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Re: [Help-gsl] Memory issues when using GSL ODE solver

From: Daniele Nicolodi
Subject: Re: [Help-gsl] Memory issues when using GSL ODE solver
Date: Mon, 25 Nov 2013 19:32:48 +0100
User-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:24.0) Gecko/20100101 Thunderbird/24.1.0

On 25/11/2013 19:19, Alex Shevtsov wrote:
>> Excellent.  This was with GSL version 1.16?
> No, I compiled it all with GSL 1.15 from Ubuntu 12.04 repositories. But
> still I see no leaks in the C-version, while there is something in the
> Cython/Python version.
>> Sometimes scripting environments or shared libraries will "hold
>> on" to memory until they exit or until they're asked to let go (e.g.
>> Intel MKL and FFTW both do this).
> Probably it is the problem of a Python interpreter. It has an automatic
> garbage collector, which is probably invoked in the end, when all the loops
> are finished. But while they were running, the memory was being consumed. I
> never had any problems with it before though.
> I have to think how to work-around these difficulties. Any suggestions are
> very appreciated.

Python memory management should not be the problem here, at least if you
are not leaking references to unused objects.

I believe Cython itself, is unlikely the responsible for the memory
leak, because it does not do much memory allocation.  If the same code
written in C does not exhibit the memory leak, I believe the problem may
be in your wrapping of GSL in Cython.  Would you like to share your
code, at least the part that exhibits the memory leak?


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