Re: [PyMOL] Memory not released after load and delete of structure
The suspension of undo doesn't have any effect on my accumulation of GB when
working with Hybrid PyMol...
Gianluigi
Da: Thomas Holder
A: pymol-users@lists.sourceforge.net
Inviato: Venerdì 21 Dicembre 2012 17:31
Oggetto: Re: [PyMOL] Memory not released after load and delete of structure
Hi Gianluigi and Martin,
thanks for reporting, this is a serious issue and we are looking into it.
As far as we can reproduce, it's related to the undo feature. Adding this to
your scripts should help:
cmd.set("suspend_undo", 1)
Cheers,
Thomas
On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano wrote:
> I have the same problem since pymol 1.5, mainly with the hybrid (I can reach
> 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and
> pymol version 1.5.0.3.
> I had to renounce working with Hybrid unless I really need some plug-in.
>
> Gianluigi
>
>
> Da: Jason Vertrees
> A: Martin Hediger
> Cc: "pymol-users@lists.sourceforge.net"
> Inviato: Giovedì 20 Dicembre 2012 17:05
> Oggetto: Re: [PyMOL] Memory not released after load and delete of structure
>
> Martin,
>
> That sounds like a memory leak in v1.3. Can you try a newer version of
> PyMOL and let us know if it still happens? We've fixed lots of bugs
> since v1.3.
>
> Also, is your script simply iterating over structures and deleting
> them when done? You sure you're not missing a cleanup step somewhere?
> (Any chance we can see the script or a stub of it?)
>
> Cheers,
>
> -- Jason
>
> On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger wrote:
> > Hi Jason,
> > I'm using PyMOL 1.3.
> >
> > Best regards
> > Martin
> >
> >
> >
> > On 20.12.12 15:53, Jason Vertrees wrote:
> >>
> >> Hi Martin,
> >>
> >> Which version of PyMOL are you using?
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger wrote:
> >>>
> >>> Dear PyMOL users
> >>> In a directory are PDB files of combined size equal to around 3MB. When
> >>> I load all files into PyMOL, I observe that the required RAM of PyMOL
> >>> (MacOS X 10.6) increases by roughly this amount.
> >>> When I delete all objects, the RAM requirement remains the same and when
> >>> I then reload all structures, the RAM requirement increases even further.
> >>> I'm currently using PyMOL to batch process a number of files where a
> >>> structure is loaded, modified and then deleted again from the objects
> >>> list. This then results in RAM requirements of over 1GB and together
> >>> with other applications, I run out of memory.
> >>> Is there a way I can prevent PyMOL from behaving this way?
> >>>
> >>> Best regards and thanks for any help
> >>> Martin
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Product Management
> Schrödinger, Inc.
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
--
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Re: [PyMOL] Memory not released after load and delete of structure
Hi Thomas, thanks for the feedback.
I would like to point out that I observe this with version PyMOL 1.3
(also Hybrid), where, correct me if I'm wrong, there is no undo feature
available (at least I have never used or seen it here). To me this would
mean, the problem has to be with something else (possibly in addition to
undo).
To perfectly reproduce my situation, you can run the script that I
posted on pastebin (http://pastebin.com/mC6Rs6wk). Let me know if you
need some guidance with all the variables, I'm sorry for the terrible
code. I can also send you the PDB file I used when I got into this
problem, then you dont need to adjust any variables.
Best regards
Martin
On 21.12.12 17:31, Thomas Holder wrote:
> Hi Gianluigi and Martin,
>
> thanks for reporting, this is a serious issue and we are looking into it.
>
> As far as we can reproduce, it's related to the undo feature. Adding this to
> your scripts should help:
>
> cmd.set("suspend_undo", 1)
>
> Cheers,
>Thomas
>
> On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano wrote:
>
>> I have the same problem since pymol 1.5, mainly with the hybrid (I can reach
>> 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and
>> pymol version 1.5.0.3.
>> I had to renounce working with Hybrid unless I really need some plug-in.
