[Chimera-users] Hbond in CLI + cacheDA

[Eric Pettersen]

Okay, I have a workaround until I get a fix in:  in the "New  
Molecules" category of Preferences, change "smart initial display"  
from true to false (then run your script, or "Save" your change if you  
want to run your script in a new Chimera).

--Eric

On Jul 28, 2011, at 1:29 PM, Eric Pettersen wrote:

> 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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