Dynamic topology phase IV #481

tokusanya · 2024-08-15T20:34:06Z

Functionality for reduction operations on groups

…haseIV

packages/seacas/libraries/ioss/src/exodus/Ioex_DatabaseIO.C

gsjaardema

Looks good. A few questions/comments/suggestions.

packages/seacas/libraries/ioss/src/Ioss_Region.C

packages/seacas/libraries/ioss/src/exodus/Ioex_DatabaseIO.C

packages/seacas/libraries/ioss/src/gen_struc/Iogs_DatabaseIO.C

packages/seacas/libraries/ioss/src/generated/Iogn_DatabaseIO.C

packages/seacas/libraries/ioss/src/text_mesh/Iotm_DatabaseIO.C

packages/seacas/libraries/ioss/src/unit_tests/UnitTestDynamicTopology.C

packages/seacas/libraries/exodus/src/ex_inquire.c

packages/seacas/libraries/ioss/src/exodus/Ioex_BaseDatabaseIO.C

packages/seacas/libraries/ioss/src/exodus/Ioex_DatabaseIO.C

packages/seacas/libraries/ioss/src/Ioss_DatabaseIO.h

…haseIV

gsjaardema

Lots of good stuff here. I didn't make it through everything yet, but tried to get a good overview. I think it looks good overall and is evolving toward where I think we want to go...

packages/seacas/libraries/ioss/src/Ioss_DatabaseIO.h

packages/seacas/libraries/ioss/src/Ioss_DynamicTopology.C

packages/seacas/libraries/ioss/src/Ioss_Region.C

packages/seacas/libraries/ioss/src/exodus/Ioex_ParallelDatabaseIO.C

…haseIV

gsjaardema

There are a few suggestions for changes. Nothing required that I remember... Looks good although lots of code, so not sure I fully covered all of it...

packages/seacas/libraries/ioss/src/Ioss_ChangeSetFactory.h

packages/seacas/libraries/ioss/src/Ioss_ChangeSet.C

packages/seacas/libraries/ioss/src/Ioss_ChangeSet.h

packages/seacas/libraries/ioss/src/Ioss_DynamicTopology.C

packages/seacas/libraries/ioss/src/Ioss_DynamicTopology.h

packages/seacas/libraries/ioss/src/exodus/Ioex_ChangeSet.h

packages/seacas/libraries/ioss/src/Ioss_Region.C

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>

* 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>

…haseIV

…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>

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>

…#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>

…#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>

tokusanya · 2024-10-16T16:14:59Z

@gsjaardema Can you help me resolve the conflict that popped up? I'm not sure which version is correct

gsjaardema · 2024-10-16T16:19:00Z

@gsjaardema Can you help me resolve the conflict that popped up? I'm not sure which version is correct

I will give it a try

Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>

tokusanya · 2024-10-16T16:31:10Z

@gsjaardema I'm ready to merge but a little surprised that the tests did not automatically run after my last commit

gsjaardema · 2024-10-16T16:32:03Z

Is this ready to merge?

tokusanya · 2024-10-16T16:34:05Z

Is this ready to merge?

Yes

gsjaardema · 2024-10-16T16:35:06Z

@gsjaardema I'm ready to merge but a little surprised that the tests did not automatically run after my last commit

It looks like they are currently running. Not sure why they don't show up here or under "checks" tab... See https://github.com/sandialabs/seacas/actions

gsjaardema · 2024-10-16T16:52:37Z

@tokusanya Looks like a couple build errors showing up. Possibly a bad merge on Ioss_DynamicTopology.C and the const should be removed from Ioss_DatabaseIO.h, reset_database() ?

tokusanya · 2024-10-16T16:55:38Z

@tokusanya Looks like a couple build errors showing up. Possibly a bad merge on Ioss_DynamicTopology.C and the const should be removed from Ioss_DatabaseIO.h, reset_database() ?

Yeah, I'm putting in a fix for the const error

gsjaardema · 2024-10-16T16:59:03Z

I'm not sure what happened on Ioss_DynamicTopology.C. Maybe the "clang-format` workflow messed it up?

tokusanya · 2024-10-16T17:22:05Z

I'm not sure what happened on Ioss_DynamicTopology.C. Maybe the "clang-format` workflow messed it up?

Possibly ... I always have issues with that file every time I do a pull. The file formatting is completely messed up

tokusanya · 2024-10-16T17:35:45Z

@gsjaardema Does it make sense to break up Ioss_DynamicTopology.C according to the classes in it? It's currently supporting 4 classes...

gsjaardema · 2024-10-16T17:37:26Z

@gsjaardema Does it make sense to break up Ioss_DynamicTopology.C according to the classes in it? It's currently supporting 4 classes...

