Re: [OBO-Edit Working Group] Notes from OEWG meeting, 5 May 2011

[David Osumi-S. <dj...@ge...>]

Hi all,

Very interested in this issue from the meeting:

"Discussion of maximum memory allocation in OE
Marcus has a computer with 6G of RAM, yet the OE installer (and config manager) only let you set the memory allocation to a max of 1860M. However, when he hand-edited oboedit.vmoptions and set it to a higher number, OE worked great (and didn't run out of memory like it did before).
This is because 32-bit JVMs can only handle 1860M. However, newer 64-bit JVMs (which some users have--such as Marcus) can use as much memory as you care to give them.
Is there some way to ask from within a running Java app whether the JVM is 32- or 64-bit? If so, we could set the max memory accordingly. (But might not be able to do that in the installer.)
Heiko investigated and didn't find any easy way to figure it out from inside a Java app."
Have been experimenting with this, but I'm running up against the basic problem of how to configure OE or my system so that OE runs over 64 bit java.

My system java, as assessed from shell, is

djs93% java -version
java version "1.6.0_24"
Java(TM) SE Runtime Environment (build 1.6.0_24-b07-334-10M3326)
Java HotSpot(TM) 64-Bit Server VM (build 19.1-b02-334, mixed mode)


But if I fire up OE and look in the activity monitor, it appears not to be running at 64 bit.  In contrast, Protege, which is also a java app, is running at 64bit. From sampling the process in each case:
OE2: Code Type:       X86 (Native)
Protege: Code Type:       X86-64 (Native)

Also supporting this - I get heap space memory errors if I try to set memory allocation above 2048M

e.g.- from console:

04/May/2011 4 May 2011 11:44:16	[0x0-0xbb5bb5].????[15137]	Invalid maximum heap size: -Xmx4096M

Would be great if we could specify which java VM to use in OE configuration manager.  In the absence of this, is there some way to specify it in OE config files?
e.g.- OBO-Edit.app/Contents/Info.plist (which I had to edit to respecify memory allocation in order to get OE to start after setting it to high).

Cheers,

David




On 4 May 2011, at 4/May/2011 06:47:45, Nomi Harris wrote:

> Some notes are at http://wiki.geneontology.org/index.php/OEWG_20110503#Discussion
> I didn't get everything down in the last two topics--can those who participated in the discussion (especially Marcus, Midori, and Chris M) take a look and edit as needed?
> 	Nomi
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David Osumi-Sutherland, PhD
Curator/ Ontologist
FlyBase / Virtual Fly Brain
Department of Genetics,
University of Cambridge,
Downing Street,
Cambridge, CB2 3EH, UK
Tel: +44 (0)1223 333 963
Fax: +44 (0)1223 766 732