Re: [Seqan-dev] memory issue when calling function in seqan

Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de> · Wed, 18 May 2011 00:15:41 +0200

Lingjie,

can you submit a minimal demo program that compiles and shows your  

error? Please compile it on your computer and run it under valgrind  

[1,2] and make sure that a memory leak is reported.

I just replaced "MyersHirschberg" with "MyersBitVector" in the demos/ 

alignment.cpp file, compiled it and ran it through valgrind. Valgrind  

[1,2] reported no memory leaks, so it is very unlikely that this  

function produces leaks per se in the current trunk version.

If it turns out that your memory leak is in another position, valgrind  

is a very useful and versatile tool to find such leaks. You will find  

many high-quality tutorials on the internet.

There are known leaks with the last release version when using SeqAn  

Strings of non-POD types (i.e. objects that allocate memory and where  

the destructor has to be called in order to free memory) that is fixed  

in the current trunk version. A workaround here, is to upgrade to the  

trunk version or use std::vector<> objects. Also, the SeqAn Map  

specialization based on skiplists is known to leak memory. Use another  

specialization or std::map<,> directly.

What SeqAn version are you using? The last release version? May I  

recommend you to try out the trunk version and check whether the  

problem persists?

Bests,
Manuel

[1] http://www.valgrind.org
[2] http://lh3lh3.users.sourceforge.net/memdebug.shtml

Am 17.05.2011 um 23:59 schrieb Lingjie Weng:

Dear Seqan team,

I am interested in our Seqan C++ library, it is really helpful. But I
got some problem when try to use the function
"globalAlignment(Align<TSource, TSpec> & align_,Score<TScoreValue,
Simple> const &, MyersBitVector" in seqan/align/align.myers.h file.

I was trying to call this function in my project, I called it in this
way (got those code from /demos/alignment.cpp) :

    typedef String<Dna> TSequence;
    TSequence seq1 = "atcgaatgcgga";
    TSequence seq2 = "actcgttgca";
    Score<int> score(0, -1, -1, -2);
    Align<TSequence, ArrayGaps> align;
    resize(rows(align), 2);
    assignSource(row(align, 0), seq1);
    assignSource(row(align, 1), seq2);
    ::std::cout << "Score = " << globalAlignment(align, score,
MyersBitVector()) << ::std::endl;

I found you have internally clean up the memory in the function
"globalAlignment ()". My question is how could clean up the memory I
allocated for initialization, for example, Tsequence, align...

When I am using it for millions  of reads alignment, the memory keeps
increasing, which turns out to be a big issue to me. Do you have any
idea how to release memory properly? I really appreciate if you could
show me how to fix it.

I am looking forward to your reply.

Thanks,
Lingjie

PhD student
University of California, Irvine

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Manuel Holtgrewe			manuel.holtgrewe@fu-berlin.de
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