VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 20 2017 - 08:58:09 CST

If you're looking for your posting from earlier this morning, it won't
show up on the web site until tomorrow. The mailing list page for
VMD is updated only once per day since there are a large number
of messages to index. This helps prevent overloading of the machines that
do the nightly web site update work.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Dec 20, 2017 at 07:40:05AM -0700, Stephen Thomas wrote:
> Hi Ashar,
>
> Thanks for your response. This is my first post in this mailing list. Why
> do I not see my question on the mailing list page?
>
> On Wed, Dec 20, 2017 at 12:38 AM, Ashar Malik <[1]asharjm_at_gmail.com>
> wrote:
>
> Multiple things to note here:Â
> 1) From the look of the submit file you may be aiming to run a
> non-Graphic instance. To run just a script -- you need to add some more
> flags to the command line to ensure only the script is run (on command
> line).Â
> so do:
> vmd -dispdev text -e run.tcl
>
> I did it. But that does not change the behavior.
>
> 2) If I run the shell script I get the display from run.tcl. Which means
> (probably) that when you are loading the module -- its not putting vmd
> in your path.Â
> So if you give more details on what is not wrking  (error details)
> someone may give a better answer.Â
>
> As I mentioned in the previous email, the symptom is that I don't see the
> print message from the tcl script if I run the shell script using the
> sbatch command. Here is the output:
>
> /cm/shared/apps/vmd/1.9.3/lib//vmd_LINUXAMD64: /lib64/libGL.so.1: no
> version information available (required by
> /cm/shared/apps/vmd/1.9.3/lib//vmd_LINUXAMD64)
> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> Info)
> [2]http://www.ks.uiuc.edu/Research/vmd/Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
> Info) Email questions and bug reports to
> [3]vmd_at_ks.uiuc.edu         Â
> Info) Please include this reference in published work using VMD:Â Â
> Info)   Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Â
> Info)Â Â Â Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 16 CPUs detected.
> Info)Â Â CPU features: SSE2 AVX AVX2 FMA
> Info) Free system memory: 61GB (96%)
> Info) Creating CUDA device pool and initializing hardware...
> Warning) thread[0] can't init GPU[0] found by device query
> Warning) thread[1] can't init GPU[1] found by device query
> Warning) CUDA error: all CUDA-capable devices are busy or unavailable
> Warning) CUDA error: all CUDA-capable devices are busy or unavailable
> CUDA error: all CUDA-capable devices are busy or unavailable,
> CUDAClearDevice.cu line 56
> CUDA error: all CUDA-capable devices are busy or unavailable,
> CUDAClearDevice.cu line 56
> Info) Detected 2 available CUDA accelerators:
> Info) [0] Tesla P100-PCIE-12GB 56 SM_6.0 @ 1.33 GHz, 12GB RAM, AE2, ZCP
> Info) [1] Tesla P100-PCIE-12GB 56 SM_6.0 @ 1.33 GHz, 12GB RAM, AE2, ZCP
> Info) Detected 2 available TachyonL/OptiX ray tracing accelerators
> Info)Â Â Compiling 1 OptiX shaders on 2 target GPUs...
> Info) Dynamically loaded 2 plugins in directory:
> Info) /cm/shared/apps/vmd/1.9.3/lib/plugins/LINUXAMD64/molfile
> ERROR) Illegal rendering mode: GLSL
> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> Info) Exiting normally.
>
> However, if I run the vmd command directly in bash, I do see the print
> message:
>
> $ vmd -dispdev text -e run.tcl
> /cm/shared/apps/vmd/1.9.3/lib//vmd_LINUXAMD64: /lib64/libGL.so.1: no
> version information available (required by
> /cm/shared/apps/vmd/1.9.3/lib//vmd_LINUXAMD64)
> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> Info)
> [4]http://www.ks.uiuc.edu/Research/vmd/Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
> Info) Email questions and bug reports to
> [5]vmd_at_ks.uiuc.edu         Â
> Info) Please include this reference in published work using VMD:Â Â
> Info)   Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Â
> Info)Â Â Â Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 16 CPUs detected.
> Info)Â Â CPU features: SSE2 AVX AVX2 FMA
> Info) Free system memory: 58GB (92%)
> Info) No CUDA accelerator devices available.
> Info) Dynamically loaded 2 plugins in directory:
> Info) /cm/shared/apps/vmd/1.9.3/lib/plugins/LINUXAMD64/molfile
> ERROR) Illegal rendering mode: GLSL
> vmd > Unable to change color name
> Unable to change color name
> Unable to change color name
> ERROR) No molecules loaded.mol operates on one molecule only.
> ERROR) No molecules loaded.mol operates on one molecule only.
> 0
> 0
> =================Running tcl script===================
> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> Info) Exiting normally.
>
> Hope this clarifies.
>
> On Wed, Dec 20, 2017 at 6:55 PM, Stephen Thomas
> <[6]stephenthomas1_at_boisestate.edu> wrote:
>
> Hi,
>
> I am unable to run a tcl from vmd using the -e option. However, this
> works fine if I just run the command directly from bash. Here is a
> minimal example to reproduce the problem.
>
> Steps to reproduce:
> 1) run submit.sh
> 2) notice that the output does not contain the text "Running tcl
> script" as seen in run.tcl
>
> Can anyone suggest what I might be doing wrong?
>
> Thanks,
> Stephen Thomas.
>
> --
> Best,
> /A
>
> References
>
> Visible links
> 1. mailto:asharjm_at_gmail.com
> 2. http://www.ks.uiuc.edu/Research/vmd/
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. http://www.ks.uiuc.edu/Research/vmd/
> 5. mailto:vmd_at_ks.uiuc.edu
> 6. mailto:stephenthomas1_at_boisestate.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/