performance measurements
Each table row shows performance measurements for this Lisp SBCL program with a particular command-line input value N.
| N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
|---|---|---|---|---|---|
| 250,000 | 4.59 | 4.60 | 47,624 | 847 | 1% 0% 0% 100% |
| 2,500,000 | Bad Output | 847 |
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
This is SBCL 1.1.7, an implementation of ANSI Common Lisp.
k-nucleotide Lisp SBCL program source code
;; The Computer Language Benchmarks Game ;; http://benchmarksgame.alioth.debian.org/ ;; contributed by James McIlree ;; Modified by Juho Snellman 2005-11-19 ;; * About 50% speedup on both SBCL and CMUCL ;; * Use SIMPLE-BASE-STRINGs instead of (SIMPLE-ARRAY CHARACTER) for ;; lower memory use on Unicode SBCL ;; * Declare the type of SEQUENCE in ACCUMULATE-FREQUENCIES (defun read-data (stream) (let ((data (make-array 0 :element-type 'base-char :adjustable t :fill-pointer 0))) (do ((line (read-line stream nil 'eof) (read-line stream nil 'eof))) ((or (eq line 'eof) (string= ">THREE" line :start2 0 :end2 6)))) (do ((line (read-line stream nil 'eof) (read-line stream nil 'eof))) ((or (eq line 'eof) (char= (schar line 0) #\>))) (if (not (char= (schar line 0) #\;)) (dotimes (char-index (length line)) (vector-push-extend (char-upcase (the base-char (schar line char-index))) data)))) (coerce data 'simple-base-string))) (defun accumulate-frequencies (hashmap sequence offset fragment-length) (declare (type (integer 0 18) fragment-length) (fixnum offset) (type (simple-base-string) sequence)) (let ((last-sequence-index (- (length sequence) fragment-length))) (do ((start offset (+ start fragment-length))) ((> start last-sequence-index)) (let ((fragment (subseq sequence start (+ start fragment-length)))) (setf (gethash fragment hashmap) (1+ (the (integer 0 999999) (gethash fragment hashmap 0)))))))) (defun calculate-frequencies (sequence fragment-length) (declare (type (integer 0 18) fragment-length)) (let ((hashmap (make-hash-table :test #'equal))) (dotimes (offset fragment-length) (accumulate-frequencies hashmap sequence offset fragment-length)) hashmap)) (defun write-frequencies (sequence length) (let ((sorted-frequencies) (sum 0)) (declare (fixnum sum)) (maphash #'(lambda (k v) (setf sum (+ sum (the fixnum v))) (setf sorted-frequencies (cons (cons k v) sorted-frequencies))) (calculate-frequencies sequence length)) (setf sorted-frequencies (sort sorted-frequencies #'(lambda (v1 v2) (cond ((> (the (integer 0 999999) (cdr v1)) (the (integer 0 999999) (cdr v2))) t) ((< (the (integer 0 999999) (cdr v1)) (the (integer 0 999999) (cdr v2))) nil) (t (string< (car v1) (car v2))))))) (dolist (entry sorted-frequencies) (format t "~A ~,3F~%" (car entry) (* (/ (the (integer 0 999999) (cdr entry)) sum) 100.0))) (terpri))) ;; ;; Delete this before including in the shootout, test method only. ;; ;;(defun test-main (filename) ;; (with-open-file (stream filename) ;; (let ((sequence (read-data stream))) ;; (declare (type (simple-array * *) sequence)) ;; (dolist (entry '(1 2)) (write-frequencies sequence entry)) ;; (dolist (entry '("GGT" "GGTA" "GGTATT" "GGTATTTTAATT" "GGTATTTTAATTTATAGT")) ;; (declare (type (simple-array * *) entry)) ;; (format t "~A~C~A~%" (gethash entry (calculate-frequencies sequence (length entry)) 0) #\Tab entry))))) (defun main () (let ((sequence (read-data *standard-input*))) (declare (type (simple-array * *) sequence)) (dolist (entry '(1 2)) (write-frequencies sequence entry)) (dolist (entry '("GGT" "GGTA" "GGTATT" "GGTATTTTAATT" "GGTATTTTAATTTATAGT")) (declare (type (simple-array * *) entry)) (format t "~A~C~A~%" (gethash entry (calculate-frequencies sequence (length entry)) 0) #\Tab entry))))
make, command-line, and program output logs
Fri, 03 May 2013 22:22:35 GMT
MAKE:
cp: ‘knucleotide.sbcl’ and ‘./knucleotide.sbcl’ are the same file
SBCL built with: /usr/local/bin/sbcl --userinit /dev/null --batch --eval '(load "knucleotide.sbcl_compile")'
### START knucleotide.sbcl_compile
(handler-bind ((sb-ext:defconstant-uneql (lambda (c) (abort c)))) (load (compile-file "knucleotide.sbcl" ))) (save-lisp-and-die "sbcl.core" :purify t)
### END knucleotide.sbcl_compile
; compiling file "/home/dunham/benchmarksgame/bench/knucleotide/knucleotide.sbcl" (written 24 JAN 2013 02:01:15 PM):
; compiling (DEFUN READ-DATA ...)
; compiling (DEFUN ACCUMULATE-FREQUENCIES ...)
; compiling (DEFUN CALCULATE-FREQUENCIES ...)
; compiling (DEFUN WRITE-FREQUENCIES ...)
; compiling (DEFUN MAIN ...)
; /home/dunham/benchmarksgame_onecore/knucleotide/tmp/knucleotide.fasl written
; compilation finished in 0:00:00.057
[undoing binding stack and other enclosing state... done]
[saving current Lisp image into sbcl.core:
writing 3512 bytes from the read-only space at 0x0x1000000
writing 2256 bytes from the static space at 0x0x1100000
writing 28205056 bytes from the dynamic space at 0x0x9000000
done]
### START knucleotide.sbcl_run
(main) (quit)
### END knucleotide.sbcl_run
0.65s to complete and log all make actions
COMMAND LINE:
/usr/local/bin/sbcl --noinform --core sbcl.core --userinit /dev/null --load knucleotide.sbcl_run 0 < knucleotide-input2500000.txt
UNEXPECTED OUTPUT
0a1,27
> A 30.297
> T 30.151
> C 19.798
> G 19.755
>
> AA 9.177
> TA 9.133
> 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 3.910
> CG 3.909
> GG 3.903
>
> 147166 GGT
> 44658 GGTA
> 4736 GGTATT
> 89 GGTATTTTAATT
> 89 GGTATTTTAATTTATAGT
PROGRAM OUTPUT:
debugger invoked on a TYPE-ERROR in thread
#<THREAD "main thread" RUNNING {AAE6B11}>:
The value 1000000 is not of type (MOD 1000000).