VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 22 2018 - 11:09:56 CDT

Hi,
  The behavior of internationalized input handlers is very
operating system specific, even among linux distributions,
so I can't really answer this in general. Here's a discussion
of one variant:
  https://www.linuxquestions.org/questions/suse-opensuse-60/how-to-disable-scim-from-starting-up-automatically-409785/

and another:
  https://access.redhat.com/documentation/en-us/red_hat_enterprise_linux/5/html/international_language_support_guide/red_hat_enterprise_linux_international_language_support_guide-smart_common_input_method

and similar issues with other software that uses Tk:
  http://www.rkeene.org/projects/tcl/tk.fossil/tkthistory/2902214fffffffffffffff
ffffffffffffffffff

Best,
  John

On Fri, Jun 22, 2018 at 11:26:18AM -0400, Mohammadjavad Mohammadi wrote:
> 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
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute
> for Advanced Science and Technology University of Illinois, 405 N. Mathews
> Ave, Urbana, IL 61801
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_-7Ejohns
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> weBfmG0Zmol7w4q4_3l4Q&e= Phone: 217-244-3349
> 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=
> = 

-- 
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/