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Add k-nucleotide to BenchmarkGames 

Changed .gitattributes to set line endings to windows ones for the input
files of this test.
Added two different tests, one with and the other without parallelism.
Used FileStream instead of BufferedStream, since the latter does not
exist in netstandard 1.4
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1 parent 0dedbd5 commit 812230630b694f14ebf0d54eb1c357f4dfb9bb5a @guhuro guhuro committed Feb 2, 2017
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2 .gitattributes
@@ -71,4 +71,6 @@ tests/src/JIT/Performance/CodeQuality/BenchmarksGame/regexdna/regexdna-input25.t
tests/src/JIT/Performance/CodeQuality/BenchmarksGame/regexdna/regexdna-input25000.txt text eol=lf
tests/src/JIT/Performance/CodeQuality/BenchmarksGame/revcomp/revcomp-input25.txt text eol=lf
tests/src/JIT/Performance/CodeQuality/BenchmarksGame/revcomp/revcomp-input25000.txt text eol=lf
+tests/src/JIT/Performance/CodeQuality/BenchmarksGame/k-nucleotide/knucleotide-input.txt text eol=lf
+tests/src/JIT/Performance/CodeQuality/BenchmarksGame/k-nucleotide/knucleotide-input-big.txt text eol=lf
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312 tests/src/JIT/Performance/CodeQuality/BenchmarksGame/k-nucleotide/k-nucleotide.cs
@@ -0,0 +1,312 @@
+/* The Computer Language Benchmarks Game
+ http://benchmarksgame.alioth.debian.org/
+ *
+ * submitted by Josh Goldfoot
+ *
+ */
+
+using System;
+using System.IO;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using Microsoft.Xunit.Performance;
+using Xunit;
+
+[assembly: OptimizeForBenchmarks]
+[assembly: MeasureInstructionsRetired]
+[assembly: MeasureGCCounts]
+
+namespace BenchmarksGame
+{
+
+public class knucleotide
+{
+#if DEBUG
+ const int Iterations = 1;
+ const string InputFile = "knucleotide-input.txt";
+ static int[] expectedCountLetter = new int[] { 1480, 974, 970, 1576 };
+ static int[] expectedCountPairs = new int[] { 420, 272, 292, 496, 273, 202, 201, 298, 316, 185, 167, 302, 470, 315, 310, 480 };
+ static int[] expectedCountFragments = new int[] { 54, 24, 4, 0, 0 };
+#else
+ const int Iterations = 10;
+ const string InputFile = "knucleotide-input-big.txt";
+ static int[] expectedCountLetter = new int[] { 302923, 198136, 197566, 301375 };
+ static int[] expectedCountPairs = new int[] { 91779, 60030, 59889, 91225, 60096, 39203, 39081, 59756, 59795, 39190, 39023, 59557, 91253, 59713, 59572, 90837 };
+ static int[] expectedCountFragments = new int[] { 11765, 3572, 380, 7, 7 };
+#endif
+
+
+ static string FindInput(string s)
+ {
+ string CoreRoot = System.Environment.GetEnvironmentVariable("CORE_ROOT");
+
+ if (CoreRoot == null)
+ {
+ Console.WriteLine("This benchmark requries CORE_ROOT to be set");
+ return null;
+ }
+
+ string inputFile = s ?? InputFile;
+
+ // Normal testing -- input file will end up next to the assembly
+ // and CoreRoot points at the test overlay dir
+ string[] pathPartsNormal = new string[] {
+ CoreRoot, "..", "..", "JIT", "Performance",
+ "CodeQuality", "BenchmarksGame", "k-nucleotide", "k-nucleotide", inputFile
+ };
+
+ string inputPathNormal = Path.Combine(pathPartsNormal);
+
