[pygr-notify] Issue 103 in pygr: Excessive memory consumption in megatests

[codesite-noreply at google.com]

Comment #1 on issue 103 by deepreds: Excessive memory consumption in  
megatests
http://code.google.com/p/pygr/issues/detail?id=103

Here are some comments on this issue.

Pygr uses excessive memory when it uses SQLTable or SQLTableClustered  
classes for
NLMSA building and querying.

You have to run full version of megatest in your machine. First, you need  
to setup
megatest machine, check necessary files at
http://biodb.bioinformatics.ucla.edu/MEGATEST/ Some of the bugs has been  
fixed and
placed in July2009_BugFix directory.

And you have to run annotation_hg18_megatest.py by protest.py or nose.  
Because you
don't have to run Collection megatest, you can place sys.exit() after def
collectionannot_test(self): The function you have to test is def  
mysqlannot_test
(self):

If you want to change ouptut directory for debugging, you can put testDir  
after def
__init__(self, testDir = None): of class PygrBuildNLMSAMegabase(object):

testDir = /tmp/mytest

Symptom is that it uses more than 2GB memory when building NLMSA or  
querying NLMSA.
It never decrease even if you set autoGC = True.


--
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings