VMD-L Mailing List

From: Mohammadjavad Mohammadi (mm14_at_wildcats.unh.edu)
Date: Fri Jun 22 2018 - 10:26:18 CDT

Hi John,

Thanks, in terminal by first using "su - <username>", VMD is running with no
crashing on startup, but without it VMD still is crashing with segmentation
fault. Could you please guide me how can I disable SCIM or any international
keyboard/input handler when running VMD?

Thanks,
Mohammadjavad

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Thursday, June 21, 2018 2:20 PM
To: Mohammadi, Mohammadjavad <mm14_at_wildcats.unh.edu>
Cc:
Subject: Re: vmd-l:

Hi,
  It seems this is caused by Tk's use (misuse) of XGetICValues() in handling
internationalized input. Are you using SCIM or another international
keyboard/input handler? That is the likely cause of the crash. Since this
is a bug in Tk, there's nothing to be done specifically for VMD itself. In
the past, others that have encountered problems with Tk and XGetICValues()
causing crashes were successful in working around the problem by disabling
internationalized input handling when running VMD (or other apps that embed
Tk).

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 21, 2018 at 01:12:40AM +0000, Mohammadi, Mohammadjavad wrote:
> Hello,
>
> I upgraded my operating system to OpenSUSE leap 15.0, and reinstall
vmd. I
> installed all of the routine nvidia and CUDA related material, but vmd
> crashes on startup with segmentation fault. I ran the vmd -debug , and
the
> below is the debuger during vmd startup. Could you please guide me how
I
> could fix this issue?
>
> Mohammadjavad
>
> **
> *** Running VMD in debugger, type 'run' at debugger prompt
> ***
> GNU gdb (GDB; openSUSE Leap 15.0) 8.1
> Copyright (C) 2018 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later
>
<https://urldefense.proofpoint.com/v2/url?u=http-3A__gnu.org_licenses_gpl.ht
ml&d=DwIBAg&c=c6MrceVCY5m5A_KAUkrdoA&r=TQeUvmRrz6AQv8QBVQs-zlEMh4I6t_xVMx1Sy
idyIKA&m=IGxO2t3k-GT9pt9_ouzUIdpnJ17u7b8pB2rPjfCUzXY&s=CgRjh3DZQue9j92bA9x8x
7gtpZfjkBt7YJyaMdmg4ew&e=>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law. Type "show
copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-suse-linux".
> Type "show configuration" for configuration details.
> For bug reporting instructions, please see:
>
<https://urldefense.proofpoint.com/v2/url?u=http-3A__bugs.opensuse.org_&d=Dw
IBAg&c=c6MrceVCY5m5A_KAUkrdoA&r=TQeUvmRrz6AQv8QBVQs-zlEMh4I6t_xVMx1SyidyIKA&
m=IGxO2t3k-GT9pt9_ouzUIdpnJ17u7b8pB2rPjfCUzXY&s=vmpf_Nv6AEpqfV8BBeqTRwFuEeGs
11_-gBgLzsyoBjM&e=>.
> Find the GDB manual and other documentation resources online at:
>
<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gnu.org_software_gd
b_documentation_&d=DwIBAg&c=c6MrceVCY5m5A_KAUkrdoA&r=TQeUvmRrz6AQv8QBVQs-zlE
Mh4I6t_xVMx1SyidyIKA&m=IGxO2t3k-GT9pt9_ouzUIdpnJ17u7b8pB2rPjfCUzXY&s=CoCQnQB
RsjRPYDtu36VHMS-B_hsfdsjSwQ32TuXNQlU&e=>.
> For help, type "help".
> Type "apropos word" to search for commands related to "word"...
> Reading symbols from /usr/local/lib/vmd/vmd_LINUXAMD64...(no debugging
> symbols found)...done.
> (gdb) run
> Starting program: /usr/local/lib/vmd/vmd_LINUXAMD64
> Missing separate debuginfo for /lib64/ld-linux-x86-64.so.2
> Try: zypper install -C