+ // Perf testing -- input file will end up next to the assembly
+ // and CoreRoot points at this directory
+ string[] pathPartsPerf = new string[] { CoreRoot, inputFile };
+
+ string inputPathPerf = Path.Combine(pathPartsPerf);
+
+ string inputPath = null;
+
+ if (File.Exists(inputPathNormal))
+ {
+ inputPath = inputPathNormal;
+ }
+ else if (File.Exists(inputPathPerf))
+ {
+ inputPath = inputPathPerf;
+ }
+
+ if (inputPath != null)
+ {
+ Console.WriteLine("Using input file {0}", inputPath);
+ }
+ else
+ {
+ Console.WriteLine("Unable to find input file {0}", inputFile);
+ }
+
+ return inputPath;
+ }
+
+ public static int Main(string[] args)
+ {
+ int iterations = Iterations;
+
+ string inputFile = FindInput(InputFile);
+ if (inputFile == null)
+ {
+ throw new Exception("unable to find input");
+ }
+
+ PrepareLookups();
+ var source = new FileStream(inputFile, FileMode.Open);
+ var buffer = GetBytesForThirdSequence(source);
+ var fragmentLengths = new[] { 1, 2, 3, 4, 6, 12, 18 };
+ var dicts =
+ (from fragmentLength in fragmentLengths.AsParallel()
+ select CountFrequency(buffer, fragmentLength)).ToArray();
+ source.Dispose();
+ int res = 100;
+ for (ulong i = 0; i < 4; ++i){
+ if (dicts[0][i].V != expectedCountLetter[i]){
+ res = -1;
+ }
+ }
+ for (ulong i = 0; i < 16; ++i){
+ if (dicts[1][i].V != expectedCountPairs[i]){
+ res = -1;
+ }
+ }
+ int buflen = dicts[0].Values.Sum(x => x.V);
+ WriteFrequencies(dicts[0], buflen, 1);
+ WriteFrequencies(dicts[1], buflen, 2);
+ if (WriteCount(dicts[2], "GGT") != expectedCountFragments[0]) { res = -1; }
+ if (WriteCount(dicts[3], "GGTA") != expectedCountFragments[1]) { res = -1; }
+ if (WriteCount(dicts[4], "GGTATT") != expectedCountFragments[2]) { res = -1; }
+ if (WriteCount(dicts[5], "GGTATTTTAATT") != expectedCountFragments[3]) { res = -1; }
+ if (WriteCount(dicts[6], "GGTATTTTAATTTATAGT") != expectedCountFragments[4]) { res = -1; }
+ //Console.ReadKey();
+ return res;
+ }
+
+ private static void WriteFrequencies(Dictionary<ulong, Wrapper> freq, int buflen, int fragmentLength)
+ {
+
+ double percent = 100.0 / (buflen - fragmentLength + 1);
+ foreach (var line in (from k in freq.Keys
+ orderby freq[k].V descending
+ select string.Format("{0} {1:f3}", PrintKey(k, fragmentLength),
+ (freq.ContainsKey(k) ? freq[k].V : 0) * percent)))
+ Console.WriteLine(line);
+ Console.WriteLine();
+ }
+
+ private static int WriteCount(Dictionary<ulong, Wrapper> dictionary, string fragment)
+ {
+ ulong key = 0;
+ var keybytes = Encoding.ASCII.GetBytes(fragment.ToLower());
+ for (int i = 0; i < keybytes.Length; i++)
+ {
+ key <<= 2;
+ key |= tonum[keybytes[i]];
+ }
+ Wrapper w;
+ int count = dictionary.TryGetValue(key, out w) ? w.V : 0;
+ Console.WriteLine("{0}\t{1}",
+ count,
+ fragment);
+ return count;
+ }
+
+ private static string PrintKey(ulong key, int fragmentLength)
+ {
+ char[] items = new char[fragmentLength];
+ for (int i = 0; i < fragmentLength; ++i)
+ {
+ items[fragmentLength - i - 1] = tochar[key & 0x3];
+ key >>= 2;
+ }
+ return new string(items);
+ }
+
+ private static Dictionary<ulong, Wrapper> CountFrequency(byte[] buffer, int fragmentLength)
+ {
+ var dictionary = new Dictionary<ulong, Wrapper>();
+ ulong rollingKey = 0;
+ ulong mask = 0;
