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

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

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.

    sortsort sort
  ×   Program Source Code CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
1.0JavaScript V8 #5 98.4398.5270,0761249  0% 1% 1% 100%
1.8Rust 28.3828.40129,3322049  0% 0% 1% 100%
1.9Pascal Free Pascal #2 78.9278.96130,5682383  0% 0% 0% 100%
1.9Ruby 8 min8 min131,052637  1% 1% 0% 100%
2.0Lisp SBCL #5 36.8636.90138,4842301  0% 0% 1% 100%
2.0Lisp SBCL #4 36.9637.00138,4882272  0% 1% 1% 100%
2.2C++ g++ #3 18.1018.13152,5521252  0% 1% 1% 100%
2.3Scala #2 24.0524.07164,1202080  0% 1% 1% 100%
2.4Ruby #2 7 min7 min167,244420  1% 1% 0% 100%
2.4Ruby #3 8 min8 min170,396540  1% 1% 0% 100%
2.5Java  #4 60.7460.79174,1041873  1% 1% 0% 100%
2.6C gcc #7 32.1532.18180,3082280  0% 1% 1% 100%
2.6C gcc #6 51.9351.97180,3122439  0% 1% 1% 100%
2.7Fortran Intel 81.6681.71186,8642238  0% 0% 0% 100%
2.8Java  #5 69.2969.36194,9602211  0% 1% 0% 100%
2.8Fortran Intel #2 59.7559.79195,7562079  0% 0% 0% 100%
3.4Clojure #5 26.3726.39237,7562723  0% 1% 1% 100%
3.5PHP #4 5 min5 min247,7321060  0% 0% 0% 100%
3.5PHP 42.6242.66247,8321036  0% 0% 0% 100%
3.6OCaml #3 56.2256.29253,6281789  0% 0% 0% 100%
3.7Ada 2005 GNAT #2 35.1235.16256,1324865  0% 1% 1% 100%
3.7Go #2 147.08150.69256,9161531  1% 1% 0% 100%
3.7Go #5 76.1376.19261,9881268  0% 1% 1% 100%
3.7Hack #4 140.97141.77262,6601061  0% 1% 1% 100%
4.3C# Mono #2 142.18142.32302,1161012  0% 1% 1% 100%
4.6Haskell GHC #3 92.0992.17322,9082749  0% 1% 1% 100%
4.7Lisp SBCL #3 141.70141.77331,2241284  1% 1% 1% 100%
4.7Lisp SBCL #2 142.03142.10331,2241277  0% 1% 1% 100%
4.8C# Mono #3 96.2196.29334,5321404  0% 0% 1% 100%
4.8OCaml #2 80.7980.90337,8841205  0% 0% 0% 100%
5.2Haskell GHC 47.7547.80362,4601693  0% 1% 1% 100%
5.3Haskell GHC #2 62.0862.15369,3321965  0% 0% 0% 100%
5.4Go 186.31192.37380,532980  2% 29% 10% 100%
5.4Smalltalk VisualWorks #5 5 min5 min380,8521153  0% 0% 0% 100%
5.5Racket #4 96.6796.91387,480881  0% 1% 1% 100%
5.7Python 3 7 min7 min402,016487  1% 0% 0% 100%
6.3OCaml 69.3569.41443,224870  0% 0% 0% 100%
6.4C# Mono #5 130.49130.66449,4282445  1% 1% 1% 100%
6.5Python 3 #8 6 min6 min456,532647  0% 1% 1% 100%
7.0Scala #6 99.8599.99493,4601380  1% 0% 1% 100%
7.2Ruby #4 112.27112.31501,972449  0% 0% 0% 100%
7.2JavaScript V8 #2 271.06271.26503,152451  0% 1% 0% 100%
7.2Java  #3 48.7948.83504,9841630  0% 1% 0% 100%
7.2Java  #2 48.5748.61505,8401602  0% 0% 1% 100%
7.7C# Mono 95.6395.67538,8081420  0% 1% 1% 100%
8.0C# Mono #4 89.3089.34559,8161696  0% 1% 0% 100%
9.0F# Mono 173.17173.43630,816701  1% 1% 1% 100%
9.3F# Mono #3 69.3469.39652,8761111  0% 0% 1% 100%
9.4F# Mono #4 67.0867.14658,4281505  1% 0% 1% 100%
10Lua #2 192.80194.92707,636613  0% 0% 0% 100%
11Perl #2 212.24215.90778,052359  0% 0% 0% 100%
15Clojure #4 5 min5 min1,054,4281944  0% 1% 1% 100%
15Clojure #6 105.62105.751,054,9121737  0% 1% 1% 100%
15Clojure #7 101.54101.631,058,4883030  0% 0% 1% 100%
16Ruby JRuby #3 7 min7 min1,086,272540  1% 1% 1% 100%
16Ruby JRuby 7 min7 min1,086,580637  0% 1% 1% 100%
17Erlang HiPE #3 292.66296.501,160,884932  0% 0% 0% 100%
19Racket 189.40189.781,308,968542  0% 1% 1% 100%
27Ruby JRuby #4 89.9090.251,862,368449  0% 1% 1% 100%
52Erlang HiPE 5 min5 min3,632,748930  8% 2% 1% 100%
C++ g++ Make Error2106
Erlang HiPE #2 Failed997
Hack Bad Output1038
JavaScript V8 #3 Timed Out5 min390
JavaScript V8 Timed Out5 min423
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
0.7C++ g++ #5 7.317.3252,0883416
1.8JavaScript V8 #4 97.4497.99123,5001177
1.8C gcc #8 8.828.83128,0402040
2.1C++ g++ #6 9.639.64144,0923415
2.5C gcc #4 8.808.81176,6122409
2.9Java  8.338.34204,9965211
4.0C gcc #5 50.8450.88281,7402519
5.4Python 3 #2 91.6091.75375,452624
5.7Ada 2005 GNAT 14.9214.93400,4006503
10C# Mono #6 35.5236.31709,1521433
missing benchmark programs
Dart 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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