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312 changes: 312 additions & 0 deletions
312
tests/src/JIT/Performance/CodeQuality/BenchmarksGame/k-nucleotide/k-nucleotide.cs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
|
|
||
|
|
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| 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; | ||
| } | ||
|
|
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| string inputFile = s ?? InputFile; | ||
|
|
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| // 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 | ||
| }; | ||
|
|
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| string inputPathNormal = Path.Combine(pathPartsNormal); | ||
|
|
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| // Perf testing -- input file will end up next to the assembly | ||
| // and CoreRoot points at this directory | ||
| string[] pathPartsPerf = new string[] { CoreRoot, inputFile }; | ||
|
|
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| string inputPathPerf = Path.Combine(pathPartsPerf); | ||
|
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| string inputPath = null; | ||
|
|
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| 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); | ||
| } | ||
|
|
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| return inputPath; | ||
| } | ||
|
|
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| public static int Main(string[] args) | ||
| { | ||
| int iterations = Iterations; | ||
|
|
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| 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; | ||
| } | ||
|
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| private static void WriteFrequencies(Dictionary<ulong, Wrapper> freq, int buflen, int fragmentLength) | ||
| { | ||
|
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| 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(); | ||
| } | ||
|
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| 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; | ||
| } | ||
|
|
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| 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; } | ||
| } | ||
|
|
||
| } | ||
53 changes: 53 additions & 0 deletions
53
tests/src/JIT/Performance/CodeQuality/BenchmarksGame/k-nucleotide/k-nucleotide.csproj
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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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Are you guaranteed to have CORE_ROOT set?