VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Mon Apr 04 2022 - 11:15:30 CDT

Hi Haochuan,

If you are just trying to merge together two structures in a way that
doesn't segfault, I think the "mergemols" command in topotools gives you
a way around this problem. Admittedly, this is now my default approach,
so I don't know how widespread this problem is with psfgen 2.0.

-Josh

On 4/4/22 11:06, 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
>
> 

-- 
Josh Vermaas
Assistant Professor
MSU-DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology
Michigan State University
https://urldefense.com/v3/__https://vermaaslab.github.io/__;!!DZ3fjg!s7U1bnDOh1OKEBnRjrfWwZYBnJFFvRF6CxPhTin0_yRRdCROInpZ44c-KYC1Lewe7Q$