JUSTUS2/Software/Gaussview: Difference between revisions

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⚫
{{Softwarepage|chem/gaussview}}


{| width=600px class="wikitable"
<!--{| align="right" {{Table|width=40%}} -->
{|{{Softwarebox}}
|-
|-
! Description !! Content
! colspan="2" style="text-align:center" | Name
|-
|-
| module load
| module load
| chem/gaussview
| chem/gaussview
⚫
|-
| Availability
| [[bwForCluster_Chemistry]]
|-
|-
| License
| License
| Commercial - see [http://gaussian.com/pricing/ Pricing for Gaussian Products]
| commercial
|-
|-
|Citing
| Citing
| [http://www.gaussian.com/g_tech/gv5ref/gv5citation.htm See Gaussview manual]
| [http://gaussian.com/gv611rn/ See section Citation of the Release Notes]
|-
|-
| Links
| Links
| [http://www.gaussian.com Homepage]; [http://www.gaussian.com/g_tech/gv5ref/gv5ref_toc.htm Manual]
| [http://www.gaussian.com Gaussian Homepage]; [http://gaussian.com/gaussview6/ GaussView Documentation]
|-
|-
| Graphical Interface
| Graphical Interface
| [[#Loading the module and starting GaussView (within VNC session)|Yes]]
⚫
| Gaussview is GUI for [[Gaussian]]
⚫
|-
| Related program
⚫
| See [[Gaussian]]
|}
|}



= Description =
= Description =
⚫
'''GaussView''' is an advanced and powerful graphical user interface for [[Gaussian]]. With the aid of GaussView you can

⚫
* build, save or load molecular structures (advanced molecule editor)
⚫
'''GaussView''' is a very advanced and powerful graphical user interface for [[Gaussian]]. With the aid of GaussView you can
* prepare Gaussian calculations (create and save Gaussian input files with all parameters)
⚫
* build, save or load molecular structures (very powerful molecule editor)
* set up, start, monitor and control Gaussian calculations (create Gaussian input files with all parameters)
* monitor progress of running Gaussian calculations (login to the compute node and change to the temporary job directory)
* load, view and analyze results (e.g. visualize 3D ISO surfaces of densities and orbitals, plot IR and Raman spectra)
* load, view and analyze results (e.g. visualize 3D ISO surfaces of densities and orbitals, plot IR and Raman spectra)
* setup, visualize and analyze parameter scans
* setup, visualize and analyze parameter scans
* setup and control QM/MM calculations
* setup QM/MM calculations
For more information on features please visit GaussView's [http://www.gaussian.com/g_prod/gv5b.htm ''Visualizing Molecules & Reactions with GaussView''] web page.
For more information on features please visit GaussView's [http://gaussian.com/gaussview6/ ''GaussView Documentation''] web page.
<br>
<br>
When running GaussView on one of the login nodes via X-forwarding please do not start long Gaussian calculations interactively in the foreground.
Instead of this you can save the Gaussian command file to disk and submit it as ordinary [[Gaussian]] job.
⚫
<br>
When running GaussView via VNC, e.g. via [[TigerVNC]], on a compute node, you may run longer interactive GaussView calculations.
Please do not start interactive jobs occupying more cores than have been requested when starting the interactive VNC session.
<br>
<br>


⚫
= Usage =


There are two methods to start GaussView remotely on JUSTUS 2:
= Versions and Availability =
* '''Remote-VNC''' method (recommended): First set up a VNC (Virtual Network Computing) remote desktop connection to one of the JUSTUS 2 login or visualization nodes. To help you with that we have pre-installed [[TigerVNC]] on JUSTUS 2. See the [[TigerVNC]] documentation for details. Thereafter you can open a terminal window in that VNC session, load the GaussView module and start GaussView via command ''gaussview''.

