Performance roadmap: reducing redraws and reducing GoslingTrackModel initializations

Question

Performance roadmap: reducing redraws and reducing GoslingTrackModel initializations

etowahadams opened this issue 6 months ago · comments

etowahadams commented 6 months ago

The frame-rate of certain Gosling visualizations is very low when zooming and panning. What are the main bottlenecks?

Flame charts

We can interact with laggy visualzations and observe their flame charts to understand what is causing poor performance.

Multiple Sequence Alignment

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Here's a flame graph when zooming in and out of :

SARS-Cov2

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Corces et al.

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Mark Displacement

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Observations

Based on the flame charts, we observe three main bottlenecks:

Redrawing over and over
Data transformations - converting a data into a form that that makes it ready to visualize. This involves use of
Creating GoslingTrackModel over over again

Reduce redrawing

Redrawing everything to the same Graphics object is expensive. There are several strategies to overcome this

Stretch the Graphics object everything is drawn to. This was implemented in #1018. However, this strategy does not work well for shapes that do not have right angle corners, since only the x-direction gets stretched.
Draw everything as a Sprite and translate the Sprites on zoom. Compared to redrawing at every frame, translating Sprites is much more performant according to my testing.

Initialize GoslingTrackModel only when needed

GoslingTrackModels are reinitialized every time draw() is called. However, it only changes when the data, spec, or theme changes. We need to persist the models unless the data, spec, or theme changes.

etowahadams · Answer 1 · Wed Feb 07 2024 01:57:27 GMT+0800 (China Standard Time)

Optimizing the point mark: 4.2X speedup

Spec:

{"layout": "linear","arrangement": "vertical","centerRadius": 0.8,"xDomain": {"chromosome": "chr1", "interval": [1, 3000500]},"views": [{"tracks": [{"id": "track-6","data": {"url": "https://server.gosling-lang.org/api/v1/tileset_info/?d=cistrome-multivec","type": "multivec","row": "sample","column": "position","value": "peak","categories": ["sample 1", "sample 2", "sample 3", "sample 4"]},"mark": "point","x": {"field": "position", "type": "genomic", "axis": "top"},"y": {"field": "peak", "type": "quantitative", "grid": true},"size": {"field": "peak", "type": "quantitative"},"color": {"field": "sample", "type": "nominal", "legend": true},"opacity": {"value": 0.5},"tooltip": [{"field": "start", "type": "genomic", "alt": "Start Position"},{"field": "end", "type": "genomic", "alt": "End Position"},{"field": "peak","type": "quantitative","alt": "Value","format": ".2"},{"field": "sample", "type": "nominal", "alt": "Sample"}],"width": 600,"height": 130}]}]}

Stack charts

Before: 5.5 ms to draw a frame

After: 1.3 ms to draw, or a 4.2X speedup

Frame charts (firefox)

After

Changes:

Persist GoslingTrackModel between draws
Looking up values using encodedPIXIvalues is expensive -> instead look up once and cache the results in GoslingTrackModel
Similarly, create UUIDs for each data point once and store with the data in GoslingTrackModel
Access the scale in the tile directly

How does draw time scale with the number of tracks?

Theoretically, it should take 1.3 ms to draw each track. Does draw time scale linearly with the number of tracks? Yes, but not with the relation that we want. Specifically, it draws 2x-1 times more than it needs to.

For example, here a visualization with 3 tracks. We expect each track to be drawn only once (3 total calls to draw) but instead we see 5.

Overall, this amounts in the following relationship: