[Biojava-dev] DP memory leak

[Thomas Down]

Did this problem ever get fixed?  I've got a DP application
leaking pretty badly right now.

If the answer is no, would anyone object to me implementing
the weak-reference solution? (which might require a little
bit of magic so that the `well known' alphabets don't get
unloaded immediately after BJ initializes.  *sigh*).

     Thomas.

Once upon a time, Matthew Pocock wrote:
> Hi,
> 
> Lachlan James Coin wrote:
> 
> >Hi,
> >
> >I came across a bit of a memory leak while using the dp code.  The 
> >problem is that AlphabetManager keeps a reference to every alphabet 
> >created, including StateAlphabetcreated when using the dp package.  I 
> >had extended the EmissionState class in such a way that the instances 
> >were of a non-trivial size.  I am also creating (one after the other) 
> >a lot of different state alphabets.  The result was that I ran out of 
> >memory farily quickly.
> 
> Hehe. That's an unforseen use-case bug.
> 
> >
> >One possible fix I thought of was to add "deregisterAlphabet(name)" 
> >method to AlphabetManager, and to call this from the finalize mehod of 
> >SimpleMarkovModel, so that when the garbage collector thinks it can 
> >clear the markov model the statealphabet is removed from the 
> >AlphabetManager registry and can then also be garbage collected.   
> >Also, it would be necessary to make alphabetToIndex a WeakHashMap.
> 
> This may work - but it adds API.
> 
> >
> >Any other suggestions?  Can I make these changes?
> 
> How transparent can we make this? How easy would it be for alphabets to 
> be dropped automatically when not needed any more? I guess we don't want 
> to drop DNA & friends :)
> 
> >
> >Thanks,
> >
> >Lachlan
> >
> Matthew
> 
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