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 performance measurements

Each table row shows performance measurements for this C# Mono program with a particular command-line input value N.

 N  CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
250,0003.241.2650,0522445  70% 69% 60% 62%
2,500,00020.066.3284,2362445  77% 77% 78% 86%
25,000,000188.3256.25539,2482445  85% 81% 81% 90%

Read the ↓ make, command line, and program output logs to see how this program was run.

Read k-nucleotide benchmark to see what this program should do.

 notes

Mono JIT compiler version 3.0.3 (tarball Tue Feb 12 21:22:20 PST 2013)
LLVM: yes(3.2svn-mono)

 k-nucleotide C# Mono #5 program source code

/* The Computer Language Benchmarks Game

   http://benchmarksgame.alioth.debian.org/

 *

 * contributed by by Robert F. Tobler

 *  + byte processing, C# 3.0 idioms, frame level paralellism

 * modified by Jonathan C. Dickinson

 *  + unsafe code, string-free, micro-optimizations, best performance practices

 *   (33% faster on MSFT CLR)

 */

using System;
using System.IO;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Threading;
using System.Diagnostics;

public sealed class ByteString : IEquatable<ByteString>, IComparable<ByteString>
{
   public readonly byte[] Array;
   public readonly int Start;
   public readonly int Length;
   private int HashCode;

   public unsafe ByteString(byte[] array, int start, int length)
   {
      Array = array; Start = start; Length = length;
      HashCode = 0;
      fixed (byte* ptrFixed = &Array[Start])
      {
         byte* ptr = ptrFixed;
         for (int i = 0; i < Length; i++)
            HashCode = HashCode * 31 + *ptr++;
      }
   }

   public unsafe ByteString(string text)
   {
      Start = 0; Length = text.Length;
      Array = Encoding.ASCII.GetBytes(text);
      HashCode = 0;
      fixed (byte* ptrFixed = &Array[Start])
      {
         byte* ptr = ptrFixed;
         for (int i = 0; i < Length; i++)
            HashCode = HashCode * 31 + *ptr++;
      }
   }

   public override int GetHashCode()
   {
      return HashCode;
   }

   public unsafe bool Equals(ByteString other)
   {
      if (Length != other.Length) return false;
      fixed (byte* thisFixed = &Array[Start], otherFixed = &other.Array[other.Start])
      {
         var tf = thisFixed;
         var of = otherFixed;
         for (int i = 0; i < Length; i++)
            if (*(tf++) != *(of++)) return false;
      }
      return true;
   }

   public unsafe int CompareTo(ByteString other)
   {
      // Converting to strings to compare is just wasteful.


      var len = Math.Min(this.Length, other.Length);
      fixed (byte* thisFixed = &Array[Start], otherFixed = &other.Array[other.Start])
      {
         var tf = thisFixed;
         var of = otherFixed;
         // We have to do this loop because of how strings compare.

         for (var i = 0; i < len; i++)
         {
            var c1 = (char)(*(tf++));
            var c2 = (char)(*(of++));
            var c = c1.CompareTo(c2);
            if (c != 0)
               return c;
         }
      }

      return this.Length.CompareTo(other.Length);
   }

   public override string ToString()
   {
      return Encoding.ASCII.GetString(Array, Start, Length);
   }
}

public static class Extensions
{
   public static readonly byte[] NewLine;

   static Extensions()
   {
      //NewLine = Environment.NewLine.Select(x => (byte)x).ToArray();

      NewLine = new[] { (byte)'\n' };
   }

   public static bool Contains(this byte[] buffer, byte[] data)
   {
      var index = 0;
      for (var i = 0; i < buffer.Length - data.Length; i++)
      {
         var b = buffer[i];

         // ToUpper

         if (b > 96 && b < 123)
            b = (byte)(b - 32);

         if (data[index] == b)
         {
            index++;
            if (index == data.Length)
            {
               return true;
            }
         }
         else
         {
            index = 0;
         }
      }
      return false;
   }

   public static IEnumerable<byte[]> ReadByteLines(this Stream stream)
   {
      // Read a stream as a set of byte arrays representing strings.

