Hi Shaun,

On Mar 10, 2011, at 10:05 AM, SHAUN WEBB wrote:

> Thanks Greg, there would be about 100 datasets in the library.

If there are only about 100 datasets, then this is likely not the cause of the 
time taken to render the library.  Whatever is going on with the environment 
that is slowing Galaxy may also be causing this. 

> 
> Can you tell me how I would pull a single changeset, I have only done batch 
> updates using the distribution depository before.

You really can't pull a single change set, you just have to pull from the 
development repo in a batch update like you've done with teh stable 
distribution.

> 
> I'm just wondering why it has become so much slower since the latest update 
> (I previously updated last December). Also wondering why the Galaxy process 
> is now taking up 25% of the memory on a 64GB machine.

Yeah, the cause of this is really needed, although I have no idea what is could 
be...


> 
> Thanks
> Shaun
> 
> Quoting Greg Von Kuster <g...@bx.psu.edu>:
> 
>> Hi Shaun,
>> 
>> Security checks are performed on every active ( undeleted ) dataset within a 
>> data library as it's contents are rendered upon opening.  For the current 
>> user, every dataset is checked to determine if the user can access it, and 
>> if so, then checks are made to see if the user has permission to perform 
>> operations on the dataset that fall into the add / modify / manage 
>> permissions areas.  These checks incur db hits for each dataset, so if your 
>> data library include many datasets ( several hundred  or more ), then it 
>> will take a bit of time to render it upon opening.  The size of the dataset 
>> files is not an issue here, but the number of datasets within the data 
>> library.
>> 
>> A solution to this is to split up the data library.  Change set 
>> 5200:ed7b6180b925 added the ability to move data library items within a 
>> library or between libraries, providing a way to split up a large library.  
>> This change set should make it to the distribution within the next few 
>> weeks, or you can pull it from our development repo.
>> 
>> Thanks Shaun,
>> 
>> Greg Von Kuster
>> 
>> 
>> On Mar 10, 2011, at 5:21 AM, SHAUN WEBB wrote:
>> 
>>> 
>>> Further to my email below.
>>> 
>>> I have a data library that contains many ~117Gb of NGS data, uploaded via 
>>> file system path. This library was always slow to open (about 10s) but now 
>>> takes several minutes or not at all.
>>> 
>>> Thanks for any help on this. I am still experiencing a memory leak that I 
>>> can't pinpoint and it is only dissipated by restarting the server. At the 
>>> moment my debugging level is set to INFO. Is there anything I can change in 
>>> the universe file to try to trace this.
>>> 
>>> Thanks!
>>> Shaun
>>> 
>>> 
>> 
>> Greg Von Kuster
>> Galaxy Development Team
>> g...@bx.psu.edu
>> 
>> 
>> 
>> 
>> 
> 
> 
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 

Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to