From: Ben Cossins (
Date: Sun Nov 14 2021 - 13:29:37 CST

Dear John, Tru and Axel,

Many thanks for your responses.

I started my installed 1.9.4a55 with the -debug flag and got the following
error message:-

Info) Detected 1 available CUDA accelerator::
Info) [0] Tesla T4 40 SM_7.5 1.6 GHz, 15GB RAM SP32 KT AE3 ZC
Missing separate debuginfo for /lib64/
Try: yum --enablerepo='*debug*' install
[New Thread 0x7fffb3f4d700 (LWP 32312)]
Info) OpenGL renderer: Tesla T4/PCIe/SSE2
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling OptiX shaders on 1 target GPU...
[New Thread 0x7fff8d573700 (LWP 32313)]
Detaching after fork from child process 32314.
Detaching after fork from child process 32315.
Detaching after fork from child process 32316.
Detaching after fork from child process 32317.
Detaching after fork from child process 32318.
Detaching after fork from child process 32320.
Detaching after fork from child process 32322.

Thread 1 "vmd_LINUXAMD64" received signal SIGSEGV, Segmentation fault.
0x00007ffff7863cc2 in XGetICValues () from /lib64/
Missing separate debuginfos, use: debuginfo-install
libX11-1.6.7-3.amzn2.0.2.x86_64 libXau-1.0.8-2.1.amzn2.0.2.x86_64
libXcursor-1.1.15-1.amzn2.x86_64 libXext-1.3.3-3.amzn2.0.2.x86_64
libXfixes-5.0.3-1.amzn2.0.2.x86_64 libXi-1.7.9-1.amzn2.0.2.x86_64
libXinerama-1.1.3-2.1.amzn2.0.2.x86_64 libXrender-0.9.10-1.amzn2.0.2.x86_64
libdrm-2.4.97-2.amzn2.x86_64 libgcc-7.3.1-13.amzn2.x86_64
libstdc++-7.3.1-13.amzn2.x86_64 libxcb-1.12-1.amzn2.0.2.x86_64
sssd-client-1.16.5-10.amzn2.10.x86_64 tcl-8.5.13-8.amzn2.0.2.x86_64

I tried the "unset XMODIFIERS" command and this allowed my std 1.9.4a55.bin
install to work normally.

I can add this to my bashrc and this should work.

Many thanks

On Tue, 9 Nov 2021 at 22:05, John Stone <> wrote:

> Hi,
> Yes, I would watch out for international input processing
> tools, as they are known to cause problems with a wide range
> of Tcl/Tk versions, causing a crash in Tk during startup.
> This has been discussed on VMD-L many times under the topic "SCIM" IIRC.
> I'd definitely suggest using VMD 1.9.4 rather than VMD 1.9.3 here as
> well, since these builds are made with much more current compilers and
> runtime libraries. If you still encounter trouble, I could give you a
> compilation made w/ Tcl/Tk 8.6.x or later, which addresses the issue
> with international input handlers, and I could also disable other
> features/libraries that may play a role in the problem you observe.
> Best,
> John Stone
> On Sun, Nov 07, 2021 at 04:13:46PM +0100, Tru Huynh wrote:
> > On Sat, Nov 06, 2021 at 03:56:34PM +0000, Ben Cossins wrote:
> > ..
> > > When we install the precompiled binaries for VMD 1.9.4 or 1.9.3 we
> get a
> > > segmentation fault.
> > > > Info)
> /opt/MD-software/vmd-1.9.3/lib/vmd/plugins/LINUXAMD64/molfile
> > > > Segmentation fault (core dumped)
> > > We have checked all of the plugins for missing libraries and they
> all seem
> > > to be covered.
> > > I had hoped this would work as I think amazon Linux is based on
> RHEL 7?
> > can you try to "unsetenv XMODIFIERS" before starting vmd?
> > We ran into this issue on CentOS-7 sometimes ago (on pristine vmd 1.9.3
> > versions)
> >
> > Cheers
> >
> > Tru
> > --
> > Tru Huynh (PhD) | | tel +33 1 45 68 87 37
> >
> > Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15
> France
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Phone: 217-244-3349

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