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Dynamic topology phase IV #481

Merged
merged 47 commits into from
Oct 16, 2024

Commits on Aug 15, 2024

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Commits on Aug 16, 2024

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Commits on Aug 18, 2024

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Commits on Aug 20, 2024

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Commits on Aug 21, 2024

  1. IOSS: Fix compiler errors

    tokusanya committed Aug 21, 2024
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Commits on Sep 3, 2024

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  3. Hush compiler issues

    tokusanya committed Sep 3, 2024
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Commits on Sep 7, 2024

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Commits on Sep 11, 2024

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  2. Bump step-security/harden-runner from 2.9.1 to 2.10.0 (sandialabs#492)

    Bumps [step-security/harden-runner](https://github.com/step-security/harden-runner) from 2.9.1 to 2.10.0.
    - [Release notes](https://github.com/step-security/harden-runner/releases)
    - [Commits](step-security/harden-runner@5c7944e...446798f)
    
    ---
    updated-dependencies:
    - dependency-name: step-security/harden-runner
      dependency-type: direct:production
      update-type: version-update:semver-minor
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
    dependabot[bot] authored and tokusanya committed Sep 11, 2024
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  3. Lossy compression (sandialabs#464)

    * EXODUS: Add support for lossy compression via netCDF quantize method
    
    * IOSS: Add support for lossy compression specifying NSD for netCDF quantize method
    
    * EXODUS: Update version date
    
    * EXODUS: Add some error checking on nsd values
    
    * EXODUS: Check if Quantization supported; include in config output
    
    * EXODUS: Cleaning up new compression support
    
    * EXODUS: Fix error handling code
    
    * EXODUS: Better error checking on compression
    
    * IOSS: Support for zstd compression
    
    * IOSS: Handle building with no netCDF-4 capability
    
    * IOSS: Change gold files to netcdf-3 so work without hdf5-supported netCDF
    
    * CI: See if can figure out intel build failure
    
    * CI: Fix hdf5 version warning message
    
    * CI: Turn on plugins; support new syntax
    
    * EXODUS: Only flush stderr if written to
    
    Signed-off-by: Greg Sjaardema <gdsjaar@sandia.gov>
    
    * Tweak compression additions
    
    * CI: Fix intel build script syntax error
    
    * EXODUS: Support new netCDF with changed _FillValue
    
    * IOSS: Fix so latest fmt version works
    
    * IOSS: Catalyst API 2 (sandialabs#463)
    
    * IOSS: Catalyst API 2
    
    Added support to database for using my_processor and
    processor_count IOSS properties when operating in
    serial parallel mode and reading Conduit files.
    
    * IOSS: Catalyst API 2
    
    Changed Conduit serial parallel test to use
    files from the one MPI rank can.ex2 test.
    
    ---------
    
    Co-authored-by: Greg Sjaardema <gsjaardema@gmail.com>
    
    * Fix export symbols (sandialabs#465)
    
    * IOSS: Catalyst API 2 (sandialabs#466)
    
    Create the cell_ids and cell_node_ids fields for
    a StructuredBlock when asked for by a reading
    application, if these fields are not already stored in
    the Conduit data. Uses the get_cell_ids() and
    get_cell_node_ids() methods on StructuredBlock.
    
    * CI: Remove hdf5-1.8 testing
    
    * IOSS: Catalyst API 2 (sandialabs#463)
    
    * IOSS: Catalyst API 2
    
    Added support to database for using my_processor and
    processor_count IOSS properties when operating in
    serial parallel mode and reading Conduit files.
    
    * IOSS: Catalyst API 2
    
    Changed Conduit serial parallel test to use
    files from the one MPI rank can.ex2 test.
    
    ---------
    
    Co-authored-by: Greg Sjaardema <gsjaardema@gmail.com>
    
    * NEM_SPREAD: Add missing include file
    
    * CI: Enable netCDF quantize option
    
    * CI: Support newest netCDF; fmt
    
    * Enable new compression options
    
    * EXODUS: Fix non-hdf5 build
    
    * EXODUS: Do not commit the kluge to repository
    
    * IOSS: See if can fix spack ci build
    
    * CI: Spack build should not run on PR
    
    * CI: Spack build on master only [ci skip]
    
    * CI: Fix spack workflow syntax [ci skip]
    
