnl.gov>
 Arlie Capps <capps2@llnl.gov>                   Arlie Capps <capps2@cab689.llnl.gov>
@@ -24,6 +25,7 @@ George Zagaris <zagaris2@llnl.gov>              George Zagaris <george.zagaris@g
 Joe Hennis <hennis1@llnl.gov>                   Hennis <hennis1@luz.llnl.gov>
 Joe Hennis <hennis1@llnl.gov>                   hennis1 <73615573+hennis1@users.noreply.github.com>
 Josh Essman <essman1@llnl.gov>                  Josh Essman <68349992+joshessman-llnl@users.noreply.github.com>
+Kae Suarez <suarez29@llnl.gov>                  Kae S <31679808+ksuarez1423@users.noreply.github.com>
 Kenneth Weiss <weiss27@llnl.gov>                Kenneth Weiss <kweiss@llnl.gov>
 Kenneth Weiss <weiss27@llnl.gov>                Kenny Weiss <kennyweiss@users.noreply.github.com>
 Kenneth Weiss <weiss27@llnl.gov>                Kenny Weiss <kenny@kennyweiss.com>
@@ -45,6 +47,8 @@ Randolph Settgast <settgast1@llnl.gov>          Randolph R. Settgast <rrsettgast
 Randolph Settgast <settgast1@llnl.gov>          Randolph R. Settgast <settgast1@llnl.gov>
 Randolph Settgast <settgast1@llnl.gov>          Randy Settgast <settgast1@llnl.gov>
 Richard D. Hornung <hornung1@llnl.gov>          Rich Hornung <hornung1@llnl.gov>
+Robert Carson <rac428@cornell.edu>              Robert <rac428@cornell.edu>
+Robert Carson <rac428@cornell.edu>              rcarson3 <rac428@cornell.edu>
 
 Axom Shared User <axom-dev@llnl.gov>            Asctoolkit Shared User <axom-dev@llnl.gov>
 Axom Shared User <axom-dev@llnl.gov>            Asctoolkit Shared User <atk@cab687.llnl.gov>

.readthedocs.yml

@@ -15,3 +15,5 @@ formats: all
 # Optionally set the version of Python and requirements required to build your docs
 python:
   version: 3.7
+  install:
+    - requirements: src/docs/requirements.txt

.uberenv_config.json

@@ -4,11 +4,11 @@
 "package_final_phase": "initconfig",
 "package_source_dir": "../..",
 "spack_url": "https://github.com/spack/spack",
-"spack_commit": "764c17053041a65f684ce565a2598d705b04a16b",
+"spack_commit": "d19105f76165857ca5f25ddb7e63a45a31b2ee92",
 "spack_configs_path": "scripts/spack/configs",
 "spack_packages_path": "scripts/spack/packages",
 "vcpkg_url": "https://github.com/microsoft/vcpkg",
-"vcpkg_commit": "b79f7675aaa82eb6c5a96ae764fb1ce379a9d5d6",
+"vcpkg_commit": "5568f110b509a9fd90711978a7cb76bae75bb092",
 "vcpkg_triplet": "x64-windows",
 "vcpkg_ports_path": "scripts/vcpkg_ports"
 }

CITATION.cff

@@ -0,0 +1,43 @@
+cff-version: 1.2.0
+message: "If you use Axom, please cite it as follows."
+title: "Axom:  CS infrastructure components for HPC applications"
+doi: 10.11578/dc.20210915.2
+url: https://github.com/llnl/axom
+license: BSD-3-Clause
+authors:
+- family-names: Capps
+  given-names: Arlie
+- family-names: Carson
+  given-names: Robert
+- family-names: Corbett
+  given-names: Benjamin
+- family-names: Elliott
+  given-names: Noah
+- family-names: Essman
+  given-names: Josh
+- family-names: Han
+  given-names: Brian
+- family-names: Harrison
+  given-names: Cyrus
+- family-names: Hornung
+  given-names: Richard
+- family-names: Larsen
+  given-names: Matthew
+- family-names: Moody
+  given-names: Adam
+- family-names: Pauli
+  given-names: Esteban
+- family-names: Settgast
+  given-names: Randolph
+- family-names: Taylor
+  given-names: Lee
+- family-names: Weiss
+  given-names: Kenneth
+  orcid:  "https://orcid.org/0000-0001-6649-8022"
+- family-names: White
+  given-names: Christopher
+- family-names: Yang
+  given-names: Max
+- family-names: Zagaris
+  given-names: George
+

RELEASE

@@ -1,22 +1,30 @@
 *******************************************************************************
 
-Axom: ................................, version 0.5.0
+Axom: ................................, version 0.6.0
 
 Copyright (c) 2017-2021, Lawrence Livermore National Security, LLC. 
 Produced at the Lawrence Livermore National Laboratory.
 All rights reserved. See details in the file axom/LICENSE.
 
+Current open source release information:
+Unclassified/Open Source - BSD Distribution
+LLNL-CODE-825966
+CP02462
+
+Previous open source releases:
 Unlimited Open Source - BSD Distribution
 LLNL-CODE-741217
 OCEC-17-187
 
 The Axom development team is comprised of:
 
-Rich Hornung (hornung1@llnl.gov)
 Arlie Capps (capps2@llnl.gov)
 Noah Elliott (elliott22@llnl.gov)
+Josh Essman (essman1@llnl.gov)
 Brian Han (han12@llnl.gov)
 Cyrus Harrison (harrison37@llnl.gov)
+Rich Hornung (hornung1@llnl.gov)
+Esteban Pauli (pauli2@llnl.gov)
 Lee Taylor (taylor16@llnl.gov)
 Kenny Weiss (kweiss@llnl.gov)
 Chris White (white238@llnl.gov)