[Chimera-users] Hbond in CLI + cacheDA

[Eric Pettersen]

This seems to be a memory leak in Chimera.  Using the 1.3 production  
release (1.3.2577) the weak key dictionary discards entries as they  
are closed, but with the 1.4 production release (1.4.1) and later the  
entries accumulate in the dictionary.  That means that some code  
somewhere in Chimera is holding onto a reference to the closed model,  
preventing it from being destroyed and its memory freed (and its weak- 
key dictionary references from being deleted).

This is why your "flush cache" trick helps some but doesn't completely  
solve the problem:  the closed models aren't freeing up memory like  
they should.  I will be investigating this and will post something  
here when I've fixed it, but memory leaks are pretty difficult to  
track down so it might take until sometime next week for me to find/ 
fix it.

--Eric

On Jul 28, 2011, at 11:24 AM, Maciek Wójcikowski wrote:

> Hello Eric,
>
> My script is quite simple, but I'm not an python expert:
>
> #! /usr/bin/env python
> # -*- coding: utf-8 -*-
>
> import os
> import glob
> import sys
>
> if len(sys.argv) < 2:
>     	print 'No directory specified.'
>     	sys.exit()
>
> path = sys.argv[1]
>
> from chimera import runCommand
> runCommand("open 0 model.mol2")
>
> i=0
>
> for files in glob.glob( os.path.join(path, '*.mol2') ):
> 	#print path+files
> 	runCommand('open 1 %s' % files)
> 	if i < 100:
> 		cache = " cacheDA true"
> 	else:
> 		cache = ""
> 		i=0
> 	try:
> 		runCommand("hbonds intramodel false distSlop 0.8 angleSlop 40" +  
> cache )
> 	except:
>     		pass
> 	runCommand("close 1")
> 	i+=1
>
> I've added the "non-cache" run every 100 iterations, since I've  
> noticed in source code that non-cache hbond check trigers  
> flushCache() and it seams to help. When I previously had all  
> iterations with "cacheDA true" chimera was eating RAM like a beast  
> (up to about 2GB per 100.000 molecules) making the cache searches  
> slow. It would be ideal to have cached only those D+A from the model  
> (protein).
>
> Some tech. details: Chimera 1.5.3, Fedora 14, CentOS 6.0, Debian Sid  
> - all have this problem.
>
> PS.
> Is it possible to get the number of donors and acceptors somehow? Or  
> should I add this to the source code? It can be achieved easily  
> since it counts them, but doesn't print such number.
>
> Thank you in advance for your help.
> ----
> Pozdrawiam,  |  Best regards,
> Maciek Wójcikowski
> maciek at wojcikowski.pl
>
>
> 2011/7/28 Eric Pettersen <pett at cgl.ucsf.edu>
> On Jul 28, 2011, at 3:35 AM, Maciek Wójcikowski wrote:
>
>> Hello everyone,
>>
>> I'm trying to compute hbonds for quite large molecular database, so  
>> i do it in CLI. I've added cacheDA parameter which speeds up whole  
>> process at first by 10 times, although after time cache is getting  
>> bigger and bigger operations slows down as one can expect, because  
>> Chimera is caching every compound. Is there a way to limit the size  
>> of a cache, or even better to tell chimera to cache only protein  
>> donors and acceptors?
>
> Hi Maciek,
> 	Are you closing the compound models after you do the H-bond  
> computation?  I ask because the caching uses a "weak key dictionary"  
> where the key is the model.  What this means is that if the model is  
> closed it should simply disappear from the cache, no fuss no muss.   
> If you are closing the models then either the slowdown is due to  
> something else, or the models aren't being properly removed from the  
> cache.  Let me know if your script is closing the models but still  
> having this problem and I will investigate.
>
> --Eric
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
>
>
>

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