      var dynamic = new byte[85];
      var lineLength = 0;

      var buffer = new byte[4096]; // Ideally the system page size but I am not sure what Linux uses.

      var index = 0;
      var readCount = 0;

      while ((readCount = stream.Read(buffer, 0, buffer.Length)) != 0)
      {
         for (var i = 0; i < readCount; i++)
         {
            var b = buffer[i];

            // ToUpper

            if (b > 96 && b < 123)
               b = (byte)(b - 32);

            // Check for a newline.

            if (NewLine[index] == b)
            {
               index++;
               if (index == NewLine.Length)
               {
                  if (lineLength == 0)
                     yield return new byte[0];
                  var result = new byte[lineLength];
                  Buffer.BlockCopy(dynamic, 0, result, 0, lineLength);
                  yield return result;
                  lineLength = 0;
                  index = 0;
               }
            }
            else
            {
               // Otherwise append what we had of the newline.

               for (var j = 0; j < index; j++)
               {
                  Append(ref dynamic, ref lineLength, NewLine[j]);
               }

               // And the data.

               index = 0;
               Append(ref dynamic, ref lineLength, b);
            }
         }
      }
   }

   private static void Append(ref byte[] dynamic, ref int lineLength, byte b)
   {
      var newLength = lineLength + 1;
      if (dynamic.Length < newLength)
      {
         // Allocate into an new array but use a DMA function

         // instead of a silly O(n) Array.Copy/Resize.

         var newArr = new byte[dynamic.Length + 85];
         Buffer.BlockCopy(dynamic, 0, newArr, 0, dynamic.Length);
         dynamic = newArr;
      }
      dynamic[lineLength] = b;
      lineLength = newLength;
   }

   public static byte[] Concat(this IList<byte[]> bytes, int totalCount)
   {
      // Once again we use DMA.

      var buffer = new byte[totalCount];
      var pos = 0;
      for (var i = 0; i < bytes.Count; i++)
      {
         var arr = bytes[i];
         Buffer.BlockCopy(arr, 0, buffer, pos, arr.Length);
         pos += arr.Length;
      }
      return buffer;
   }
}

public static class Program
{
   public static int TaskCount;
   public static int Current = -1;
   public static KNucleotide[] kna;

   public static void Main(string[] args)
   {
      // The help page asks to deal with command-line args.

      var source = Console.OpenStandardInput();
      var input = new List<byte[]>();
      var totalCount = 0;

      var hasSeenThree = false;
      foreach (var line in source.ReadByteLines())
      {
         if (!hasSeenThree)
         {
            hasSeenThree = line.Contains(new[] { (byte)'>', (byte)'T', (byte)'H', (byte)'R', (byte)'E', (byte)'E' });
            continue;
         }
         if (line[0] == (byte)'>') break;
         if (line[0] != (byte)';')
         {
            totalCount += line.Length;
            input.Add(line);
         }
      }

      var lengths = new[] { 1, 2, 3, 4, 6, 12, 18 };
      TaskCount = lengths.Aggregate(0, (cnt, len) => cnt + len); // Wasteful but likely not an issue.

      kna = new KNucleotide[TaskCount];

      var bytes = input.Concat(totalCount);
      lengths.Aggregate(0, (cnt, len) =>
      {
         for (int i = 0; i < len; i++)
            kna[cnt + i] = new KNucleotide(bytes, len, i);
         return cnt + len;
      });

      // This technically should be faster, but my profiler is broken.

      var events = new AutoResetEvent[Environment.ProcessorCount];
      for (int i = 0; i < events.Length; i++)
      {
         events[i] = new AutoResetEvent(false);
         new Thread(CountFrequencies).Start(events[i]);
      }

      WaitHandle.WaitAll(events);

      // Converting these to byte arrays at compile time is slightly wasteful but likely premature.

