Merge branch 'next' into docs_fifth_pass

.github/workflows/ci.yml

@@ -167,7 +167,7 @@ jobs:
     - name: 'ethier FP32 cimode 2'
       working-directory: ${{ env.NEKRS_EXAMPLES }}/ethier
       run: |
-        NEKRS_FP32=1 NEKRS_CACHE_DIR=${{ env.NEKRS_EXAMPLES }}/ethier/custom-cache-dir ${{ env.NEKRS_HOME }}/bin/nrsmpi ethier 1 --cimode 22 
+        FP32=1 NEKRS_CACHE_DIR=${{ env.NEKRS_EXAMPLES }}/ethier/custom-cache-dir ${{ env.NEKRS_HOME }}/bin/nrsmpi ethier 1 --cimode 22 
 
   lowMach:
     needs: install

3rd_party/adios/.circleci/config.yml

@@ -0,0 +1,52 @@
+defaults: &defaults
+  steps:
+    - checkout:
+        path: source
+    - run:
+        # https://discuss.circleci.com/t/circle-working-directory-doesnt-expand/17007
+        name: "Fix CIRCLE_WORKING_DIRECTORY"
+        command: echo 'CIRCLE_WORKING_DIRECTORY="${CIRCLE_WORKING_DIRECTORY/#\~/$HOME}"' >> $BASH_ENV
+    - run:
+        name: CDash
+        command: bash source/scripts/ci/circle/postCDashStatus.sh
+    - run:
+        name: Update
+        command: bash source/scripts/ci/circle/run.sh update
+    - run:
+        name: Configure
+        command: bash source/scripts/ci/circle/run.sh configure
+    - run:
+        name: Build
+        command: bash source/scripts/ci/circle/run.sh build
+    - run:
+        name: Sanitize
+        command: bash source/scripts/ci/circle/run.sh memcheck
+
+version: 2
+
+jobs:
+  "fedora-ubsan":
+    <<: *defaults
+    docker:
+      - image: ornladios/adios2:ci-fedora-ubsan
+  "fedora-asan":
+    <<: *defaults
+    docker:
+      - image: ornladios/adios2:ci-fedora-asan
+  "fedora-msan":
+    <<: *defaults
+    docker:
+      - image: ornladios/adios2:ci-fedora-msan
+  "fedora-tsan":
+    <<: *defaults
+    docker:
+      - image: ornladios/adios2:ci-fedora-tsan
+
+workflows:
+  version: 2
+  sanitizers:
+    jobs:
+      - "fedora-ubsan"
+      - "fedora-asan"
+      - "fedora-msan"
+      - "fedora-tsan"

3rd_party/adios/.clang-format

@@ -0,0 +1,31 @@
+Language:  Cpp
+BasedOnStyle:  LLVM
+BreakBeforeBraces:  Custom
+ConstructorInitializerIndentWidth:  0
+IndentWidth: 4
+ContinuationIndentWidth: 4
+AccessModifierOffset: -4
+AlwaysBreakTemplateDeclarations:  true
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+FixNamespaceComments: false
+Standard: Cpp11
+ColumnLimit: 100
+AllowAllParametersOfDeclarationOnNextLine: true
+AlignEscapedNewlines: Right
+AlignAfterOpenBracket: Align
+SortUsingDeclarations: false
+BraceWrapping:
+  AfterClass: true
+  AfterControlStatement: true
+  AfterEnum: true
+  AfterExternBlock: false
+  AfterFunction: true
+  AfterNamespace: true
+  AfterStruct: true
+  AfterUnion: true
+  BeforeCatch: true
+  BeforeElse: true
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: false

3rd_party/adios/.clang-tidy

@@ -0,0 +1,5 @@
+Checks: -*,cppcoreguidelines-*,google-*,llvm-*,misc-*,modernize-*,performance-*,-cppcoreguidelines-pro-type-vararg,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-cppcoreguidelines-pro-type-reinterpret-cast,-google-runtime-int
+
+CheckOptions:
+  - key: 	google-runtime-int.TypeSuffix
+    value:	_t

3rd_party/adios/.e4s/e4s.yaml

@@ -0,0 +1,8 @@
+- e4s_product: adios2
+  version: 0.1.0
+  website: https://github.com/ornladios/adios2
+  docs: [ReadMe.md, LICENSE]
+  spack_name: adios2
+  area: Data & Viz
+  Description: "ADIOS2 is the latest implementation of the Adaptable Input Output System, a modular high performance framework for HPC I/O."
+  MemberProduct: False

3rd_party/adios/.flake8

@@ -0,0 +1,6 @@
+[flake8]
+max-line-length = 100
+max-complexity = 1000
+format = pylint
+ignore = E302,F401,F403,F405,F999,W504
+exclude = thirdparty/,.gitlab/config/SpackCIBridge.py

3rd_party/adios/.gitattributes

@@ -0,0 +1,22 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+*       text=auto
+
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+*.cxx   text
+*.h     text
+*.hxx   text
+*.tcc   text
+*.cu    text
+*.c     text
+*.h     text
+*.py    text
+*.f90   text
+*.F90   text
+*.sh    text
+
+*.cmake whitespace=tab-in-indent
+*.md    whitespace=tab-in-indent whitespace=-blank-at-eol conflict-marker-size=79
+*.rst   whitespace=tab-in-indent conflict-marker-size=79
+*.txt   whitespace=tab-in-indent
+*.xml   whitespace=tab-in-indent

3rd_party/adios/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,35 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+We ask the community to always report bugs. Please open a new issue if some other comes up in the conversation. It will help us stay on topic and manage tasks more efficiently.
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+Example: Reader failing to extract compressed values with SZ
+
+**To Reproduce**
+A minimal reproducible example is preferred.
+Or Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Desktop (please complete the following information):**
+ - OS/Platform: [e.g. Ubuntu 18.04, Cori, Summit]
+ - Build [e.g. compiler version gcc 7.4.0, cmake version, build type: static ]
+
+**Additional context**
+Add any other context about the problem here.
+
+**Following up**
+Was the issue fixed? Please report back.

