[SciPy-user] MemoryError in scipy_core

Travis Oliphant oliphant at ee.byu.edu
Fri Nov 4 12:38:05 CST 2005


Chris Fonnesbeck wrote:

>In the course of moving PyMC from Numeric to scipy_core, I am running
>into some pretty serious memory issues. For those of you unfamilair
>with PyMC, it is simply a Bayesian simulation module that estimates
>model paramters by iteratively sampling from the joint posterior
>distribution of the model, and saving each sample to an array. Under
>Numeric, I could safely run several hundered thousand iterations of
>pretty complex models (i.e. lots of paramters) without trouble. Under
>scipy_core, PyMC hogs most of the system resources (you really cant do
>anything else while its running), and crashes after just over 10K
>iterations, under a pretty simple model. Here is the end of the
>  
>
>output:
>  
>

It's possible that it's a memory leak.   I would love to close it if it 
is.   Is there someway I could run the model you are using?   Also, 
which version of scipy core are you using?

All arrays are created and deleted from the same section of code and so 
it wouldn't be too difficult to track down if certain arrays that were 
created were not getting deleted.

Can you monitor memory usage somehow and report.  I will also look more 
closely at memory usage on some simple tests and try to figure this one 
out.

Thanks for your report and assistance.

-Travis



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