+ int cursor;
+ for (cursor = 0; cursor < fragmentLength - 1; cursor++)
+ {
+ rollingKey <<= 2;
+ rollingKey |= tonum[buffer[cursor]];
+ mask = (mask << 2) + 3;
+ }
+ mask = (mask << 2) + 3;
+ int stop = buffer.Length;
+ Wrapper w;
+ byte cursorByte;
+ while (cursor < stop)
+ {
+ if ((cursorByte = buffer[cursor++]) < (byte)'a')
+ cursorByte = buffer[cursor++];
+ rollingKey = ((rollingKey << 2) & mask) | tonum[cursorByte];
+ if (dictionary.TryGetValue(rollingKey, out w))
+ w.V++;
+ else
+ dictionary.Add(rollingKey, new Wrapper(1));
+ }
+ return dictionary;
+ }
+
+ private static byte[] GetBytesForThirdSequence(FileStream source)
+ {
+ const int buffersize = 2500120;
+ byte[] threebuffer = null;
+ var buffer = new byte[buffersize];
+ int amountRead, threebuflen, indexOfFirstByteInThreeSequence, indexOfGreaterThan, threepos, tocopy;
+ amountRead = threebuflen = indexOfFirstByteInThreeSequence = indexOfGreaterThan = threepos = tocopy = 0;
+ bool threeFound = false;
+ //var source = new FileStream(inputFile, FileMode.Open);
+ source.Seek(0, SeekOrigin.Begin);
+ while (!threeFound && (amountRead = source.Read(buffer, 0, buffersize)) > 0)
+ {
+ indexOfGreaterThan = Array.LastIndexOf(buffer, (byte)'>');
+ threeFound = (indexOfGreaterThan > -1 &&
+ buffer[indexOfGreaterThan + 1] == (byte)'T' &&
+ buffer[indexOfGreaterThan + 2] == (byte)'H');
+ if (threeFound)
+ {
+ threepos += indexOfGreaterThan;
+ threebuflen = threepos - 48;
+ threebuffer = new byte[threebuflen];
+ indexOfFirstByteInThreeSequence = Array.IndexOf<byte>(buffer, 10, indexOfGreaterThan) + 1;
+ tocopy = amountRead - indexOfFirstByteInThreeSequence;
+ if (amountRead < buffersize)
+ tocopy -= 1;
+ Buffer.BlockCopy(buffer, indexOfFirstByteInThreeSequence, threebuffer, 0, tocopy);
+ buffer = null;
+ }
+ else
+ threepos += amountRead;
+ }
+ int toread = threebuflen - tocopy;
+ source.Read(threebuffer, tocopy, toread);
+ return threebuffer;
+ }
+
+ private static byte[] tonum = new byte[256];
+ private static char[] tochar = new char[4];
+ private static void PrepareLookups()
+ {
+ tonum['a'] = 0;
+ tonum['c'] = 1;
+ tonum['g'] = 2;
+ tonum['t'] = 3;
+ tochar[0] = 'A';
+ tochar[1] = 'C';
+ tochar[2] = 'G';
+ tochar[3] = 'T';
+ }
+
+ [Benchmark(InnerIterationCount=Iterations)]
+ public static void Bench_Parallel()
+ {
+ PrepareLookups();
+ string inputFile = FindInput(InputFile);
+ var source = new FileStream(inputFile, FileMode.Open);
+
+ if (inputFile == null)
+ {
+ throw new Exception("unable to find input");
+ }
+ foreach (var iteration in Benchmark.Iterations)
+ {
+ using (iteration.StartMeasurement())
+ {
+ for (int i = 0; i < Benchmark.InnerIterationCount; ++i)
+ {
+ var buffer = GetBytesForThirdSequence(source);
+ var fragmentLengths = new[] { 1, 2, 3, 4, 6, 12, 18 };
+ var dicts =
+ (from fragmentLength in fragmentLengths.AsParallel()
+ select CountFrequency(buffer, fragmentLength)).ToArray();
+ }
+ }
+ }
+ source.Dispose();
+ }
+ [Benchmark(InnerIterationCount=Iterations)]
+ public static void Bench_No_Parallel()
+ {
+ string inputFile = FindInput(InputFile);
+ var source = new FileStream(inputFile, FileMode.Open);
+
+ if (inputFile == null)
+ {
+ throw new Exception("unable to find input");
