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Diffstat (limited to 'tests/src/JIT/Performance/CodeQuality/BenchmarksGame/k-nucleotide/k-nucleotide.cs')
| -rw-r--r-- | tests/src/JIT/Performance/CodeQuality/BenchmarksGame/k-nucleotide/k-nucleotide.cs | 312 |
1 files changed, 312 insertions, 0 deletions
diff --git a/tests/src/JIT/Performance/CodeQuality/BenchmarksGame/k-nucleotide/k-nucleotide.cs b/tests/src/JIT/Performance/CodeQuality/BenchmarksGame/k-nucleotide/k-nucleotide.cs new file mode 100644 index 0000000000..54bd10702c --- /dev/null +++ b/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; } +} + +}
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