    * IOSS: Add progress output to chain/face generation
    
    * IOSS: Reduce Face memory
    
    * EXODUS: Better control over exodus verbosity
    
    * EXODUS:, IOSS:  Add bzip2 compression support
    
    * Further testing of non-lossy compression with plugins
    
    * CI: Update cmake-sems to work with current sems
    
    * Default netcdf should be 4.9.2
    
    Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>
    
    * Clean up copyright dates
    
    Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>
    
    * Clean up copyright dates
    
    Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>
    
    * accidentally added to pr; removed
    
    Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>
    
    ---------
    
    Signed-off-by: Greg Sjaardema <gdsjaar@sandia.gov>
    Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>
    Co-authored-by: Greg Sjaardema <gdsjaar@sandia.gov>
    Co-authored-by: tjotaha <tjotaha@sandia.gov>
    Co-authored-by: Spiros Tsalikis <spiros.tsalikis@kitware.com>
    4 people authored and tokusanya committed Sep 11, 2024
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Commits on Sep 23, 2024

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Commits on Sep 25, 2024

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Commits on Sep 26, 2024

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Commits on Oct 3, 2024

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  3. Merge branch 'master' into DynamicTopology-PhaseIV

    Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>
    gsjaardema authored Oct 3, 2024
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Commits on Oct 4, 2024

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Commits on Oct 8, 2024

  1. Fix issue with invalid exodus file pointer

    I think this is the correct change (deleting this block of code) since `handle_output_file` is returning a  `m_exodusFilePtr` and sets`m_groupName`, so that is redundant with calling `ex_get_group_id` and even  worse, `ex_get_group_id` is looking for a child group of itself...
    
    I'm not sure whether the code in this block is needed for an input file though...
    gsjaardema authored Oct 8, 2024
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Commits on Oct 9, 2024

  1. IOSS: Remove commented out code

    Remove code commented out in last commit.
    gsjaardema authored Oct 9, 2024
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Commits on Oct 14, 2024

  1. Merge branch 'master' into DynamicTopology-PhaseIV

    Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>
    gsjaardema authored Oct 14, 2024
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  5. Update io_shell_ts.C

    gsjaardema authored Oct 14, 2024
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Commits on Oct 16, 2024

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  2. Bump sphinx from 8.1.1 to 8.1.3 in /cmake/tribits/doc/sphinx (sandial…

    …abs#523)
    
    Bumps [sphinx](https://github.com/sphinx-doc/sphinx) from 8.1.1 to 8.1.3.
    - [Release notes](https://github.com/sphinx-doc/sphinx/releases)
    - [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES.rst)
    - [Commits](sphinx-doc/sphinx@v8.1.1...v8.1.3)
    
    ---
    updated-dependencies:
    - dependency-name: sphinx
      dependency-type: direct:production
      update-type: version-update:semver-patch
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
    dependabot[bot] authored and tokusanya committed Oct 16, 2024
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  3. Bump github/codeql-action from 3.26.12 to 3.26.13 (sandialabs#524)

    Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3.26.12 to 3.26.13.
    - [Release notes](https://github.com/github/codeql-action/releases)
    - [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
    - [Commits](github/codeql-action@c36620d...f779452)
    
    ---
    updated-dependencies:
    - dependency-name: github/codeql-action
      dependency-type: direct:production
      update-type: version-update:semver-patch
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
    dependabot[bot] authored and tokusanya committed Oct 16, 2024
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  4. Bump ubuntu from b359f10 to ab64a83 in /docker/seacas (sandialabs…

    …#525)
    
    Bumps ubuntu from `b359f10` to `ab64a83`.
    
    ---
    updated-dependencies:
    - dependency-name: ubuntu
      dependency-type: direct:production
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
    Co-authored-by: Greg Sjaardema <gsjaardema@gmail.com>
    2 people authored and tokusanya committed Oct 16, 2024
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  5. Bump ubuntu from b359f10 to ab64a83 in /docker/exodus (sandialabs…

    …#526)
    
    Bumps ubuntu from `b359f10` to `ab64a83`.
    
    ---
    updated-dependencies:
    - dependency-name: ubuntu
      dependency-type: direct:production
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
    dependabot[bot] authored and tokusanya committed Oct 16, 2024
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  6. CI: Add harden runner to clang-format

    gdsjaar authored and tokusanya committed Oct 16, 2024
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  8. Merge branch 'master' into DynamicTopology-PhaseIV

    Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>
    gsjaardema authored Oct 16, 2024
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