VMD-L Mailing List
From: Matic Kisovec (Matic.Kisovec_at_ki.si)
Date: Wed Jan 28 2015 - 09:53:11 CST
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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
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- Next message: John Stone: "Re: making self-adjustable high resolution images"
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- Next in thread: John Stone: "Re: VMD Segmentation fault (core dumped)"
- Reply: John Stone: "Re: VMD Segmentation fault (core dumped)"
- Reply: Axel Kohlmeyer: "Re: VMD Segmentation fault (core dumped)"
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