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Release v3 compatible ASTE version #182

Merged
merged 82 commits into from
Mar 22, 2024
Merged

Release v3 compatible ASTE version #182

merged 82 commits into from
Mar 22, 2024

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davidscn
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@davidscn davidscn commented Feb 2, 2024

Main changes of this PR

TODO: add more detailed changes.

Author's checklist

  • I used the pre-commit hook and used pre-commit run --all to apply all available hooks.
  • I added a test to cover the proposed changes in our test suite.
  • I updated the documentation in docs/README.md.
  • I updated potential breaking changes in the tutorial precice/tutorials/aste-turbine.

davidscn and others added 30 commits October 5, 2022 15:23
* Add Halton mesh generator
* Update requirements for tools
* Change from vtk to meshio
* Add README fix format
* Add a unit grid generator
* Update tools/mesh-generators/README.md

Co-authored-by: Frédéric Simonis <[email protected]>

Co-authored-by: David Schneider <[email protected]>
* Limit local logging to application log
* Indentation using clang-format
* Handle log entries from ASTE and preCICE
* Hide preCICE log location in non-verbose runs
* Add severity and rank filter control
* Fix filter expression
* Make mapping tester tests verbose
* Indentation using clang-format
* Remove log sinks from ASTE configuration files
* Update flag documentation

Co-authored-by: David Schneider <[email protected]>
* Update from C++14 to C++17 Standart
* Change CMake and Boost versions

Co-authored-by: David Schneider <[email protected]>
* Limit local logging to application log
* Indentation using clang-format
* Handle log entries from ASTE and preCICE
* Hide preCICE log location in non-verbose runs
* Add severity and rank filter control
* Fix filter expression
* Make mapping tester tests verbose
* Indentation using clang-format
* Remove log sinks from ASTE configuration files
* Update flag documentation

Co-authored-by: David Schneider <[email protected]>
* Update from C++14 to C++17 Standart
* Change CMake and Boost versions

Co-authored-by: David Schneider <[email protected]>
* Create dependabot.yml
* Remove stale file
Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 3.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v2...v3)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump actions/setup-python from 3 to 4

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 4.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v3...v4)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>

* Add python version to CI

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: David Schneider <[email protected]>
* Use ubuntu codename preCICE CI packages
* Use correct syntax
davidscn and others added 28 commits August 4, 2023 12:29
- necessary due to deprecated python functions used in libvtk-7
Compatibility with preCICE version 3
Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v3...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
* Set vertex resolution in partitioner/joiner to double

* Fix second occurrence in mesh joiner
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
* Add lints for website integration

* Apply preCICE config formatting

* Remove the redundant workflow
* Change test name from test to precice-aste-test

* Update test!

* Rename precice-test-aste to test-aste

* Rename precice-test-aste to test-precice-aste

---------

Co-authored-by: David Schneider <[email protected]>
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davidscn commented Mar 21, 2024

Some status update and summary:

The CI is currently failing and I can reproduce this behavior on my local machine. The issue occurs when using precice-aste-evaluate and storing a mesh in VTU file format and trying to read it afterwards, using any of the VTK facilities (python or C++).

The error message:

 (   0.373s) [        9D6DFE00]       vtkXMLParser.cxx:375    ERR| vtkXMLDataParser (0x5639d4af14c0): Error parsing XML in stream at line 24, column 19, byte index 1649: not well-formed (invalid token)
 (   0.373s) [        9D6DFE00]       vtkXMLReader.cxx:521    ERR| vtkXMLUnstructuredGridReader (0x5639d4bb6080): Error parsing input file.  ReadXMLInformation aborting.
 (   0.373s) [        9D6DFE00]       vtkExecutive.cxx:752    ERR| vtkCompositeDataPipeline (0x5639d4b00ed0): Algorithm vtkXMLUnstructuredGridReader(0x5639d4bb6080) returned failure for request: vtkInformation (0x5639d4bff260)
  Debug: Off
  Modified Time: 153
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_INFORMATION
  ALGORITHM_AFTER_FORWARD: 1
  FORWARD_DIRECTION: 0

The curious thing: Yesterday (before I executed my apt upgrade) I was not able to reproduce the issue and everything was ok.

After some digging, my best guess is the upgrade of libexpat1-dev (xml parser). I found a recent issue in the arch package and it is also discussed in the paraview discourse. We can also see in our CI, that the tests passed on develop four weeks before, whereas now they are failing without obious reasons.

EDIT: Although the arch discussion is referring to version 2.6 and in ubuntu we are talking about an update from 2.4.7-1ubuntu0.2 to 2.4.7-1ubuntu0.3, running apt changelog libexpat1 points to the same problematic changes as discussed in the corresponding libexpat1 issues where the discussion bisects to (this changes backported to the ubuntu package 2.4.7-1ubuntu0.3).

@davidscn davidscn merged commit 765f405 into master Mar 22, 2024
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5 participants