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 #2 223.14226.16708,152359  65% 0% 0% 34%
1.2Ruby #2 12 min12 min160,396420  100% 1% 1% 0%
1.3Ruby JRuby #4 100.3592.161,824,852449  25% 29% 48% 9%
1.3Ruby #4 197.74197.79501,532449  0% 1% 100% 0%
1.3Perl #4 234.9278.201,049,332472  81% 95% 65% 61%
1.4Python 3 9 min9 min391,748487  1% 100% 0% 0%
1.4Perl #3 280.1690.611,126,916507  95% 80% 70% 65%
1.5Ruby #3 13 min13 min169,176540  27% 24% 26% 24%
1.5Ruby JRuby #3 8 min173.58881,064540  87% 72% 87% 57%
1.5Racket 219.87220.011,419,712542  96% 0% 1% 4%
1.7Dart 252.27250.50317,204595  2% 78% 5% 18%
1.8Ruby JRuby 8 min170.50878,712637  74% 89% 70% 76%
1.8Ruby 13 min249.47130,416637  69% 69% 95% 97%
1.8Python 3 #8 8 min161.33364,488647  89% 60% 98% 56%
1.8Perl 242.0769.891,774,668648  82% 88% 85% 92%
2.0F# Mono 5 min110.39644,644701  76% 73% 72% 74%
2.6Erlang HiPE #3 5 min124.55980,820932  69% 81% 58% 77%
2.7Go 152.6345.14396,976980  97% 76% 90% 76%
2.8Ruby #5 52.7817.28356,824996  69% 71% 69% 98%
2.8C# Mono #2 175.09175.13292,4761012  40% 1% 44% 17%
2.9PHP 48.5943.11246,9681036  4% 4% 90% 16%
3.0PHP #4 5 min87.70246,8841060  78% 94% 84% 88%
3.1F# Mono #3 62.4327.21999,4921111  51% 45% 56% 79%
3.2PHP #2 55.4120.16247,1841141  62% 65% 58% 91%
3.5C++ g++ #3 23.447.22139,1361252  76% 76% 78% 97%
3.5Go #5 50.6719.02274,2121268  93% 83% 45% 46%
3.6Lisp SBCL #2 161.15161.23366,5601277  0% 1% 1% 100%
3.6Lisp SBCL #3 160.20160.29366,5601284  0% 1% 100% 1%
3.9C# Mono #3 101.2634.92319,1761404  97% 65% 61% 68%
4.0C# Mono 113.26113.30517,2041420  8% 0% 1% 93%
4.2F# Mono #4 59.1224.631,007,2601505  50% 55% 46% 90%
4.3Go #2 129.4043.58270,9281531  88% 93% 60% 57%
4.3C gcc #9 35.8912.38130,7561535  94% 63% 91% 43%
4.5Java  #2 45.0512.92516,2081602  95% 88% 85% 81%
4.5Java  #3 45.5413.06516,7721630  85% 98% 85% 84%
4.7Haskell GHC 7 min111.20264,4361693  97% 96% 96% 97%
4.7C# Mono #4 104.3634.12515,5281696  98% 68% 71% 70%
4.8Clojure #6 106.2934.98999,2241737  81% 69% 89% 66%
5.1Java  #7 35.8910.661,200,3201844  82% 83% 92% 82%
5.2Java  #4 52.5751.48195,5761873  1% 2% 67% 33%
5.4Clojure #4 189.5763.42994,8521944  76% 68% 79% 78%
5.5Haskell GHC #2 70.5319.10260,1881965  91% 91% 91% 98%
5.8Fortran Intel #2 70.6828.99158,1242079  35% 42% 99% 68%
5.9Rust 27.089.04148,3162113  62% 82% 60% 98%
6.2Java  #5 77.9433.76197,5682211  85% 26% 28% 94%
6.2Fortran Intel 122.78122.86166,9522238  92% 0% 8% 0%
6.3Lisp SBCL #4 67.2367.30111,1922272  91% 1% 10% 0%
6.4C gcc #7 40.7214.77165,8002280  90% 46% 96% 45%
6.4Lisp SBCL #5 67.1467.21111,1882301  0% 39% 1% 62%
6.6Pascal Free Pascal #2 46.2246.24130,0682383  0% 100% 1% 1%
6.8C gcc #6 53.4416.99163,7882439  64% 97% 61% 97%
6.8C# Mono #5 183.2252.74333,7202445  91% 84% 87% 88%
7.6Clojure #5 39.8515.07375,7842723  69% 82% 79% 36%
7.7Haskell GHC #3 113.8037.68496,0202749  59% 83% 61% 100%
8.4Clojure #7 99.9831.11993,3763030  82% 72% 81% 89%
14Ada 2005 GNAT #2 21.189.72273,9404865  57% 81% 27% 55%
C++ g++ Make Error2106
Erlang HiPE Failed930
Erlang HiPE #2 Failed997
Go #3 Bad Output1399
Lisp SBCL Timed Out5 min847
OCaml #3 Failed1789
OCaml Failed870
OCaml #2 Failed1205
Racket #2 Bad Output842
Racket #4 Bad Output881
Ruby JRuby #5 Failed996
Ruby JRuby #2 Failed421
Scala #4 Failed1287
Scala #6 Failed1380
Scala Failed1625
Scala #2 Failed2080
"wrong" (different) algorithm / less comparable programs
1.7Python 3 #2 126.3773.25351,796624
4.0C# Mono #6 44.0616.4782,2321433
5.7C gcc #8 16.1616.18125,9962040
5.9Java  #6 19.1619.03156,2202115
6.7C gcc #4 13.333.76155,0002409
7.0C gcc #5 48.2714.80277,2202519
9.5C++ g++ #6 11.623.49132,9843415
9.5C++ g++ #5 9.072.9645,0123416
15Java  14.224.00173,6245211
18Ada 2005 GNAT 10.564.66407,8886503

 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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