VMD-L Mailing List

From: yjcoshc (yjcoshc_at_gmail.com)
Date: Mon Apr 04 2022 - 11:18:41 CDT

Hi Josh,

Thanks for your information. I have tried VMD 1.9.3 with psfgen 1.6,
which works without the segfault. The generated files look correct, so I
have used them. I will try topotools if I have time.

Thanks,

Haochuan Chen

On 4/4/22 11:15, Josh Vermaas wrote:
> 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
>>
>>