> "debuginfo(build-id)=3b92738c1958b86aee8b14adbebf9d2dc4a84c02"
> /usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib64/libGL.so.1: no version
> information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
> Missing separate debuginfo for /usr/lib64/libGL.so.1
> Try: zypper install -C
> "debuginfo(build-id)=3f6a5a08196a28c3e3bb7b0da22c196e4863314e"
> Missing separate debuginfo for /usr/lib64/libX11.so.6
> Try: zypper install -C
> "debuginfo(build-id)=ff867c578f2ecf893655d95d851f9c455706ea56"
> Missing separate debuginfo for /usr/lib64/libXinerama.so.1
> Try: zypper install -C
> "debuginfo(build-id)=764d559bdc75ec52c17065bb5df95f7acff88473"
> Missing separate debuginfo for /usr/lib64/libXi.so.6
> Try: zypper install -C
> "debuginfo(build-id)=ceeab058dec326fc3505fe5d2bef69fd67cebf47"
> Missing separate debuginfo for /lib64/libpthread.so.0
> Try: zypper install -C
> "debuginfo(build-id)=00ad8e7c413091d45bb349f105a4b3e466e367a7"
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/lib64/libthread_db.so.1".
> Missing separate debuginfo for /lib64/libm.so.6
> Try: zypper install -C
> "debuginfo(build-id)=918225cf6b6ff0c6c8dd92643b45c81b25a92c63"
> Missing separate debuginfo for /lib64/libdl.so.2
> Try: zypper install -C
> "debuginfo(build-id)=afe13cfdcf1d5312417df860e5cbe4fee96d8c62"
> Missing separate debuginfo for /lib64/libutil.so.1
> Try: zypper install -C
> "debuginfo(build-id)=d61646ebd72474426ff0edc24dca54f8ed2c4154"
> Missing separate debuginfo for /usr/lib64/libstdc++.so.6
> Try: zypper install -C
> "debuginfo(build-id)=5173cf3c20dbaf430ec13b12bb8fa4730e17f048"
> Missing separate debuginfo for /lib64/libgcc_s.so.1
> Try: zypper install -C
> "debuginfo(build-id)=642b28ab8de504fa60c105e7a178e1a2805181cc"
> Missing separate debuginfo for /lib64/libc.so.6
> Try: zypper install -C
> "debuginfo(build-id)=b5b558c30ba01bc47a8201373569afa3df140522"
> Missing separate debuginfo for /lib64/librt.so.1
> Try: zypper install -C
> "debuginfo(build-id)=0df32935357efd4230b61ff61c86d41b451bf4a5"
> Missing separate debuginfo for /usr/lib64/libGLX.so.0
> Try: zypper install -C
> "debuginfo(build-id)=1ad40bdfe9fa6c5f4597769e8fd76ea2d9e9760e"
> Missing separate debuginfo for /usr/lib64/libGLdispatch.so.0
> Try: zypper install -C
> "debuginfo(build-id)=ddeeafa18db92852cb4bd8cf1cf829ea203e9d38"
> Missing separate debuginfo for /usr/lib64/libxcb.so.1
> Try: zypper install -C
> "debuginfo(build-id)=f452cb119f2b0a56cd2b9fda126731693c914619"
> Missing separate debuginfo for /usr/lib64/libXext.so.6
> Try: zypper install -C
> "debuginfo(build-id)=fe1f9107049ede7c35286dab93700b798365b895"
> Missing separate debuginfo for /usr/lib64/libXau.so.6
> Try: zypper install -C
> "debuginfo(build-id)=9ad19a9b77ab3c7217d4e01f9d3369848a2a5d2e"
> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> Info)
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research
_vmd_&d=DwIBAg&c=c6MrceVCY5m5A_KAUkrdoA&r=TQeUvmRrz6AQv8QBVQs-zlEMh4I6t_xVMx
1SyidyIKA&m=IGxO2t3k-GT9pt9_ouzUIdpnJ17u7b8pB2rPjfCUzXY&s=BG-PxexJ8HoCV4DBYd
jYr6Bdmzj0t9uQLmW9k5XuS1E&e=
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 20 CPUs detected.
> Info) CPU features: SSE2 AVX AVX2 FMA
