Hi Divya,
OpenBabel became part of your environment when you added the
Avogadro SoftEnv key I sent to you. We use PBS (Torque actually)
with a Maui Scheduler on top. It is much easier than Big Red's LoadLeveler.
You can add "-I" to your qsub command. When your job starts, you
have an interactive connection to the cluster where you can launch a
remote X11
session. More on Quarry's PBS is here: http://kb.iu.edu/data/avmy.html
More on Remote X11 in general is here: http://kb.iu.edu/data/adhh.html
and on Quarry specifically is here: http://kb.iu.edu/data/ahgh.html
I'll hush again while y'all discuss what y'all do and how you do it.
Ray
On 3/13/2012 12:42 PM, Divya Neelagiri wrote:
Hello David,
I thought since avogadro has python extension we can write scripts in
python and run them. I tried to execute a python script like that but
the problem is I cant turn off the graphics in avogadro. I will look
into openbabel and see if it does everything we need.
Thank you,
Divya
On Tue, Mar 13, 2012 at 12:26 PM, David Lonie <lonieda...@gmail.com
<mailto:lonieda...@gmail.com>> wrote:
Hi Divya,
On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri
<divne...@umail.iu.edu <mailto:divne...@umail.iu.edu>> wrote:
> I need avogadro to perform minimization and some other operations on
> proteins.
I'm not sure how you would perform any operations without the GUI, as
there is no real command line interface to Avogadro. I think your best
bet is to use the openbabel utilities. For instance, obminimize will
perform a geometry relaxation using the same forcefield
implementations that Avogadro uses:
http://openbabel.org/wiki/Obminimize
There are quite a few others that may help with the other tasks
you need:
http://openbabel.org/wiki/Guides
Another option that I use with our remote clusters is to forward an X
connection over SSH by using the -X or -Y options to ssh. This will
launch the avogadro GUI on your workstation, even though it's actually
running on the remote cluster.
Hope this helps,
Dave
> We installed avogadro on quarry which is a super computer at IU.
> In quarry we cant see the interface (graphics), we can only work
with the
> scripts and commands. For other softwares like VMD for example
have an
> option specified of how to turn off the graphics eg., "vmd
-dispdev eof
> -exit". I was wondering if there was any such similar command
for avogadro
> because in quarry if we are not able to turn off graphics it
wont execute.
> It just quits. Please suggest me what to fo on this issue.
>
> Thank you,
> Divya
>
> On Sun, Mar 11, 2012 at 7:36 PM, Ray Sheppard <rshep...@iu.edu
<mailto:rshep...@iu.edu>> wrote:
>>
>> Hi Dave, Thorsten,
>> Please meet Divya. Hi Divya. Divya is the researcher in the
School of
>> Pharmacology
>> who is taking the lead in this project. I am just an old
physicist that
>> got pressed into
>> supercomputer duty about 30 years ago and hasn't figured out
how to escape
>> yet :)
>> Divya can explain what she was trying to do and the issues
she is trying
>> to overcome.
>> Please just keep me in the loop in case I need to build,
rebuild or modify
>> something.
>> I have a GAMESS-UK copy on the machine, but it is getting a bit
old. I do
>> not think we have
>> GAMESS-US on this machine. It might be living on Big Red.
Thanks guys
>> for helping.
>> Ray
>>
>> On 3/11/2012 1:20 PM, Thorsten Hoffmann wrote:
>>
>> Why not use Gamess (US)? Avogadro can create an inputfile for
Gamess.
>> Gamess (and cfour) run on clusters.
>> sincerely,
>> Thorsten
>>
>> On Fri, Mar 9, 2012 at 1:28 PM, Ray Sheppard
<rshep...@indiana.edu <mailto:rshep...@indiana.edu>> wrote:
>>
>> Hello Avogadro Development folks,
>> I recently installed Avogadro on a supercomputer for the
School of
>> Pharmacology.
>> These machines work within a batch job environment. I was asked:
>> "can you please tell me the command to execute avogadro without
>> graphics?"
>>
>> I don't think this is possible with Avogadro -- AFAIK we never
>> anticipated a use case that wouldn't need the display. What do they
>> need to do in avogadro without graphics?
>>
>> It may be possible to accomplish what they need with some of the
>> openbabel command-line tools? See
>>
>> http://openbabel.org/wiki/Guides
>>
>> Hope this helps,
>>
>> Dave
>>
>>
>>
------------------------------------------------------------------------------
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>> Cloud computing makes use of virtualization - but cloud computing
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>>
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>>
>>
------------------------------------------------------------------------------
>> Virtualization & Cloud Management Using Capacity Planning
>> Cloud computing makes use of virtualization - but cloud computing
>> also focuses on allowing computing to be delivered as a service.
>> http://www.accelacomm.com/jaw/sfnl/114/51521223/
>>
>>
>>
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>>
>
>
>
> --
> Thanks
> Divya
>
--
Thanks
Divya
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