performance measurements

Each table row shows performance measurements for this Ada 2005 GNAT program with a particular command-line input value N.

 N  CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
250,0000.160.16?6503  0% 0% 0% 100%
2,500,0001.121.1347,3886503  2% 6% 1% 100%
25,000,00010.9610.97407,4326503  1% 0% 1% 100%

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.



gcc version 4.8.2 (Ubuntu 4.8.2-19ubuntu1)

 k-nucleotide Ada 2005 GNAT program source code

--  The Computer Language Benchmarks Game
--  Contributed by Martin Krischik
--  Modified by Georg Bauhaus and Jonathan Parker (Oct 2012)

--  Uses representation for compacting. Idea for uppercasing on the
--  fly taken from Rikard Mustajärvi's Java program.

pragma Profile (Ravenscar);

with Data_Input;          use Data_Input;
with Data;                use Data;
with Statistics.Setup;    use Statistics;
with Statistics.Aux;
with GNAT.OS_Lib;

procedure KNucleotide is
   Input_Text : Writable_String_Access;
   Input_Text  := new String'(Read);
   Setup.Buffer := To_Compressed (Plain_View (Input_Text));
   Free (Input_Text);


   GNAT.OS_Lib.OS_Exit (0);
end KNucleotide;

package Statistics is
   pragma Pure;
   type Fragment_Lengths is range 1 .. 18;
end Statistics;

with Statistics.Work;
with Data.Text_Fragments;
with Interfaces;
with Ada.Unchecked_Conversion;
package Statistics.Setup is

   generic function UC renames Ada.Unchecked_Conversion;

   subtype U8 is Interfaces.Unsigned_8;
   subtype U16 is Interfaces.Unsigned_16;
   subtype U32 is Interfaces.Unsigned_32;
   subtype U64 is Interfaces.Unsigned_64;

   type F is array (Fragment_Lengths range <>) of Data.Symbol;
   for F'Component_Size use Data.Symbol'Size;

   subtype FX1 is Fragment_Lengths range 1 .. 1;
   type F1 is new F (FX1);
   for F1'Size use U8'Size;
   function To_U is new UC (F1, U8);

   subtype FX2 is Fragment_Lengths range 1 .. 2;
   type F2 is new F (FX2);
   for F2'Size use U8'Size;
   function To_U is new UC (F2, U8);

   subtype FX3 is Fragment_Lengths range 1 .. 3;
   type F3 is new F (FX3);
   for F3'Size use U8'Size;
   function To_U is new UC (F3, U8);

   subtype FX4 is Fragment_Lengths range 1 .. 4;
   type F4 is new F (FX4);
   for F4'Size use U8'Size;
   function To_U is new UC (F4, U8);

   subtype FX6 is Fragment_Lengths range 1 .. 6;
   type F6 is new F (FX6);
   for F6'Size use U16'Size;
   function To_U is new UC (F6, U16);

   subtype FX12 is Fragment_Lengths range 1 .. 12;
   type F12 is new F (FX12);
   for F12'Size use U32'Size;
   function To_U is new UC (F12, U32);

   subtype FX18 is Fragment_Lengths range 1 .. 18;
   type F18 is new F (FX18);
   for F18'Size use U64'Size;
   function To_U is new UC (F18, U64);

   package Fragments_1 is new Data.Text_Fragments (FX1, F1, U8);
   package Fragments_2 is new Data.Text_Fragments (FX2, F2, U8);
   package Fragments_3 is new Data.Text_Fragments (FX3, F3, U8);
   package Fragments_4 is new Data.Text_Fragments (FX4, F4, U8);
   package Fragments_6 is new Data.Text_Fragments (FX6, F6, U16);
   package Fragments_12 is new Data.Text_Fragments (FX12, F12, U32);
   package Fragments_18 is new Data.Text_Fragments (FX18, F18, U64);

   package Work_On_1 is new Work (Fragments_1);
   package Work_On_2 is new Work (Fragments_2);
   package Work_On_3 is new Work (Fragments_3);
   package Work_On_4 is new Work (Fragments_4);
   package Work_On_6 is new Work (Fragments_6);
   package Work_On_12 is new Work (Fragments_12);
   package Work_On_18 is new Work (Fragments_18);

