Hi Stuart, I just tested it again just to be sure. Here's what I'm doing:
1. Open Taverna 2.1 beta 2 2. Open fetch_today_s_xkcd_comic_841305.t2flow as an example 3. Press the play button several times (~30 times) 4. Wait some time until all runs are completed 5. Remove all results (6. Switch to design view, if you want to) Voilà, Taverna now uses around 150 Threads. Regards, Simon > -----Original Message----- > From: Stuart Owen [mailto:[email protected]] > Sent: Dienstag, 6. Oktober 2009 16:42 > To: [email protected] > Subject: Re: [Taverna-users] memory management > > Simon Felix wrote: > > Hi Anja, > > > > there are two leaks in Taverna I'm aware of: > > 1. When you run a workflow Taverna leaks some threads. Try running > your workflow over and over again while watching thread usage in > jvisualvm (comes with JDK). When I ran the workflow 20 times Taverna > used >100 active threads (70 of which are daemon threads). Maybe that's > related to your problem... ? > > > Are you referring to Taverna 1 or Taverna 2? I've done some testing > with > Taverna 2 and didn't find any evidence of thread leaks. (I did find > some > evidence of a memory leak though when using beanshells). > There are a few threads held by the results view after you run a > workflow, but these should disappear after you close the results. > > thanks, > Stuart > > 2. Raven leaks classes (--> JVM runs out of PermGen space). That is > probably not a problem when using workbench however. > > > > Simon > > > > > >> -----Original Message----- > >> From: Anja Le Blanc [mailto:[email protected]] > >> Sent: Montag, 5. Oktober 2009 09:49 > >> To: [email protected] > >> Subject: Re: [Taverna-users] memory management > >> > >> Many thanks for your answer. > >> > >> Stian Soiland-Reyes wrote: > >> > >>> When you run Taverna on Windows, and launching using the > taverna.exe > >>> file (the default), it will use up to a minimum 300 MB, but if you > >>> have more free memory it will use up to 50% of the amount that is > >>> available - calculated when you start Taverna. > >>> > >>> If this is the case for your example I guess you have about 3 GB of > >>> memory installed on your machine? (with ~2.2 GB free at start up). > >>> > >> Yes, the machine has 3GB memory. > >> > >> > >>> The Java virtual machine does not typically reduce the memory usage > >>> once it's occupied, even if the garbage collector is run and the > >>> memory is freed internally inside Taverna. If the garbage collector > >>> > >> is > >> > >>> not run earlier than more memory could be used than strictly > >>> necessary, if the JVM decides it's faster to delay garbage > >>> > >> collection. > >> > >> Yes, that's the reason why I waited for 15 minutes after closing all > >> workflows and results. The JVM had all opportunity to run garbage > >> collection. > >> > >> > >>> That said, it is still odd that you said your Taverna has allocated > >>> that much memory, had you been running any particularly heavyweight > >>> workflows when you got that number? > >>> > >> I would not think so. The memory usage was build up over time. I > would > >> change something in a workflow - let it run - delete the run - > change > >> the workflow and so on. My impression was that for all the runs new > >> memory was allocated but at a delete none was freed. > >> > >> > >>> It could also be that the memory usage you see includes shared > memory > >>> pages used for accessing the graphic system and system libraries - > >>> > >> but > >> > >>> in that case this bit is not 'real' memory and is actually shared > >>> between all other programs on your operating system. Windows Task > >>> Manager typically shows the "Memory (private working set)" which I > >>> believe excludes such memory pages. > >>> > >>> > >>> If you want to reduce the maximum memory allowance for Java, you > can > >>> edit taverna-debug.bat and modify the -Xmx300m parameter to say > >>> -Xmx450m if you want to assign a maximum of 450 MB. Run > >>> taverna-debug.bat instead of taverna.exe for this parameter to be > >>> picked up - if you want you can modify the Taverna startup menu > item > >>> by right clicking and selecting Properties. > >>> > >> Actually I don't want to reduce the memory used by Taverna, if it > needs > >> it. All I want is to work for a day without having to restart > Taverna. > >> I > >> wouldn't have looked at memory if a workflow which had run happily > >> before hadn't slowed down dramatically. (I now understand that > Taverna > >> had reached the 50% memory limit.) > >> > >> Best regards, > >> Anja > >> > >> > >> > >>> On Thu, Oct 1, 2009 at 15:39, Anja Le Blanc > >>> <[email protected]> wrote: > >>> > >>>> Dear Taverna Developers, > >>>> > >>>> After working with Taverna for a good part of a day, I noticed > that > >>>> Taverna was using 1,115,872 KBytes of my memory. I closed all open > >>>> workflows, removed all results and waited 15 minutes. The memory > >>>> > >> usage > >> > >>>> stayed the same. Could there be a problem with freeing memory, or > is > >>>> > >> the > >> > >>>> garbage collection not happening? > >>>> > >>>> I don't know whether it is already reported as bug (in a quick > >>>> > >> search I > >> > >>>> have not found it). > >>>> > >>>> Best regards, > >>>> Anja > >>>> > >>>> ------------------ > >>>> System Windows XP SP3 > >>>> Taverna Workbench 2.1 beta 2 > >>>> java 1.6.0_15 > >>>> ------------------ > >>>> > >>>> -- > >>>> Anja Le Blanc > >>>> Research Computing Services > >>>> University of Manchester > >>>> > >>>> ------------------------------------------------------------------ > -- > >>>> > >> ---------- > >> > >>>> Come build with us! The BlackBerry® Developer Conference in > SF, > >>>> > >> CA > >> > >>>> is the only developer event you need to attend this year. > Jumpstart > >>>> > >> your > >> > >>>> developing skills, take BlackBerry mobile applications to market > and > >>>> > >> stay > >> > >>>> ahead of the curve. Join us from November 9-12, 2009. Register > >>>> > >> now! > >> > >>>> http://p.sf.net/sfu/devconf > >>>> _______________________________________________ > >>>> taverna-users mailing list > >>>> [email protected] > >>>> [email protected] > >>>> Web site: http://www.taverna.org.uk > >>>> Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ > >>>> > >>>> > >>> > >>> > >> -------------------------------------------------------------------- > --- > >> ------- > >> Come build with us! The BlackBerry® Developer Conference in SF, > CA > >> is the only developer event you need to attend this year. Jumpstart > >> your > >> developing skills, take BlackBerry mobile applications to market and > >> stay > >> ahead of the curve. Join us from November 9-12, 2009. Register > >> now! > >> http://p.sf.net/sfu/devconf > >> _______________________________________________ > >> taverna-users mailing list > >> [email protected] > >> [email protected] > >> Web site: http://www.taverna.org.uk > >> Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ > >> > > > > --------------------------------------------------------------------- > --------- > > Come build with us! The BlackBerry® Developer Conference in SF, > CA > > is the only developer event you need to attend this year. Jumpstart > your > > developing skills, take BlackBerry mobile applications to market and > stay > > ahead of the curve. Join us from November 9-12, 2009. Register > now! > > http://p.sf.net/sfu/devconf > > _______________________________________________ > > taverna-users mailing list > > [email protected] > > [email protected] > > Web site: http://www.taverna.org.uk > > Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ > > > > > ----------------------------------------------------------------------- > ------- > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9-12, 2009. Register > now! > http://p.sf.net/sfu/devconf > _______________________________________________ > taverna-users mailing list > [email protected] > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/