      var seqs = new[] { null, null,
            "GGT", "GGTA", "GGTATT", "GGTATTTTAATT",
            "GGTATTTTAATTTATAGT"};

      int index = 0;
      lengths.Aggregate(0, (cnt, len) =>
      {
         if (len < 3)
         {
            for (int i = 1; i < len; i++)
               kna[cnt].AddFrequencies(kna[cnt + i]);
            kna[cnt].WriteFrequencies();
         }
         else
         {
            var fragment = seqs[index];
            int freq = 0;
            for (int i = 0; i < len; i++)
               freq += kna[cnt + i].GetCount(fragment);
            Console.WriteLine("{0}\t{1}", freq, fragment);
         }
         index++;
         return cnt + len;
      });
   }

   static void CountFrequencies(object state)
   {
      int index;
      while ((index = Interlocked.Increment(ref Current)) < TaskCount)
         kna[index].KFrequency();
      ((AutoResetEvent)state).Set();
   }

}

public sealed class KNucleotide
{

   private sealed class Count
   {
      public int V;
      public Count(int v) { V = v; }
   }

   private Dictionary<ByteString, Count> frequencies
      = new Dictionary<ByteString, Count>();

   private byte[] sequence;
   int length;
   int frame;

   public KNucleotide(byte[] s, int l, int f)
   {
      sequence = s; length = l; frame = f;
   }

   public void AddFrequencies(KNucleotide other)
   {
      foreach (var kvp in other.frequencies)
      {
         Count count;
         if (frequencies.TryGetValue(kvp.Key, out count))
            count.V += kvp.Value.V;
         else
            frequencies[kvp.Key] = kvp.Value;
      }
   }

   public void WriteFrequencies()
   {
      var items = frequencies.ToArray();
      Array.Sort(items, SortByFrequencyAndCode); // Apparantly faster, who knows?

      double percent = 100.0 / (sequence.Length - length + 1);
      foreach (var item in items)
         Console.WriteLine("{0} {1:f3}",
                  item.Key.ToString(), item.Value.V * percent);
      Console.WriteLine();
   }

   public int GetCount(string fragment)
   {
      Count count;
      if (!frequencies.TryGetValue(new ByteString(fragment), out count))
         count = new Count(0);
      return count.V;
   }

   public void KFrequency()
   {
      int n = sequence.Length - length + 1;
      for (int i = frame; i < n; i += length)
      {
         var key = new ByteString(sequence, i, length);
         Count count;
         if (frequencies.TryGetValue(key, out count))
            count.V++;
         else
            frequencies[key] = new Count(1);
      }
   }

   int SortByFrequencyAndCode(
         KeyValuePair<ByteString, Count> i0,
         KeyValuePair<ByteString, Count> i1)
   {
      int order = i1.Value.V.CompareTo(i0.Value.V);
      if (order != 0) return order;
      return i0.Key.CompareTo(i1.Key);
   }
}

 make, command-line, and program output logs

Wed, 13 Feb 2013 07:40:44 GMT

MAKE:
mv knucleotide.csharp-5.csharp knucleotide.csharp-5.cs
/usr/local/bin/mcs -unsafe+ -optimize+ -platform:x64 -out:knucleotide.csharp-5.csharp_run knucleotide.csharp-5.cs
rm knucleotide.csharp-5.cs
0.31s to complete and log all make actions

COMMAND LINE:
/usr/local/bin/mono --llvm knucleotide.csharp-5.csharp_run 0 < knucleotide-input25000000.txt

PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754

AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902

1471758	GGT
446535	GGTA
47336	GGTATT
893	GGTATTTTAATT
893	GGTATTTTAATTTATAGT

<premain>: CommandLine Error: Argument 'misched' defined more than once!
<premain>: CommandLine Error: Argument 'print-machineinstrs' defined more than once!
-simplifycfg: CommandLine Error: Argument 'misched' defined more than once!
-simplifycfg: CommandLine Error: Argument 'print-machineinstrs' defined more than once!

Revised BSD license

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