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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	14.80	4.31	132,452	3415	81% 80% 99% 84%
1.3	C++ GNU g++ #2	20.12	5.50	161,516	2673	89% 88% 89% 99%
1.7	C++ GNU g++ #3	26.85	7.48	153,276	2313	100% 86% 87% 87%
1.9	C++ GNU g++	30.09	8.32	156,512	2106	88% 99% 87% 88%
2.7	Ada 2005 GNAT #2	28.18	11.47	254,024	4504	49% 72% 40% 82%
3.3	Java 6 -server #2	47.53	14.24	762,548	1602	80% 80% 95% 79%
5.3	Java 6 -server	77.03	22.84	759,536	1330	81% 81% 92% 82%
8.0	C# Mono #3	107.38	34.34	479,860	1404	87% 76% 69% 79%
9.2	Scala #4	120.61	39.80	608,340	1287	78% 75% 75% 74%
12	Haskell GHC #3	112.51	52.02	407,916	2749	47% 38% 71% 37%
13	C GNU gcc #2	53.96	53.96	802,928	1141	0% 0% 0% 100%
14	Pascal Free Pascal #2	62.42	62.42	127,780	2383	0% 0% 0% 100%
15	Lua LuaJIT #2	65.87	65.87	601,104	613	0% 0% 100% 0%
15	Lua LuaJIT	65.97	65.98	569,900	601	70% 0% 0% 30%
21	Perl	281.57	88.72	2,774,904	648	78% 73% 88% 83%
22	Clean	92.87	92.87	1,573,432	1511	0% 100% 0% 0%
24	C# Mono	104.84	104.13	472,012	1420	100% 0% 1% 0%
32	Fortran Intel	137.67	137.66	205,660	2238	0% 0% 0% 100%
33	Python CPython #6	6 min	144.14	439,968	520	56% 88% 50% 96%
34	PHP #3	8 min	144.96	247,900	1268	96% 75% 85% 96%
34	C GNU gcc	143.17	146.39	134,108	1340	1% 98% 0% 0%
35	Lisp SBCL #3	150.84	150.85	392,552	1284	100% 0% 0% 0%
36	Python CPython #5	7 min	157.21	439,968	557	77% 54% 93% 76%
37	Erlang HiPE #3	7 min	160.31	558,128	932	82% 62% 62% 77%
40	Erlang HiPE	7 min	174.56	2,204,632	930	50% 80% 67% 61%
41	C# Mono #2	176.16	175.53	597,996	1012	0% 87% 13% 0%
47	Python 3 #4	10 min	204.52	842,860	577	77% 54% 94% 72%
50	Lua	216.59	216.58	619,440	601	100% 0% 0% 0%
52	Lua #2	221.91	223.26	670,844	613	1% 1% 98% 1%
60	Perl #2	253.06	256.79	709,264	359	99% 1% 0% 0%
60	Haskell GHC #2	5 min	258.56	2,739,252	1767	23% 30% 47% 32%
63	Go 6g 8g	266.92	270.49	391,788	874	96% 9% 6% 2%
65	Python 3 #2	10 min	279.00	842,864	563	31% 32% 66% 93%
69	Java 6 -Xint #2	17 min	297.28	299,196	1602	85% 86% 86% 100%
72	Scheme PLT	5 min	5 min	1,294,924	623	2% 3% 2% 93%
81	JavaScript V8 #3	5 min	5 min	332,956	390	0% 100% 0% 0%
90	JavaScript V8	6 min	6 min	332,884	423	1% 1% 1% 98%
94	Lisp SBCL	6 min	6 min	379,584	847	2% 93% 3% 2%
103	Java 6 -Xint	27 min	7 min	685,072	1330	93% 93% 93% 95%
118	Ruby JRuby #2	8 min	8 min	423,736	420	38% 61% 2% 2%
122	PHP #2	8 min	8 min	247,900	914	0% 0% 0% 100%
127	JavaScript TraceMonkey	9 min	9 min	659,444	423	2% 97% 0% 0%
130	Python CPython	9 min	9 min	439,248	475	0% 0% 99% 0%
165	Python 3	11 min	11 min	840,244	487	4% 96% 0% 0%
168	JavaScript TraceMonkey #3	12 min	12 min	427,744	390	0% 100% 0% 0%
184	Ruby 1.9 #2	13 min	13 min	163,236	420	1% 99% 0% 1%
196	Ruby MRI #2	14 min	14 min	147,980	420	0% 0% 0% 100%
	ATS	Make Error			1336
	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	9.90	3.15	41,468	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).