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.

     sortsortsort
  ×   Program Source Code CPU secs Elapsed secs Memory KB Code B ≈ CPU Load
1.0Ada 2005 GNAT #2 21.189.72273,9404865  57% 81% 27% 55%
1.1C++ g++ #3 23.447.22139,1361252  76% 76% 78% 97%
1.3Rust 26.508.74154,5162118  79% 78% 85% 63%
1.7C gcc #9 35.8912.38130,7561535  94% 63% 91% 43%
1.7Java  #7 35.8910.661,200,3201844  82% 83% 92% 82%
1.9Clojure #5 39.8515.07375,7842723  69% 82% 79% 36%
1.9C gcc #7 40.7214.77165,8002280  90% 46% 96% 45%
2.1Java  #2 45.0512.92516,2081602  95% 88% 85% 81%
2.2Java  #3 45.5413.06516,7721630  85% 98% 85% 84%
2.2Pascal Free Pascal #2 46.2246.24130,0682383  0% 100% 1% 1%
2.2PHP 46.7441.46246,9721036  91% 13% 4% 6%
2.4Go #5 50.6719.02274,2121268  93% 83% 45% 46%
2.5Java  #4 52.5751.48195,5761873  1% 2% 67% 33%
2.5C gcc #6 53.4416.99163,7882439  64% 97% 61% 97%
2.8F# Mono #4 59.1224.631,007,2601505  50% 55% 46% 90%
2.9F# Mono #3 62.4327.21999,4921111  51% 45% 56% 79%
3.1C# Mono #7 64.9324.05515,5241822  93% 57% 60% 61%
3.2Lisp SBCL #5 67.1467.21111,1882301  0% 39% 1% 62%
3.2Lisp SBCL #4 67.2367.30111,1922272  91% 1% 10% 0%
3.2Fortran Intel #2 68.1027.09172,0642079  37% 54% 83% 79%
3.6Haskell GHC #2 76.8120.49268,8201965  97% 93% 94% 92%
3.7Java  #5 77.9433.76197,5682211  85% 26% 28% 94%
4.7Clojure #7 99.9831.11993,3763030  82% 72% 81% 89%
4.8C# Mono #3 101.2634.92319,1761404  97% 65% 61% 68%
4.9C# Mono #4 104.3634.12515,5281696  98% 68% 71% 70%
5.0Haskell GHC #3 106.2735.58501,9802749  49% 100% 59% 92%
5.0Clojure #6 106.2934.98999,2241737  81% 69% 89% 66%
5.2Ruby JRuby #4 109.3499.111,917,404449  21% 5% 6% 80%
5.3C# Mono 113.26113.30517,2041420  8% 0% 1% 93%
5.4Fortran Intel 113.76113.82192,3202238  1% 0% 0% 100%
6.1Go #2 129.4043.58270,9281531  88% 93% 60% 57%
7.2Go 152.6345.14396,976980  97% 76% 90% 76%
7.6Lisp SBCL #3 160.20160.29366,5601284  0% 1% 100% 1%
7.6Lisp SBCL #2 161.15161.23366,5601277  0% 1% 1% 100%
8.3C# Mono #2 175.09175.13292,4761012  40% 1% 44% 17%
8.7C# Mono #5 183.2252.74333,7202445  91% 84% 87% 88%
8.7Ruby #4 184.06187.14501,072449  6% 93% 0% 1%
9.0Clojure #4 189.5763.42994,8521944  76% 68% 79% 78%
10Racket 219.87220.011,419,712542  96% 0% 1% 4%
10Perl #2 221.40224.30464,944359  4% 31% 37% 29%
11Perl #4 228.7466.991,051,292472  75% 74% 96% 97%
11Perl 240.8465.841,012,832648  90% 93% 93% 91%
12Perl #3 255.0274.611,140,456507  96% 89% 83% 76%
12Dart 260.74258.83321,408595  43% 37% 1% 22%
14Python 3 #3 294.0977.49141,2161937  97% 94% 95% 97%
15PHP #4 5 min87.95246,8281060  92% 100% 80% 83%
15F# Mono 5 min110.39644,644701  76% 73% 72% 74%
17Erlang HiPE #3 5 min124.55980,820932  69% 81% 58% 77%
21Haskell GHC 7 min113.49264,5321693  99% 99% 99% 100%
23Python 3 #8 8 min161.33364,488647  89% 60% 98% 56%
26Python 3 9 min9 min391,748487  1% 100% 0% 0%
33Ruby #2 11 min11 min158,504420  0% 1% 0% 100%
37Ruby 13 min238.96129,896637  97% 92% 73% 67%
38Ruby #3 13 min13 min164,540540  22% 28% 30% 21%
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 #3 Timed Out1h 00 min540
Ruby JRuby #2 Failed421
Ruby JRuby Timed Out1h 00 min637
Scala #4 Failed1287
Scala #6 Failed1380
Scala Failed1625
Scala #2 Failed2080
"wrong" (different) algorithm / less comparable programs
0.4C++ g++ #5 9.072.9645,0123416
0.5Ada 2005 GNAT 10.564.66407,8886503
0.5C++ g++ #6 11.623.49132,9843415
0.6C gcc #4 13.333.76155,0002409
0.7Java  14.224.00173,6245211
0.8C gcc #8 16.1616.18125,9962040
0.9Java  #6 19.1619.03156,2202115
2.1C# Mono #6 44.0616.4782,2321433
2.3C gcc #5 48.2714.80277,2202519
6.0Python 3 #2 126.3773.25351,796624

 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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