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 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
1.0C++ g++ #3 24.417.33155,9241252  79% 80% 81% 95%
1.0Clojure #5 24.8610.20241,9602723  48% 98% 26% 73%
1.0Scala #2 25.109.23171,4642080  55% 76% 69% 73%
1.2Rust 28.4128.44129,3322049  1% 1% 0% 100%
1.3Ada 2005 GNAT #2 31.9012.52256,1284865  85% 65% 52% 54%
1.5Lisp SBCL #4 37.0837.12138,4882272  0% 1% 1% 100%
1.5Lisp SBCL #5 37.0937.13138,4842301  0% 0% 1% 100%
1.8PHP 43.0837.93247,8321036  4% 91% 4% 16%
1.8C gcc #7 43.9916.22180,3722280  38% 97% 97% 41%
1.8Java  #2 44.8512.81504,3121602  93% 86% 87% 84%
1.9Java  #3 46.4913.13504,9521630  86% 84% 86% 99%
2.3OCaml #3 55.5020.29253,6241789  39% 57% 79% 100%
2.4C gcc #6 59.6819.71180,3722439  97% 98% 54% 55%
2.5Java  #4 61.2260.65186,3801873  70% 1% 1% 31%
2.7Fortran Intel #2 65.5225.74196,2122079  48% 38% 90% 83%
2.7Haskell GHC 65.9917.73363,7801693  92% 93% 93% 97%
2.8OCaml 69.4569.51443,232870  96% 0% 0% 4%
3.0F# Mono #3 73.2331.12628,3841111  70% 69% 34% 65%
3.1F# Mono #4 74.5627.44663,1761505  99% 49% 66% 59%
3.1Haskell GHC #2 74.8220.03365,1121965  96% 92% 95% 92%
3.1Go #5 76.0628.90261,9961268  37% 48% 83% 97%
3.2Java  #5 78.9336.26193,2162211  17% 88% 20% 95%
3.4OCaml #2 82.4737.09325,7401205  26% 80% 36% 82%
3.5Pascal Free Pascal #2 86.0586.09130,5682383  91% 0% 0% 9%
3.6Fortran Intel 88.6088.68187,1202238  0% 0% 100% 0%
3.6C# Mono #4 89.0428.88563,9961696  71% 96% 70% 72%
3.8Ruby JRuby #4 92.2383.491,825,996449  5% 55% 47% 5%
3.9C# Mono 95.7095.74538,8121420  3% 1% 1% 97%
4.0C# Mono #3 96.5831.05334,6721404  97% 68% 70% 78%
4.4Racket #4 106.84106.83387,480881  0% 0% 1% 100%
4.6Clojure #7 112.5135.881,062,0363030  95% 74% 79% 67%
4.6Ruby #4 112.75112.79501,972449  1% 100% 0% 0%
5.0Haskell GHC #3 122.1146.26313,5082749  54% 89% 43% 80%
5.4Clojure #6 132.7050.501,027,6321737  81% 54% 49% 81%
5.6Hack #4 137.0542.82221,9601061  66% 94% 74% 89%
5.8Lisp SBCL #3 141.54141.61331,2201284  0% 1% 1% 100%
5.9C# Mono #2 143.28143.31302,1121012  95% 1% 1% 5%
5.9Go #2 144.3849.56256,9161531  62% 57% 88% 87%
6.0C# Mono #5 145.4951.21449,7442445  69% 78% 70% 69%
6.0Lisp SBCL #2 145.75145.86331,2201277  0% 0% 1% 100%
7.8Go 189.2863.63380,512980  86% 60% 92% 61%
7.8Racket 190.80190.941,308,984542  29% 1% 66% 5%
7.8Scala #6 191.4252.66492,5801380  91% 91% 91% 91%
8.7Clojure #4 213.0966.311,061,7001944  72% 89% 82% 78%
9.1Perl #2 221.13224.63778,212359  97% 1% 0% 0%
9.1Perl #4 221.6971.041,066,204472  61% 96% 90% 67%
9.9Perl 240.6070.321,886,164648  84% 90% 82% 87%
11Perl #3 278.3584.541,143,524507  72% 75% 94% 90%
12F# Mono 295.43103.51662,576701  77% 73% 74% 59%
13PHP #4 5 min94.40247,7241060  97% 76% 76% 82%
15Python 3 #8 6 min124.40498,756647  59% 58% 87% 98%
15Erlang HiPE #3 6 min143.111,133,724932  68% 78% 64% 60%
16Erlang HiPE 6 min181.003,734,268930  84% 50% 53% 68%
18Ruby #2 7 min7 min167,228420  1% 100% 0% 0%
18Erlang #3 7 min157.60996,280932  80% 73% 64% 57%
18Erlang 7 min195.373,684,516930  82% 49% 58% 73%
19Python 3 7 min7 min402,016487  0% 1% 100% 0%
20Ruby #3 7 min7 min170,312540  26% 25% 23% 27%
20Ruby 8 min143.44131,008637  96% 80% 95% 72%
22Ruby JRuby 8 min167.76944,148637  91% 79% 82% 65%
24Ruby JRuby #3 9 min183.31907,264540  76% 91% 66% 85%
C++ g++ Make Error2106
Erlang #2 Failed997
Erlang HiPE #2 Failed997
Hack Bad Output1038
Lisp SBCL Timed Out10 min847
Racket #2 Bad Output842
Ruby JRuby #2 Failed421
Scala Failed1625
Scala #4 Failed1287
"wrong" (different) algorithm / less comparable programs
0.3C++ g++ #5 7.432.4549,4003416
0.4C gcc #4 8.852.65174,4682409
0.4C gcc #8 8.868.87128,1082040
0.4C++ g++ #6 10.803.08139,0203415
0.5Java  12.643.64200,9245211
0.6Ada 2005 GNAT 14.127.04395,1126503
1.8C# Mono #6 43.8115.191,013,2081433
2.3C gcc #5 57.1618.05282,0202519
3.8Python 3 #2 93.3351.67376,064624
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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