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

From: Alex Shevtsov
Subject: Re: [Help-gsl] Memory issues when using GSL ODE solver
Date: Mon, 25 Nov 2013 20:56:21 +0100


I will of course share it. It is quite messy because it involves a lot of
function declarations, ODE solution and double integration.

I append 4 files, which can be used to reproduce the behavior I mentioned.
First of all I use CythonGSL ( as a Cython
wrapper to GSL. So, in the attached files there is:

1) lib_SI_CI_V6.pyx - the library, which is to be compiled using the
2) - python file, which calls the compiled library and
performs calculations.
3) In order to see how the memory is getting full quickly, I use mpi4py to
lauch several substances of the program. The commands to run are in the
'commands file provided'. -n 7 must be substituted by -n x, where x is the
number of CPU cores you want to use.

So, in order to use the files do:
1) Compile the .pyx file by using
python build_ext --inplace
you will be prompted for the name..type the name of the .pyx file without
2) Use one of the commands provided in the 'commands' file from the
terminal or launch the whole bunch of them by using chmod +x commands &&
3) Use htop to see how quickly the memory is being filled.

P.S. In my version of CythonGSL I fixed the gsl_odeiv2_driver_free return
type from int to void, as it should be, but the problem persists.

I understand that the program is very messy, sorry for that.

Thank you!

Best wishes,

Attachment: Shevtsov_code.tar.gz
Description: GNU Zip compressed data

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