   Buffer : aliased Data.Compressed_View;

   Worker_1 : Work_On_1.Counting_Job (Buffer'Access, 1, null);
   Worker_2 : Work_On_2.Counting_Job (Buffer'Access, 2, null);
   Worker_3 : Work_On_3.Counting_Job (Buffer'Access, 3, new F3'("GGT"));
   Worker_4 : Work_On_4.Counting_Job (Buffer'Access, 4, new F4'("GGTA"));
   Worker_6 : Work_On_6.Counting_Job (Buffer'Access, 6, new F6'("GGTATT"));
   Worker_12 : Work_On_12.Counting_Job
     (Buffer'Access, 12, new F12'("GGTATTTTAATT"));
   Worker_18 : Work_On_18.Counting_Job
     (Buffer'Access, 18, new F18'("GGTATTTTAATTTATAGT"));

end Statistics.Setup;

package Data is

   pragma Preelaborate (Data);

   type Symbol is ('A', 'C', 'G', 'T');
   for Symbol'Size use 2;

   type Compressed is array (Positive range <>) of Symbol;
   for Compressed'Component_Size use Symbol'Size;

   type Translation_Table is array (Character range <>) of Symbol;
   To_Symbol : constant Translation_Table ('A' .. 't') :=
     ('A' => 'A', 'a' => 'A',
      'C' => 'C', 'c' => 'C',
      'G' => 'G', 'g' => 'G',
      'T' => 'T', 't' => 'T', others => 'A');

   type Elbat_Noitalsnart is array (Symbol range <>) of Character;
   To_Character : constant Elbat_Noitalsnart ('A' .. 'T') :=
     ('A' => 'A',
      'C' => 'C',
      'G' => 'G',
      'T' => 'T');

   type Plain_View is access constant String;
   type Compressed_View is access constant Compressed;

   function To_Compressed (Buffer : Plain_View) return Compressed_View;

end Data;

package body Data is

   type Compressed_Access is access Compressed;

   function To_Compressed (Buffer : Plain_View) return Compressed_View is
      Result : constant Compressed_Access := new Compressed (Buffer'Range);
      for K in Buffer'Range loop
         Result (K) := To_Symbol (Buffer (K));
      end loop;
      return Compressed_View (Result);
   end To_Compressed;

end Data;

with Statistics;    use Statistics;
with Ada.Containers;
   type Fragment_Index is new Fragment_Lengths;
   type Compact is array (Fragment_Index) of Symbol;
   type Rep_Type is mod <>;
   with function To_U (S : Compact) return Rep_Type is <>;
package Data.Text_Fragments is

   pragma Preelaborate (Text_Fragments);

   type Fragment is array (Fragment_Index) of Character;

   function Hash (Key : Compact) return Ada.Containers.Hash_Type;
   function Eq (Left, Right : Compact) return Boolean;
   function "=" (Left, Right : Compact) return Boolean is abstract;

   function To_Fragment (Source : Compact) return Fragment;

end Data.Text_Fragments;

package body Data.Text_Fragments is

   Size : constant Fragment_Index := Fragment_Index'Last;

   function Hash (Key : Compact) return Ada.Containers.Hash_Type is
      subtype HT is Ada.Containers.Hash_Type;
      pragma Assert (HT'Size <= 32);
      if    Size <=  4 then return HT (To_U (Key) and 16#FF#);
      elsif Size <=  8 then return HT (To_U (Key) and 16#FFFF#);
      elsif Size <= 16 then return HT (To_U (Key));
         return HT (To_U (Key) and 16#FFFF_FFFF#);
      end if;
   end Hash;

   function Eq (Left, Right : Compact) return Boolean is
      if    Size <=  4 then
         return (To_U (Left) and 16#FF#) = (To_U (Right) and 16#FF#);
      elsif Size <=  8 then
         return (To_U (Left) and 16#FFFF#) = (To_U (Right) and 16#FFFF#);
      elsif Size <= 16 then
         return To_U (Left) = To_U (Right);
         return To_U (Left) = To_U (Right);
      end if;
   end Eq;

   function To_Fragment (Source : Compact) return Fragment is
      Result : Fragment;
      for K in Source'Range loop
         Result (K) := To_Character (Source (K));
      end loop;
      return Result;
   end To_Fragment;

end Data.Text_Fragments;

with Data.Text_Fragments;
   with package Fragments is new Data.Text_Fragments (<>);
package Statistics.Calculator is

   use Fragments;

