k-nucleotide benchmark ≈240MB N=25,000,000

Each chart bar shows how many times more Code, one ↓ k-nucleotide program used, compared to the program that used least Code.

These are not the only programs that could be written. These are not the only compilers and interpreters. These are not the only programming languages.

Column × shows how many times more each program used compared to the benchmark program that used least.

    sortsortsort 
  ×   Program Source Code CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
1.0Perl #2 221.40224.30464,944359  4% 31% 37% 29%
1.2Ruby #2 11 min11 min158,504420  0% 1% 0% 100%
1.3Ruby JRuby #4 108.1399.062,186,060449  50% 27% 26% 7%
1.3Ruby #4 184.06187.14501,072449  6% 93% 0% 1%
1.3Perl #4 228.7466.991,051,292472  75% 74% 96% 97%
1.4Perl #3 255.0274.611,140,456507  96% 89% 83% 76%
1.5Ruby #3 13 min13 min164,540540  22% 28% 30% 21%
1.5Racket 206.91206.991,421,872542  87% 4% 11% 1%
1.7Dart 264.31262.40327,412595  1% 23% 74% 4%
1.8Ruby 13 min238.96129,896637  97% 92% 73% 67%
1.8Python 3 #8 8 min167.03375,368647  87% 54% 97% 59%
1.8Perl 240.8465.841,012,832648  90% 93% 93% 91%
2.0F# Mono 9 min247.50642,016701  64% 54% 51% 62%
2.6Erlang HiPE #3 5 min124.55980,820932  69% 81% 58% 77%
2.7Go 152.6345.14396,976980  97% 76% 90% 76%
2.9PHP 46.7441.46246,9721036  91% 13% 4% 6%
3.0PHP #4 5 min87.95246,8281060  92% 100% 80% 83%
3.1F# Mono #3 66.1028.521,145,9441111  68% 74% 46% 46%
3.5C++ g++ #3 23.607.22132,7401252  78% 77% 76% 98%
3.5Go #5 50.6719.02274,2121268  93% 83% 45% 46%
3.6Lisp SBCL #2 164.32164.40370,0921277  0% 17% 1% 84%
3.6Lisp SBCL #3 164.79164.93368,5761284  85% 16% 1% 0%
3.9C# Mono #3 164.1150.07492,3681404  75% 95% 70% 90%
4.0C# Mono 118.76118.59507,5481420  1% 0% 100% 0%
4.2F# Mono #4 64.7623.701,144,3121505  54% 57% 97% 67%
4.3Go #2 129.4043.58270,9281531  88% 93% 60% 57%
4.3C gcc #9 36.5812.35131,9041535  37% 71% 95% 94%
4.5Java  #2 44.6212.83518,0361602  94% 85% 84% 85%
4.5Java  #3 44.7912.87517,6321630  95% 86% 84% 84%
4.7Haskell GHC 7 min113.49264,5321693  99% 99% 99% 100%
4.7C# Mono #4 115.1135.47505,6001696  96% 76% 77% 76%
5.1C# Mono #7 71.7624.59505,8721822  66% 68% 94% 65%
5.1Java  #7 35.2710.611,199,1841844  79% 78% 90% 88%
5.2Java  #4 59.5258.48196,4041873  2% 2% 100% 1%
5.4Python 3 #3 291.9475.78148,1921937  97% 97% 100% 97%
5.5Haskell GHC #2 76.8120.49268,8201965  97% 93% 94% 92%
5.8Rust 27.669.47155,5802078  99% 57% 80% 57%
5.8Fortran Intel #2 68.1027.09172,0642079  37% 54% 83% 79%
6.2Java  #5 77.0832.87209,1482211  54% 69% 24% 89%
6.2Fortran Intel 113.76113.82192,3202238  1% 0% 0% 100%
6.3Lisp SBCL #4 67.3667.43114,5082272  0% 0% 100% 1%
6.4C gcc #7 42.1515.39164,3242280  42% 42% 100% 91%
6.4Lisp SBCL #5 67.6667.73115,0402301  93% 2% 6% 0%
6.6Pascal Free Pascal #2 46.2246.24130,0682383  0% 100% 1% 1%
6.8C gcc #6 55.4017.53168,4362439  97% 94% 62% 64%
6.8C# Mono #5 136.5241.14330,9722445  80% 80% 95% 79%
7.7Haskell GHC #3 106.2735.58501,9802749  49% 100% 59% 92%
7.8Clojure #6 96.2931.94999,0082793  72% 69% 77% 86%
7.9Clojure #5 40.4815.35393,5282852  59% 65% 71% 70%
8.6Clojure #4 160.9751.381,000,3123081  73% 80% 78% 84%
12Clojure #7 101.8131.321,003,9684387  83% 91% 82% 70%
14Ada 2005 GNAT #2 19.298.91271,5044865  22% 49% 80% 67%
C# Mono #2 Failed1012
C++ g++ Make Error2106
Erlang HiPE Failed930
Erlang HiPE #2 Failed997
Go #3 Bad Output1399
Lisp SBCL Bad Output847
OCaml #3 Failed1789
OCaml Failed870
OCaml #2 Failed1205
Racket #2 Bad Output842
Racket #4 Bad Output881
Ruby JRuby #3 Timed Out1h 00 min540
Ruby JRuby #2 Failed421
Ruby JRuby Timed Out1h 00 min637
Scala #4 Failed1287
Scala #6 Failed1380
Scala Failed1625
Scala #2 Failed2080
"wrong" (different) algorithm / less comparable programs
1.7Python 3 #2 128.5573.75329,280624
4.0C# Mono #6 44.7415.90105,1401433
5.7C gcc #8 15.945.87130,3882040
5.9Java  #6 19.3319.15161,4202115
6.7C gcc #4 13.183.73158,3922409
7.0C gcc #5 50.8014.76277,1482519
9.5C++ g++ #6 11.943.56134,5563415
9.5C++ g++ #5 9.383.0245,1243416
15Java  14.544.17176,8845211
18Ada 2005 GNAT 9.854.57410,5806503

 k-nucleotide benchmark : Hashtable update and k-nucleotide strings

You can write your own program for this task and contribute to the benchmarks game by following these general instructions.

More specifically:

diff program output for this 250KB input file (generated with the fasta program N = 25000) with this output file to check your program is correct before contributing.

We are trying to show the performance of various programming language implementations - so we ask that contributed programs not only give the correct result, but also use the same algorithm to calculate that result.

We use FASTA files generated by the fasta benchmark as input for this benchmark. Note: the file may include both lowercase and uppercase codes.

Each program should

In practice, less brute-force would be used to calculate k-nucleotide frequencies, for example Virus Classification using k-nucleotide Frequencies and A Fast Algorithm for the Exhaustive Analysis of 12-Nucleotide-Long DNA Sequences. Applications to Human Genomics (105KB pdf).

Revised BSD license

  Home   Conclusions   License   Play