>>
>> Gianluigi
>>
>>
>> Da: Jason Vertrees
>> A: Martin Hediger
>> Cc: "pymol-users@lists.sourceforge.net"
>> Inviato: Giovedì 20 Dicembre 2012 17:05
>> Oggetto: Re: [PyMOL] Memory not released after load and delete of structure
>>
>> Martin,
>>
>> That sounds like a memory leak in v1.3. Can you try a newer version of
>> PyMOL and let us know if it still happens? We've fixed lots of bugs
>> since v1.3.
>>
>> Also, is your script simply iterating over structures and deleting
>> them when done? You sure you're not missing a cleanup step somewhere?
>> (Any chance we can see the script or a stub of it?)
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger wrote:
>>> Hi Jason,
>>> I'm using PyMOL 1.3.
>>>
>>> Best regards
>>> Martin
>>>
>>>
>>>
>>> On 20.12.12 15:53, Jason Vertrees wrote:
>>>> Hi Martin,
>>>>
>>>> Which version of PyMOL are you using?
>>>>
>>>> Cheers,
>>>>
>>>> -- Jason
>>>>
>>>> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger wrote:
>>>>> Dear PyMOL users
>>>>> In a directory are PDB files of combined size equal to around 3MB. When
>>>>> I load all files into PyMOL, I observe that the required RAM of PyMOL
>>>>> (MacOS X 10.6) increases by roughly this amount.
>>>>> When I delete all objects, the RAM requirement remains the same and when
>>>>> I then reload all structures, the RAM requirement increases even further.
>>>>> I'm currently using PyMOL to batch process a number of files where a
>>>>> structure is loaded, modified and then deleted again from the objects
>>>>> list. This then results in RAM requirements of over 1GB and together
>>>>> with other applications, I run out of memory.
>>>>> Is there a way I can prevent PyMOL from behaving this way?
>>>>>
>>>>> Best regards and thanks for any help
>>>>> Martin
>> --
>> Jason Vertrees, PhD
>> Director of Core Modeling Product Management
>> Schrödinger, Inc.
>>
>> (e) jason.vertr...@schrodinger.com
>> (o) +1 (603) 374-7120
--
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Re: [PyMOL] Memory not released after load and delete of structure
Hi Gianluigi and Martin,
thanks for reporting, this is a serious issue and we are looking into it.
As far as we can reproduce, it's related to the undo feature. Adding this to
your scripts should help:
cmd.set("suspend_undo", 1)
Cheers,
Thomas
On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano wrote:
> I have the same problem since pymol 1.5, mainly with the hybrid (I can reach
> 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and
> pymol version 1.5.0.3.
> I had to renounce working with Hybrid unless I really need some plug-in.
>
> Gianluigi
>
>
> Da: Jason Vertrees
> A: Martin Hediger
> Cc: "pymol-users@lists.sourceforge.net"
> Inviato: Giovedì 20 Dicembre 2012 17:05
> Oggetto: Re: [PyMOL] Memory not released after load and delete of structure
>
> Martin,
>
> That sounds like a memory leak in v1.3. Can you try a newer version of
> PyMOL and let us know if it still happens? We've fixed lots of bugs
> since v1.3.
>
> Also, is your script simply iterating over structures and deleting
> them when done? You sure you're not missing a cleanup step somewhere?
> (Any chance we can see the script or a stub of it?)
>
> Cheers,
>
> -- Jason
>
> On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger wrote:
> > Hi Jason,
> > I'm using PyMOL 1.3.
> >
> > Best regards
> > Martin
> >
> >
> >
> > On 20.12.12 15:53, Jason Vertrees wrote:
> >>
> >> Hi Martin,
> >>
> >> Which version of PyMOL are you using?
> >>
> >> Cheers,
> >>
> >> -- Jason
> >>
> >> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger wrote:
> >>>
> >>> Dear PyMOL users
> >>> In a directory are PDB files of combined size equal to around 3MB. When
> >>> I load all files into PyMOL, I observe that the required RAM of PyMOL
> >>> (MacOS X 10.6) increases by roughly this amount.
> >>> When I delete all objects, the RAM requirement remains the same and when
> >>> I then reload all structures, the RAM requirement increases even further.
> >>> I'm currently using PyMOL to batch process a number of files where a
> >>> structure is loaded, modified and then deleted again from the objects
> >>> list. This then results in RAM requirements of over 1GB and together
> >>> with other applications, I run out of memory.
