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 23.447.22139,1361252  76% 76% 78% 97%
1.3Rust 26.399.27154,5682075  77% 77% 57% 74%
1.3Ada 2005 GNAT #2 21.189.72273,9404865  57% 81% 27% 55%
1.5Java  #7 35.8910.661,200,3201844  82% 83% 92% 82%
1.7C gcc #9 35.8912.38130,7561535  94% 63% 91% 43%
1.8Java  #2 45.0512.92516,2081602  95% 88% 85% 81%
1.8Java  #3 45.5413.06516,7721630  85% 98% 85% 84%
2.0C gcc #7 40.7214.77165,8002280  90% 46% 96% 45%
2.1Clojure #5 39.8515.07375,7842723  69% 82% 79% 36%
2.4C gcc #6 53.4416.99163,7882439  64% 97% 61% 97%
2.6Go #5 50.6719.02274,2121268  93% 83% 45% 46%
2.8Haskell GHC #2 76.8120.49268,8201965  97% 93% 94% 92%
3.3C# Mono #7 64.9324.05515,5241822  93% 57% 60% 61%
3.4F# Mono #4 59.1224.631,007,2601505  50% 55% 46% 90%
3.8Fortran Intel #2 68.1027.09172,0642079  37% 54% 83% 79%
3.8F# Mono #3 62.4327.21999,4921111  51% 45% 56% 79%
4.3Clojure #7 99.9831.11993,3763030  82% 72% 81% 89%
4.7Java  #5 77.9433.76197,5682211  85% 26% 28% 94%
4.7C# Mono #4 104.3634.12515,5281696  98% 68% 71% 70%
4.8C# Mono #3 101.2634.92319,1761404  97% 65% 61% 68%
4.8Clojure #6 106.2934.98999,2241737  81% 69% 89% 66%
4.9Haskell GHC #3 106.2735.58501,9802749  49% 100% 59% 92%
5.7PHP 46.7441.46246,9721036  91% 13% 4% 6%
6.0Go #2 129.4043.58270,9281531  88% 93% 60% 57%
6.3Go 152.6345.14396,976980  97% 76% 90% 76%
6.4Pascal Free Pascal #2 46.2246.24130,0682383  0% 100% 1% 1%
7.1Java  #4 52.5751.48195,5761873  1% 2% 67% 33%
7.3C# Mono #5 183.2252.74333,7202445  91% 84% 87% 88%
8.8Clojure #4 189.5763.42994,8521944  76% 68% 79% 78%
9.1Perl 240.8465.841,012,832648  90% 93% 93% 91%
9.3Perl #4 228.7466.991,051,292472  75% 74% 96% 97%
9.3Lisp SBCL #4 67.3667.43114,5082272  0% 0% 100% 1%
9.4Lisp SBCL #5 67.6667.73115,0402301  93% 2% 6% 0%
10Perl #3 255.0274.611,140,456507  96% 89% 83% 76%
11Python 3 #3 291.9475.78148,1921937  97% 97% 100% 97%
12PHP #4 5 min87.95246,8281060  92% 100% 80% 83%
14Ruby JRuby #4 109.3499.111,917,404449  21% 5% 6% 80%
15F# Mono 5 min110.39644,644701  76% 73% 72% 74%
16C# Mono 113.26113.30517,2041420  8% 0% 1% 93%
16Haskell GHC 7 min113.49264,5321693  99% 99% 99% 100%
16Fortran Intel 113.76113.82192,3202238  1% 0% 0% 100%
17Erlang HiPE #3 5 min124.55980,820932  69% 81% 58% 77%
23Lisp SBCL #2 164.32164.40370,0921277  0% 17% 1% 84%
23Lisp SBCL #3 164.79164.93368,5761284  85% 16% 1% 0%
23Python 3 #8 8 min167.03375,368647  87% 54% 97% 59%
24C# Mono #2 175.09175.13292,4761012  40% 1% 44% 17%
26Ruby #4 184.06187.14501,072449  6% 93% 0% 1%
29Racket 206.91206.991,421,872542  87% 4% 11% 1%
31Perl #2 221.40224.30464,944359  4% 31% 37% 29%
33Ruby 13 min238.96129,896637  97% 92% 73% 67%
36Dart 260.74258.83321,408595  43% 37% 1% 22%
97Ruby #2 11 min11 min158,504420  0% 1% 0% 100%
110Ruby #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 Bad Output847
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
0.5C++ g++ #6 11.623.49132,9843415
0.5C gcc #4 13.333.76155,0002409
0.6Java  14.224.00173,6245211
0.6Ada 2005 GNAT 10.564.66407,8886503
2.1C gcc #5 48.2714.80277,2202519
2.2C gcc #8 16.1616.18125,9962040
2.3C# Mono #6 44.0616.4782,2321433
2.6Java  #6 19.1619.03156,2202115
10Python 3 #2 128.5573.75329,280624

 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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