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 #2 212.24215.90778,052359  0% 0% 0% 100%
1.1JavaScript V8 #3 5 min5 min456,392390  4% 25% 19% 100%
1.2Ruby #2 7 min7 min163,892420  1% 1% 0% 100%
1.2JavaScript V8 266.48266.67458,036423  0% 1% 1% 100%
1.3Ruby JRuby #4 86.1086.231,875,096449  1% 0% 0% 100%
1.3Ruby #4 111.85111.90503,728449  1% 1% 0% 100%
1.3JavaScript V8 #2 261.99262.18533,424451  2% 13% 13% 100%
1.4Python 3 7 min7 min402,016487  1% 0% 0% 100%
1.5Ruby JRuby #3 7 min7 min944,788540  1% 0% 0% 100%
1.5Ruby #3 8 min8 min175,020540  1% 1% 0% 100%
1.5Racket 189.40189.781,308,968542  0% 1% 1% 100%
1.7Dart 290.40290.60413,124595  0% 1% 1% 100%
1.7Lua #2 192.80194.92707,636613  0% 0% 0% 100%
1.8Ruby JRuby 7 min7 min946,844637  1% 1% 0% 100%
1.8Ruby 8 min8 min132,992637  1% 0% 1% 100%
1.8Python 3 #8 6 min6 min456,532647  0% 1% 1% 100%
2.4OCaml 69.3569.41443,224870  0% 0% 0% 100%
2.5Racket #4 96.6796.91387,480881  0% 1% 1% 100%
2.6Erlang HiPE 5 min6 min3,646,340930  6% 8% 9% 100%
2.6Erlang HiPE #3 292.20295.911,096,972932  1% 1% 1% 100%
2.7Go 195.30195.44399,016980  0% 1% 1% 100%
2.8Ruby #5 37.0137.04457,952996  1% 1% 0% 100%
2.9PHP 46.6946.71247,8201036  1% 0% 0% 100%
3.0PHP #4 5 min5 min247,7321060  0% 0% 0% 100%
3.0Hack #4 132.73133.20219,5961061  0% 0% 1% 100%
3.1F# Mono #3 61.3261.381,025,7281111  0% 1% 1% 100%
3.2PHP #2 52.2652.29248,0441141  1% 0% 1% 100%
3.2Smalltalk VisualWorks #5 5 min5 min380,8521153  0% 0% 0% 100%
3.4OCaml #2 80.7980.90337,8841205  0% 0% 0% 100%
3.5JavaScript V8 #5 128.05128.1976,4361249  0% 1% 1% 100%
3.5C++ g++ #3 18.1018.13152,5521252  0% 1% 1% 100%
3.5Go #5 73.7173.77272,6961268  1% 0% 0% 100%
3.6Lisp SBCL #2 136.36137.47307,8801277  1% 1% 1% 100%
3.6Lisp SBCL #3 136.86136.93310,2481284  1% 3% 1% 100%
3.9Go #3 30.7530.77254,5801399  0% 0% 1% 100%
3.9C# Mono #3 94.4494.52344,2281404  0% 0% 1% 100%
4.0C# Mono 85.8185.85531,3561420  0% 1% 0% 100%
4.2F# Mono #4 58.8258.881,021,3841505  0% 0% 1% 100%
4.3Go #2 142.68142.78267,7801531  1% 1% 1% 100%
4.3C gcc #9 36.5436.57128,6401535  1% 1% 0% 100%
4.5Java  #2 46.8146.85462,6001602  0% 1% 1% 100%
4.5Java  #3 47.0247.05466,8201630  1% 0% 0% 100%
4.7Haskell GHC 47.7547.80362,4601693  0% 1% 1% 100%
4.7C# Mono #4 80.8580.90533,6681696  0% 1% 1% 100%
4.8Clojure #6 104.41104.521,007,3921737  1% 1% 0% 100%
5.0OCaml #3 56.2256.29253,6281789  0% 0% 0% 100%
5.1Java  #7 34.7834.841,119,0841844  0% 1% 1% 100%
5.2Java  #4 48.7448.78180,6601873  0% 0% 1% 100%
5.4Clojure #4 268.29268.541,010,2601944  1% 1% 0% 100%
5.5Haskell GHC #2 62.0862.15369,3321965  0% 0% 0% 100%
5.8Fortran Intel #2 59.7559.79195,7562079  0% 0% 0% 100%
5.9Rust 27.2127.23152,5082113  0% 1% 1% 100%
6.2Java  #5 60.5860.63181,4242211  0% 1% 1% 100%
6.2Fortran Intel 81.6681.71186,8642238  0% 0% 0% 100%
6.3Lisp SBCL #4 33.0933.13152,1842272  0% 1% 1% 100%
6.4C gcc #7 32.1532.18180,3082280  0% 1% 1% 100%
6.4Lisp SBCL #5 33.1133.14152,1842301  0% 1% 0% 100%
6.6Pascal Free Pascal #2 79.9780.04132,5002383  1% 0% 0% 100%
6.8C gcc #6 51.9351.97180,3122439  0% 1% 1% 100%
6.8C# Mono #5 106.43106.58406,3922445  0% 1% 0% 100%
7.6Clojure #5 21.4221.44400,0042723  0% 1% 0% 100%
7.7Haskell GHC #3 92.0992.17322,9082749  0% 1% 1% 100%
8.4Clojure #7 76.0676.131,012,7723030  1% 1% 0% 100%
14Ada 2005 GNAT #2 32.1832.23276,1924865  1% 1% 1% 100%
C# Mono #2 Failed1012
C++ g++ Make Error2106
Erlang HiPE #2 Failed997
F# Mono Failed701
Hack Bad Output1038
Lisp SBCL Timed Out5 min847
Perl #3 Failed507
Perl Failed648
Perl #4 Failed472
Racket #2 Bad Output842
Ruby JRuby #5 Failed996
Ruby JRuby #2 Failed421
Scala Failed1625
Scala #4 Failed1287
Scala #2 Failed2080
Scala #6 Failed1380
"wrong" (different) algorithm / less comparable programs
1.7Python 3 #2 91.6091.75375,452624
3.3JavaScript V8 #4 98.4098.51155,8521177
 C# Mono #6 Failed  1433
5.7C gcc #8 8.828.83128,0402040
5.9Java  #6 17.1417.16162,7882115
6.7C gcc #4 8.808.81176,6122409
7.0C gcc #5 50.8450.88281,7402519
9.5C++ g++ #6 9.639.64144,0923415
9.5C++ g++ #5 7.317.3252,0883416
15Java  7.357.36217,7685211
18Ada 2005 GNAT 12.1812.20409,7526503

 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

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