performance measurements
Each table row shows performance measurements for this Smalltalk VisualWorks program with a particular command-line input value N.
| N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
|---|---|---|---|---|---|
| 250,000 | 3.98 | 4.04 | 77,436 | 1153 | 0% 0% 0% 100% |
| 2,500,000 | 34.97 | 35.01 | 131,556 | 1153 | 0% 0% 0% 100% |
| 25,000,000 | 343.20 | 343.48 | 380,852 | 1153 | 0% 0% 0% 100% |
Read the ↓ make, command line, and program output logs to see how this program was run.
Read k-nucleotide benchmark to see what this program should do.
notes
VisualWorks® Personal Use Edition Release 7.9 of May 11, 2012
k-nucleotide Smalltalk VisualWorks #5 program source code
"* The Computer Language Benchmarks Game http://benchmarksgame.alioth.debian.org/ contributed by Andres Valloud *"! !SequenceableCollection methodsFor: 'computer language shootout'! substringFrequencies5: aLength using: aDictionary | buffer | buffer := String new: aLength. 1 to: self size - aLength + 1 do: [:i | | answer | buffer replaceFrom: 1 to: aLength with: self startingAt: i. answer := aDictionary at: buffer putValueOf: [:sum | sum + 1] ifAbsentPutValueOf: 1. answer = 1 ifTrue: [buffer := String new: aLength]. ]. ^aDictionary! ! !Dictionary methodsFor: 'computer language shootout'! at: key putValueOf: putBlock ifAbsentPutValueOf: absentBlock "* Set the value at key to be the value of evaluating putBlock with the existing value. If key is not found, create a new entry for key and set is value to the evaluation of absentBlock. Answer the result of evaluating either block. *" | index element anObject | key == nil ifTrue: [^self subscriptBoundsErrorFor: #at:putValueOf:ifAbsentPutValueOf: index: key value: absentBlock value]. index := self findKeyOrNil: key. element := self basicAt: index. element == nil ifTrue: [self atNewIndex: index put: (self createKey: key value: (anObject := absentBlock value))] ifFalse: [element value: (anObject := putBlock value: element value)]. ^anObject ! ! !Tests class methodsFor: 'benchmarking'! readFasta: sequenceName from: input | prefix newline buffer description line char | prefix := '>',sequenceName. newline := Character lf. "* find start of particular fasta sequence *" [(input atEnd) or: [ (input peek = $>) ifTrue: [((line := input upTo: newline) indexOfSubCollection: prefix startingAt: 1) = 1] ifFalse: [input skipThrough: newline. false]] ] whileFalse. "* line-by-line read - it would be a lot faster to block read *" description := line. buffer := ReadWriteStream on: (String new: 1028). [(input atEnd) or: [(char := input peek) = $>]] whileFalse: [ (char = $;) ifTrue: [input upTo: newline] ifFalse: [buffer nextPutAll: (input upTo: newline)] ]. ^Association key: description value: buffer contents ! ! !Tests class methodsFor: 'benchmarking'! knucleotide5From: input to: output "Same as av3, but create less strings while updating the frequencies" | sequence writeFrequencies writeCount | sequence := (self readFasta: 'THREE' from: input) value asUppercase. writeFrequencies := [:k | | frequencies count | frequencies := SortedCollection sortBlock: [:a :b| (a value = b value) ifTrue: [b key < a key] ifFalse: [b value < a value]]. count := 0.0. (sequence substringFrequencies5: k using: (Dictionary new: 1024)) associationsDo: [:each| frequencies add: each. count := count + each value]. frequencies do: [:each | | percentage | percentage := (each value / count) * 100.0. output nextPutAll: each key; space; print: percentage digits: 3; nl]]. writeCount := [:nucleotideFragment | | frequencies count | frequencies := sequence substringFrequencies5: nucleotideFragment size using: (Dictionary new: 1024). count := frequencies at: nucleotideFragment ifAbsent: [0]. output print: count; tab; nextPutAll: nucleotideFragment; nl]. writeFrequencies value: 1. output nl. writeFrequencies value: 2. output nl. writeCount value: 'GGT'. writeCount value: 'GGTA'. writeCount value: 'GGTATT'. writeCount value: 'GGTATTTTAATT'. writeCount value: 'GGTATTTTAATTTATAGT'.! ! !Tests class methodsFor: 'benchmark scripts'! knucleotide5 self knucleotide5From: self stdinSpecial to: self stdout. ^''! !
make, command-line, and program output logs
Thu, 07 Feb 2013 01:51:20 GMT COMMAND LINE: /usr/local/src/vw7.9pul/bin/linuxx86_64/vwlinuxx86_64 /usr/local/src/vw7.9pul/image/benchmarks.im -nogui -evaluate "Tests knucleotide5" -a 0 < knucleotide-input25000000.txt PROGRAM OUTPUT: A 30.295 T 30.151 C 19.800 G 19.754 AA 9.177 TA 9.132 AT 9.131 TT 9.091 CA 6.002 AC 6.001 AG 5.987 GA 5.984 CT 5.971 TC 5.971 GT 5.957 TG 5.956 CC 3.917 GC 3.911 CG 3.909 GG 3.902 1471758 GGT 446535 GGTA 47336 GGTATT 893 GGTATTTTAATT 893 GGTATTTTAATTTATAGT