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 13 min13 min156,256420  0% 99% 1% 0%
1.3Ruby JRuby #4 97.4489.931,952,044449  58% 5% 14% 33%
1.3Ruby #4 201.00201.08499,252449  0% 0% 0% 100%
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 JRuby #3 8 min176.561,194,036540  78% 68% 71% 87%
1.5Ruby #3 14 min14 min161,372540  19% 31% 32% 20%
1.5Racket 219.87220.011,419,712542  96% 0% 1% 4%
1.7Dart 287.74285.80345,924595  1% 3% 3% 96%
1.8Ruby 14 min257.66128,344637  68% 94% 100% 67%
1.8Ruby JRuby 10 min201.011,060,796637  67% 85% 86% 66%
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 6 min137.89864,700932  99% 48% 49% 72%
2.7Go 161.1054.14392,272980  91% 68% 80% 62%
2.8Ruby #5 52.9517.66357,344996  69% 68% 72% 95%
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 50.7619.05270,1441268  46% 45% 84% 93%
3.6Lisp SBCL #2 162.33162.44363,1041277  1% 100% 0% 1%
3.6Lisp SBCL #3 161.76161.83364,2401284  1% 0% 100% 1%
3.8Scala #6 156.4041.51473,5241380  95% 94% 94% 95%
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 #2 153.6648.21267,0961531  100% 90% 66% 64%
4.3C gcc #9 35.8912.38130,7561535  94% 63% 91% 43%
4.5Java  #2 49.7014.28909,1081602  85% 96% 81% 86%
4.5Java  #3 45.3313.06923,0681630  81% 83% 85% 99%
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 #6 106.3836.21984,5281737  83% 83% 70% 58%
5.2Java  #4 55.3854.37176,9761873  97% 6% 6% 2%
5.4Clojure #4 187.8564.51984,0121944  94% 66% 63% 70%
5.5Haskell GHC #2 70.5319.10260,1881965  91% 91% 91% 98%
5.8Fortran Intel #2 70.6828.99158,1242079  35% 42% 99% 68%
5.8Scala #2 30.2511.00209,6602080  74% 87% 54% 60%
6.2Java  #5 81.2336.06178,6442211  86% 32% 85% 24%
6.2Fortran Intel 122.78122.86166,9522238  92% 0% 8% 0%
6.3Lisp SBCL #4 65.4165.47109,2082272  0% 1% 1% 100%
6.4C gcc #7 40.7214.77165,8002280  90% 46% 96% 45%
6.4Lisp SBCL #5 65.7065.77108,8042301  1% 0% 100% 1%
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 42.6516.70369,9642723  75% 73% 55% 54%
7.7Haskell GHC #3 113.8037.68496,0202749  59% 83% 61% 100%
8.4Clojure #7 114.4636.68985,7923030  84% 78% 60% 91%
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 Out10 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 Failed1625
"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 19.2219.10155,7682115
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  14.164.00183,2165211
18Ada 2005 GNAT 10.564.66407,8886503
missing benchmark programs
Rust No program

 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