improved getMarkersAverage performance

- use lut
- add performance tests

src/mol-geo/geometry/marker-data.ts

@@ -17,10 +17,42 @@ export type MarkerData = {
     markerStatus: ValueCell<number>
 }
 
+const MarkerCountLut = new Uint8Array(0x0303 + 1);
+MarkerCountLut[0x0001] = 1;
+MarkerCountLut[0x0002] = 1;
+MarkerCountLut[0x0003] = 1;
+MarkerCountLut[0x0100] = 1;
+MarkerCountLut[0x0200] = 1;
+MarkerCountLut[0x0300] = 1;
+MarkerCountLut[0x0101] = 2;
+MarkerCountLut[0x0201] = 2;
+MarkerCountLut[0x0301] = 2;
+MarkerCountLut[0x0102] = 2;
+MarkerCountLut[0x0202] = 2;
+MarkerCountLut[0x0302] = 2;
+MarkerCountLut[0x0103] = 2;
+MarkerCountLut[0x0203] = 2;
+MarkerCountLut[0x0303] = 2;
+
+/**
+ * Calculates the average number of entries that have any marker flag set.
+ *
+ * For alternative implementations and performance tests see
+ * `src\perf-tests\markers-average.ts`.
+ */
 export function getMarkersAverage(array: Uint8Array, count: number): number {
     if (count === 0) return 0;
+
+    const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
+    const viewEnd = (count - 4) >> 2;
+    const backStart = 4 * viewEnd;
+
     let sum = 0;
-    for (let i = 0; i < count; ++i) {
+    for (let i = 0; i < viewEnd; ++i) {
+        const v = view[i];
+        sum += MarkerCountLut[v & 0xFFFF] + MarkerCountLut[v >> 16];
+    }
+    for (let i = backStart; i < count; ++i) {
         sum += array[i] && 1;
     }
     return sum / count;

