VMD-L Mailing List

From: Yjcoshc (yjcoshc_at_gmail.com)
Date: Tue Feb 25 2025 - 14:20:58 CST

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 tovmd_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