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[bioontology-support] NCBO memory problem

Jean-Paul jean.paul.ik at
Tue Dec 6 01:58:49 PST 2011

Thank you.
I am giving only 2G of memory to the VM. But I see that the Xmx parameter
of tomcat (/etc/init.d/tomcat) is set to 4500m. So is this a minimum
requirement for the app to work properly?. I only have one user accessing,
and very few ontologies. (for instance this one: I load it, parse it and
it works well. But when i browse the terms in the tree, the application
dies after navigating some of the tree elements.


2011/12/5 Paul R Alexander <palexander at>

> Memory usage will vary on how you are utilizing the Virtual Appliance and
> exactly what is happening on the system at any given point. The portions of
> the application that tend to use a lot of memory include: Lucene search
> index, ontology parsing, and the Rails application when experiencing
> mid-high traffic loads (~20 concurrent users).
> We haven't heard of other users having memory issues, but again it is very
> dependent on how you are using the Appliance. Your virtualization
> environment should include options for increasing the memory available to
> the Appliance, so starting there is what I would do.
> Best,
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> On 12/2/11 12:03 AM, jpcik wrote:
>> I am using v 0.3 of NCBO. We followed the instructions and the
>> documentation
>> a couple of weeks ago. It seemed tu run fine, but I noticed that
>>  Bioportal becomes unresponsive after a while, (we get database connection
>> errors constanly). I am under the impression that it might be a memory
>> problem ( the VM is running on a machine with only 3GB of memory). Does
>> Bioportal require more than 4G of memory to run properly or maybe the
>> source
>> of our problem is something else. I  thought about that because you have
>> this heavy cache implementation that might require lots of resources....
>> --
>> View this message in context: http://ncbo-support.2288202.**
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>> bioontology-support mailing list
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