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MathGroup Archive 2004

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Re: Timing of statements inside a cell

  • To: mathgroup at smc.vnet.net
  • Subject: [mg50852] Re: [mg50841] Timing of statements inside a cell
  • From: János <janos.lobb at yale.edu>
  • Date: Fri, 24 Sep 2004 04:41:26 -0400 (EDT)
  • References: <200409230927.FAA08079@smc.vnet.net>
  • Sender: owner-wri-mathgroup at wolfram.com

To answer my own question, wrapping Timing with a Print works just fine 
from inside the cell.  I found it shortly after I sent my e-mail to the 
group.  Sorry...

My other question is still pending regarding the replacement of Append 
with REAP and SOW.  I read all I could on it in the Book, I looked many 
archived messages, but my brain is still not on it.

János
On Sep 23, 2004, at 5:27 AM, János wrote:

> 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)
>
>

-------------------------------------------------------------------
János Löbb
Yale University School of Medicine
Department of Pathology
Phone: 203-737-5204
Fax:      203-785-7303
E-mail: janos.lobb at yale.edu


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