VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Wed Feb 26 2025 - 01:42:36 CST

Hi Barry,

I need to run multiple times at every launch.

Regards,
Raman

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________________________________
From: Isralewitz, Barry <isralewi_at_illinois.edu>
Sent: Wednesday, 26 February 2025 00:44:06
To: Raman Preet Singh <ramanpreetsingh_at_hotmail.com>
Cc: Diego Gomes <diego.enry_at_gmail.com>; Julien Devemy <julien.devemy_at_uca.fr>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: VMD 2.0 Segmentation Fault on Ubuntu 24.04 and Containers

Hi Raman,

Thanks for the this report. To clarify, do you need to make the 3 to 4 attempts every time you attempt to run VMD -- or is this something happening only after initial install and not seen afterwards?

Cheers,
Barry

On Feb 25, 2025, at 1:03 PM, Raman Preet Singh <ramanpreetsingh_at_hotmail.com> wrote:

Hi Diego,

I too get Segmentation fault on Ubuntu 20.04 LTS.
Info) VMD for LINUXAMD64, version 2.0.0a4 (February 17, 2025)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu<mailto: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, 12 CPUs.
Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 AVX512F AVX512CD HT
Info) Free system memory: 38GB (96%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator::
Info) [0] NVIDIA GeForce RTX 3070 46 SM_8.6 1.7 GHz, 7.8GB RAM SP32 KT AE2 ZC
Info) OpenGL renderer: Mesa Intel(R) Graphics (RKL GT1)
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8)
OpenGLDisplayDevice) Creating OptiX RTRT context...
OpenGLDisplayDevice) OptiX RTRT context created.
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling OptiX shaders on 1 target GPU...
Segmentation fault (core dumped)

I need to run VMD 3-4 times and then VMD finally starts. VMD 1.9.4 used to work fine. I have CUDA 12.3 installed and driver version 525.85.05.

Regards,
Raman

________________________________
From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> <owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of Diego Gomes <diego.enry_at_gmail.com<mailto:diego.enry_at_gmail.com>>
Sent: Tuesday, February 25, 2025 9:08 PM
To: Julien Devemy <julien.devemy_at_uca.fr<mailto:julien.devemy_at_uca.fr>>
Cc: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: Re: vmd-l: VMD 2.0 Segmentation Fault on Ubuntu 24.04 and Containers

Thank you for reporting the issue, we'll look into it ASAP.

Friendly,
Diego.

On Tue, Feb 25, 2025 at 7:50 AM Julien Devemy <julien.devemy_at_uca.fr<mailto:julien.devemy_at_uca.fr>> wrote:
Hi,

I successfully installed and ran VMD 2.0 on my laptop (Ubuntu 24.10),
but I’m encountering issues when trying to run it in other environments.

On Ubuntu 24.04 (within a Virtual Machine), VMD crashes with a
Segmentation Fault. The stack trace is:
#0 0x00000000008fd1a0 in
GraphicsFltkRepOrbital::GraphicsFltkRepOrbital(void (*)(Fl_Widget*,
void*), void*) ()
#1 0x00000000008f1cf5 in GraphicsFltkBuilder::repcontrol_addname(int) ()
#2 0x00000000008f5caa in
GraphicsFltkBuilder::GraphicsFltkBuilder(MainFltkMenu*, VMDApp*, int,
int) ()
#3 0x000000000090af41 in MainFltkMenu::MainFltkMenu(VMDApp*) ()
#4 0x00000000008646ba in VMDApp::activate_menus() ()
#5 0x00000000008665ac in VMDApp::VMDinit(int, char**, char const*,
int*, int*) ()
#6 0x00000000005650eb in main ()

I also tested it in a Singularity container with both Ubuntu 24.10 and
Alma 8, and I encountered the same issue.

Please let me know if you need any additional tests or information. I’d
be happy to help troubleshoot further.

Best regards,
Julien Devémy 

--
Diego Enry B. Gomes, PhD
Department of Physics at Auburn University &
NIH Center for Macromolecular Modeling and Visualization
Leach Science Center - Ste. 3182 - Auburn, AL
dgomes_at_auburn.edu<mailto:dgomes_at_auburn.edu>
--
Barry Isralewitz
Theoretical and Computational Biophysics Group
3143 Beckman, University of Illinois at Urbana-Champaign
Work Phone: (217) 300-1988
Email: isralewi_at_illinois.edu
https://www.ks.uiuc.edu/~barryi