performance measurements

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

 N  CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
250,0002.651.0349,268472  38% 56% 89% 77%
2,500,00022.957.66153,956472  95% 59% 83% 66%
25,000,000221.6971.041,066,204472  61% 96% 90% 67%

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

This is perl 5, version 18, subversion 0 (v5.18.0) built for x86_64-linux-thread-multi

Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
                        PERL_DONT_CREATE_GVSV
                        PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
                        PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
                        PERL_PRESERVE_IVUV PERL_SAWAMPERSAND USE_64_BIT_ALL
                        USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
                        USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
                        USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
                        USE_REENTRANT_API

 k-nucleotide Perl #4 program source code

# The Computer Language Benchmarks Game
#  http://benchmarksgame.alioth.debian.org/
#
#  contributed by Mykola Zubach

use strict;
use integer;
use threads;

my($sequence, $seq_len, $thr, @threads, %h);

sub count_frame {
   my $len = shift;
   for (0 .. $seq_len - $len) {
      $h{substr($sequence, $_, $len)} ++;
   }
}

sub count_len {
   my $len = shift;
   my $out;
   count_frame($len);

   no integer;
   if(@_) {
      $out = join '', map sprintf("%d\t%s\n", $h{$_}, $_), @_;
   } else {
      my $sum = $seq_len - $len + 1;
      for (sort { $h{$b} <=> $h{$a} || $a cmp $b } keys %h) {
         $out .= sprintf "%s %.3f\n", $_, $h{$_} * 100 / $sum;
      }
      $out .= "\n";
   }
   return $out;
}

## MAIN()

while(<STDIN>) {
   last if /^>THREE /;
}
while(<STDIN>) {
   last if /^>/;
   chomp;
   $sequence .= uc;
}
$seq_len = length($sequence);

for (1,2) {
   push @threads, threads->create(\&count_len, $_);
}

for (qw(GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT)) {
   push @threads, threads->create(\&count_len, length, $_);
}

foreach $thr (@threads) {
   print $thr->join();
}

 make, command-line, and program output logs

Tue, 14 Jan 2014 20:59:58 GMT

COMMAND LINE:
/usr/local/src/perl-5.18.0/bin/perl knucleotide.perl-4.perl 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

Revised BSD license

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