fasta benchmark ≈240MB N=25,000,000

Each chart bar shows how many times slower, one ↓ fasta 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 gcc #6 5.291.812,3521914  89% 53% 54% 100%
1.0Java  #5 5.901.8231,6002457  80% 83% 80% 82%
1.0Go #3 6.581.902,7601344  87% 86% 89% 87%
1.2Haskell GHC #7 3.342.1115,5321550  44% 21% 44% 50%
1.2Haskell GHC #6 6.052.2113,2161567  61% 61% 91% 62%
1.4Haskell GHC #5 3.812.545,0361378  38% 27% 21% 66%
1.7Fortran Intel #4 2.992.992601327  0% 1% 100% 1%
1.8C gcc #5 3.243.256761261  100% 0% 2% 1%
2.0Haskell GHC #2 3.923.652,440979  100% 3% 3% 2%
2.4C++ g++ #2 4.284.281,1681105  1% 1% 1% 100%
2.4Ada 2005 GNAT #5 4.314.321,7042186  100% 0% 1% 0%
2.4C++ g++ #3 4.334.331,1281286  0% 0% 0% 100%
2.5Fortran Intel #3 4.444.445241190  0% 1% 100% 0%
2.5C# Mono #4 10.534.55130,1161505  66% 61% 62% 44%
2.6Java  #4 4.784.6824,9481507  1% 65% 36% 2%
2.7C++ g++ 4.834.841,1681033  0% 100% 1% 0%
2.8C gcc #4 5.025.036321221  0% 0% 0% 100%
2.9Rust 5.205.216,1161211  0% 0% 1% 100%
3.5Scala #3 6.396.2629,4881053  2% 89% 11% 1%
3.5C++ g++ #4 6.266.275841266  0% 100% 1% 0%
3.5Fortran Intel 6.326.335241155  0% 0% 100% 0%
3.9C gcc 7.047.056681185  0% 97% 4% 0%
4.1C# Mono #2 7.467.4739,4121180  100% 1% 0% 1%
4.2Java  #2 7.627.5225,2361240  89% 2% 7% 6%
4.3Lisp SBCL #6 7.867.867,8361751  0% 0% 100% 1%
4.4Pascal Free Pascal #4 7.937.9381112  0% 100% 1% 0%
4.6Go #2 13.538.2710,3801388  33% 57% 49% 27%
4.8Ada 2005 GNAT 8.588.591,6321346  0% 0% 0% 100%
4.8Dart 8.708.6021,6081386  1% 79% 22% 1%
4.9Go 8.778.777601036  0% 1% 1% 100%
5.4Clojure #6 11.159.7261,1281692  7% 98% 5% 7%
5.6Scala 10.3010.1330,9281080  2% 99% 1% 2%
5.8F# Mono 10.4310.4340,548978  1% 100% 1% 0%
5.9Clojure #5 12.1810.6363,0761964  23% 62% 27% 7%
6.5Lisp SBCL #3 11.7211.737,8441579  0% 1% 0% 100%
6.7OCaml #3 12.0512.066001042  1% 1% 100% 0%
7.4Racket #3 13.4213.4319,6481276  0% 0% 1% 100%
8.2Lisp SBCL 14.8314.8324,4921419  1% 0% 100% 0%
8.9Lisp SBCL #2 16.0516.0624,4841617  0% 1% 100% 1%
25Python 3 #5 127.5445.962,479,9041933  76% 65% 78% 80%
28Erlang HiPE #2 49.8749.8824,1161164  1% 1% 1% 99%
28Racket 50.1350.1218,0281054  0% 0% 1% 100%
54Erlang HiPE 97.2997.3215,2881039  100% 1% 0% 1%
61Python 3 #3 109.42109.464,332977  23% 2% 100% 53%
63Perl 113.68113.7251,420838  1% 0% 0% 100%
66PHP #3 118.72118.762,5921030  0% 100% 1% 1%
132Python 3 238.94239.194,296792  11% 11% 62% 18%
133Ruby #5 240.42240.855,124987  45% 20% 29% 9%
133Ruby #4 240.98241.22197,180904  44% 47% 4% 7%
157Ruby #2 284.20284.29128,236732  16% 42% 1% 42%
172Perl #4 5 min5 min2,560934  20% 38% 7% 38%
206PHP #2 6 min6 min2,5881006  1% 35% 22% 44%
234Perl #2 7 min7 min2,556886  31% 35% 0% 36%
Haskell GHC #4 Bad Output1413
Haskell GHC Bad Output1421
OCaml #6 Failed1161
Ruby JRuby Failed760
"wrong" (different) algorithm / less comparable programs
1.3Perl #5 2.302.3015,2321113
1.3C gcc #2 2.392.391,2801169
1.6C++ g++ #5 2.902.911,1761543
6.9Haskell GHC #3 13.4312.538,0361408

 fasta benchmark : Generate and write random DNA sequences

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 N = 1000 with this 10KB 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.

Each program should

We'll use the generated FASTA file as input for other benchmarks (reverse-complement, k-nucleotide).

Random DNA sequences can be based on a variety of Random Models (554KB pdf). You can use Markov chains or independently distributed nucleotides to generate random DNA sequences online.

Revised BSD license

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