Fix issue #265

[lohedges]

This PR closes #265 by changing the way that periodic box vectors are updated in the SOMD OpenMM context. This change is needed due to this issue from OpenMM. We now only need to update the default box vectors in the system, then reinitialise the context, after which the updated vectors will be propagated. Without this, calling setPeriodicBoxVectors() directly on the context will trigger an exception when using certain platforms, e.g. CUDA.

I've added tests for this update in BioSimSpace here. Note that these will always pass in the CI since the CPU platform is unaffected by this issue. As such, the test will need to be run manually on a GPU enabled device in order to validate. (The CUDA platform is conditionally used in the tests when CUDA_VISIBLE_DEVICES is set.)

• I confirm that I have merged the latest version of devel into this branch before issuing this pull request (e.g. by running git pull origin devel): [y]
• I confirm that I have added a changelog entry to the changelog (we will add a link to this PR as part of the review): [y]
• I confirm that I have permission to release this code under the GPL3 license: [y]

[mb2055]

All good 👍

Just to clarify, does this mean that SOMD is now only compatible with openmm versions 8.2+?

[lohedges]

No, this works for any version. The previous logic was unnecessary, but still (thankfully) gives the same result.

[lohedges]

Despite the CI passing for the PR, it's now repeatedly failing for Windows for the devel build. I'll check next week, but presumably some dependency in the environment has changed.

[lohedges]

This is the exception raise during compilation of the wrappers on Windows, which worked on the CI only a few days ago:

2024-12-14T09:18:04.9473896Z   Generating Code...
2024-12-14T09:18:04.9475005Z      Creating library C:/Users/runneradmin/miniconda3/envs/sire_build/conda-bld/sire_1734161070384/work/build/conda_build_wrapper/Mol/Release/Mol.lib and object C:/Users/runneradmin/miniconda3/envs/sire_build/conda-bld/sire_1734161070384/work/build/conda>
2024-12-14T09:18:04.9476345Z   LINK : /LTCG specified but no code generation required; remove /LTCG from the link command line to improve linker performance
2024-12-14T09:18:04.9476901Z   Mol.vcxproj -> %SRC_DIR%\build\conda_build_wrapper\Mol\Release\_Mol.pyd
2024-12-14T09:18:04.9477240Z SOMETHING WENT WRONG WHEN COMPILING THE WRAPPERS!

@chryswoods: Any ideas? The LTCG bit looks to be a warning, not an error, so I'm not sure why it failed.

This is the setup for the failing runner:

Current runner version: '2.321.0'
Operating System
  Microsoft Windows Server 2022
  10.0.20348
  Datacenter
Runner Image
  Image: windows-2022
  Version: 20241211.1.0
  Included Software: https://github.com/actions/runner-images/blob/win22/20241211.1/images/windows/Windows2022-Readme.md
  Image Release: https://github.com/actions/runner-images/releases/tag/win22%2F20241211.1
Runner Image Provisioner
  2.0.385.1

The last one that worked was:

Current runner version: '2.321.0'
Operating System
  Microsoft Windows Server 2022
  10.0.20348
  Datacenter
Runner Image
  Image: windows-2022
  Version: 20241201.2.0
  Included Software: https://github.com/actions/runner-images/blob/win22/20241201.2/images/windows/Windows2022-Readme.md
  Image Release: https://github.com/actions/runner-images/releases/tag/win22%2F20241201.2
Runner Image Provisioner
  2.0.385.1

The only difference appears to be the Runner image version, which is 20241211.1.0 for the one that doesn't work and 20241201.2.0 for the one that does.

[lohedges]

The LTCG bit is a red herring, since the same message appears in the working build.