> >>> Is there a way I can prevent PyMOL from behaving this way?
> >>>
> >>> Best regards and thanks for any help
> >>> Martin
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Product Management
> Schrödinger, Inc.
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
--
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Re: [PyMOL] Memory not released after load and delete of structure
I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3. I had to renounce working with Hybrid unless I really need some plug-in. Gianluigi Da: Jason Vertrees A: Martin Hediger Cc: "pymol-users@lists.sourceforge.net" Inviato: Giovedì 20 Dicembre 2012 17:05 Oggetto: Re: [PyMOL] Memory not released after load and delete of structure Martin, That sounds like a memory leak in v1.3. Can you try a newer version of PyMOL and let us know if it still happens? We've fixed lots of bugs since v1.3. Also, is your script simply iterating over structures and deleting them when done? You sure you're not missing a cleanup step somewhere? (Any chance we can see the script or a stub of it?) Cheers, -- Jason On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger wrote: > Hi Jason, > I'm using PyMOL 1.3. > > Best regards > Martin > > > > > > On 20.12.12 15:53, Jason Vertrees wrote: >> >> Hi Martin, >> >> Which version of PyMOL are you using? >> >> Cheers, >> >> -- Jason >> >> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger wrote: >>> >>> Dear PyMOL users >>> In a directory are PDB files of combined size equal to around 3MB. When >>> I load all files into PyMOL, I observe that the required RAM of PyMOL >>> (MacOS X 10.6) increases by roughly this amount. >>> When I delete all objects, the RAM requirement remains the same and when >>> I then reload all structures, the RAM requirement increases even further. >>> I'm currently using PyMOL to batch process a number of files where a >>> structure is loaded, modified and then deleted again from the objects >>> list. This then results in RAM requirements of over 1GB and together >>> with other applications, I run out of memory. >>> Is there a way I can prevent PyMOL from behaving this way? >>> >>> Best regards and thanks for any help >>> Martin >>> >>> >>> -- >>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial >>> Remotely access PCs and mobile devices and provide instant support >>> Improve your efficiency, and focus on delivering more value-add services >>> Discover what IT Professionals Know. Rescue delivers >>> http://p.sf.net/sfu/logmein_12329d2d >>> ___ >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> >> > -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net-- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Memory not released after load and delete of structure
I'll give it a try with the newer versions. I just checked, and I believe I'm doing some cleaning up. Sure, I posted the scripte on this pastebin: http://pastebin.com/mC6Rs6wk Sorry for the layout (all pretty in development). In production, the script is invoked from the "frag" function. Martin On 20.12.12 17:05, Jason Vertrees wrote: > Martin, > > That sounds like a memory leak in v1.3. Can you try a newer version of > PyMOL and let us know if it still happens? We've fixed lots of bugs > since v1.3. > > Also, is your script simply iterating over structures and deleting > them when done? You sure you're not missing a cleanup step somewhere? > (Any chance we can see the script or a stub of it?) > > Cheers, > > -- Jason > > On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger wrote: >> Hi Jason, >> I'm using PyMOL 1.3. >> >> Best regards >> Martin >> >> >> >> >> >> On 20.12.12 15:53, Jason Vertrees wrote: >>> Hi Martin, >>> >>> Which version of PyMOL are you using? >>> >>> Cheers, >>> >>> -- Jason >>> >>> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger wrote: Dear PyMOL users In a directory are PDB files of combined size equal to around 3MB. When I load all files into PyMOL, I observe that the required RAM of PyMOL (MacOS X 10.6) increases by roughly this amount. When I delete all objects, the RAM requirement remains the same and when I then reload all structures, the RAM requirement increases even further. I'm currently using PyMOL to batch process a number of files where a structure is loaded, modified and then deleted again from the objects list. This then results in RAM requirements of over 1GB and together with other applications, I run out of memory. Is there a way I can prevent PyMOL from behaving this way? Best regards and thanks for any help Martin -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >>> >>> > > -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Memory not released after load and delete of structure
