From: Diego Gomes (diego.enry_at_gmail.com)
Date: Tue Feb 25 2025 - 17:02:46 CST

Thank you Haochuan, we're merging this fix to the main branch.

On Tue, Feb 25, 2025 at 2:21 PM Yjcoshc <yjcoshc_at_gmail.com> wrote:

> Hi Diego,
>
> That's not weird. I have submitted the patch on Slack that solved this
> issue.
>
> Best,
> Haochuan
>
>
> On 2025/2/25 13:18, Diego Gomes wrote:
>
> 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
>
>

-- 
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