VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 28 2015 - 10:04:03 CST
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Hi,
How much RAM does your computer contain? Each of the trajectories
you're loading would use about 1.8GB of memory (7500 * 20000 * 12 bytes)
just for the single-precision atomic coordinates, not counting anything else.
If you're loading 5 such trajectories, you would need roughly 10GB of
memory free (5 * 1.8GB) just for the atomic coordinates. By the time you
start drawing the structures and load other per-atom information the memory
usage will be higher, but since we're only talking about 7500 atoms, I would
expect it to fall in the range of 11-12GB of memory. If you have less than
12GB of RAM in your machine, this is likely why you're running into trouble.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Wed, Jan 28, 2015 at 03:53:11PM +0000, Matic Kisovec wrote:
> Dear VMD users,
>
> I have been googling around a bit and I couldn't find a similar issue so I
> think this is a good place to start. I am using linux Ubuntu 14.04.1 and
> VMD 1.9.2.
>
> Lately I have been working with molecular dynamics (MD) trajectories that
> were produced with GROMACS software.
> The trajectories consist of ~7500 atoms and 20000 frames. I work mainly
> with .xtc files that are compressed trajectory files. They can be easily
> opened in VMD.
> The problem usually appears when I try to open more than one trajectory
> (so multiple molecules each with 20000 frames). Sooner or later during the
> loading I get a 'Segmentation fault (core dumped)' and VMD crashes.
> Sometime it happens when I am opening the first trajectory (rarely) but
> after the first one is loaded it is more and more likely that VMD will
> crash during the load of the next trajectory.
> If I run VMD with 'vmd -debug' this is reported (I command 'where' after
> the core dump happened):
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x0000000000790bbd in stringdup(char const*) ()
> (gdb) where
> #0 0x0000000000790bbd in stringdup(char const*) ()
> #1 0x00000000006dfb29 in MolFilePlugin::read_metadata(Molecule*) ()
> #2 0x0000000000760d59 in VMDApp::molecule_load(int, char const*, char
> const*, FileSpec const*) ()
> #3 0x00000000007d908b in FileChooserFltkMenu::load_cb(Fl_Widget*,
> void*) ()
> #4 0x0000000000ba3786 in Fl_Button::handle(int) ()
> #5 0x0000000000b9ea9e in send(int, Fl_Widget*, Fl_Window*) ()
> #6 0x0000000000b9ed81 in Fl::handle(int, Fl_Window*) ()
> #7 0x0000000000bb588d in fl_handle(_XEvent const&) ()
> #8 0x0000000000bb646b in do_queued_events() ()
> #9 0x0000000000bb689f in fl_wait(double) ()
> #10 0x0000000000b9e32d in Fl::wait(double) ()
> #11 0x00000000007933ea in VMDupdateFltk() ()
> #12 0x00000000007955e0 in main ()
>
> When I did manage to get lets say three (max 5) trajectories loaded I
> could work with them just fine. Problem appears only during trajectory
> loading. I tried to save VMD visualisation state but that works even more
> randomly. It saves the state just fine but when I select Load Visualistion
> State I very often get 'core dump' during the loading of molecules. Below
> I pasted another report from 'debug' that occured after trying to load a
> visualisation state.
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x0000000000790bbd in stringdup(char const*) ()
> (gdb) where
> #0 0x0000000000790bbd in stringdup(char const*) ()
> #1 0x00000000006dfb29 in MolFilePlugin::read_metadata(Molecule*) ()
> #2 0x0000000000760d59 in VMDApp::molecule_load(int, char const*, char
> const*, FileSpec const*) ()
> #3 0x00000000007ca39f in text_cmd_mol(void*, Tcl_Interp*, int, char
> const**) ()
> #4 0x0000000000a59f78 in TclInvokeStringCommand ()
> #5 0x0000000000a5cb97 in TclEvalObjvInternal ()
> #6 0x0000000000a9ee56 in TclExecuteByteCode ()
> #7 0x0000000000aa4d74 in TclCompEvalObj ()
> #8 0x0000000000a5e723 in TclEvalObjEx ()
> #9 0x0000000000aaa7bc in Tcl_RecordAndEvalObj ()
> #10 0x00000000007b57ee in TclTextInterp::evalFile(char const*) ()
> #11 0x00000000007b4d08 in text_cmd_play(void*, Tcl_Interp*, int, char
> const**) ()
> #12 0x0000000000a59f78 in TclInvokeStringCommand ()
> #13 0x0000000000a5cb97 in TclEvalObjvInternal ()
> #14 0x0000000000a9ee56 in TclExecuteByteCode ()
> #15 0x0000000000aa4d74 in TclCompEvalObj ()
> #16 0x0000000000a5e723 in TclEvalObjEx ()
> #17 0x0000000000aaa7bc in Tcl_RecordAndEvalObj ()
> #18 0x0000000000aaa835 in Tcl_RecordAndEval ()
> #19 0x00000000007b56f1 in TclTextInterp::evalString(char const*) ()
> #20 0x00000000007b6127 in TclTextInterp::tcl_cb(char const*) ()
> #21 0x0000000000758b94 in TclEvalEvent::do_callback(TextInterp*) ()
> #22 0x0000000000758b42 in UIText::act_on_command(int, Command*) ()
> #23 0x0000000000630a77 in CommandQueue::runcommand(Command*) ()
> #24 0x00000000007fe74e in loadstate_cb(Fl_Widget*, void*) ()
> #25 0x0000000000bac96b in Fl_Menu_::picked(Fl_Menu_Item const*) ()
> #26 0x0000000000bad0fe in Fl_Menu_Bar::handle(int) ()
> #27 0x0000000000ba4f31 in Fl_Group::handle(int) ()
> #28 0x0000000000b9ea9e in send(int, Fl_Widget*, Fl_Window*) ()
> #29 0x0000000000b9ebec in Fl::handle(int, Fl_Window*) ()
> #30 0x0000000000bb588d in fl_handle(_XEvent const&) ()
> #31 0x0000000000bb646b in do_queued_events() ()
> #32 0x0000000000bb689f in fl_wait(double) ()
> #33 0x0000000000b9e32d in Fl::wait(double) ()
> #34 0x00000000007933ea in VMDupdateFltk() ()
> #35 0x00000000007955e0 in main ()
>
> I was checking the memory consumption but it never got above 85% of total
> RAM.
> So it seem a fairly random thing that gets more and more likely to occur
> with an increasing number of molecules(with trajectories) loaded in VMD.
>
> I also tried the Windows version of VMD and in that case I am unable to
> open even a single .xtc before a crash happens.
> Could the GROMACS output files be a problem? But then I would expect them
> to fail every time.
> If anybody is interested in this I would be very happy to provide
> additional information and also to see this issue fixed (if it is of
> course even a VMD issue).
>
> Thank you all and kind regards,
> Matic Kisovec
> begin:vcard
> fn:Matic Kisovec
> n:Kisovec;Matic
> org:National Institute of Chemistry Slovenia;Laboratory for Molecular Biology and Nanobiotechnology
> adr:;;Hajdrihova ulica 19;Ljubljana;;SI-1000;Slovenia
> email;internet:matic.kisovec_at_ki.si
> title:PhD student
> tel;work:+386 1 4760 427
> x-mozilla-html:TRUE
> url:www.ki.si
> version:2.1
> end:vcard
>
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/
- Next message: Axel Kohlmeyer: "Re: VMD Segmentation fault (core dumped)"
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- In reply to: Matic Kisovec: "VMD Segmentation fault (core dumped)"
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- Reply: Axel Kohlmeyer: "Re: VMD Segmentation fault (core dumped)"
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