From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 16 2019 - 15:37:23 CDT

Hi Steven,
  This is a known issue with certain Tcl/Tk versions that occurs if
you're running X-windows with an international input handler (e.g. for
chinese characters) such as SCIM or similar.
If you disable the SCIM input handler, the problem should go away.

Best,
  John Stone

On Tue, Jul 16, 2019 at 12:43:55PM -0700, Steven Wang wrote:
> Hi all,
>
> I recently upgraded my operating system to OpenSUSE 15.1 and VMD stopped
> working. Starting VMD (19.4a31
> LINUXAMD64-CUDA9-OptiX600-RTX-OSPRay170.opengl) will lead to "Segmentation
> fault (core dumped)", but "vmd -dispdev text" works. I am using an Nvidia
> GPU (GeForce GTS 1080) with CUDA 10.2 installed. I tried different version
> of VMD. All had the same issue. Can someone let me know how to fix this?
> Thanks.
>
> Steven Wang
> P.S.
> Here are my Nvidia GPU information from nvidia-smi.
> +-----------------------------------------------------------------------------+
> | NVIDIA-SMI 430.26 Driver Version: 430.26 CUDA Version:
> 10.2 |
> |-------------------------------+----------------------+----------------------+
> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile
> Uncorr. ECC |
> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
> Compute M. |
> |===============================+======================+======================|
> | 0 GeForce GTX 1080 Off | 00000000:17:00.0 On |
> N/A |
> | 28% 40C P5 10W / 180W | 444MiB / 8116MiB |
> 1% Default |
> +-------------------------------+----------------------+----------------------+
>
> Here is the Linux kernel info.
> Linux version 4.12.14-lp151.28.7-default (geeko_at_buildhost) (gcc version
> 7.4.0 (SUSE Linux) ) #1 SMP Mon Jun 17 16:36:38 UTC 2019 (f8a1872)
> Here is the "vmd -debug" message.
> vmd -debug
> ***
> *** Running VMD in debugger, type 'run' at debugger prompt
> ***
> GNU gdb (GDB; openSUSE Leap 15.1) 8.2
> Copyright (C) 2018 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later
> <[1]http://gnu.org/licenses/gpl.html>
> 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:
> <[2]http://bugs.opensuse.org/>.
> Find the GDB manual and other documentation resources online at:
> <[3]http://www.gnu.org/software/gdb/documentation/>.
>
> For help, type "help".
> Type "apropos word" to search for commands related to "word"...
> Reading symbols from
> /data/stevenw/install/vmd/1.9.4.a31/lib/vmd/vmd_LINUXAMD64...done.
> (gdb) run
> Starting program:
> /data/stevenw/install/vmd/1.9.4.a31/lib/vmd/vmd_LINUXAMD64
> Missing separate debuginfo for /lib64/ld-linux-x86-64.so.2
> Try: zypper install -C
> "debuginfo(build-id)=d7ca383add0385765c8e3456aa714ae42b6a6e83"
> /data/stevenw/install/vmd/1.9.4.a31/lib/vmd/vmd_LINUXAMD64:
