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How can I profile a HYPHY execution? (Read 1906 times)
avilella
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How can I profile a HYPHY execution?
Oct 17th, 2005 at 5:31am
 
Dears,

HYPHY is taking a lot of time with the "Replace stop codons with gaps
in codon data" with a file of very long sequences:

echo -e "4\n1\n1\n/home/avb/wallace/eukarya/drosophila/concat/obacs/data/Dmsye.fasta\n4\
n3\n1\n1\n/home/avb/wallace/eukarya/drosophila/concat/obacs/data/Dmsye.nogaps.fa
sta\n" | ./HYPHYMP

And I was wondering how can I profile, somehow, where is it spending
so much time to do the job.

Are there any tools that you, the HYPHY gurus, use for that?

Bests,

    Albert.
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avilella
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Re: How can I profile a HYPHY execution?
Reply #1 - Oct 17th, 2005 at 5:36am
 
http://gromit.bio.ub.es/Dmsye.fasta.bz2

This is an example file with large sequences and a good amount of stop codons.
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Sergei
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Re: How can I profile a HYPHY execution?
Reply #2 - Oct 17th, 2005 at 4:31pm
 
Dear Albert,

I fixed the bug which was causing the slowdown.

Effectively it's a 'stream problem'. Effectively, what happens is this imagine you have a very long string A and a string B, which you want to populate with a modified version of A.

The code I had in the file (and it works fine for short sequences) is like this:

[code]
B="";

for (k=0; k<Abs(A); k=k+1)
{
     if (A[k] == something)
    {
           B = B + function of A[k]);
    }
    else
    {
           B = B + another function of A[k];
    }
}
[/code]

The slowdown comes when Abs(A) is large. Effectively in B=B+something, new memory has to be allocated of length(B)+length(something). When length (B) is large, the cost of reallocating length(B)+length (something) can be order (length (B)). Thus the overall complexity of the algorithm can be order (length (A)^2).

Here's a streamed version of the same alrgorithm:

[code]
B="";
B*8192; /* make B into a stream string and allocate some initial storage */

for (k=0; k<Abs(A); k=k+1)
{
     if (A[k] == something)
    {
           B * function of A[k]); /* '*' in this context is an 'add to stream' operation */
    }
    else
    {
           B * another function of A[k];
    }
}
B*0; /*trim unused memory; B is now a regular string */
[/code]

Now, when time comes to allocate more memory to stream B, new allocation is not length (function of A[k]), but rather length (B)/2 (i.e. if the string is already long, we allocate a lot more memory that immediately needed, but then save on memory allocations). Now we only have Log (length (A)) allocations (assuming functions of A[k] return constant length strings), and execution time is Log(length (A)) * length (A).

Fixed version of CleanStopCodons.bf [url] http://www.hyphy.org/pubs/BFs/CleanStopCodons.bf[/url] and will be rolled into the next update.

Having a HyPhy batch code profiler is a good idea! I will add it soon.

Cheers,
Sergei

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Division of Infectious Diseases
Division of Biomedical Informatics
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University of California San Diego
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Sergei
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Re: How can I profile a HYPHY execution?
Reply #3 - Oct 21st, 2005 at 3:39pm
 
Dear Albert,

I have added a simple code profiler to HyPhy as of today's (Oct 21st) build. Take a look at the profile_test.bf file in Examples/BatchLanguage for a trivial example.

Cheers,
Sergei
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Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
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