From: Warren D. <wa...@de...> - 2006-04-26 15:14:51
|
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.=20 Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Peter Adrian Meyer > Sent: Tuesday, April 25, 2006 3:15 PM > To: pym...@li... > Subject: [PyMOL] pse/session files increase memory usage? >=20 > Hi all, >=20 > For complex scenes, I've noticed that pymol 0.99rc6 (with=20 > ext0.99rc1) on linux appears to use more memory when started=20 > from a pse file than it does when loading the models/maps=20 > manually or from a pml script (based on the fact that I get=20 > out of memory errors during ray-tracing after starting from a=20 > pse, but not after starting from pml scripts). >=20 > The easy work-around is to use pml scripts instead of pse=20 > files, but I was curious if anyone else had run into this=20 > (or, for that matter if it's a known issue...my best guess=20 > would be that there's a memory leak somewhere, or that the=20 > configuration flags I used to build python were causing problems). >=20 > Pete >=20 >=20 > Pete Meyer > Fu Lab > BMCB grad student > Cornell University >=20 >=20 >=20 > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web=20 > services, security? > Get stuff done quickly with pre-integrated technology to make=20 > your job easier Download IBM WebSphere Application Server=20 > v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057& dat=3D121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |
From: Warren D. <wa...@de...> - 2006-04-26 19:33:23
|
Pete, Thanks -- I ran some tests too and wasn't able to find any convincing = memory leaks either. =20 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. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Peter Adrian Meyer > Sent: Wednesday, April 26, 2006 9:02 AM > To: Warren DeLano > Cc: pym...@li... > Subject: RE: [PyMOL] pse/session files increase memory usage? >=20 > Warren, >=20 > I did a bit of testing (memory figures from top VIRT column,=20 > after pymol > had finished executing commands and was responsive to input): >=20 > >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 >=20 > > pymol test.pse (532MB) >=20 > It looks to me like there's a small memory leak when=20 > 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. >=20 >=20 > Pete >=20 > > Pete, > > > > It is a PyMOL fact of life that session files take more=20 > memory, because > > all state information must transient exist in both Python=20 > and C while the > > session is being loading. However, we should get that=20 > memory back after > > the session is fully loaded. If not, then you may be right=20 > about a memory > > leak. A good way to test this is to see what happens if=20 > you load the same > > session over and over again without restarting PyMOL. Does=20 > memory usage > > consistently increase or does it level off? > > > > The most likely cause of this would be PyMOL failing to=20 > 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:wa...@de... > > > > > >> -----Original Message----- > >> From: pym...@li... > >> [mailto:pym...@li...] On Behalf Of > >> Peter Adrian Meyer > >> Sent: Tuesday, April 25, 2006 3:15 PM > >> To: pym...@li... > >> 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=3Dlnk&kid=3D120709&bid=3D263057& > > dat=3D121642 > >> _______________________________________________ > >> PyMOL-users mailing list > >> PyM...@li... > >> https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > >> > >> > >> > > >=20 >=20 > Pete Meyer > Fu Lab > BMCB grad student > Cornell University >=20 >=20 >=20 > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web=20 > services, security? > Get stuff done quickly with pre-integrated technology to make=20 > your job easier > Download IBM WebSphere Application Server v.1.0.1 based on=20 > Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057& > dat=3D121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 |
From: Peter A. M. <pa...@co...> - 2006-04-26 15:54:47
|
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:wa...@de... > > >> -----Original Message----- >> From: pym...@li... >> [mailto:pym...@li...] On Behalf Of >> Peter Adrian Meyer >> Sent: Tuesday, April 25, 2006 3:15 PM >> To: pym...@li... >> 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 >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> >> >> >> > Pete Meyer Fu Lab BMCB grad student Cornell University |