> /usr/lib64/libGL.so.1: no version information available (required by
> /data/stevenw/install/vmd/1.9.4.a31/lib/vmd/vmd_LINUXAMD64)
> Missing separate debuginfo for /usr/lib64/libGL.so.1
> Try: zypper install -C
> "debuginfo(build-id)=cf4175e5d66d87ce9e3a63f2004f8618e74720ae"
> Missing separate debuginfo for /usr/lib64/libX11.so.6
> Try: zypper install -C
> "debuginfo(build-id)=df52beb86f5c40e875345eb6a5ff7c1e3ac22dee"
> Missing separate debuginfo for /lib64/librt.so.1
> Try: zypper install -C
> "debuginfo(build-id)=e51c445381402916aeff8fa555a7779d518fd1ac"
> Missing separate debuginfo for /usr/lib64/libXinerama.so.1
> Try: zypper install -C
> "debuginfo(build-id)=2a7d9e7cff2feee5ed1ce01d3bcbb28a1c77346b"
> Missing separate debuginfo for /usr/lib64/libXi.so.6
> Try: zypper install -C
> "debuginfo(build-id)=c3e259a5a1abfc0b95c8448fb7734c022caad334"
> Missing separate debuginfo for /lib64/libpthread.so.0
> Try: zypper install -C
> "debuginfo(build-id)=68cc1007b0e595b758221977d554be6164b0fb07"
> [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)=7412b90a9c901afc33370ce58e796df47882c62c"
> Missing separate debuginfo for /lib64/libdl.so.2
> Try: zypper install -C
> "debuginfo(build-id)=62f0af5febe3a20dee53bd8e52eed5a0a2a23d38"
> Missing separate debuginfo for /lib64/libutil.so.1
> Try: zypper install -C
> "debuginfo(build-id)=769185def058cacc2d02e1b37bb16ee48cc219aa"
> Missing separate debuginfo for /usr/lib64/libstdc++.so.6
> Try: zypper install -C
> "debuginfo(build-id)=9dc2c7c42b9bccf5b065ab5038d7ea7dd13dbbf1"
> Missing separate debuginfo for /lib64/libgcc_s.so.1
> Try: zypper install -C
> "debuginfo(build-id)=3951fe59642d19b2a914f3cfa0834548338baf4a"
> Missing separate debuginfo for /lib64/libc.so.6
> Try: zypper install -C
> "debuginfo(build-id)=5f5808c2afdf0ace734ad8c317e6d5fd14b6048b"
> Missing separate debuginfo for /usr/lib64/libGLX.so.0
> Try: zypper install -C
> "debuginfo(build-id)=c46ac1043b5ea9de5fafbacc529288b544963d31"
> Missing separate debuginfo for /usr/lib64/libGLdispatch.so.0
> Try: zypper install -C
> "debuginfo(build-id)=78563d78f59a00e890fee76435e9439dc8cc2a08"
> Missing separate debuginfo for /usr/lib64/libxcb.so.1
> Try: zypper install -C
> "debuginfo(build-id)=9fd896ed29cfe7df608513940be70e1884da1371"
> Missing separate debuginfo for /usr/lib64/libXext.so.6
> Try: zypper install -C
> "debuginfo(build-id)=23bae5cf3751002e7065bcdcd01312f4b3a9c0e7"
> Missing separate debuginfo for /usr/lib64/libXau.so.6
> Try: zypper install -C
> "debuginfo(build-id)=78c9f9354c6549cb94288e580439bce59d3473bc"
> Info) VMD for LINUXAMD64, version 1.9.4a31 (March 13, 2019)
> Info) [4]http://www.ks.uiuc.edu/Research/vmd/
>
> Info) Email questions and bug reports to [5]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, 48 CPUs detected.
