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

Each chart bar shows how many times slower, one ↓ k-nucleotide program was, compared to the fastest program.

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.

    sort sortsort
  ×   Program Source Code CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
1.0C++ g++ #3 18.1018.13152,5521252  0% 1% 1% 100%
1.3Scala #2 24.0524.07164,1202080  0% 1% 1% 100%
1.5Clojure #5 26.3726.39237,7562723  0% 1% 1% 100%
1.7Go #3 30.7130.74252,4441399  1% 0% 1% 100%
1.8C gcc #7 32.1532.18180,3082280  0% 1% 1% 100%
1.8Ada 2005 GNAT #2 32.1832.23276,1924865  1% 1% 1% 100%
1.8Lisp SBCL #5 32.9432.98152,3482301  0% 1% 0% 100%
1.8Lisp SBCL #4 32.9533.00152,3482272  0% 0% 1% 100%
2.0C gcc #9 36.5436.57128,6401535  1% 1% 0% 100%
2.6PHP 46.6946.71247,8201036  1% 0% 0% 100%
2.6Haskell GHC 47.7547.80362,4601693  0% 1% 1% 100%
2.7Java  #2 48.5748.61505,8401602  0% 0% 1% 100%
2.7Java  #3 48.7948.83504,9841630  0% 1% 0% 100%
2.9C gcc #6 51.9351.97180,3122439  0% 1% 1% 100%
2.9PHP #2 52.2652.29248,0441141  1% 0% 1% 100%
3.1OCaml #3 56.2256.29253,6281789  0% 0% 0% 100%
3.3F# Mono #4 59.4559.52987,7721505  1% 1% 0% 100%
3.3Fortran Intel #2 59.7559.79195,7562079  0% 0% 0% 100%
3.4Java  #4 60.7460.79174,1041873  1% 1% 0% 100%
3.4Haskell GHC #2 62.0862.15369,3321965  0% 0% 0% 100%
3.5F# Mono #3 62.7262.781,022,6681111  1% 0% 1% 100%
3.8Java  #5 69.2969.36194,9602211  0% 1% 0% 100%
3.8OCaml 69.3569.41443,224870  0% 0% 0% 100%
4.1Go #5 73.3973.46271,3401268  1% 1% 1% 100%
4.4Pascal Free Pascal #2 79.9780.04132,5002383  1% 0% 0% 100%
4.5OCaml #2 80.7980.90337,8841205  0% 0% 0% 100%
4.5C# Mono #4 81.4181.46530,9961696  1% 0% 1% 100%
4.5Fortran Intel 81.6681.71186,8642238  0% 0% 0% 100%
4.8C# Mono 86.3586.39536,6401420  1% 1% 0% 100%
5.0Ruby JRuby #4 89.9090.251,862,368449  0% 1% 1% 100%
5.1Haskell GHC #3 92.0992.17322,9082749  0% 1% 1% 100%
5.2C# Mono #3 94.7394.82344,4601404  1% 1% 0% 100%
5.3Racket #4 96.6796.91387,480881  0% 1% 1% 100%
5.4JavaScript V8 #5 97.1697.2871,5081249  0% 1% 1% 100%
5.5Scala #6 99.8599.99493,4601380  1% 0% 1% 100%
5.6Clojure #7 101.54101.631,058,4883030  0% 0% 1% 100%
5.8Clojure #6 105.62105.751,054,9121737  0% 1% 1% 100%
5.9C# Mono #5 107.30107.45401,6362445  1% 1% 1% 100%
6.2Ruby #4 112.27112.31501,972449  0% 0% 0% 100%
7.4Lisp SBCL #3 134.25134.34310,4161284  0% 1% 1% 100%
7.4Lisp SBCL #2 134.54134.62312,3681277  0% 1% 1% 100%
7.6Go #2 134.51138.18263,4761531  1% 1% 1% 100%
7.6C# Mono #2 138.24138.39309,2321012  1% 1% 0% 100%
7.8Hack #4 140.97141.77262,6601061  0% 1% 1% 100%
9.1F# Mono 165.36165.62675,440701  1% 1% 0% 100%
9.8Go 177.98178.13389,020980  1% 0% 1% 100%
10Racket 189.40189.781,308,968542  0% 1% 1% 100%
11Lua #2 192.80194.92707,636613  0% 0% 0% 100%
12Perl #2 212.24215.90778,052359  0% 0% 0% 100%
16JavaScript V8 #2 290.88291.12558,680451  0% 1% 1% 100%
16JavaScript V8 291.92294.05422,792423  0% 1% 1% 100%
16Erlang HiPE #3 292.66296.501,160,884932  0% 0% 0% 100%
17PHP #4 5 min5 min247,7321060  0% 0% 0% 100%
17Dart 5 min5 min518,324595  0% 1% 1% 100%
19Smalltalk VisualWorks #5 5 min5 min380,8521153  0% 0% 0% 100%
19Clojure #4 5 min5 min1,054,4281944  0% 1% 1% 100%
19Erlang HiPE 5 min5 min3,632,748930  8% 2% 1% 100%
20JavaScript V8 #3 6 min6 min467,276390  1% 1% 1% 100%
21Python 3 #8 6 min6 min456,532647  0% 1% 1% 100%
24Python 3 7 min7 min402,016487  1% 0% 0% 100%
25Ruby JRuby #3 7 min7 min1,086,272540  1% 1% 1% 100%
26Ruby #2 7 min7 min167,244420  1% 1% 0% 100%
26Ruby JRuby 7 min7 min1,086,580637  0% 1% 1% 100%
27Ruby #3 8 min8 min170,396540  1% 1% 0% 100%
27Ruby 8 min8 min131,052637  1% 1% 0% 100%
C++ g++ Make Error2106
Erlang HiPE #2 Failed997
Hack Bad Output1038
Lisp SBCL Timed Out10 min847
Perl #3 Failed507
Perl Failed648
Perl #4 Failed472
Racket #2 Bad Output842
Ruby JRuby #2 Failed421
Scala Failed1625
Scala #4 Failed1287
"wrong" (different) algorithm / less comparable programs
0.4C++ g++ #5 7.317.3252,0883416
0.5Java  8.338.34204,9965211
0.5C gcc #4 8.808.81176,6122409
0.5C gcc #8 8.828.83128,0402040
0.5C++ g++ #6 9.639.64144,0923415
0.7Ada 2005 GNAT 12.1812.20409,7526503
1.2Java  #6 22.4122.44165,4882115
1.8C# Mono #6 31.8232.63110,4641433
2.8C gcc #5 50.8450.88281,7402519
5.1Python 3 #2 91.6091.75375,452624
5.6JavaScript V8 #4 101.05101.18146,7401177
missing benchmark programs
Rust No program

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

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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