VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 05 2024 - 19:26:07 CST

Something seems to be messed up with your paths or similar.
But since your machine is in a bad shape altogether, it is impossible to
debug and fix this from remote.

On Mon, Feb 5, 2024 at 7:11 PM He, Xibing <xibing.he_at_pitt.edu> wrote:

> Hi Axel,
>
> Thanks for your reply!
>
> I do have .vmdrc file under my home directory, but it already contains
> "menu main on" and "menu graphics on". Previously the main window and the
> graphic window would pop out automatically, but not any more now.
>
> I just deleted the ~/.vmdrc file, and typed vmd. Again, only the OpenGL
> Display window appeared, and the text message got stuck there after showing:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
>
> Regards,
>
> Xibing He, Ph.D.
> Research Scientist
> Department of Pharmaceutical Sciences
> School of Pharmacy
> University of Pittsburgh
> ------------------------------
> *From:* Axel Kohlmeyer <akohlmey_at_gmail.com>
> *Sent:* Monday, February 5, 2024 5:58 PM
> *To:* He, Xibing <xibing.he_at_pitt.edu>
> *Cc:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: unable to open VMD as normal
>
> What you describe about your system suggests that it is not completely
> repaired.
> Only a local person can help you with that.
>
> The situation of having the OpenGL window but not the main VMD window can
> happen, when you have a .vmdrc file in your home directory but it does not
> include the command "menu main on" or there is an error when processing the
> file *before* it reaches the "menu main on" command.
>
> Again, this is something local and usually self-inflicted.
>
> On Mon, Feb 5, 2024 at 1:16 PM He, Xibing <xibing.he_at_pitt.edu> wrote:
>
> Dear all,
>
> Previously I had been running VMD smoothly on my Linux desktop (CentOS7)
> before the mother board and the power supply of the computer were replaced
> with the exact same models as the old ones.
>
> After replacing the mother board and the power supply, my Linux desktop
> have several weird behaviors including failure of starting VMD:
> (1) It cannot be rebooted to the normal login interface unless I choose
> the 2nd Linux core at the beginning process.
> (2) It cannot find the inserted data hard drives. I have to unplug the
> data hard drives, then start the computer, then manually insert the hard
> drives one at each time and type commands to mount the hard drives one by
> one.
> (3) When I type 'vmd', only the VMD OpenGL Display window is popped out,
> but the "main" window never appears. It seems that VMD is hanging there and
> waiting for something forever. The text messages on the terminal is as
> follows:
>
> [xibing_at_qin ~]$ which vmd
> /usr/local/bin/vmd
> [xibing_at_qin ~]$ vmd
> Info) VMD for LINUXAMD64, version 1.9.4a57 (April 27, 2022)
> 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, 64 CPUs.
> Info) CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 HT
> Info) Free system memory: 231GB (91%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator::
> Info) [0] GeForce GTX 1080 Ti 28 SM_6.1 1.6 GHz, 11GB RAM SP32 KT AE2 ZC
> Info) OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture
> (4)
> Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> Info) Compiling OptiX shaders on 1 target GPU...
> Info) Dynamically loaded 3 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl /home2/xibing/scripts/vmd/la1.0
> /usr/local/lib/vmd/scripts/tcl8.5 /usr/local/lib/vmd/scripts
> /usr/local/lib/lib /Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
> /usr/local/lib/vmd/scripts/tk8.5 /usr/local/lib/vmd/scripts/tk8.5/ttk
> /usr/local/lib/vmd/scripts/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
> /usr/local/lib/vmd/plugins/noarch/tcl /home2/xibing/scripts/vmd/la1.0
> /home2/xibing/scripts/vmd/orient
>
> Can anyone help me figure out the reason behind? We can schedule a Zoom
> meeting so that you may access to my Linux desktop remotely.
>
> Thanks!
>
> Xibing He, Ph.D.
> Research Scientist
> Department of Pharmaceutical Sciences
> School of Pharmacy
> University of Pittsburgh
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__https://goo.gl/1wk0__;!!DZ3fjg!61QGQ9ZajmuJHty_Q8xoXST_9qVOBUljvK0Em8Ukt9doJRFhMJ3UjTwaTut1wQ1kzMWTQaN7XI8Vgom4_g$
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> Institute for Computational Molecular Science and HPC, https://urldefense.com/v3/__https://icmshpc.com__;!!DZ3fjg!61QGQ9ZajmuJHty_Q8xoXST_9qVOBUljvK0Em8Ukt9doJRFhMJ3UjTwaTut1wQ1kzMWTQaN7XI9rTzkR6Q$
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>
> College of Science & Technology, Temple University, Philadelphia PA, USA
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__https://goo.gl/1wk0__;!!DZ3fjg!61QGQ9ZajmuJHty_Q8xoXST_9qVOBUljvK0Em8Ukt9doJRFhMJ3UjTwaTut1wQ1kzMWTQaN7XI8Vgom4_g$ 
Institute for Computational Molecular Science and HPC, https://urldefense.com/v3/__https://icmshpc.com__;!!DZ3fjg!61QGQ9ZajmuJHty_Q8xoXST_9qVOBUljvK0Em8Ukt9doJRFhMJ3UjTwaTut1wQ1kzMWTQaN7XI9rTzkR6Q$ 
College of Science & Technology, Temple University, Philadelphia PA, USA