VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 04 2022 - 10:11:51 CDT

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/