Ubuntu : Intel® Q6600® quad-core
Computer Language Benchmarks Game      [[ Play ]]

- all benchmarks - n-body fannkuch-redux meteor-contest fasta fasta-redux spectral-norm reverse-complement mandelbrot k-nucleotide regex-dna pidigits chameneos-redux thread-ring binary-trees-redux binary-trees - all languages - Ada 2005 GNAT ATS C gcc Clojure C# Mono C++ g++ Dart Erlang HiPE F# Mono Fortran Intel Go Haskell GHC Java 7 Lisp SBCL OCaml Pascal Free Pascal Perl PHP Python 3 Racket Ruby 2.0 Ruby JRuby Scala x86 one core x64 quad-core x86 quad-core x64 one core

 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		sort	sort
×	Program Source Code	CPU secs	Elapsed secs	Memory KB	Code B	≈ CPU Load
1.0	C++ g++ #3	23.39	7.40	138,100	1252	73% 74% 74% 97%
1.3	Ada 2005 GNAT #2	22.36	9.60	253,480	4865	29% 66% 39% 100%
1.4	Scala #2	27.51	10.18	217,308	2080	70% 74% 51% 76%
1.7	Java 7  #2	44.83	12.93	494,264	1602	84% 81% 85% 99%
1.8	Java 7  #3	46.77	13.37	494,772	1630	96% 82% 87% 87%
2.0	C gcc #7	39.88	14.64	153,688	2280	96% 92% 50% 36%
2.2	ATS #3	54.99	16.09	159,484	3810	83% 81% 82% 98%
2.3	C gcc #6	54.70	17.40	153,668	2439	91% 51% 77% 96%
2.5	Go #5	48.81	18.28	260,256	1268	97% 34% 66% 72%
2.9	Haskell GHC #2	79.26	21.34	374,364	1965	91% 91% 95% 95%
3.9	Fortran Intel #2	70.68	28.99	158,124	2079	35% 42% 99% 68%
4.2	C# Mono #3	99.69	31.43	317,812	1404	70% 96% 83% 69%
4.4	C# Mono #4	105.85	32.27	545,852	1696	78% 100% 78% 74%
4.4	ATS #2	32.32	32.33	124,132	3238	0% 1% 100% 0%
4.9	Haskell GHC #3	103.97	36.40	359,728	2749	49% 46% 96% 95%
5.3	Clojure #6	118.43	39.22	1,015,780	1737	82% 66% 74% 82%
5.4	C# Mono #5	123.30	39.92	363,616	2445	74% 74% 74% 88%
6.0	Scala #6	160.68	44.49	485,572	1380	90% 91% 91% 91%
6.3	Pascal Free Pascal #2	46.88	46.91	128,396	2383	89% 0% 0% 11%
7.4	Clojure #7	181.72	54.79	1,014,076	3030	86% 78% 86% 84%
8.3	Go	171.44	61.26	379,332	980	45% 70% 66% 100%
9.4	Lisp SBCL #4	69.14	69.22	105,244	2272	0% 0% 0% 100%
9.4	Lisp SBCL #5	69.46	69.54	105,248	2301	1% 92% 9% 1%
9.4	Clojure #4	211.81	69.85	1,006,452	1944	77% 75% 77% 87%
9.4	Perl	242.07	69.89	1,774,668	648	82% 88% 85% 92%
11	PHP #4	292.63	82.96	246,808	1060	90% 98% 83% 83%
12	Haskell GHC	5 min	87.82	263,752	1693	98% 98% 99% 98%
13	F# Mono	265.02	94.57	647,280	701	61% 58% 80% 80%
15	C# Mono	113.58	113.64	526,612	1420	0% 0% 0% 100%
17	Fortran Intel	122.78	122.86	166,952	2238	92% 0% 8% 0%
19	Erlang HiPE #3	6 min	137.89	864,700	932	99% 48% 49% 72%
22	C# Mono #2	159.72	159.77	290,440	1012	3% 97% 1% 0%
22	Python 3 #8	8 min	161.22	422,160	647	62% 55% 97% 90%
23	Lisp SBCL #2	173.66	173.80	355,100	1277	0% 88% 12% 0%
24	Lisp SBCL #3	174.52	174.63	355,100	1284	0% 0% 0% 100%
25	Ruby JRuby #3	9 min	182.01	920,168	540	88% 80% 86% 92%
25	Ruby JRuby	10 min	186.63	920,900	637	72% 90% 92% 74%
30	Racket	218.65	219.02	1,419,368	542	93% 1% 6% 0%
31	Perl #2	223.14	226.16	708,152	359	65% 0% 0% 34%
33	Ruby 2.0	13 min	247.46	128,020	637	94% 74% 96% 76%
75	Python 3	9 min	9 min	353,020	487	0% 0% 100% 0%
105	Ruby 2.0 #2	12 min	12 min	158,088	420	27% 54% 17% 3%
135	Ruby 2.0 #3	19 min	16 min	216,296	540	48% 10% 14% 43%
	C++ g++	Make Error			2106
	Erlang HiPE	Failed			930
	Erlang HiPE #2	Failed			997
	Lisp SBCL	Bad Output			847
	OCaml #3	Failed			1789
	OCaml	Failed			870
	OCaml #2	Failed			1205
	Racket #2	Bad Output			842
	Racket #4	Bad Output			881
	Ruby JRuby #2	Failed			421
	Scala #4	Failed			1287
	Scala	Failed			1625
"wrong" (different) algorithm / less comparable programs
0.4	C++ g++ #5	9.81	3.14	41,340	3416
0.5	C++ g++ #6	11.92	3.57	131,184	3415
0.5	C gcc #4	12.62	3.60	161,956	2409
0.5	Java 7	14.23	4.01	151,788	5211
0.7	Ada 2005 GNAT	11.32	5.15	398,804	6503
2.0	C# Mono #6	42.11	15.05	82,464	1433
2.1	C gcc #5	51.45	15.36	267,440	2519
9.7	Python 3 #2	125.64	72.05	459,992	624
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

• read line-by-line a redirected FASTA format file from stdin
• extract DNA sequence THREE
• define a procedure/function to update a hashtable of k-nucleotide keys and count values, for a particular reading-frame — even though we'll combine k-nucleotide counts for all reading-frames (grow the hashtable from a small default size)
• use that procedure/function and hashtable to
  • count all the 1-nucleotide and 2-nucleotide sequences, and write the code and percentage frequency, sorted by descending frequency and then ascending k-nucleotide key
  • count all the 3- 4- 6- 12- and 18-nucleotide sequences, and write the count and code for the specific sequences GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT

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).

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