   --  Elements used to store inside hash table:

   type Element_Type is private;
   type Element_Access is access Element_Type;
   for Element_Access'Storage_Size use 16#40_00_00#;

   --  Iteration:

   function Get_First return Element_Access;
   function Get_Next return Element_Access;

   --  Key and value:

   function Count_Of (Element : not null Element_Access) return Natural;
   function Fragment_Of (Element : not null Element_Access) return Compact;

   --  Calculate frequency of occurrences of the nucleotides:

   procedure Get_Frequencies_Big (Buffer : Data.Compressed);
   procedure Get_Frequencies_Small (Buffer : Data.Compressed);

   function Occurrences (Nucleotide_Fragment : Compact) return Natural;
   procedure Get_Totals (Total : out Natural; Count : out Natural);

   type Element_Type is record
      Count : Natural := 0;
      Key   : Compact;
      Next  : Element_Access;
   end record;
end Statistics.Calculator;

with GNAT.HTable;
with Ada.Containers;
with Ada.Unchecked_Conversion;
with Interfaces;

package body Statistics.Calculator is

   --  Prepare table.

   Log_Table_Size : constant Natural :=
     Natural'Min (Natural (Fragment'Last) * 2 + 4, 17);

   Table_Size     : constant Natural := 2 ** Log_Table_Size;

   subtype Hash_Type is Natural range 0 .. Table_Size - 1;

   function Hash (Key : Compact) return Hash_Type is
      use type Ada.Containers.Hash_Type;
      return Hash_Type (Fragments.Hash (Key)
                           mod Ada.Containers.Hash_Type (Table_Size));
   end Hash;

   function Next (E : Element_Access) return Element_Access is
      return E.all.Next;
   end Next;

   procedure Set_Next (E : Element_Access; Next_Element : Element_Access) is
      E.all.Next := Next_Element;
   end Set_Next;

   function Get_Key (E : not null Element_Access) return Compact is
      return E.all.Key;
   end Get_Key;

   package Table is new GNAT.HTable.Static_HTable
     (Header_Num => Hash_Type,
      Element    => Element_Type,
      Elmt_Ptr   => Element_Access,
      Null_Ptr   => null,
      Key        => Compact,
      Hash       => Hash,
      Equal      => Fragments.Eq,
      Set_Next   => Set_Next,
      Next       => Next,
      Get_Key    => Get_Key);

   --  Counting

   function To_Compact is new Ada.Unchecked_Conversion (Rep_Type, Compact);

   Bits_per_Fragment : constant Positive :=
     Data.Symbol'Size * Fragments.Compact'Length;

      type U is mod <>;
   procedure TAdd (Value : U);
   procedure TAdd (Value : U) is
      Key : constant Compact := To_Compact (Rep_Type (Value));
      Element : constant Element_Access := Table.Get (Key);
      if Element /= null then
         Element.all.Count := Natural'Succ (Element.all.Count);
         Table.Set (new Element_Type'(Count => 1,
                                      Key => Key,
                                      Next => null));
      end if;
   end TAdd;

      type U is mod <>;
      with function Shift_Left (Value : U; Amount : Natural) return U is <>;
      with function Shift_Right (Value : U; Amount : Natural) return U is <>;
   procedure Get_Frequencies (Buffer : Data.Compressed);
   procedure Get_Frequencies (Buffer : Data.Compressed) is

      procedure Add_to_Table is new TAdd (U);

      S : constant          := Data.Symbol'Size;
      W : constant Positive := U'Size / 16 - 1;
      Symbols_per_U : constant Positive := U'Size / S;
      No_of_U       : constant Natural  := (S * Buffer'Length) /  U'Size;
      Mask          : constant U        := 2**Bits_per_Fragment - 1;

