Re: [Avogadro-devel] How to turn off graphics?
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 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 Sheppardrshep...@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 -- 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 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] How to turn off graphics?
Hi Divya, On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri 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 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 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 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] How to turn off graphics?
On Tue, Mar 13, 2012 at 12:26 PM, David Lonie lonieda...@gmail.com wrote: Hi Divya, On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri 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. 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 -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ Avogadro-devel mailing list Avogadro-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-devel
Re: [Avogadro-devel] How to turn off graphics?
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 -- 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/