+ }
+ foreach (var iteration in Benchmark.Iterations)
+ {
+ using (iteration.StartMeasurement())
+ {
+ for (int i = 0; i < Benchmark.InnerIterationCount; ++i)
+ {
+ PrepareLookups();
+ var buffer = GetBytesForThirdSequence(source);
+ var fragmentLengths = new[] { 1, 2, 3, 4, 6, 12, 18 };
+ var dicts =
+ (from fragmentLength in fragmentLengths
+ select CountFrequency(buffer, fragmentLength)).ToArray();
+ }
+ }
+ }
+ source.Dispose();
+ }
+}
+
+public class Wrapper
+{
+ public int V;
+ public Wrapper(int v) { V = v; }
+}
+
+}
View
53 tests/src/JIT/Performance/CodeQuality/BenchmarksGame/k-nucleotide/k-nucleotide.csproj
@@ -0,0 +1,53 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="12.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+ <Import Project="$([MSBuild]::GetDirectoryNameOfFileAbove($(MSBuildThisFileDirectory), dir.props))\dir.props" />
+ <PropertyGroup>
+ <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
+ <Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
+ <SchemaVersion>2.0</SchemaVersion>
+ <ProjectGuid>{95DFC527-4DC1-495E-97D7-E94EE1F7140D}</ProjectGuid>
+ <OutputType>Exe</OutputType>
+ <AppDesignerFolder>Properties</AppDesignerFolder>
+ <FileAlignment>512</FileAlignment>
+ <ProjectTypeGuids>{786C830F-07A1-408B-BD7F-6EE04809D6DB};{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}</ProjectTypeGuids>
+ <ReferencePath>$(ProgramFiles)\Common Files\microsoft shared\VSTT\11.0\UITestExtensionPackages</ReferencePath>
+ <SolutionDir Condition="$(SolutionDir) == '' Or $(SolutionDir) == '*Undefined*'">..\..\</SolutionDir>
+ <NuGetPackageImportStamp>7a9bfb7d</NuGetPackageImportStamp>
+ <NuGetTargetMoniker>.NETStandard,Version=v1.4</NuGetTargetMoniker>
+ </PropertyGroup>
+ <!-- Default configurations to help VS understand the configurations -->
+ <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
+ </PropertyGroup>
+ <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
+ </PropertyGroup>
+ <PropertyGroup>
+ <DebugType>pdbonly</DebugType>
+ <Optimize>true</Optimize>
+ </PropertyGroup>
+ <ItemGroup>
+ <CodeAnalysisDependentAssemblyPaths Condition=" '$(VS100COMNTOOLS)' != '' " Include="$(VS100COMNTOOLS)..\IDE\PrivateAssemblies">
+ <Visible>False</Visible>
+ </CodeAnalysisDependentAssemblyPaths>
+ </ItemGroup>
+ <ItemGroup>
+ <Service Include="{82A7F48D-3B50-4B1E-B82E-3ADA8210C358}" />
+ </ItemGroup>
+ <ItemGroup>
+ <Compile Include="k-nucleotide.cs" />
+ </ItemGroup>
+ <ItemGroup>
+ <Content Include="knucleotide-input.txt">
+ <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+ </Content>
+ <Content Include="knucleotide-input-big.txt">
+ <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+ </Content>
+ </ItemGroup>
+ <PropertyGroup>
+ <ProjectJson>$(JitPackagesConfigFileDirectory)benchmark\project.json</ProjectJson>
+ <ProjectLockJson>$(JitPackagesConfigFileDirectory)benchmark\project.lock.json</ProjectLockJson>
+ </PropertyGroup>
+ <Import Project="$([MSBuild]::GetDirectoryNameOfFileAbove($(MSBuildThisFileDirectory), dir.targets))\dir.targets" />
+ <PropertyGroup Condition=" '$(MsBuildProjectDirOverride)' != '' ">
+ </PropertyGroup>
+</Project>
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