3rd_party/adios/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,21 @@
+---
+name: Feature request
+about: Propose a new feature
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+Remember to motivate and summarize considering the community. Provide enough information to motivate such as:
+
+**Why is this feature important?**
+**What is the potential impact of this feature in the community?**
+**Is your feature request related to a problem? Please describe.**
+**Describe the solution you'd like and potential required effort**
+**Describe alternatives you've considered and potential required effort**
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
+
+Note: contents adapted from the [VTK contribution guidelines](https://github.com/Kitware/VTK/blob/master/Documentation/dev/git/develop.md#create-a-merge-request)

3rd_party/adios/.github/ISSUE_TEMPLATE/new_release.md

@@ -0,0 +1,73 @@
+<!--
+  Replace the following vars with its corresponding values:
+  - @VERSION@ (example 2.9.0)
+  - @MAJOR@ (example 2)
+  - @MINOR@ (example 9)
+  - @OLD_RELEASE@ (example 2.8.3)
+
+-->
+Instructions for performing an ADIOS2 release:
+
+- [ ] Make sure that the milestone for @VERSION@ has no pending issues/PRs.
+- [ ] Update your remotes
+``
+git fetch origin
+git fetch github #if needed
+``
+- [ ] Create a branch that updates the version
+<!-- If the release_@MAJOR@@MINOR@ already exists -->
+```
+git checkout -b bump-release-version origin/release_@MAJOR@@MINOR@
+```
+<!-- else -->
+```
+git checkout -b bump-release-version origin/master
+```
+<!-- endif -->
+- [ ] Add Commit that updates the version in the repo
+```
+git grep --name-only @OLD_RELEASE@ | xargs -n1 sed -i 's/@OLD_RELEASE@/@VERSION@/g'
+git commit -am 'Bump version to v@VERSION@'
+git push
+```
+- [ ] Create PR (BASE to master if release_@MAJOR@@MINOR@ does not exists; otherwise release_@MAJOR@@MINOR@)
+- [ ] Ask for review
+- [ ] Merge PR
+- [ ] Create Tag commit `git tag -a -m 'v@VERSION' v@VERSION@ the_merge_commit`
+- [ ] Create Release in GitHub page
+  - Use the following script for getting the PR of this release
+    - `./scripts/developer/create-changelog.sh v@VERSION@ v@OLD_RELEASE@`
+  - Copy its content to the release description
+<!-- If the release_@MAJOR@@MINOR@ does not exists -->
+- [ ] Create the release_@MAJOR@@MINOR@ branch
+```
+git fetch origin
+git checkout -b release_@MAJOR@@MINOR@ origin/master
+# Use the following command with care
+git push origin release_@MAJOR@@MINOR@:release_@MAJOR@@MINOR@
+```
+<!-- else -->
+- [ ] Remove older patch releases for @MAJOR@.@MINOR@.X in ReadTheDocs.
+- [ ] Create merge -sours commit in master:
+```
+git fetch origin
+git checkout master
+git reset --hard origin/master
+# We do not want the changes master from the release branch
+git -s ours release_@MAJOR@@MINOR@
+# Be very careful here
+git push origin master
+```
+<!-- endif -->
+- [ ] Submit a PR in Spack that adds this new version of ADIOS (if not RC mark this new version as preferred)
+  - Run `spack checksum -a adios2` to add it, create commit; push it; Create
+    PR in Spack repo.
+- [ ] Submit a PR in Conda that adds this new version of ADIOS (if not RC mark this new version as preferred)
+  - CondaForge robot should do this for you automatically, expect a new PR at
+    https://github.com/conda-forge/adios2-feedstock a couple of hours after the
+    release.
+- [ ] Submit a MR for ParaView Superbuild to use v@VERSION@ release.
+- [ ] Update the website to point to the v@VERSION@ release
+- [ ] Write an announcement in the ADIOS-ECP mail-list
+  (https://groups.google.com/a/kitware.com/g/adios-ecp)
+

3rd_party/adios/.github/actions/save-context-artifacts/action.yml

@@ -0,0 +1,41 @@
+name: Upload Contexts
+description: Dump GitHub Action CI contexts and upload as artifacts
+runs:
+  using: composite
+  steps:
+    - name: Dump github context
+      shell: bash
+      run: echo '${{ toJSON(github) }}' > context-github.json
+    - name: Dump env context
+      shell: bash
+      run: echo '${{ toJSON(env) }}' > context-env.json
+    - name: Dump job context
+      shell: bash
+      run: echo '${{ toJSON(job) }}' > context-job.json
+    - name: Dump steps context
+      shell: bash
+      run: echo '${{ toJSON(steps) }}' > context-steps.json
+    - name: Dump runner context
+      shell: bash
+      run: echo '${{ toJSON(runner) }}' > context-runner.json
+    - name: Dump strategy context
+      shell: bash
+      run: echo '${{ toJSON(strategy) }}' > context-strategy.json
+    - name: Dump matrix context
+      shell: bash
+      run: echo '${{ toJSON(matrix) }}' > context-matrix.json
+    - name: Upload contexts as artifacts
+      uses: actions/upload-artifact@v3
+      with:
+        name: contexts
+        path: |
+          ${{ github.event_path }}
+          context-github.json
+          context-env.json
+          context-job.json
+          context-steps.json
+          context-runner.json
+          context-secrets.json
+          context-strategy.json
+          context-matrix.json
+          context-inputs.json