VMD-L Mailing List

From: Stephen Thomas (stephenthomas1_at_boisestate.edu)
Date: Wed Dec 20 2017 - 08:40:05 CST

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 <asharjm_at_gmail.com> wrote:

> Multiple things to note here:
>
> 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).
> 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.
> So if you give more details on what is not wrking (error details) someone
> may give a better answer.
>
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) http://www.ks.uiuc.edu/Research/vmd/
<http://www.ks.uiuc.edu/Research/vmd/> Info) Email
questions and bug reports to vmd_at_ks.uiuc.edu <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, 16 CPUs detected.Info) 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 queryWarning) thread[1] can't init GPU[1] found by device
queryWarning) CUDA error: all CUDA-capable devices are busy or
unavailableWarning) CUDA error: all CUDA-capable devices are busy or
unavailableCUDA error: all CUDA-capable devices are busy or unavailable,
CUDAClearDevice.cu line 56CUDA error: all CUDA-capable devices are busy or
unavailable, CUDAClearDevice.cu line 56Info) Detected 2 available CUDA
accelerators:Info) [0] Tesla P100-PCIE-12GB 56 SM_6.0 @ 1.33 GHz, 12GB RAM,
AE2, ZCPInfo) [1] Tesla P100-PCIE-12GB 56 SM_6.0 @ 1.33 GHz, 12GB RAM, AE2,
ZCPInfo) Detected 2 available TachyonL/OptiX ray tracing
acceleratorsInfo) 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/molfileERROR) Illegal
rendering mode: GLSLInfo) 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) http://www.ks.uiuc.edu/Research/vmd/
<http://www.ks.uiuc.edu/Research/vmd/> Info) Email
questions and bug reports to vmd_at_ks.uiuc.edu <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, 16 CPUs detected.Info) 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/molfileERROR) Illegal
rendering mode: GLSLvmd > Unable to change color nameUnable to change color
nameUnable to change color nameERROR) No molecules loaded.mol operates on
one molecule only.ERROR) No molecules loaded.mol operates on one molecule
only.00=================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 <
> 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
>