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- all benchmarks - binary-trees chameneos-redux fannkuch fasta k-nucleotide mandelbrot meteor-contest n-body pidigits regex-dna reverse-complement spectral-norm thread-ring - all languages - Ada 2005 GNAT ATS C GNU gcc C# Mono C++ GNU g++ Clean Erlang HiPE F# Mono Fortran Intel Go 6g 8g Haskell GHC Java 6 -server Java 6 -Xint Java 6 steady state JavaScript TraceMonkey JavaScript V8 Lisaac Lisp SBCL Lua Lua LuaJIT Mozart/Oz OCaml Pascal Free Pascal Perl PHP Python 3 Python CPython Ruby 1.9 Ruby JRuby Ruby MRI Scala Scheme PLT Smalltalk VisualWorks

 How big is the measured performance difference?

Each chart bar shows how many times more Time or how many times more Memory one unidentified ↓ k-nucleotide program used, compared to the program that used least Time or the program that used least Memory.

 k-nucleotide benchmark ~240MB N=25,000,000

This table shows 5 measurements - CPU Time, Elapsed Time, Memory, Code and ~ CPU Load.

Compare how much Memory the k-nucleotide programs used - sort Memory KB. Compare how much Code the programs used - sort Code B

Column × shows how many times more each program used compared to the program that used least.

		sort	sort	sort	sort
×	Program Source Code	CPU secs	Elapsed secs	Memory KB	Code B	~ CPU Load
1.0	C++ GNU g++ #6	13.61	13.61	132,864	3415	0% 0% 0% 100%
1.3	C++ GNU g++ #3	18.05	18.05	130,796	2313	0% 0% 0% 100%
1.4	C++ GNU g++ #2	18.51	18.51	137,236	2673	0% 0% 0% 100%
1.5	C++ GNU g++	21.09	21.09	130,776	2106	0% 2% 6% 100%
2.1	Ada 2005 GNAT #2	28.50	28.51	254,024	4504	0% 0% 0% 100%
3.5	Java 6 -server #2	46.90	46.95	351,004	1602	0% 0% 0% 100%
4.0	C GNU gcc #2	53.84	53.83	843,132	1141	0% 0% 0% 100%
4.6	Pascal Free Pascal #2	62.78	62.77	127,780	2383	0% 0% 0% 100%
4.8	Lua LuaJIT #2	65.63	65.63	487,092	613	0% 0% 0% 100%
4.8	Lua LuaJIT	65.78	65.77	609,124	601	0% 0% 0% 100%
6.3	Java 6 -server	85.16	85.23	758,456	1330	0% 0% 0% 100%
6.9	Haskell GHC #3	93.79	93.79	409,216	2749	0% 0% 0% 100%
7.4	C# Mono #3	100.95	100.95	567,808	1404	0% 0% 0% 100%
7.7	C# Mono	104.23	104.22	467,872	1420	0% 0% 0% 100%
8.5	Scala #4	116.00	116.03	607,968	1287	0% 0% 0% 100%
9.1	Clean	124.30	124.29	1,049,148	1511	0% 0% 0% 100%
10	Fortran Intel	137.35	137.34	205,660	2238	0% 0% 0% 100%
11	C GNU gcc	141.91	144.32	134,104	1340	0% 0% 0% 100%
11	Lisp SBCL #3	151.12	151.12	392,548	1284	0% 0% 0% 100%
13	C# Mono #2	180.34	180.61	526,364	1012	0% 0% 0% 100%
16	Lua	217.60	217.59	675,524	601	0% 0% 0% 100%
16	Lua #2	223.02	223.43	667,400	613	0% 0% 0% 100%
19	Perl #2	249.61	252.46	709,264	359	0% 0% 0% 100%
20	Go 6g 8g	269.17	271.79	389,740	874	0% 0% 0% 100%
20	Perl	269.61	272.49	2,697,908	648	0% 0% 0% 100%
22	Erlang HiPE #3	294.36	295.52	574,028	932	0% 99% 0% 0%
23	Scheme PLT	5 min	5 min	1,294,916	623	0% 0% 0% 100%
23	Haskell GHC #2	5 min	5 min	2,745,104	1767	0% 0% 0% 100%
26	JavaScript V8 #3	5 min	5 min	332,880	390	0% 1% 0% 100%
26	JavaScript V8	6 min	6 min	332,964	423	0% 0% 0% 100%
30	Lisp SBCL	6 min	6 min	379,596	847	6% 11% 3% 100%
31	Python CPython #6	7 min	7 min	439,968	520	0% 0% 0% 100%
35	Python CPython #5	7 min	7 min	439,972	557	8% 4% 4% 100%
38	PHP #2	8 min	8 min	247,916	914	0% 0% 0% 100%
38	PHP #3	8 min	8 min	247,912	1268	0% 0% 0% 100%
38	Ruby JRuby #2	8 min	8 min	423,656	420	0% 0% 0% 100%
40	JavaScript TraceMonkey	9 min	9 min	659,444	423	0% 0% 0% 100%
41	Python CPython	9 min	9 min	439,248	475	0% 0% 0% 100%
45	Python 3 #2	10 min	10 min	842,860	563	0% 0% 0% 100%
46	Python 3 #4	10 min	10 min	842,860	577	0% 0% 0% 100%
51	Python 3	11 min	11 min	840,240	487	0% 0% 0% 100%
53	JavaScript TraceMonkey #3	12 min	12 min	427,748	390	0% 0% 0% 100%
59	Ruby 1.9 #2	13 min	13 min	163,236	420	0% 0% 0% 100%
62	Ruby MRI #2	14 min	14 min	147,984	420	0% 0% 0% 100%
71	Java 6 -Xint #2	16 min	16 min	299,116	1602	0% 0% 0% 100%
89	Java 6 -Xint	20 min	20 min	600,768	1330	0% 0% 0% 100%
	ATS	Make Error			1336
	Erlang HiPE	Failed			930
	Erlang HiPE #2	Failed			997
	JavaScript TraceMonkey #2	Bad Output			400
	JavaScript V8 #2	Failed			400
	Lisaac	Make Error			1242
	Lisp SBCL #4	Failed			1434
	Mozart/Oz #2	Failed			771
	Mozart/Oz	Failed			791
	OCaml #3	Failed			1095
	OCaml	Failed			870
	OCaml #2	Failed			1205
	Pascal Free Pascal	Bad Output			2380
	Smalltalk VisualWorks	Bad Output			1191
	Smalltalk VisualWorks #4	Bad Output			1296
interesting alternative programs
0.7	C++ GNU g++ #5	9.27	9.27	41,324	3416
missing programs
	F# Mono	No program
	Java 6 steady state	No program

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

diff program output for this 100KB input file (generated with the fasta program N = 10000) with this output file to check your program is correct before contributing.

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).