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
