[ome-users] java.lang.OutOfMemoryError: PermGen space

[Josh Moore]

On Mar 31, 2011, at 4:46 PM, Wood, Christopher wrote:

> Josh, 
> 
> Thanks for your help.

Gladly.

> Would you suggest increasing the heap size to 1024m?

If you can spare it, it's definitely worth it. Typically the more heap the better, up to some pretty large limit like 4+ GB, at which point garbage collection times can become prohibitive.

> Chris

~Josh


> -----Original Message-----
> From: Josh Moore [mailto:josh at glencoesoftware.com] 
> Sent: Thursday, March 31, 2011 9:33 AM
> To: Wood, Christopher
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] java.lang.OutOfMemoryError: PermGen space
> 
> 
> On Mar 31, 2011, at 4:00 PM, Wood, Christopher wrote:
> 
>> Josh,
> 
> Hi Chris,
> 
>> I attached the Blitz-0.log and the master.err files.
> 
> The master.err was very helpful:
> 
> 3/30/11 16:55:23:101 error: Blitz-0-Ice.ThreadPool.Server-9: java.lang.OutOfMemoryError: PermGen space
> 
> PermGen errors are not affected by changes to -Xmx. Rather you need to add an element of the form:
> 
>  <option>-XX:MaxPermSize=256m</option>
> 
> and restart your server. PermGen errors are dependent on OS and whether your system is 32 or 64 bit, but 256m tends to be a very safe value. If you leave your server at -Xmx512m (which is the maximum heap size), then you probably want a smaller value, like 128m, for MaxPermSize.
> 
> Hope that helps.
> Cheers,
> ~Josh. 
> 
>> I imported one image, about 11 MB, with 300 planes (z = 150, channels=2). I tested the Make Movie script and some of the other scripts in Insight (on mac), and tried to view them through the web client a windows computer.
>> 
>> Thanks
>> Chris
>> -----Original Message-----
>> From: Josh Moore [mailto:josh at glencoesoftware.com] 
>> Sent: Thursday, March 31, 2011 2:35 AM
>> To: Wood, Christopher
>> Cc: OME Users
>> Subject: Re: [ome-users] java.lang.OutOfMemoryError: PermGen space
>> 
>> 
>> On Mar 31, 2011, at 12:05 AM, Wood, Christopher wrote:
>> 
>>> Hi,
>> 
>> Hi Chris,
>> 
>>> I am getting (I restarted omero in the meantime) errors like this in master.err:
>>> 
>>> 3/30/11 16:55:02:131 error: Blitz-0-Ice.ThreadPool.Server-7: java.lang.OutOfMemoryError: PermGen space
>>> 
>>> 3/30/11 16:55:23:101 error: Blitz-0-Ice.ThreadPool.Server-9: java.lang.OutOfMemoryError: PermGen space
>> 
>> Do you know what series of operations (e.g. importing a file of size X, then viewing it) lead to the OutOfMemoryError? I ask to try to help judge how much memory you are going to need. If you'd like to send your Blitz-0.log (again), we should be able to track down what happened.
>> 
>>> I assume there is a setting somewhere to increase the JVM memory, but I am not sure where that is.
>> 
>> In etc/grid/template.xml on line 174 or so, in the <server-template id="BlitzTemplate"> element, there's an element:
>> 
>> <option>-Xmx512M</option>
>> 
>> If there are resources available on that system, you might try "-Xmx1024M".
>> 
>>> I currently have 2 GB of memory on this machine.
>>> 
>>> Here are the java commands from ps:
>>> 
>>> 2696 ?        Sl     0:21 java -Xmx512M -Djava.awt.headless=true -Dlog4j.configuration=etc/log4j.xml -Domero.logfile=var/log/${omero.name}.log -Domero.name=Blitz-0 -jar lib/server/blitz.jar --Ice.Config=/OMERO/OMERO.server-Beta-4.2.2/var/master/servers/Blitz-0/config/config
>>> 2702 ?        Sl     0:20 java -Xmx256M -Djava.awt.headless=true -Dlog4j.configuration=etc/log4j-indexing.xml -Domero.logfile=var/log/${omero.name}.log -Domero.name=Indexer-0 -jar lib/server/blitz.jar ome.fulltext --Ice.Config=/OMERO/OMERO.server-Beta-4.2.2/var/master/servers/Indexer-0/config/config
>>> 
>>> Thanks
>>> Chris
>> 
>> Cheers,
>> ~Josh
>> <logfiles.tgz>
>