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MathGroup Archive 2004

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Timing of statements inside a cell

  • To: mathgroup at smc.vnet.net
  • Subject: [mg50841] Timing of statements inside a cell
  • From: János <janos.lobb at yale.edu>
  • Date: Thu, 23 Sep 2004 05:27:24 -0400 (EDT)
  • Sender: owner-wri-mathgroup at wolfram.com

Hi,

I have a cell with some code in it containing many statements.  Like:

Cell starts here
...
...
currentTargetPartitioned = Partition[currentTarget, primerLength, 1];
prposBin = {{1}, {currentTargetLength}};

(* Do as long as the Mean of
the distance between
     neighbouring primers is bigger than averagePrimerDistance *)
While[Mean[Flatten[Map[#[[2]] - #[[1]] &, Partition[prposBin, 2, 1]]] ] 
 > \
averagePrimerDistance, (
       pr = random[currentTargetPartitioned];
       prpos = Position[currentTargetPartitioned, pr];
       prposBin = Sort[Flatten[Append[prposBin, Flatten[prpos] ] ] ];
       )];

(* Create a double strand
             from the currentTarget in such a way that the double starts 
from
       the first primer position and file it into collectedDnaBin *)
prposBinDouble = Most[Map[{#, Last[prposBin]} &, prposBin] ];
collectpr = Take[currentTarget, prposBinDouble[[2]] ];
...
...
Cell ends here

I would like to time every single statement as they are executing.  
Just adding //Timing after every statement  or wrapping them with 
Timing[statement;] does not work.
Any good hint ?  /I am sure I am not the only one needing it :)/

In general,  what kind of profiling Mathematica allows to pinpoint the 
statements inside a single cell which spend the most time in the kernel 
?

If it cannot be done inside a cell, what is possible baring to break 
the cell into single statements cells ?  What should I read ?

Other question:  In the While loop above I am collecting positions into 
a list
       prposBin = Sort[Flatten[Append[prposBin, Flatten[prpos] ] ] ];
/Just realized that I should do the Sort outside of the loop :)/
How can I do the collection with Sow and Reap to avoid Append ?

Thanks ahead,

János
P.S.
----------------------------------------------
Trying to argue with a politician is like lifting up the head of a 
corpse.
(S. Lem: His Master Voice)


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