VMD-L Mailing List

From: Diego Gomes (diego.enry_at_gmail.com)
Date: Tue Feb 25 2025 - 13:18:44 CST

Thank you all for reporting issues with VMD 2 alpha :)

It is weird that one needs to start VMD 2-3 times to work, but don't worry,
it is the *first VMD 2.0 alpha* version to be out in the wild.

We're tracing this segmentation fault to find & fix the issue!

Friendly,
Diego.

On Tue, Feb 25, 2025 at 1:14 PM Isralewitz, Barry <isralewi_at_illinois.edu>
wrote:

> 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
> 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 <owner-vmd-l_at_ks.uiuc.edu> on behalf of
> Diego Gomes <diego.enry_at_gmail.com>
> *Sent:* Tuesday, February 25, 2025 9:08 PM
> *To:* Julien Devemy <julien.devemy_at_uca.fr>
> *Cc:* 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
>
> 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>
> 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
>
>
> --
> 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
>
>
>
>
>
>
>
>
> 

-- 
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