VMD-L Mailing List

From: Andrea Spitaleri (andrea.spitaleri_at_iit.it)
Date: Tue Sep 29 2015 - 10:58:41 CDT

Hi,
you may think to remotely mount your cluster on your local machine by
using sshfs protocol and the use your vmd to open files from the cluster

and

On 29/09/2015 17:23, John Stone wrote:
> Hi,
> Do you have the DISPLAY environment variable set when you're logged
> into the remote cluster? From your description, it would seem that your
> colleagues are able to run it, so it is likely an issue with the DISPLAY
> environment variable not being set properly. Can you run 'xterm' or
> other programs like 'glxgears' successfully?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Sep 25, 2015 at 03:32:25PM -0700, Payal Chatterjee wrote:
>> Dear Admin
>> I am a graduate student at the Western University of Health Sciences. I am
>> unable to call VMD from the cluster, from any system/laptop, even after
>> installing the X11 application! Everyone else in my lab can however,
>> easily do the same! Could you help me find out what is the problem? When I
>> type vmd on the terminal, after logging in into the cluster, all I see is
>> the following script, whereas no VMD window pops up:
>> id: cannot find name for group ID 1019
>> [payal_at_headnode ~]$ vmd
>> id: cannot find name for group ID 1019
>> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
>> Info) [1]http://www.ks.uiuc.edu/Research/vmd/ A A A A A A A A A
>> A A A A
>> Info) Email questions and bug reports to [2]vmd_at_ks.uiuc.edu A A A A
>> A A
>> Info) Please include this reference in published work using VMD: A A
>> Info) A A Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual A A
>> Info) A A Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
>> Info) -------------------------------------------------------------
>> Info) Multithreading available, 8 CPUs detected.
>> Info) Free system memory: 30592MB (95%)
>> Warning) Detected a mismatch between CUDA runtime and GPU driver
>> Warning) Check to make sure that GPU drivers are up to date.
>> Info) No CUDA accelerator devices available.
>> Info) Dynamically loaded 2 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/vmd /usr/local/lib/vmd/plugins/LINUXAMD64/tcl
>> /usr/local/lib/vmd/plugins/noarch/tcl /home/lyna/vmd_diffusion
>> diffusion_coefficient_gui:diffusion_coefficient_tk {Analysis/Diffusion
>> Coefficient Tool}
>> Thanks
>> Payal
>> Department of Pharmaceutical Sciences
>> Western University of Health Sciences
>> Pomona, CA
>>
>> References
>>
>> Visible links
>> 1. http://www.ks.uiuc.edu/Research/vmd/
>> 2. mailto:vmd_at_ks.uiuc.edu 

-- 
Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/0000-0003-3012-3557