      Overlay       : array (1 .. No_of_U) of U;
      pragma Import (Ada, Overlay);
      for Overlay'Address use Buffer (Buffer'First)'Address;
      Bits          : U;
      Bits := Overlay (Overlay'First);
      for K in  2 .. Overlay'Last  loop
         for HW in 0 .. W loop
            for j in 1 .. 16/S loop
               Add_to_Table (Bits and Mask);
               Bits := Shift_Right (Bits, S);
            end loop;
            Bits := Shift_Left (Shift_Right (Overlay (K), HW * 16),
                                W * 16) or Bits;
         end loop;
      end loop;

      for j in 1 .. Symbols_per_U - Compact'Length + 1 loop
         Add_to_Table (Bits and Mask);
         Bits := Shift_Right (Bits, S);
      end loop;

      for k in Symbols_per_U * No_of_U + 1 - Compact'Length + 1
        .. Buffer'Length - Compact'Length + 1
         Add_to_Table (U (Fragments.To_U
                           (Compact (Buffer (k .. k + Compact'Length - 1)))));
      end loop;
   end Get_Frequencies;

   use Interfaces;
   procedure FSmall is new Get_Frequencies (Unsigned_32);
   procedure FBig is new Get_Frequencies (Unsigned_64);

   procedure Get_Frequencies_Small (Buffer : Data.Compressed) renames FSmall;
   procedure Get_Frequencies_Big (Buffer : Data.Compressed) renames FBig;

   function Count_Of (Element : not null Element_Access) return Natural is
      return Element.all.Count;
   end Count_Of;

   function Occurrences (Nucleotide_Fragment : Compact) return Natural is
      The_Element : constant Element_Access := Table.Get (Nucleotide_Fragment);
      if The_Element /= null then
         return The_Element.all.Count;
         return 0;
      end if;
   end Occurrences;

   function Get_First return Element_Access renames Table.Get_First;
   function Get_Next return Element_Access renames Table.Get_Next;

   procedure Get_Totals (Total : out Natural; Count : out Natural) is
      The_Element : Element_Access := Table.Get_First;
      Total := 0;
      Count := 0;
      while The_Element /= null loop
         Total       := Total + The_Element.all.Count;
         Count       := Count + 1;
         The_Element := Table.Get_Next;
      end loop;
   end Get_Totals;

   function Fragment_Of (Element : not null Element_Access) return Compact is
      return Element.all.Key;
   end Fragment_Of;

end Statistics.Calculator;

package Statistics.Aux is

   pragma Elaborate_Body (Aux);

   type Summary is abstract tagged limited null record;
   type Report is access constant Summary'Class;

   procedure Print (Info : Summary) is abstract;

   protected Printer is
      procedure Log_Percent (L : Fragment_Lengths; Result : Report);
      procedure Log_Count (L : Fragment_Lengths; Result : Report);
   end Printer;

   procedure Print_When_Finished;

   --  Tasks will start once their suspension objects become true:
   procedure Unlock;
   procedure Wait (Lock_Number : Fragment_Lengths);

end Statistics.Aux;

with Ada.Synchronous_Task_Control;    use Ada.Synchronous_Task_Control;
package body Statistics.Aux is

   type Task_ID is range 1 .. 7;

   Lock  : array (Task_ID) of Suspension_Object;
   Ready : Suspension_Object;

   Percents : array (Fragment_Lengths range 1 .. 2) of Report;
   Counts   : array (Fragment_Lengths range 3 .. 18) of Report;

   Selection : constant array (Task_ID) of Fragment_Lengths :=
     (1, 2, 3, 4, 6, 12, 18);

   function All_Present return Boolean is
      for K in Selection'First .. Selection'First + 1 loop
         if Percents (Selection (K)) = null then
            return False;
         end if;
      end loop;
      for K in Selection'First + 2 .. Selection'Last loop
         if Counts (Selection (K)) = null then
            return False;
         end if;
      end loop;
      return True;
   end All_Present;

   protected body Printer is

      procedure Log_Percent (L : Fragment_Lengths; Result : Report) is
         Percents (L) := Result;
         if All_Present then
            Set_True (Ready);
         end if;
      end Log_Percent;

