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
1.0Lisp SBCL #4 67.3667.43114,5082272  0% 0% 100% 1%
1.0Lisp SBCL #5 67.6667.73115,0402301  93% 2% 6% 0%
1.1Ruby 13 min238.96129,896637  97% 92% 73% 67%
1.1Pascal Free Pascal #2 46.2246.24130,0682383  0% 100% 1% 1%
1.1C gcc #9 35.8912.38130,7561535  94% 63% 91% 43%
1.2C++ g++ #3 23.447.22139,1361252  76% 76% 78% 97%
1.3Python 3 #3 291.9475.78148,1921937  97% 97% 100% 97%
1.3Rust 26.399.27154,5682075  77% 77% 57% 74%
1.4Ruby #2 11 min11 min158,504420  0% 1% 0% 100%
1.4C gcc #6 53.4416.99163,7882439  64% 97% 61% 97%
1.4Ruby #3 13 min13 min164,540540  22% 28% 30% 21%
1.4C gcc #7 40.7214.77165,8002280  90% 46% 96% 45%
1.5Fortran Intel #2 68.1027.09172,0642079  37% 54% 83% 79%
1.7Fortran Intel 113.76113.82192,3202238  1% 0% 0% 100%
1.7Java  #4 52.5751.48195,5761873  1% 2% 67% 33%
1.7Java  #5 77.9433.76197,5682211  85% 26% 28% 94%
2.2PHP #4 5 min87.95246,8281060  92% 100% 80% 83%
2.2PHP 46.7441.46246,9721036  91% 13% 4% 6%
2.3Haskell GHC 7 min113.49264,5321693  99% 99% 99% 100%
2.3Haskell GHC #2 76.8120.49268,8201965  97% 93% 94% 92%
2.4Go #2 129.4043.58270,9281531  88% 93% 60% 57%
2.4Ada 2005 GNAT #2 21.189.72273,9404865  57% 81% 27% 55%
2.4Go #5 50.6719.02274,2121268  93% 83% 45% 46%
2.6C# Mono #2 175.09175.13292,4761012  40% 1% 44% 17%
2.8C# Mono #3 101.2634.92319,1761404  97% 65% 61% 68%
2.8Dart 260.74258.83321,408595  43% 37% 1% 22%
2.9C# Mono #5 183.2252.74333,7202445  91% 84% 87% 88%
3.2Lisp SBCL #3 164.79164.93368,5761284  85% 16% 1% 0%
3.2Lisp SBCL #2 164.32164.40370,0921277  0% 17% 1% 84%
3.3Python 3 #8 8 min167.03375,368647  87% 54% 97% 59%
3.3Clojure #5 39.8515.07375,7842723  69% 82% 79% 36%
3.5Go 152.6345.14396,976980  97% 76% 90% 76%
4.1Perl #2 221.40224.30464,944359  4% 31% 37% 29%
4.4Ruby #4 184.06187.14501,072449  6% 93% 0% 1%
4.4Haskell GHC #3 106.2735.58501,9802749  49% 100% 59% 92%
4.5C# Mono #7 64.9324.05515,5241822  93% 57% 60% 61%
4.5C# Mono #4 104.3634.12515,5281696  98% 68% 71% 70%
4.5Java  #2 45.0512.92516,2081602  95% 88% 85% 81%
4.5Java  #3 45.5413.06516,7721630  85% 98% 85% 84%
4.5C# Mono 113.26113.30517,2041420  8% 0% 1% 93%
5.6F# Mono 5 min110.39644,644701  76% 73% 72% 74%
8.6Erlang HiPE #3 5 min124.55980,820932  69% 81% 58% 77%
8.7Clojure #7 99.9831.11993,3763030  82% 72% 81% 89%
8.7Clojure #4 189.5763.42994,8521944  76% 68% 79% 78%
8.7Clojure #6 106.2934.98999,2241737  81% 69% 89% 66%
8.7F# Mono #3 62.4327.21999,4921111  51% 45% 56% 79%
8.8F# Mono #4 59.1224.631,007,2601505  50% 55% 46% 90%
8.8Perl 240.8465.841,012,832648  90% 93% 93% 91%
9.2Perl #4 228.7466.991,051,292472  75% 74% 96% 97%
10Perl #3 255.0274.611,140,456507  96% 89% 83% 76%
10Java  #7 35.8910.661,200,3201844  82% 83% 92% 82%
12Racket 206.91206.991,421,872542  87% 4% 11% 1%
17Ruby JRuby #4 109.3499.111,917,404449  21% 5% 6% 80%
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
0.7C# Mono #6 44.0616.4782,2321433
1.1C gcc #8 16.1616.18125,9962040
1.2C++ g++ #6 11.623.49132,9843415
1.4C gcc #4 13.333.76155,0002409
1.4Java  #6 19.1619.03156,2202115
1.5Java  14.224.00173,6245211
2.4C gcc #5 48.2714.80277,2202519
2.9Python 3 #2 128.5573.75329,280624
3.6Ada 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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