> Info) CPU features: SSE2 AVX AVX2 FMA AVX512F AVX512CD
> Info) Free system memory: 53GB (85%)
> [New Thread 0x7ffff1d8f700 (LWP 44288)]
> [New Thread 0x7ffff158e700 (LWP 44289)]
> [New Thread 0x7ffff0d8d700 (LWP 44290)]
> [New Thread 0x7ffff058c700 (LWP 44291)]
> [New Thread 0x7fffefd8b700 (LWP 44292)]
> [New Thread 0x7fffef58a700 (LWP 44293)]
> [New Thread 0x7fffeed89700 (LWP 44294)]
> [New Thread 0x7fffee588700 (LWP 44295)]
> [New Thread 0x7fffedd87700 (LWP 44296)]
> [New Thread 0x7fffed586700 (LWP 44297)]
> [New Thread 0x7fffecd85700 (LWP 44298)]
> [New Thread 0x7fffec584700 (LWP 44299)]
> [New Thread 0x7fffebd83700 (LWP 44300)]
> [New Thread 0x7fffeb582700 (LWP 44301)]
> [New Thread 0x7fffead81700 (LWP 44302)]
> [New Thread 0x7fffea580700 (LWP 44303)]
> [New Thread 0x7fffe9d7f700 (LWP 44304)]
> [New Thread 0x7fffe957e700 (LWP 44305)]
> [New Thread 0x7fffe8d7d700 (LWP 44306)]
> [New Thread 0x7fffe857c700 (LWP 44307)]
> [New Thread 0x7fffe7d7b700 (LWP 44308)]
> [New Thread 0x7fffe757a700 (LWP 44309)]
> [New Thread 0x7fffe6d79700 (LWP 44310)]
> [New Thread 0x7fffe6578700 (LWP 44311)]
> [New Thread 0x7fffe5d77700 (LWP 44312)]
> [New Thread 0x7fffe5576700 (LWP 44313)]
> [New Thread 0x7fffe4d75700 (LWP 44314)]
> [New Thread 0x7fffe4574700 (LWP 44315)]
> [New Thread 0x7fffe3d73700 (LWP 44316)]
> [New Thread 0x7fffe3572700 (LWP 44317)]
> [New Thread 0x7fffe2d71700 (LWP 44318)]
> [New Thread 0x7fffe2570700 (LWP 44319)]
> [New Thread 0x7fffe1d6f700 (LWP 44320)]
> [New Thread 0x7fffe156e700 (LWP 44321)]
> [New Thread 0x7fffe0d6d700 (LWP 44322)]
> [New Thread 0x7fffe056c700 (LWP 44323)]
> [New Thread 0x7fffdfd6b700 (LWP 44324)]
> [New Thread 0x7fffdf56a700 (LWP 44325)]
> [New Thread 0x7fffded69700 (LWP 44326)]
> [New Thread 0x7fffde568700 (LWP 44327)]
> [New Thread 0x7fffddd67700 (LWP 44328)]
> [New Thread 0x7fffdd566700 (LWP 44329)]
> [New Thread 0x7fffdcd65700 (LWP 44330)]
> [New Thread 0x7fffdc564700 (LWP 44331)]
> [New Thread 0x7fffdbd63700 (LWP 44332)]
> [New Thread 0x7fffdb562700 (LWP 44333)]
> [New Thread 0x7fffdad61700 (LWP 44334)]
> [New Thread 0x7fffda560700 (LWP 44335)]
> [Detaching after fork from child process 44336]
> [New Thread 0x7fffd29a1700 (LWP 44338)]
> Info) Creating CUDA device pool and initializing hardware...
> [New Thread 0x7fffd21a0700 (LWP 44339)]
> [New Thread 0x7fffd199f700 (LWP 44340)]
> [New Thread 0x7fffd101b700 (LWP 44341)]
> Info) Detected 1 available CUDA accelerator:
> Info) [0] GeForce GTX 1080 20 SM_6.1 1.73 GHz, 7.9GB RAM, KTO, AE2,
> ZCP
> Missing separate debuginfo for /usr/lib64/libdrm.so.2
> Try: zypper install -C
> "debuginfo(build-id)=9457cd03018db62905ed9cdd97df90042cf4142a"
> Missing separate debuginfo for /usr/lib64/libXcursor.so.1
> Try: zypper install -C
> "debuginfo(build-id)=b11feef95ee2e8377af6ae42b28c472ba9f103b4"
> Missing separate debuginfo for /usr/lib64/libXrender.so.1
> Try: zypper install -C
> "debuginfo(build-id)=22892a1a7852d4c7f7e6c6f04c5d733fa15f9a02"
> Missing separate debuginfo for /usr/lib64/libXfixes.so.3
> Try: zypper install -C
> "debuginfo(build-id)=e7d452c128c20137b7fef3a7da54a5ef09a1d00d"
> Info) OpenGL renderer: GeForce GTX 1080/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 (32768x32768), 3-D (16384x16384x16384),
> Multitexture (4)
> Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> Info) Compiling 1 OptiX shaders on 1 target GPU...
