Pete, Thanks -- I ran some tests too and wasn't able to find any convincing memory leaks either.
Instead, it appears that Python simply caching memory previously used, all of which appears to remain available to Python for loading of subsequent session. As it turns out, this inefficiency in Python is something people are aware of and thinking about: http://evanjones.ca/memoryallocator Since we are currently dependent upon Python for our platform-independent session save & restore capability, we are stuck with this behavior until Python itself is fixed. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Peter Adrian Meyer > Sent: Wednesday, April 26, 2006 9:02 AM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] pse/session files increase memory usage? > > Warren, > > I did a bit of testing (memory figures from top VIRT column, > after pymol > had finished executing commands and was responsive to input): > > >pymol set.pml (316MB) > save test.pse (537MB) > reinitialize ; load test.pse (539MB after load) > reinitialize ; load test.pse (540MB after load) > reinitialize ; load test.pse (542MB after load) > quit > > > pymol test.pse (532MB) > > It looks to me like there's a small memory leak when > reloading the same > session file, but that this is fairly minor compared to the difference > between loading objects from a script and loading from a session file. > > > Pete > > > Pete, > > > > It is a PyMOL fact of life that session files take more > memory, because > > all state information must transient exist in both Python > and C while the > > session is being loading. However, we should get that > memory back after > > the session is fully loaded. If not, then you may be right > about a memory > > leak. A good way to test this is to see what happens if > you load the same > > session over and over again without restarting PyMOL. Does > memory usage > > consistently increase or does it level off? > > > > The most likely cause of this would be PyMOL failing to > decrement the > > reference counts on certain session data. > > > > Cheers, > > Warren > > -- > > Warren L. DeLano, Ph.D. > > Principal Scientist > > > > . DeLano Scientific LLC > > . 400 Oyster Point Blvd., Suite 213 > > . South San Francisco, CA 94080 USA > > . Biz:(650)-872-0942 Tech:(650)-872-0834 > > . Fax:(650)-872-0273 Cell:(650)-346-1154 > > . mailto:war...@delsci.com > > > > > >> -----Original Message----- > >> From: pymol-users-ad...@lists.sourceforge.net > >> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > >> Peter Adrian Meyer > >> Sent: Tuesday, April 25, 2006 3:15 PM > >> To: pymol-users@lists.sourceforge.net > >> Subject: [PyMOL] pse/session files increase memory usage? > >> > >> Hi all, > >> > >> For complex scenes, I've noticed that pymol 0.99rc6 (with > >> ext0.99rc1) on linux appears to use more memory when started > >> from a pse file than it does when loading the models/maps > >> manually or from a pml script (based on the fact that I get > >> out of memory errors during ray-tracing after starting from a > >> pse, but not after starting from pml scripts). > >> > >> The easy work-around is to use pml scripts instead of pse > >> files, but I was curious if anyone else had run into this > >> (or, for that matter if it's a known issue...my best guess > >> would be that there's a memory leak somewhere, or that the > >> configuration flags I used to build python were causing problems). > >> > >> Pete > >> > >> > >> Pete Meyer > >> Fu Lab > >> BMCB grad student > >> Cornell University > >> > >> > >> > >> ------------------------------------------------------- > >> Using Tomcat but need to do more? Need to support web > >> services, security? > >> Get stuff done quickly with pre-integrated technology to make > >> your job easier Download IBM WebSphere Application Server > >> v.1.0.1 based on Apache Geronimo > >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&; > > dat=121642 > >> _______________________________________________ > >> PyMOL-users mailing list > >> PyMOL-users@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > >> > >> > >> > > > > > Pete Meyer > Fu Lab > BMCB grad student > Cornell University > > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web > services, security? > Get stuff done quickly with pre-integrated technology to make > your job easier > Download IBM WebSphere Application Server v.1.0.1 based on > Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&; > dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