      procedure Log_Count (L : Fragment_Lengths; Result : Report) is
         Counts (L) := Result;
         if All_Present then
            Set_True (Ready);
         end if;
      end Log_Count;

   end Printer;

   procedure Print_When_Finished is
      Suspend_Until_True (Ready);
      for K in Selection'First .. Selection'First + 1 loop
         Percents (Selection (K)).Print;
      end loop;
      for K in Selection'First + 2 .. Selection'Last loop
         Counts (Selection (K)).Print;
      end loop;
   end Print_When_Finished;

   procedure Unlock is
      for Id in Lock'Range loop
         Set_True (Lock (Id));
      end loop;
   end Unlock;

   procedure Wait (Lock_Number : Fragment_Lengths) is
      Id_Map : constant array (Fragment_Lengths) of Task_ID :=
        (1, 2, 3, 4, 5, 5, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7);
      Suspend_Until_True (Lock (Id_Map (Lock_Number)));
   end Wait;

end Statistics.Aux;

with Data.Text_Fragments;
with System;
   with package Fragments is new Data.Text_Fragments (<>);
package Statistics.Work is

   pragma Elaborate_Body (Work);

   task type Counting_Job
     (Buffer : access constant Data.Compressed_View;
      Length : Fragment_Lengths;
      Nucleotide_Fragment : access constant Fragments.Compact)
      pragma Storage_Size (2**18);
      pragma Priority (Positive'Min
                         (System.Default_Priority + Positive (Length),
   end Counting_Job;

end Statistics.Work;

with Ada.Containers.Generic_Constrained_Array_Sort;
with Ada.Text_IO, Ada.Float_Text_IO, Ada.Integer_Text_IO;
with Ada.Characters.Latin_1;
with Statistics.Aux;
with Statistics.Calculator;

package body Statistics.Work is

   package Stats is new Statistics.Calculator (Fragments);

   type Summary_Data is array (Natural range <>) of Stats.Element_Access;

   type Summary_Info (Num_Table_Entries : Natural;
                      Sum_of_Counts     : Natural) is new Aux.Summary with
         Data : Summary_Data (1 .. Num_Table_Entries);
      end record;

   procedure Print (Info : Summary_Info) is
      for I in 1 .. Info.Data'Last loop
           (String (Fragments.To_Fragment
                      (Stats.Fragment_Of (Info.Data (I)))) & ' ');
           (Item => (100.0
                       * Float (Stats.Count_Of (Info.Data (I)))
                       / Float (Info.Sum_of_Counts)),
            Fore => 1,
            Aft  => 3,
            Exp  => 0);
      end loop;
   end Print;

   type Fragment_Info is new Aux.Summary with
         Counted : Natural;
         Nucleotide_Fragment : Fragments.Fragment;
      end record;

   procedure Print (Info : Fragment_Info) is
        (Item => Info.Counted,
         Width => 1);
      Ada.Text_IO.Put (Ada.Characters.Latin_1.HT);
      Ada.Text_IO.Put_Line (String (Info.Nucleotide_Fragment));
   end Print;

   Num_Table_Entries : Natural;
   Sum_of_Counts     : Natural;

   procedure Perform_Counting (Buffer : Data.Compressed) is
      if Fragments.Compact'Length >= 12 then
         Stats.Get_Frequencies_Big (Buffer);
         Stats.Get_Frequencies_Small (Buffer);
         if Fragments.Compact'Length <= 2 then
              (Total => Sum_of_Counts,
               Count => Num_Table_Entries);
         end if;
      end if;
   end Perform_Counting;

   procedure Write_Percent (Nucleotide_Length : Fragment_Lengths) is
      use Fragments;
      subtype Index is Natural range 1 .. Num_Table_Entries;
      subtype List_of_Results is Summary_Data (Index);

      Sheet : List_of_Results;

      function Less_Than (Left, Right : Stats.Element_Access) return Boolean is
         return Stats.Count_Of (Left) > Stats.Count_Of (Right);
      end Less_Than;

      procedure Sort is new Ada.Containers.Generic_Constrained_Array_Sort
        (Index_Type   => Index,
         Element_Type => Stats.Element_Access,
         Array_Type   => List_of_Results,
         "<"          => Less_Than);