Yes, that would probably be good.

gsjaardema · 2024-10-16T23:44:21Z

@tokusanya Looks like builds succeeded. Should this be merged now?

tokusanya · 2024-10-16T23:46:33Z

@tokusanya Looks like builds succeeded. Should this be merged now?

Just merged it :)

tokusanya · 2024-10-16T23:47:13Z

@gsjaardema All that's needed now is a SEACAS snapshot into Sierra

gsjaardema · 2024-10-16T23:52:30Z

@tokusanya Do you want to try the snapshot, or should I?

tokusanya · 2024-10-17T14:31:54Z

@gsjaardema Is there a workflow for how to do the snapshot? I've never done it before so it might be easier if you tried it

gsjaardema · 2024-10-17T14:44:59Z

There is a list of the steps at https://github.com/sandialabs/seacas/wiki#developer-oriented-things under the bullet Snapshot into Sierra

I will do this snapshot since it has lots of other changes in addition to the Dynamic Toplogy changes, so more difficult to create a coherent set of commits...

tokusanya added 2 commits August 15, 2024 14:27

IOSS: More changes to support Dynamic Topology

feb7c5a

Merge remote-tracking branch 'upstream/master' into DynamicTopology-P…

ef77556

…haseIV

tokusanya commented Aug 15, 2024

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packages/seacas/libraries/ioss/src/exodus/Ioex_DatabaseIO.C Show resolved Hide resolved

gsjaardema requested changes Aug 15, 2024

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tokusanya added 2 commits August 16, 2024 00:20

IOSS: Dynamic Topology changes based on code review

f273e85

IOSS:: More functonality to support Dynamic Topology

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gsjaardema requested changes Aug 19, 2024

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tokusanya added 5 commits August 20, 2024 17:42

IOSS: Attempt to provide "change set" concept instead of "groups"

779e765

Merge remote-tracking branch 'upstream/master' into DynamicTopology-P…

e7c1db2

…haseIV

IOSS: Fix compiler errors

d1b1732

Merge remote-tracking branch 'upstream/master' into DynamicTopology-P…

14aef54

…haseIV

IOSS: Refactoring and unit test fix

90f97ec

gsjaardema reviewed Aug 27, 2024

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tokusanya added 5 commits September 3, 2024 02:11

IOSS: Introduce concept of Change Sets

14be761

Merge remote-tracking branch 'upstream/master' into DynamicTopology-P…

4c21e0b

…haseIV

Hush compiler issues

2c71918

Fix for Dynamic Topology unit test

2791f05

Merge branch 'master' into DynamicTopology-PhaseIV

61236e4

gsjaardema requested changes Sep 9, 2024

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gsjaardema reviewed Sep 10, 2024

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packages/seacas/libraries/ioss/src/Ioss_Region.C Outdated Show resolved Hide resolved

gsjaardema reviewed Sep 10, 2024

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packages/seacas/libraries/ioss/src/Ioss_Region.C Outdated Show resolved Hide resolved

gsjaardema reviewed Sep 10, 2024

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packages/seacas/libraries/ioss/src/Ioss_Region.C Outdated Show resolved Hide resolved

tokusanya and others added 7 commits September 11, 2024 14:25

Hush more compiler warnings and address some review comments

2794a19

Merge branch 'master' into DynamicTopology-PhaseIV

1351b3c

Merge branch 'master' into DynamicTopology-PhaseIV

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Bug fixes and some more refactoring

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Merge remote-tracking branch 'upstream/master' into DynamicTopology-P…

dfa841c

…haseIV

tokusanya force-pushed the DynamicTopology-PhaseIV branch from d939b3a to dfa841c Compare September 25, 2024 20:35

dependabot bot and others added 6 commits October 16, 2024 08:44

CI: Add harden runner to clang-format

19db1ff

CI: Try different trailing whitespace [ci skip]

697207b

gsjaardema and others added 2 commits October 16, 2024 10:19

Merge branch 'master' into DynamicTopology-PhaseIV

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Signed-off-by: Greg Sjaardema <gsjaardema@gmail.com>

Committing clang-format changes

550a642

tokusanya and others added 3 commits October 16, 2024 17:00

DTIO: Fix for bad merge and compiler complaints

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DTIO: Split files into individual classes

4626efd

Committing clang-format changes

a37070b

tokusanya merged commit 027dd04 into sandialabs:master Oct 16, 2024

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Dynamic topology phase IV #481

Dynamic topology phase IV #481

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Dynamic topology phase IV #481

Dynamic topology phase IV #481

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