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Add solution by flippingbits - Use SIMD for computing aggregates

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* feat(flippingbits): First revision

* chore(flippingbits): Clean up output

* fix(flippingbits): Use ShortVector.SPECIES_MAX
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Stefan Sprenger 2024-01-06 18:13:52 +01:00 committed by GitHub
parent 1a9b1cb7da
commit 749d2d8f78
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calculate_average_flippingbits.sh Executable file
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#!/bin/sh
#
# Copyright 2023 The original authors
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
source "$HOME/.sdkman/bin/sdkman-init.sh"
sdk use java 21.0.1-graal 1>&2
JAVA_OPTS="--add-modules=jdk.incubator.vector"
time java $JAVA_OPTS --class-path target/average-1.0.0-SNAPSHOT.jar dev.morling.onebrc.CalculateAverage_flippingbits

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src/main/java/dev/morling/onebrc/CalculateAverage_flippingbits.java Normal file
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/*
* Copyright 2023 The original authors
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package dev.morling.onebrc;
import jdk.incubator.vector.ShortVector;
import jdk.incubator.vector.VectorOperators;
import java.io.IOException;
import java.io.RandomAccessFile;
import java.util.*;
/**
* Approach:
* - Use memory-mapped file to speed up loading data into memory
* - Partition data, compute aggregates for partitions in parallel, and finally combine results from all partitions
* - Apply SIMD instructions for computing min/max/sum aggregates
* - Use Shorts for storing aggregates of partitions, so we maximize the SIMD parallelism
*/
public class CalculateAverage_flippingbits {
private static final String FILE = "./measurements.txt";
private static final long CHUNK_SIZE = 100 * 1024 * 1024; // 100 MB
private static final int SIMD_LANE_LENGTH = ShortVector.SPECIES_MAX.length();
public static void main(String[] args) throws IOException {
try (var file = new RandomAccessFile(FILE, "r")) {
// Calculate chunk boundaries
long[][] chunkBoundaries = getChunkBoundaries(file);
// Process chunks
var result = Arrays.asList(chunkBoundaries).stream()
.map(chunk -> {
try {
return processChunk(chunk[0], chunk[1]);
}
catch (IOException e) {
throw new RuntimeException(e);
}
})
.parallel()
.reduce((firstMap, secondMap) -> {
for (var entry : secondMap.entrySet()) {
PartitionAggregate firstAggregate = firstMap.get(entry.getKey());
if (firstAggregate == null) {
firstMap.put(entry.getKey(), entry.getValue());
}
else {
firstAggregate.mergeWith(entry.getValue());
}
}
return firstMap;
})
.map(hashMap -> new TreeMap(hashMap)).get();
System.out.println(result);
}
}
private static long[][] getChunkBoundaries(RandomAccessFile file) throws IOException {
var fileSize = file.length();
// Split file into chunks, so we can work around the size limitation of channels
var chunks = (int) (fileSize / CHUNK_SIZE);
long[][] chunkBoundaries = new long[chunks + 1][2];
var endPointer = 0L;
for (var i = 0; i <= chunks; i++) {
// Start of chunk
chunkBoundaries[i][0] = Math.min(Math.max(endPointer, i * CHUNK_SIZE), fileSize);
// Seek end of chunk, limited by the end of the file
file.seek(Math.min(chunkBoundaries[i][0] + CHUNK_SIZE - 1, fileSize));
// Extend chunk until end of line or file
while (true) {
var character = file.read();
if (character == '\n' || character == -1) {
break;
}
}
// End of chunk
endPointer = file.getFilePointer();
chunkBoundaries[i][1] = endPointer;
}
return chunkBoundaries;
}
private static Map<String, PartitionAggregate> processChunk(long startOfChunk, long endOfChunk)
throws IOException {
Map<String, PartitionAggregate> stationAggregates = new HashMap<>(10_000);
byte[] byteChunk = new byte[(int) (endOfChunk - startOfChunk)];
try (var file = new RandomAccessFile(FILE, "r")) {
file.seek(startOfChunk);
file.read(byteChunk);
var i = 0;
while (i < byteChunk.length) {
final var startPosStation = i;
// read station name
while (byteChunk[i] != ';') {
i++;
}
var station = new String(Arrays.copyOfRange(byteChunk, startPosStation, i));
i++;
// read measurement
final var startPosMeasurement = i;
while (byteChunk[i] != '\n') {
i++;
}
var measurement = Arrays.copyOfRange(byteChunk, startPosMeasurement, i);
var aggregate = stationAggregates.getOrDefault(station, new PartitionAggregate());
aggregate.addMeasurementAndComputeAggregate(measurement);
stationAggregates.put(station, aggregate);
i++;
}
stationAggregates.values().forEach(PartitionAggregate::aggregateRemainingMeasurements);
}
return stationAggregates;
}
private static class PartitionAggregate {
final short[] lane = new short[SIMD_LANE_LENGTH * 2];
// Assume that we do not have more than Integer.MAX_VALUE measurements for the same station per partition
int count = 0;
long sum = 0;
short min = Short.MAX_VALUE;
short max = Short.MIN_VALUE;
public void addMeasurementAndComputeAggregate(byte[] measurementBytes) {
// Parse measurement and exploit that we know the format of the floating-point values
var measurement = measurementBytes[measurementBytes.length - 1] - '0';
var digits = 1;
for (var i = measurementBytes.length - 3; i > 0; i--) {
var num = measurementBytes[i] - '0';
measurement = measurement + (num * (int) Math.pow(10, digits));
digits++;
}
// Check if measurement is negative
if (measurementBytes[0] == '-') {
measurement = measurement * -1;
}
else {
var num = measurementBytes[0] - '0';
measurement = measurement + (num * (int) Math.pow(10, digits));
}
// Add measurement to buffer, which is later processed by SIMD instructions
lane[count % lane.length] = (short) measurement;
count++;
// Once lane is full, use SIMD instructions to calculate aggregates
if (count % lane.length == 0) {
var firstVector = ShortVector.fromArray(ShortVector.SPECIES_MAX, lane, 0);
var secondVector = ShortVector.fromArray(ShortVector.SPECIES_MAX, lane, SIMD_LANE_LENGTH);
var simdMin = firstVector.min(secondVector).reduceLanes(VectorOperators.MIN);
min = (short) Math.min(min, simdMin);
var simdMax = firstVector.max(secondVector).reduceLanes(VectorOperators.MAX);
max = (short) Math.max(max, simdMax);
sum += firstVector.add(secondVector).reduceLanes(VectorOperators.ADD);
}
}
public void aggregateRemainingMeasurements() {
for (var i = 0; i < count % lane.length; i++) {
var measurement = lane[i];
min = (short) Math.min(min, measurement);
max = (short) Math.max(max, measurement);
sum += measurement;
}
}
public void mergeWith(PartitionAggregate otherAggregate) {
min = (short) Math.min(min, otherAggregate.min);
max = (short) Math.max(max, otherAggregate.max);
count = count + otherAggregate.count;
sum = sum + otherAggregate.sum;
}
public String toString() {
return String.format(
Locale.US,
"%.1f/%.1f/%.1f",
(min / 10.0),
(sum / 10.0) / count,
(max / 10.0));
}
}
}