      Sheet (1) := Stats.Get_First;
      for I in 2 .. Sheet'Last loop
         Sheet (I) := Stats.Get_Next;
      end loop;

      Sort (Sheet);

         new Summary_Info'(Num_Table_Entries,
   end Write_Percent;

   procedure Write_Count (Nucleotide_Fragment : Fragments.Compact) is
      No_of_Occurrences : constant Natural :=
        Stats.Occurrences (Nucleotide_Fragment);
         new Fragment_Info'(No_of_Occurrences,
                            Fragments.To_Fragment (Nucleotide_Fragment)));
   end Write_Count;

   task body Counting_Job is
      Aux.Wait (Lock_Number => Length);

      Perform_Counting (Buffer.all.all);

      case Length is
         when 1 | 2 =>
            Write_Percent (Length);

         when 3 | 4 | 6 | 12 | 18 =>
            Write_Count (Nucleotide_Fragment.all);

         when others =>
            raise Program_Error;
      end case;

   end Counting_Job;

end Statistics.Work;

with Ada.Unchecked_Deallocation;
package Data_Input is

   --  Read data from Standard_Input and return section THREE as String:

   function Read return String;

   type Writable_String_Access is access all String;
   procedure Free is new Ada.Unchecked_Deallocation
     (String, Writable_String_Access);

end Data_Input;

with Ada.IO_Exceptions;
with Ada.Strings.Unbounded;
with Line_IO;

package body Data_Input is

   use Ada.Strings;

   Data_Buffer : Unbounded.Unbounded_String := Unbounded.Null_Unbounded_String;

   Section_Marker : constant Character := '>';
   Section        : constant String    := Section_Marker & "THREE";

   --  Read next data section until EOF oder a line beginning with > is found.

   procedure Read_Section is
      Buffer     : Writable_String_Access;
      Read_First : Natural;
      Read_Last  : Natural;
      Buffer := new String (1 .. 1024 * 1024 * 16);
      Get_Data : loop
         Read_First := Buffer'First;
         Read_Last  := Buffer'First - 1;
         --  fill Buffer and append to Data_Buffer when filled
               Line : String renames Line_IO.Get_Line;
               Read_Last := Read_First + Line'Length - 1;
               if Read_Last >= Buffer'Last then
                    (Data_Buffer, New_Item => Buffer (1 .. Read_First - 1));
                  Unbounded.Append (Data_Buffer, New_Item => Line);
               end if;
               Buffer (Read_First .. Read_Last) := Line;
            exit Get_Data when Buffer (Read_First) = Section_Marker;
            Read_First := Read_Last + 1;
         end loop;
      end loop Get_Data;
      Unbounded.Append (Data_Buffer, Buffer (1 .. Read_Last));
      Free (Buffer);
      when Ada.IO_Exceptions.End_Error =>
         Unbounded.Append (Data_Buffer, Buffer (1 .. Read_Last));
         Free (Buffer);
   end Read_Section;

   --  Skip data on Standard_Input until ">THREE" is found

   procedure Skip_To_Section is
            Line : constant String := Line_IO.Get_Line;
            exit when Line (1) = Section (1)
              and then Line (Section'Range) = Section;
      end loop;
   end Skip_To_Section;

   function Read return String is
      return Unbounded.To_String (Data_Buffer);
   end Read;

end Data_Input;

package Line_IO is

   pragma Elaborate_Body (Line_IO);

   Separator : constant String := (1 => ASCII.LF);  --  ends a line

   function Get_Line return String;

end Line_IO;

with Ada.Streams.Stream_IO;
package body Line_IO is

   use Ada.Streams;

   Stdin : Stream_IO.File_Type;

   --  Declarations associated with filling a text buffer.

