VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 04 2022 - 10:20:26 CDT

Haochuan,
  Thanks. Can you send me (not the whole VMD list) the input files and
the minimum steps to reproduce the crash you see with the a55 build?
I should be able to run it inside of valgrind/address-sanitizer or gdb and
track down what's going amiss there.

Best regards,
  John Stone

On Mon, Apr 04, 2022 at 10:14:48AM -0500, yjcoshc wrote:
> Hi Jone,
>
> VMD 1.9.4a55 also crashes in the same manner.
>
> Thanks,
>
> Haochuan Chen
>
>
> On 4/4/22 10:11, John Stone wrote:
> >Hi Haochuan,
> > Can you try running the more recent VMD 1.9.4 test builds? In particular
> >I will note that there were a number of bugs that got fixed both with psfgen
> >and also in VMD itself that could be related to the crash you observe,
> >in the VMD versions between a51 and the a55 version currently
> >posted for download. The a51 version you're using is almost 18 months
> >old, so it lacks many of the bug fixes that took place last year.
> >Let me know if you still encounter the same or related issue(s) with the
> >a55 test version.
> >
> >Best,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Mon, Apr 04, 2022 at 10:06:35AM -0500, yjcoshc wrote:
> >>Dear VMD developers,
> >>
> >>I am using the "Merge Structures" plugin in VMD 1.9.4a51, and after
> >>setting all the options and clicking the "Merge" button, VMD
> >>encounters a segmentation fault. The VMD binary is download from the
> >>official website. I have also tried to compile VMD from source with
> >>debug options, and the backtrace is attached as following:
> >>
> >>Thread 1 "vmd_LINUXAMD64" received signal SIGSEGV, Segmentation fault.
> >>0x00007fc70f04aded in __GI__IO_fflush (fp=0x46ac450) at iofflush.c:39
> >>39            _IO_acquire_lock (fp);
> >>(gdb) bt
> >>#0  0x00007fc70f04aded in __GI__IO_fflush (fp=0x46ac450) at iofflush.c:39
> >>#1  0x00007fc6f4ef6c82 in newhandle_msg_text (psfcontext=0x516c090,
> >>interp=interp_at_entry=0x4158b60, msg=msg_at_entry=0x7ffef16f7590 "reading
> >>topology file /home/hanatok/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all27_prot_lipid_na.inp\n")
> >>at src/tcl_psfgen.c:71
> >>#2  0x00007fc6f4ef6d35 in newhandle_msg
> >>(vdata=vdata_at_entry=0x4be8230, v=v_at_entry=0x4158b60,
> >>msg=msg_at_entry=0x7ffef16f7590 "reading topology file /home/hanatok/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all27_prot_lipid_na.inp\n")
> >>at src/tcl_psfgen.c:95
> >>#3  0x00007fc6f4ef7183 in tcl_topology (data=0x4be8230,
> >>interp=0x4158b60, argc=<optimized out>, argv=<optimized out>) at
> >>src/tcl_psfgen.c:736
> >>#4  0x00007fc70f8da815 in TclInvokeStringCommand () from /lib64/libtcl8.6.so
> >>#5  0x00007fc70f8dbad2 in TclNRRunCallbacks () from /lib64/libtcl8.6.so
> >>#6  0x00007fc70f8e200a in ?? () from /lib64/libtcl8.6.so
> >>#7  0x00007fc70f8e2833 in Tcl_EvalEx () from /lib64/libtcl8.6.so
> >>#8  0x00007fc70f8e2856 in Tcl_Eval () from /lib64/libtcl8.6.so
> >>#9  0x00007fc6f4ef98fd in tcl_psfcontext (data=0x4be8230,
> >>interp=0x4158b60, argc=<optimized out>, argv=0x415cf90) at
> >>src/tcl_psfgen.c:560
> >>#10 0x00007fc70f8da815 in TclInvokeStringCommand () from /lib64/libtcl8.6.so
> >>#11 0x00007fc70f8dbad2 in TclNRRunCallbacks () from /lib64/libtcl8.6.so
> >>#12 0x00007fc70f9aa1ac in ?? () from /lib64/libtcl8.6.so
> >>#13 0x00007fc70f9a9d97 in TclServiceIdle () from /lib64/libtcl8.6.so
> >>#14 0x00007fc70f98ce9c in Tcl_DoOneEvent () from /lib64/libtcl8.6.so
> >>#15 0x0000000000a30f09 in TclTextInterp::doTkUpdate (this=0x4158ac0)
> >>at TclTextInterp.C:543
> >>#16 0x00000000009aaecb in UIText::check_event (this=0x4156990) at
> >>UIText.C:186
> >>#17 0x0000000000894ee3 in CommandQueue::check_events
> >>(this=0x3a677f0) at CommandQueue.C:92
> >>#18 0x00000000009af65a in VMDApp::VMDupdate (this=0x3a3f030,
> >>check_for_events=1) at VMDApp.C:915
> >>#19 0x0000000000a045ef in main (argc=1, argv=0x7ffef16f8468) at vmdmain.C:93
> >>
> >>I suspect it may be caused by incorrect file descriptor
> >>psfcontext->PSFGENLOGFILE (or wild pointer) in the new psfgen 2.0.
> >>The crash does not happen in VMD 1.9.3, which uses psfgen 1.6. Any
> >>ideas?
> >>
> >>Thanks,
> >>
> >>Haochuan Chen
> >> 

-- 
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/