Martin, That sounds like a memory leak in v1.3. Can you try a newer version of PyMOL and let us know if it still happens? We've fixed lots of bugs since v1.3. Also, is your script simply iterating over structures and deleting them when done? You sure you're not missing a cleanup step somewhere? (Any chance we can see the script or a stub of it?) Cheers, -- Jason On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger wrote: > Hi Jason, > I'm using PyMOL 1.3. > > Best regards > Martin > > > > > > On 20.12.12 15:53, Jason Vertrees wrote: >> >> Hi Martin, >> >> Which version of PyMOL are you using? >> >> Cheers, >> >> -- Jason >> >> On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger wrote: >>> >>> Dear PyMOL users >>> In a directory are PDB files of combined size equal to around 3MB. When >>> I load all files into PyMOL, I observe that the required RAM of PyMOL >>> (MacOS X 10.6) increases by roughly this amount. >>> When I delete all objects, the RAM requirement remains the same and when >>> I then reload all structures, the RAM requirement increases even further. >>> I'm currently using PyMOL to batch process a number of files where a >>> structure is loaded, modified and then deleted again from the objects >>> list. This then results in RAM requirements of over 1GB and together >>> with other applications, I run out of memory. >>> Is there a way I can prevent PyMOL from behaving this way? >>> >>> Best regards and thanks for any help >>> Martin >>> >>> >>> -- >>> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial >>> Remotely access PCs and mobile devices and provide instant support >>> Improve your efficiency, and focus on delivering more value-add services >>> Discover what IT Professionals Know. Rescue delivers >>> http://p.sf.net/sfu/logmein_12329d2d >>> ___ >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> >> > -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Memory not released after load and delete of structure
Hi Jason, I'm using PyMOL 1.3. Best regards Martin On 20.12.12 15:53, Jason Vertrees wrote: > Hi Martin, > > Which version of PyMOL are you using? > > Cheers, > > -- Jason > > On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger wrote: >> Dear PyMOL users >> In a directory are PDB files of combined size equal to around 3MB. When >> I load all files into PyMOL, I observe that the required RAM of PyMOL >> (MacOS X 10.6) increases by roughly this amount. >> When I delete all objects, the RAM requirement remains the same and when >> I then reload all structures, the RAM requirement increases even further. >> I'm currently using PyMOL to batch process a number of files where a >> structure is loaded, modified and then deleted again from the objects >> list. This then results in RAM requirements of over 1GB and together >> with other applications, I run out of memory. >> Is there a way I can prevent PyMOL from behaving this way? >> >> Best regards and thanks for any help >> Martin >> >> -- >> LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial >> Remotely access PCs and mobile devices and provide instant support >> Improve your efficiency, and focus on delivering more value-add services >> Discover what IT Professionals Know. Rescue delivers >> http://p.sf.net/sfu/logmein_12329d2d >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Memory not released after load and delete of structure
Hi Martin, Which version of PyMOL are you using? Cheers, -- Jason On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger wrote: > Dear PyMOL users > In a directory are PDB files of combined size equal to around 3MB. When > I load all files into PyMOL, I observe that the required RAM of PyMOL > (MacOS X 10.6) increases by roughly this amount. > When I delete all objects, the RAM requirement remains the same and when > I then reload all structures, the RAM requirement increases even further. > I'm currently using PyMOL to batch process a number of files where a > structure is loaded, modified and then deleted again from the objects > list. This then results in RAM requirements of over 1GB and together > with other applications, I run out of memory. > Is there a way I can prevent PyMOL from behaving this way? > > Best regards and thanks for any help > Martin > > -- > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Memory not released after load and delete of structure
Dear PyMOL users In a directory are PDB files of combined size equal to around 3MB. When I load all files into PyMOL, I observe that the required RAM of PyMOL (MacOS X 10.6) increases by roughly this amount. When I delete all objects, the RAM requirement remains the same and when I then reload all structures, the RAM requirement increases even further. I'm currently using PyMOL to batch process a number of files where a structure is loaded, modified and then deleted again from the objects list. This then results in RAM requirements of over 1GB and together with other applications, I run out of memory. Is there a way I can prevent PyMOL from behaving this way? Best regards and thanks for any help Martin -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