> [New Thread 0x7fff9db6d700 (LWP 44343)]
> [New Thread 0x7fff9d36c700 (LWP 44344)]
> [New Thread 0x7fff9cb6b700 (LWP 44345)]
> [New Thread 0x7fff8ffff700 (LWP 44346)]
> [New Thread 0x7fff8f7fe700 (LWP 44347)]
> [New Thread 0x7fff8effd700 (LWP 44348)]
> [New Thread 0x7fff8e7fc700 (LWP 44349)]
> [New Thread 0x7fff8dffb700 (LWP 44350)]
> [New Thread 0x7fff8d7fa700 (LWP 44351)]
> [New Thread 0x7fff8cff9700 (LWP 44352)]
> [New Thread 0x7fff6ffff700 (LWP 44353)]
> [New Thread 0x7fff6f7fe700 (LWP 44354)]
> [New Thread 0x7fff6effd700 (LWP 44355)]
> [New Thread 0x7fff6e7fc700 (LWP 44356)]
> [New Thread 0x7fff6dffb700 (LWP 44357)]
> [New Thread 0x7fff6d7fa700 (LWP 44358)]
> [New Thread 0x7fff6cff9700 (LWP 44359)]
> [New Thread 0x7fff4ffff700 (LWP 44360)]
> [New Thread 0x7fff4f7fe700 (LWP 44361)]
> [New Thread 0x7fff4effd700 (LWP 44362)]
> [New Thread 0x7fff4e7fc700 (LWP 44363)]
> [New Thread 0x7fff4dffb700 (LWP 44364)]
> [New Thread 0x7fff4d7fa700 (LWP 44365)]
> [New Thread 0x7fff4cff9700 (LWP 44366)]
> [New Thread 0x7fff2ffff700 (LWP 44367)]
> [New Thread 0x7fff2f7fe700 (LWP 44368)]
> [New Thread 0x7fff2effd700 (LWP 44369)]
> [New Thread 0x7fff2e7fc700 (LWP 44370)]
> [New Thread 0x7fff2dffb700 (LWP 44371)]
> [New Thread 0x7fff2d7fa700 (LWP 44372)]
> [New Thread 0x7fff2cff9700 (LWP 44373)]
> [New Thread 0x7fff0ffff700 (LWP 44374)]
> [New Thread 0x7fff0f7fe700 (LWP 44375)]
> [New Thread 0x7fff0effd700 (LWP 44376)]
> [New Thread 0x7fff0e7fc700 (LWP 44377)]
> [New Thread 0x7fff0dffb700 (LWP 44378)]
> [New Thread 0x7fff0d7fa700 (LWP 44379)]
> [New Thread 0x7fff0cff9700 (LWP 44380)]
> [New Thread 0x7ffeeffff700 (LWP 44381)]
> [New Thread 0x7ffeef7fe700 (LWP 44382)]
> [New Thread 0x7ffeeeffd700 (LWP 44383)]
> [New Thread 0x7ffeee7fc700 (LWP 44384)]
> [New Thread 0x7ffeedffb700 (LWP 44385)]
> [New Thread 0x7ffeed7fa700 (LWP 44386)]
> [New Thread 0x7ffeecff9700 (LWP 44387)]
> [New Thread 0x7ffecffff700 (LWP 44388)]
> [New Thread 0x7ffecf7fe700 (LWP 44389)]
> [New Thread 0x7ffeceffd700 (LWP 44390)]
> [New Thread 0x7ffece7fc700 (LWP 44391)]
> [New Thread 0x7ffecdffb700 (LWP 44392)]
> [New Thread 0x7ffecd7fa700 (LWP 44393)]
> [New Thread 0x7ffeccff9700 (LWP 44394)]
> [New Thread 0x7ffeaffff700 (LWP 44395)]
> [New Thread 0x7ffeaf7fe700 (LWP 44396)]
> [New Thread 0x7ffeaeffd700 (LWP 44397)]
> [New Thread 0x7ffeae7fc700 (LWP 44398)]
