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 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 #3 14 min14 min161,372540  19% 31% 32% 20%
1.5Ruby JRuby #3 8 min176.561,194,036540  78% 68% 71% 87%
1.5Racket 219.87220.011,419,712542  96% 0% 1% 4%
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 min111.81626,276701  72% 77% 75% 74%
2.6Erlang HiPE #3 6 min137.89864,700932  99% 48% 49% 72%
2.7Go 170.0958.59379,444980  81% 62% 57% 93%
2.8C# Mono #2 177.41177.45289,7641012  94% 1% 2% 5%
2.9PHP 45.7940.06246,9521036  4% 90% 14% 7%
3.0PHP #4 5 min87.70246,8841060  78% 94% 84% 88%
3.1F# Mono #3 65.7528.151,005,4401111  39% 86% 50% 59%
3.5C++ g++ #3 23.317.26137,2161252  74% 97% 76% 75%
3.5Go #5 52.7219.59260,0801268  96% 51% 82% 42%
3.6Lisp SBCL #2 171.83172.18355,4841277  99% 1% 1% 1%
3.6Lisp SBCL #3 171.44171.54355,4681284  0% 100% 0% 1%
3.8Scala #6 156.4041.51473,5241380  95% 94% 94% 95%
3.9C# Mono #3 164.0057.33316,3441404  85% 95% 57% 50%
4.0C# Mono 116.56116.60525,7361420  0% 99% 0% 1%
4.2F# Mono #4 64.4826.081,004,9361505  57% 92% 47% 53%
4.3Go #2 170.0654.60256,4401531  100% 65% 62% 90%
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 #4 107.3434.65543,9201696  100% 71% 72% 68%
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%
5.7Rust 30.3730.39126,6962049  1% 0% 100% 0%
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 71.9271.99104,2082272  0% 1% 0% 100%
6.4C gcc #7 43.3015.85153,6722280  96% 96% 37% 46%
6.4Lisp SBCL #5 71.9372.01104,2242301  0% 1% 1% 100%
6.6Pascal Free Pascal #2 46.8846.91128,3962383  89% 0% 0% 11%
6.8C gcc #6 56.2018.61153,6762439  95% 54% 54% 100%
6.8C# Mono #5 127.8241.28361,9962445  83% 73% 73% 79%
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 21.9610.11253,4924865  24% 36% 100% 60%
C++ g++ Make Error2106
Erlang HiPE Failed930
Erlang HiPE #2 Failed997
Lisp SBCL Bad Output847
OCaml #3 Failed1789
OCaml Failed870
OCaml #2 Failed1205
Racket #2 Bad Output842
Racket #4 Bad Output881
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 47.9317.32106,7881433
5.7C gcc #8 16.7716.78126,0162040
6.7C gcc #4 13.513.83162,2282409
7.0C gcc #5 50.3415.23267,4842519
9.5C++ g++ #6 11.943.56131,6883415
9.5C++ g++ #5 9.273.0241,4483416
15Java  14.164.00183,2165211
18Ada 2005 GNAT 11.345.04398,5606503
missing benchmark programs
Dart No program

 k-nucleotide benchmark : Hashtable update and k-nucleotide strings

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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