src/perf-tests/markers-average.ts

@@ -0,0 +1,207 @@
+import * as B from 'benchmark';
+
+function uint8ForLoop(array: Uint8Array, count: number): number {
+    if (count === 0) return 0;
+    let sum = 0;
+    for (let i = 0; i < count; ++i) {
+        sum += array[i] && 1;
+    }
+    return sum / count;
+}
+
+function uint32ForLoop(array: Uint8Array, count: number): number {
+    if (count === 0) return 0;
+
+    const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
+    const viewEnd = (count - 4) >> 2;
+    const backStart = 4 * viewEnd;
+
+    let sum = 0;
+    for (let i = 0; i < viewEnd; ++i) {
+        const v = view[i];
+        sum += ((v & 0xFF) && 1) + ((v & 0xFF00) && 1) + ((v & 0xFF0000) && 1) + ((v & 0xFF000000) && 1);
+    }
+    for (let i = backStart; i < count; ++i) {
+        sum += array[i] && 1;
+    }
+    return sum / count;
+}
+
+function uint32ForLoopAddOnlyBaseline(array: Uint8Array, count: number): number {
+    if (count === 0) return 0;
+
+    const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
+    const viewEnd = (count - 4) >> 2;
+    const backStart = 4 * viewEnd;
+
+    let sum = 0;
+    for (let i = 0; i < viewEnd; ++i) {
+        const v = view[i];
+        sum += v;
+    }
+    for (let i = backStart; i < count; ++i) {
+        sum += array[i] && 1;
+    }
+    return sum / count;
+}
+
+function createTypedLut() {
+    const lut = new Uint8Array(0x0303 + 1);
+    lut[0x0001] = 1;
+    lut[0x0002] = 1;
+    lut[0x0003] = 1;
+    lut[0x0100] = 1;
+    lut[0x0200] = 1;
+    lut[0x0300] = 1;
+    lut[0x0101] = 2;
+    lut[0x0201] = 2;
+    lut[0x0301] = 2;
+    lut[0x0102] = 2;
+    lut[0x0202] = 2;
+    lut[0x0302] = 2;
+    lut[0x0103] = 2;
+    lut[0x0203] = 2;
+    lut[0x0303] = 2;
+    return lut;
+}
+
+function createNativeLut() {
+    const lut: number[] = [];
+    for (let i = 0, il = 0x0303 + 1; i < il; ++i) lut[i] = 0;
+    lut[0x0000] = 0;
+    lut[0x0001] = 1;
+    lut[0x0002] = 1;
+    lut[0x0003] = 1;
+    lut[0x0100] = 1;
+    lut[0x0200] = 1;
+    lut[0x0300] = 1;
+    lut[0x0101] = 2;
+    lut[0x0201] = 2;
+    lut[0x0301] = 2;
+    lut[0x0102] = 2;
+    lut[0x0202] = 2;
+    lut[0x0302] = 2;
+    lut[0x0103] = 2;
+    lut[0x0203] = 2;
+    lut[0x0303] = 2;
+    return lut;
+}
+
+function createTypedLut2bits() {
+    const lut = new Uint8Array(256);
+    for (let a = 0; a < 4; ++a) {
+        for (let b = 0; b < 4; ++b) {
+            for (let c = 0; c < 4; ++c) {
+                for (let d = 0; d < 4; ++d) {
+                    const i = d | c << 2 | b << 4 | a << 6;
+                    const v = (a && 1) + (b && 1) + (c && 1) + (d && 1);
+                    lut[i] = v;
+                    // console.log([a, b, c, d], i, v);
+                }
+            }
+        }
+    }
+    return lut;
+}
+
+const lutNative = createNativeLut();
+const lutTyped = createTypedLut();
+const lutTyped2bits = createTypedLut2bits();
+
+function uint32ForLoopWithLutNative(array: Uint8Array, count: number): number {
+    if (count === 0) return 0;
+
+    const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
+    const viewEnd = (count - 4) >> 2;
+    const backStart = 4 * viewEnd;
+
+    let sum = 0;
+    for (let i = 0; i < viewEnd; ++i) {
+        const v = view[i];
+        sum += lutNative[v & 0xFFFF] + lutNative[v >> 16];
+    }
+    for (let i = backStart; i < count; ++i) {
+        sum += array[i] && 1;
+    }
+    return sum / count;
+}
+
+function uint32ForLoopWithLutTyped(array: Uint8Array, count: number): number {
+    if (count === 0) return 0;
+
+    const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
+    const viewEnd = (count - 4) >> 2;
+    const backStart = 4 * viewEnd;
+
+    let sum = 0;
+    for (let i = 0; i < viewEnd; ++i) {
+        const v = view[i];
+        sum += lutTyped[v & 0xFFFF] + lutTyped[v >> 16];
+    }
+    for (let i = backStart; i < count; ++i) {
+        sum += array[i] && 1;
+    }
+    return sum / count;
+}
+
+function uint32ForLoopWithLut2bits(array: Uint8Array, count: number): number {
+    if (count === 0) return 0;
+
+    const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
+    const viewEnd = (count - 4) >> 2;
+    const backStart = 4 * viewEnd;
+
+    let sum = 0;
+    for (let i = 0; i < viewEnd; ++i) {
+        const v = view[i];
+        sum += lutTyped2bits[(v >> 18 | v >> 12 | v >> 6 | v) & 0xFF];
+    }
+    for (let i = backStart; i < count; ++i) {
+        sum += array[i] && 1;
+    }
+    return sum / count;
+}
+
+function createData(elements: number, instances: number) {
+    const data = new Uint8Array(4000 * 5000);
+    const start = Math.floor(instances / 2);
+    data.fill(1, start, start + elements);
+    return data;
+};
+
+export function run(elements: number, instances: number) {
+    const suite = new B.Suite();
+    const count = elements * instances;
+    const data = createData(elements, instances);
+
+    console.log('uint8ForLoop', uint8ForLoop(data, count));
+    console.log('uint32ForLoop', uint32ForLoop(data, count));
+    console.log('uint32ForLoopWithLutNative', uint32ForLoopWithLutNative(data, count));
+    console.log('uint32ForLoopWithLutTyped', uint32ForLoopWithLutTyped(data, count));
+    console.log('uint32ForLoopWithLut2bits', uint32ForLoopWithLut2bits(data, count));
+
+    suite
+        .add('uint8ForLoop', () => uint8ForLoop(data, count))
+        .add('uint32ForLoop', () => uint32ForLoop(data, count))
+        .add('uint32ForLoopAddOnlyBaseline', () => uint32ForLoopAddOnlyBaseline(data, count))
+        .add('uint32ForLoopWithLutNative', () => uint32ForLoopWithLutNative(data, count))
+        .add('uint32ForLoopWithLutTyped', () => uint32ForLoopWithLutTyped(data, count))
+        .add('uint32ForLoopWithLut2bits', () => uint32ForLoopWithLut2bits(data, count))
+        .on('cycle', (e: any) => console.log(String(e.target)))
+        .run();
+}
+
+// console.log(createTypedLut2bits());
+
+// run(5000, 4000);
+// uint8ForLoop 0.00025
+// uint32ForLoop 0.00025
+// uint32ForLoopWithLutNative 0.00025
+// uint32ForLoopWithLutTyped 0.00025
+// uint32ForLoopWithLut2bits 0.00025
+// uint8ForLoop x 49.84 ops/sec ±3.30% (64 runs sampled)
+// uint32ForLoop x 97.70 ops/sec ±1.71% (71 runs sampled)
+// uint32ForLoopAddOnlyBaseline x 220 ops/sec ±2.49% (85 runs sampled)
+// uint32ForLoopWithLutNative x 135 ops/sec ±1.71% (76 runs sampled)
+// uint32ForLoopWithLutTyped x 137 ops/sec ±1.69% (77 runs sampled)
+// uint32ForLoopWithLut2bits x 111 ops/sec ±2.73% (70 runs sampled)