> [New Thread 0x7ffeadffb700 (LWP 44399)]
> [New Thread 0x7ffead7fa700 (LWP 44400)]
> [New Thread 0x7ffeacff9700 (LWP 44401)]
> [New Thread 0x7ffe8ffff700 (LWP 44402)]
> [New Thread 0x7ffe8f7fe700 (LWP 44403)]
> [New Thread 0x7ffe8effd700 (LWP 44404)]
> [New Thread 0x7ffe8e7fc700 (LWP 44405)]
> [New Thread 0x7ffe8dffb700 (LWP 44406)]
> [New Thread 0x7ffe8d7fa700 (LWP 44407)]
> [New Thread 0x7ffe8cff9700 (LWP 44408)]
> [New Thread 0x7ffe6ffff700 (LWP 44409)]
> [New Thread 0x7ffe6f7fe700 (LWP 44410)]
> [New Thread 0x7ffe6effd700 (LWP 44411)]
> [New Thread 0x7ffe6e7fc700 (LWP 44412)]
> [New Thread 0x7ffe6dffb700 (LWP 44413)]
> [New Thread 0x7ffe6d7fa700 (LWP 44414)]
> [New Thread 0x7ffe6cff9700 (LWP 44415)]
> [New Thread 0x7ffe4ffff700 (LWP 44416)]
> [New Thread 0x7ffe4f7fe700 (LWP 44417)]
> [New Thread 0x7ffe4effd700 (LWP 44418)]
> [New Thread 0x7ffe4e7fc700 (LWP 44419)]
> [New Thread 0x7ffe4dffb700 (LWP 44420)]
> [New Thread 0x7ffe4d7fa700 (LWP 44421)]
> [New Thread 0x7ffe4cff9700 (LWP 44422)]
> [New Thread 0x7ffe2ffff700 (LWP 44423)]
> [New Thread 0x7ffe2f7fe700 (LWP 44424)]
> [New Thread 0x7ffe2effd700 (LWP 44425)]
> [New Thread 0x7ffe2e7fc700 (LWP 44426)]
> [New Thread 0x7ffe2dffb700 (LWP 44427)]
> [New Thread 0x7ffe2d7fa700 (LWP 44428)]
> [New Thread 0x7ffe2cff9700 (LWP 44429)]
> [New Thread 0x7ffe0ffff700 (LWP 44430)]
> [New Thread 0x7ffe0f7fe700 (LWP 44431)]
> [New Thread 0x7ffe0effd700 (LWP 44432)]
> [New Thread 0x7ffe0e7fc700 (LWP 44433)]
> [New Thread 0x7ffe0dffb700 (LWP 44434)]
> [New Thread 0x7ffe0d7fa700 (LWP 44435)]
> [New Thread 0x7ffe0cff9700 (LWP 44436)]
> [New Thread 0x7ffdeffff700 (LWP 44437)]
> [New Thread 0x7ffdef7fe700 (LWP 44438)]
> Missing separate debuginfo for /usr/lib64/libexpat.so.1
> Try: zypper install -C
> "debuginfo(build-id)=a204d46cc1defae0557404b7eeacf0eaf4d9c339"
> Info) Dynamically loaded 3 plugins in directory:
> Info)
> /data/stevenw/install/vmd/1.9.4.a31/lib/vmd/plugins/LINUXAMD64/molfile
>
> Thread 1 "vmd_LINUXAMD64" received signal SIGSEGV, Segmentation fault.
> 0x00007ffff7858242 in XGetICValues () from /usr/lib64/libX11.so.6
>
> References
>
> Visible links
> 1. http://gnu.org/licenses/gpl.html
> 2. http://bugs.opensuse.org/
> 3. http://www.gnu.org/software/gdb/documentation/
> 4. http://www.ks.uiuc.edu/Research/vmd/
> 5. mailto:vmd_at_ks.uiuc.edu

-- 
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/