How to turn off graphics?

Ray_Sheppard1 · March 9, 2012, 6:28pm

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 am just an old physicist that tries to keep work moving on our
machines. I looked
around through your documentation, but could not find an "off switch."
Any help
would be appreciated. Thanks.
Ray

–
Respectfully,
Ray Sheppard
RSheppar@iu.edu
http://rc.uits.iu.edu/hpa/
317-274-0016

                Principal Analyst
                High Performance Applications
                Research Technologies
                University Information Technological Services
                IUPUI campus
                Indiana University

My "pithy" saying:  Science is the art of translating the world
    into language. Unfortunately, that language is mathematics.
Bumper sticker wisdom: Make it idiot-proof and they will make a
    better idiot.

allison.vacanti · March 11, 2012, 1:46pm

On Fri, Mar 9, 2012 at 1:28 PM, Ray Sheppard rsheppar@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

Thorsten_Hoffmann · March 11, 2012, 5:20pm

Why not use Gamess (US)? Avogadro can create an inputfile for Gamess.
Gamess (and cfour) run on clusters.
cid:part1.01010004.09000400@students.uni-mainz.de
sincerely,
Thorsten

cid:part1.01010004.09000400@students.uni-mainz.de

On Fri, Mar 9, 2012 at 1:28 PM, Ray Sheppardrsheppar@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

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/

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

Ray_Sheppard · March 11, 2012, 11:36pm

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.
cid:part1.01010004.09000400@students.uni-mainz.de
sincerely,
Thorsten

On Fri, Mar 9, 2012 at 1:28 PM, Ray Sheppardrsheppar@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

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/

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

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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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https://lists.sourceforge.net/lists/listinfo/avogadro-devel

Divya_Neelagiri · March 13, 2012, 3:27pm

Hello everyone,

I need avogadro to perform minimization and some other operations on
proteins. 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 rsheppar@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 rsheppar@indiana.edu rsheppar@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

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/

Avogadro-devel mailing listAvogadro-devel@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/avogadro-devel

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

Ray_Sheppard · March 13, 2012, 4:19pm

Hi All,
Ray here. If it helps, I am a reasonably competent programmer. I
can apply
patches/code changes if they might be needed.
Ray

On 3/13/2012 11:27 AM, Divya Neelagiri wrote:

Hello everyone,

I need avogadro to perform minimization and some other operations on
proteins. 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 <rsheppar@iu.edu
mailto:rsheppar@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<rsheppar@indiana.edu>  <mailto:rsheppar@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

------------------------------------------------------------------------------
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/
_______________________________________________
Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net  <mailto:Avogadro-devel@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

------------------------------------------------------------------------------
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/


_______________________________________________
Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net  <mailto:Avogadro-devel@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

–
Thanks
Divya

allison.vacanti · March 13, 2012, 4:26pm

Hi Divya,

On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri divneela@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 rsheppar@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 rsheppar@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

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/

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

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/

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

–
Thanks
Divya

Divya_Neelagiri · March 13, 2012, 4:42pm

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 loniedavid@gmail.com wrote:

Hi Divya,

On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri divneela@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 rsheppar@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 rsheppar@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

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/

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

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/

Avogadro-devel mailing list
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–
Thanks
Divya

–
Thanks
Divya

mhanwell · March 13, 2012, 5:04pm

On Tue, Mar 13, 2012 at 12:26 PM, David Lonie loniedavid@gmail.com wrote:

Hi Divya,

On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri divneela@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.

I would agree with David here. There are several command line
components that have things like the underlying forcefields used in
the GUI, Python bindings can make it easy to script them too. We never
developed a powerful command line mode for Avogadro, because
everything is in a library I think our efforts would be best focused
in developing a command line frontend if it was useful, rather than
trying to make the gui do both.

I am having trouble understanding how you are using Avogadro in a
non-graphical context.

Marcus

Ray_Sheppard · March 13, 2012, 5:11pm

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 <loniedavid@gmail.com
mailto:loniedavid@gmail.com> wrote:

Hi Divya,

On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri
<divneela@umail.iu.edu <mailto:divneela@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 <rsheppar@iu.edu
<mailto:rsheppar@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
<rsheppar@indiana.edu <mailto:rsheppar@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
>>
>>
>>
------------------------------------------------------------------------------
>> 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/
>> _______________________________________________
>> Avogadro-devel mailing list
>> Avogadro-devel@lists.sourceforge.net
<mailto:Avogadro-devel@lists.sourceforge.net>
>> https://lists.sourceforge.net/lists/listinfo/avogadro-devel
>>
>>
>>
>>
>>
>>
------------------------------------------------------------------------------
>> 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/
>>
>>
>>
>> _______________________________________________
>> Avogadro-devel mailing list
>> Avogadro-devel@lists.sourceforge.net
<mailto:Avogadro-devel@lists.sourceforge.net>
>> https://lists.sourceforge.net/lists/listinfo/avogadro-devel
>>
>>
>
>
>
> --
> Thanks
> Divya
>

–
Thanks
Divya

Divya_Neelagiri · March 13, 2012, 5:23pm

Hi,

Hello Marcus, the problem we are facing is that we need to run scripts on
many molecules and we thought writing a script in python which would loop
through all the molecules would really help us but what happened is we
installed avogadro on a machine which cant bring up the graphic mode i.e.,
if we try to trigger the graphics the execution stops there. We installed
avogadro on that machine because it has computational power which is
require to perform our calculations. Openbabel supports some operations we
want. But I am not sure if openbabel will suffice all our requirements.

hello ray, thank you. I performed minimization using openbabel and it
worked for me. I will contact jing-yuan about it and see if openbabel would
meet our requirements.

Thank you very much for for your support.

Thank you,
Divya

On Tue, Mar 13, 2012 at 1:11 PM, Ray Sheppard rsheppar@iu.edu wrote:

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 loniedavid@gmail.comwrote:

Hi Divya,

On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri divneela@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 rsheppar@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 rsheppar@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

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/

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

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/

Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

–
Thanks
Divya

–
Thanks
Divya

–
Thanks
Divya

ghutchis · March 14, 2012, 2:01pm

Hello Marcus, the problem we are facing is that we need to run scripts on many molecules and we thought writing a script in python which would loop through all the molecules would really help us but what happened is we installed avogadro on a machine which cant bring up the graphic mode i.e., if we try to trigger the graphics the execution stops there. We installed avogadro on that machine because it has computational power which is require to perform our calculations. Openbabel supports some operations we want. But I am not sure if openbabel will suffice all our requirements.

I’m pretty sure Open Babel and/or Pybel can do everything you require. All force field minimizations, charge assignments, conformer searching in Avogadro are done through libopenbabel.

You can, of course, easily script Open Babel in python.
http://openbabel.org/wiki/Python
http://openbabel.org/docs/2.3.1/UseTheLibrary/Python_Pybel.html

Hope that helps,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/