I can't remember if tree mipmaps and/or trilinear filtering are on by default, but for me these two options add a significant amount of time to the time taken between creating the atlas and moving onto loading sounds:
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1.318 Initial atlas bitmap size is 16384
1.320 Created atlas bitmap 16384x5589
1.320 Created atlas bitmap 4096x968
1.320 Created atlas bitmap 4096x3652
19.545 Sprites loaded
19.546 Convert atlas 4096x968 to: trilinear-filtering
19.584 Convert atlas 4096x3652 to: mipmap
20.249 Loading sounds...
With these changes combined, i.e.:
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cache-sprite-atlas=true
tree-sprite-mipmaps=false
trilinear-filtering=false
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1.291 Initial atlas bitmap size is 16384
1.295 Created atlas bitmap 16384x9492
2.506 Atlases loaded from disk cache.
2.703 Sprites loaded
3.391 Loading sounds...
Also having a e.g. sandbox save that you can auto-load by passing "--load-game yoursandbox" on the command line also helps from a workflow perspective since all the loading/waiting happens up front rather than having to explicitly click through the main menu each and every time.
One final startup "optimisation" I made was to replace all oggs in data\base with a short, silent file.
Before:
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3.389 Loading sounds...
5.699 Custom inputs active: 0
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3.403 Loading sounds...
4.037 Custom inputs active: 0