performance measurements
Each table row shows performance measurements for this OCaml program with a particular command-line input value N.
| N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
|---|---|---|---|---|---|
| 250,000 | 0.78 | 0.79 | 20,988 | 870 | 0% 1% 100% 3% |
| 2,500,000 | 7.15 | 7.16 | 65,316 | 870 | 1% 0% 0% 100% |
| 25,000,000 | 70.22 | 70.30 | 411,188 | 870 | 0% 0% 100% 0% |
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
The OCaml native-code compiler, version 4.00.1
k-nucleotide OCaml program source code
(* * The Computer Language Benchmarks Game * http://benchmarksgame.alioth.debian.org/ * * contributed by Troestler Christophe * modified by Mauricio Fernandez *) module S = struct type t = string let size = 0x40000 let equal (s1:string) s2 = (s1 = s2) let hash s = let h = ref 0 in for i = 0 to String.length s - 1 do h := !h * 5 + Char.code s.[i] done; !h end module H = Hashtbl.Make(S) (* [counts k dna] fills and return the hashtable [count] of k-nucleotide keys and count values for a particular reading-frame of length [k] of the string [dna]. Keys point to mutable values for speed (to avoid looking twice the same key to reinsert the value). *) let count = H.create S.size let counts k dna = H.clear count; let key = String.create k in for i = 0 to String.length dna - k do String.unsafe_blit dna i key 0 k; try incr(H.find count key) with Not_found -> H.add count (String.copy key) (ref 1) done; count (* [write_frequencies k dna] writes the frequencies for a reading-frame of length [k] sorted by descending frequency and then ascending k-nucleotide key. *) let compare_freq ((k1:string),(f1:float)) (k2, f2) = if f1 > f2 then -1 else if f1 < f2 then 1 else compare k1 k2 let write_frequencies k dna = let cnt = counts k dna in let tot = float(H.fold (fun _ n t -> !n + t) cnt 0) in let frq = H.fold (fun k n l -> (k, 100. *. float !n /. tot) :: l) cnt [] in let frq = List.sort compare_freq frq in List.iter (fun (k,f) -> Printf.printf "%s %.3f\n" k f) frq; print_string "\n" let write_count seq dna = let cnt = counts (String.length seq) dna in Printf.printf "%d\t%s\n" (try !(H.find cnt seq) with Not_found -> 0) seq (* Extract DNA sequence "THREE" from stdin *) let dna_three = let is_not_three s = try String.sub s 0 6 <> ">THREE" with _ -> true in while is_not_three(input_line stdin) do () done; let buf = Buffer.create 1000 in (* Skip possible comment *) (try while true do let line = input_line stdin in if line.[0] <> ';' then (Buffer.add_string buf (String.uppercase line); raise Exit) done with _ -> ()); (* Read the DNA sequence *) (try while true do let line = input_line stdin in if line.[0] = '>' then raise End_of_file; Buffer.add_string buf (String.uppercase line) done with End_of_file -> ()); Buffer.contents buf let () = Gc.set { (Gc.get()) with Gc.minor_heap_size = 1024 * 2048 } let () = List.iter (fun i -> write_frequencies i dna_three) [1; 2]; List.iter (fun k -> write_count k dna_three) ["GGT"; "GGTA"; "GGTATT"; "GGTATTTTAATT"; "GGTATTTTAATTTATAGT"]
make, command-line, and program output logs
Sat, 02 Feb 2013 20:29:15 GMT MAKE: mv knucleotide.ocaml knucleotide.ml /usr/local/bin/ocamlopt -noassert -unsafe -fno-PIC -nodynlink -inline 100 unix.cmxa knucleotide.ml -o knucleotide.ocaml_run rm knucleotide.ml 0.22s to complete and log all make actions COMMAND LINE: ./knucleotide.ocaml_run 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