pythonPackages.ovito: init at 3.0.0

[costrouc]

Motivation for this change

ovito is a visualization package for visualizing molecules and doing quick analysis.

Things done

pythonPackages.ovito: init at 3.0.0

• Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
• Built on platform(s)
  • NixOS
  • macOS
  • other Linux distributions
• Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
• Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
• Tested execution of all binary files (usually in ./result/bin/)
• Determined the impact on package closure size (by running nix path-info -S before and after)
• Fits CONTRIBUTING.md.

---

[costrouc]

Currently builds but I am running into a QT error when trying to run the binary.

/nix/store/2xgw34ydjhkdhq18wd448qprm4j6nwrf-ovito-3.0.0/bin $ ./ovito
qt.qpa.plugin: Could not find the Qt platform plugin "xcb" in ""
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

aborted (core dumped)

I have seen similar errors. Is this how the fix is done?

  postFixup = ''
     wrapProgram $out/bin/ovito \
         --prefix QT_PLUGIN_PATH : "${pkgs.qt5.qtbase}/${pkgs.qt5.qtbase.qtPluginPrefix}"
  '';

Any help would be much appreciated!

[FRidh]

It's typically not possible to run a Qt application from the store, because Qt applications are impure, that is, they check for certain things in your nix-profile. Install it with e.g. nix-env and see what happens. Note it may still fail when the Qt version is different from the one installed system-wide.

[costrouc]

Tried to run it in a pure nix-shell environment however it still segfaulted...

let pkgs = import <nixpkgs> { config = { }; };
in
pkgs.mkShell {
  buildInputs = [ pkgs.python36Packages.ovito ];

  shellHook = ''
    export QT_PLUGIN_PATH=${pkgs.qt5.qtbase.bin}/${pkgs.qt5.qtbase.qtPluginPrefix}
  '';
}

[costrouc]

Fixed and ready to merge. I have tested that the qt5 application works in NixOS. The QT5 documentation on nixpkgs was invaluable for fixing the issue.

[costrouc]

@GrahamcOfBorg build python36Packages.ovito

[GrahamcOfBorg]

Failure on aarch64-linux (full log)

Attempted: python36Packages.ovito

Partial log (click to expand)

[ 24%] Built target PyScript_PCH
[ 24%] Built target Gui_PCH
[ 24%] Built target StdObjGui_PCH
[ 24%] Built target StdModGui_PCH
[ 24%] Built target ParticlesGui_PCH
[ 24%] Linking CXX shared library ../../../lib/ovito/libQwt.so
[ 24%] Built target Qwt
make: *** [Makefile:163: all] Error 2
builder for '/nix/store/r89lm06ws66rbfvqcql8n1mnffjip6x1-ovito-3.0.0.drv' failed with exit code 2
error: build of '/nix/store/r89lm06ws66rbfvqcql8n1mnffjip6x1-ovito-3.0.0.drv' failed

[GrahamcOfBorg]

Timed out, unknown build status on x86_64-linux (full log)

Attempted: python36Packages.ovito

Partial log (click to expand)

[ 72%] Building CXX object src/plugins/particles/CMakeFiles/Particles.dir/modifier/analysis/bondangle/BondAngleAnalysisModifier.cpp.o
[ 73%] Building CXX object src/plugins/particles/CMakeFiles/Particles.dir/modifier/analysis/cna/CommonNeighborAnalysisModifier.cpp.o
[ 73%] Building CXX object src/plugins/particles/CMakeFiles/Particles.dir/modifier/analysis/coordination/CoordinationNumberModifier.cpp.o
[ 73%] Building CXX object src/plugins/particles/CMakeFiles/Particles.dir/modifier/analysis/displacements/CalculateDisplacementsModifier.cpp.o
[ 73%] Building CXX object src/plugins/particles/CMakeFiles/Particles.dir/modifier/analysis/centrosymmetry/CentroSymmetryModifier.cpp.o
[ 73%] Building CXX object src/plugins/particles/CMakeFiles/Particles.dir/modifier/analysis/strain/AtomicStrainModifier.cpp.o
[ 73%] Building CXX object src/plugins/particles/CMakeFiles/Particles.dir/modifier/analysis/diamond/IdentifyDiamondModifier.cpp.o
[ 73%] Building CXX object src/plugins/particles/CMakeFiles/Particles.dir/modifier/analysis/voronoi/VoronoiAnalysisModifier.cpp.o
building of '/nix/store/qxx4adgwxsij6gk9sw4bik0vzlfrfpnm-ovito-3.0.0.drv' timed out after 3600 seconds
error: build of '/nix/store/qxx4adgwxsij6gk9sw4bik0vzlfrfpnm-ovito-3.0.0.drv' failed

[costrouc]

This package takes a long time to build but I can promise that it works on x86_64-linux

[costrouc]

Bump. Ready for merge. Build takes over an hour and I can verify that the qt application works.

[FRidh]

If it's a Python library, then it needs to be moved under python-modules/.

[costrouc]

Fixed. Move to python-modules, added toPythonModule, and removed pkgs from derivation.

[FRidh]

I just has a look at the source code, and they vendor a lot. It's likely a lot of work to replace their vendored dependencies with our Nixpkgs builds, however, I don't think it is reasonable to let Hydra build this package.

[costrouc]

What if I were to patchelf the binary that they provide? https://ovito.org/index.php/download

Not ideal but would make the build trivial.

[FRidh]

Not sure if it would actually work well, considering also the Python dependencies.
In any case, you can have it like this but set platforms = [] so Hydra won't build it.

[costrouc]

Fixed. Set platforms = [ ].

[FRidh]

Ah, wait, it was hydraPlatforms. See the Nixpkgs manual.

[costrouc]

Makes more sense thanks for showing me that. Fixed with `hydraPlayforms = [ ];'

[costrouc]

Bump. Ready for merge. I have added hydraPlatforms = [ ]. No actual builds will be done on hydra.