   BUFSIZ : constant := 8_192 * 2;
   pragma Assert (Character'Size = Stream_Element'Size);

   SL : constant Natural := Separator'Length;

   subtype Extended_Buffer_Index is Positive range 1 .. BUFSIZ + SL;
   subtype Buffer_Index is Extended_Buffer_Index
     range Extended_Buffer_Index'First .. Extended_Buffer_Index'Last - SL;
   subtype Extended_Bytes_Index is Stream_Element_Offset
     range 1 .. Stream_Element_Offset (Extended_Buffer_Index'Last);
   subtype Bytes_Index is Extended_Bytes_Index
     range Extended_Bytes_Index'First
     .. (Extended_Bytes_Index'Last - Stream_Element_Offset (SL));

   subtype Buffer_Data is String (Extended_Buffer_Index);
   subtype Buffer_Bytes is Stream_Element_Array (Extended_Bytes_Index);

   Buffer : Buffer_Data;
   Bytes  : Buffer_Bytes;
   for Bytes'Address use Buffer'Address;
   pragma Import (Ada, Bytes);

   --  start of next substring and last valid character in buffer
   Position : Natural range 0 .. Extended_Buffer_Index'Last;
   Last     : Natural range 0 .. Buffer_Index'Last;
   End_of_Input : Boolean;

   function Get_Line return String is

      procedure Reload is
         --  fill Buffer with bytes available
         Last_Filled : Stream_Element_Offset;
         if Last < Buffer_Index'Last then
            raise Stream_IO.End_Error;
         end if;
         Stream_IO.Read (Stdin,
           Item => Bytes (Bytes_Index),
           Last => Last_Filled);
         Last := Natural (Last_Filled);
         Position := 1;
         Buffer (Last + 1 .. Last + SL) := Separator;
      end Reload;

      function Separator_Position return Natural is
         --   index of next Separator (may be sentinel)
         K : Extended_Buffer_Index := Position;
            if Buffer (K) = Separator (1) then
            elsif Buffer (K+1) = Separator (1) then
               K := K + 1; exit;
               K := K + 2;
            end if;
         end loop;
         return K;
      end Separator_Position;

      Next_Separator : Natural range 0 .. Extended_Buffer_Index'Last;
   begin  --  Get_Line

      if End_of_Input then
         raise Stream_IO.End_Error;
      end if;

      Next_Separator := Separator_Position;

      if Next_Separator > Last then
            Result : constant String := Buffer (Position .. Last);
            subtype XString is String (1 .. Last - Position + 1);
               return XString (Result) & Get_Line;
               when Stream_IO.End_Error =>
                  End_of_Input := True;
                  return XString (Result);
            Result : String renames Buffer (Position .. Next_Separator - 1);
            subtype XString is String (1 .. Next_Separator - Position);
            Position := Next_Separator + SL;
            return XString (Result);
      end if;

   end Get_Line;

   Stream_IO.Open (Stdin,
     Mode => Stream_IO.In_File,
     Name => "/dev/stdin");

   Buffer (Buffer_Index'Last + 1 .. Buffer'Last) := Separator;
   Position := Buffer_Index'Last + 1;
   Last := Buffer_Index'Last;
   End_of_Input := False;
end Line_IO;

 make, command-line, and program output logs

Sat, 26 Apr 2014 17:24:29 GMT

/usr/bin/gnatchop -r -w knucleotide.gnat
splitting knucleotide.gnat into:
/usr/bin/gnatmake -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp -f knucleotide.adb -o knucleotide.gnat_run 
gcc-4.6 -c -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp knucleotide.adb
gcc-4.6 -c -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp data.adb
gcc-4.6 -c -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp data_input.adb
gcc-4.6 -c -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp
gcc-4.6 -c -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp statistics-aux.adb
gcc-4.6 -c -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp
gcc-4.6 -c -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp line_io.adb
gcc-4.6 -c -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp data-text_fragments.adb
gcc-4.6 -c -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp statistics-calculator.adb
gcc-4.6 -c -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -gnatNp statistics-work.adb
gnatbind -x knucleotide.ali
gnatlink knucleotide.ali -O3 -fomit-frame-pointer -march=native -msse3 -mfpmath=sse -o knucleotide.gnat_run
4.38s to complete and log all make actions

./knucleotide.gnat_run 0 < knucleotide-input25000000.txt

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

Revised BSD license

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