> Info) Free system memory: 12GB (77%)
> [New Thread 0x7ffff1140700 (LWP 10401)]
> [New Thread 0x7ffff093f700 (LWP 10402)]
> [New Thread 0x7ffff013e700 (LWP 10403)]
> [New Thread 0x7fffef93d700 (LWP 10404)]
> [New Thread 0x7fffef13c700 (LWP 10405)]
> [New Thread 0x7fffee93b700 (LWP 10406)]
> [New Thread 0x7fffee13a700 (LWP 10407)]
> [New Thread 0x7fffed939700 (LWP 10408)]
> [New Thread 0x7fffed138700 (LWP 10409)]
> [New Thread 0x7fffec937700 (LWP 10410)]
> [New Thread 0x7fffec136700 (LWP 10411)]
> [New Thread 0x7fffeb935700 (LWP 10412)]
> [New Thread 0x7fffeb134700 (LWP 10413)]
> [New Thread 0x7fffea933700 (LWP 10414)]
> [New Thread 0x7fffea132700 (LWP 10415)]
> [New Thread 0x7fffe9931700 (LWP 10416)]
> [New Thread 0x7fffe9130700 (LWP 10417)]
> [New Thread 0x7fffe892f700 (LWP 10418)]
> [New Thread 0x7fffe812e700 (LWP 10419)]
> [New Thread 0x7fffe792d700 (LWP 10420)]
> [New Thread 0x7fffe6340700 (LWP 10421)]
> Info) Creating CUDA device pool and initializing hardware...
> [New Thread 0x7fffe5b3f700 (LWP 10422)]
> [New Thread 0x7fffe533e700 (LWP 10423)]
> [New Thread 0x7fffe4b3d700 (LWP 10424)]
> [New Thread 0x7fffdffff700 (LWP 10425)]
> [New Thread 0x7fffdf7fe700 (LWP 10426)]
> [New Thread 0x7fffdeffd700 (LWP 10427)]
> Info) Detected 2 available CUDA accelerators:
> Info) [0] Quadro K2200 5 SM_5.0 @ 1.12 GHz, 3.9GB RAM, AE1, ZCP
> Info) [1] Quadro K2200 5 SM_5.0 @ 1.12 GHz, 3.9GB RAM, KTO, AE1,
> ZCP
> Warning) Detected X11 'Composite' extension: if incorrect display
occurs
> Warning) try disabling this X server option. Most OpenGL drivers
> Warning) disable stereoscopic display when 'Composite' is enabled.
> Missing separate debuginfo for /usr/lib64/libXcursor.so.1
> Try: zypper install -C
> "debuginfo(build-id)=45886473becd10a9bf1705a7cff86d5276af76b1"
> Missing separate debuginfo for /usr/lib64/libXrender.so.1
> Try: zypper install -C
> "debuginfo(build-id)=26742b2ff984147a2c7508148704b3cb2f752038"
> Missing separate debuginfo for /usr/lib64/libXfixes.so.3
> Try: zypper install -C
> "debuginfo(build-id)=aa047315ac397f95aa829f479b1039b63aa05809"
> Info) OpenGL renderer: Quadro K2200/PCIe/SSE2
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (4096x4096x4096), Multitexture
> (4)
> Missing separate debuginfo for /usr/local/lib/vmd/libexpat.so.0
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd
/usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl /home/mm14/bin
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd
/usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl /home/mm14/bin
> /home/mm14/bin/Routines/Lib
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd
/usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl /home/mm14/bin
> /home/mm14/bin/Routines/Lib /home/mm14/bin/Routines/Other/bwidget
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd
/usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl /home/mm14/bin
> /home/mm14/bin/Routines/Lib /home/mm14/bin/Routines/Other/bwidget
> /home/mm14/bin/Routines/Other/tablelist4.11
>
> Thread 1 "vmd_LINUXAMD64" received signal SIGSEGV, Segmentation fault.
> 0x00007ffff78581c2 in XGetICValues () from /usr/lib64/libX11.so.6 

--
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