On Wed, Jul 15, 2009 at 16:31, Mark Wilkinson<[email protected]> wrote: > Quick Q: Will Taverna 2.1 run (usefully ;-) ) with a JVM limit of 312MB?
The default is 300MB, so I hope so! But as pointed out - it all depends on the workflow. Although the reference manager should reduce the memory footprint of data compared to earlier Tavernas, you might still run out of memory in some circumstances, depending on what combination of services that's in your workflow. For instance if you combine BioMoby, Soaplab, Biomart, WSDL and local workers all in the same workflow this would use more memory than if you only used say Soaplab. If you run workflows with larger data you can also sacrifice some workflow execution speed by turning off data caching, in File -> Preferences go to Data Storage and select "On-disk storage" instead of "On-disk (with cache) storage", this means that all data produced is written to disk immediately, with 'caching' this happens in the background, allowing the workflow to continue executing. In some circumstances the workflow runs so fast that it builds up too much data waiting to be written out. We've talked about having a threshold (depending on the amount of free memory and the size of the data) of when the reference manager would stop caching and block until say 50% of the cache was written out. Part of the trickiness of doing this is that Java does not allow you directly to ask how much memory some objects occupies, you can only do guestimates. In this case of large data you probably also want to turn off recording of intermediate values, under "Provenance" remove the tickbox for "Enable provenance capture from workflow runs". As this is currently not working very well with BioMoby this might be a good option for you anyway. You can also reduce the memory footprint by disabling plugins you don't need, for instance under Advanced -> Updates and plugins you can disable Compatibility, you would no longer be able to open Taverna 1 workflows, but you save some memory. That said Taverna shouldn't use much memory on Taverna 1 libraries until you open a Taverna 1 workflow for the first time, but I can't guarantee that, as the default selection in File Open is 'All supported types' which just tries to open as both Taverna 1 and Taverna 2. For a specialised Taverna you can disable Services and add your own limited plugin that has only some of the service types enabled, you can find the dependencies added by 'Services' now by looking at http://taverna.googlecode.com/svn/taverna/products/net.sf.taverna.t2.taverna-workbench/tags/taverna-workbench-2.1-beta-2/plugins/activities-plugin/pom.xml - http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/tags/activities-0.8/all-activities/pom.xml and http://taverna.googlecode.com/svn/taverna/ui/net.sf.taverna.t2.ui-activities/tags/ui-activities-0.12/all-activity-uis/pom.xml if you didn't want say Biomart support, you could make your own plugin definition that had all of these <dependency> sections listed (you don't need to make the intermediate modules like all-activity-ui and activities-plugin). We originally had the plugin like that, but it turned out it was easy to forget to add a module, so we made the collective ones instead. Ideally there should be one plugin per service type, but since that would mean the user would have to click to upgrade perhaps 10-15 plugins on an update we didn't go down that route. (In the same way you could disable bits of the GUI by reducing the 'components' plugin - but don't turn it off, or you won't have a workbench!) -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ------------------------------------------------------------------------------ Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge _______________________________________________ taverna-hackers mailing list [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ Developers Guide: http://www.mygrid.org.uk/tools/developer-information