* '''X-forwarding''' method (usually slow): First log in to the JUSTUS 2 login or visualization nodes with X-forwarding enabled (i.e. ''ssh -X''). Then load the GaussView module and start GaussView via command ''gaussview''. Major disadvantage: X-forwarding requires a very fast network connection with low latency. Usually home or Wi-Fi networks are too slow.
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/gaussview CIS Information on GaussView].
⚫
<br>

'''NEVER start long running large calculations interactively on login or visualization nodes. Use GaussView to prepare and save the input. Then submit a [[Gaussian]] job with the input created by GaussView.'''
On the command line interface of a particular bwHPC cluster a list of all available GaussView versions can be inquired as followed
<pre>
⚫
$ module avail chem/gaussview
</pre>


== Parallel computing ==
== Parallel computing ==
Line 58: Line 50:
within ''Gaussian Calculation Setup'' window.
within ''Gaussian Calculation Setup'' window.


Please make sure that the speed up of the calculation is reasonable when requesting
more cores. When doubling the number of cores, the speed up should be at least a
factor 1.7, better 1.8.


Please keep in mind that our Gaussian version is only shared-memory parallel.
⚫
= Usage =
Therefore requesting more than one node does not make any sense.


== Loading the module and starting GaussView (within VNC session) ==
== Loading the module and starting GaussView (within VNC session) ==


The best method to use GaussView is to start it within an interactive
The best method to use GaussView is to start it within an interactive
remote VNC session. Details on how to start an interactive VNC session
remote VNC session or a (Linux-)System with X-forwarding (e.g.: ssh -X 'your-id'@FQDN-of-cluster.de).
⚫
<br>
running on a compute node can be found here: [[TigerVNC]]
Details on how to start an interactive VNC session running on a compute node can be found here: [[TigerVNC]]


Within the X11 session open a terminal window (e.g. xterm) and execute:
Within the X11 session open a terminal window (e.g. xterm) and execute:

<pre>
<pre>
$ module load chem/gaussian
$ module load chem/gaussview
gaussview
gaussview &
</pre>
</pre>


The GaussView module automatically loads the corresponding Gaussian module.
The GaussView module automatically loads the corresponding Gaussian module.


[[File:Gaussview.jpg]]
If you wish to load a specific version you may do so by specifying the version
<br>
explicitly, e.g. specify
<br>
See [[#GaussView example session|GaussView example session]] for more infos how to work with the GUI.
<br>
<br>
It is recommended to always specify the full module name including
the version of the module, e.g. specify
<pre>
<pre>
$ module load chem/gaussview/5.0.9
$ module load chem/gaussview/6.1.1
</pre>
</pre>
to load version ''5.0.9'' of GaussView.
to load version ''6.1.1'' of GaussView.
<br>
<br>


Line 93: Line 95:
the run time of the interactive VNC session ends. Furthermore
the run time of the interactive VNC session ends. Furthermore
your should never occupy more cores (GaussView setting '''Shared Processors''', default 1 core)
your should never occupy more cores (GaussView setting '''Shared Processors''', default 1 core)
than specified when submitting the VNC session (Moab option '''PPN''', default 1 core).
than specified when submitting the VNC session (Slurm option '''--ntasks-per-node''', default 1 core).
Finally be aware that your job might get killed if it uses more memory
Finally be aware that your job might get killed if it uses more memory
than requested.
than requested.
Line 100: Line 102:


First you can construct your Gaussian job interactively with GaussView.
First you can construct your Gaussian job interactively with GaussView.
When set up of the job is done one may store the Gaussian command file to disk
When done with setting up of the job, save the Gaussian command file to disk
and submit that *.com file as described in the documentation of [[Gaussian]].
and submit that *.com file as described in the documentation of [[Gaussian]].
Please read the Gaussian documentation as well and make sure that you
Please read the Gaussian documentation as well and make sure that you
specify reasonable values for the number of cores, memory usage,
specify reasonable values for the number of cores, memory usage,
disk usage and job run time when submitting the job.
disk usage and job run time when submitting the job.



= Examples =
= Examples =
Line 111: Line 112:
== GaussView example session ==
== GaussView example session ==


* When 'gaussview' is started, the 'Builder Fragment' of the programs main window (gray background) displays the 'Carbon Tetrahedral' by default.
* When 'gaussview' is started, the [[#Loading the module and starting GaussView (within VNC session)|'Builder Fragment']] of the programs main window (gray background) displays the 'Carbon Tetrahedral' by default.
* Click in the middle of the construction window (blue background). The selected fragment should now be displayed there (undo clicks via 'Menu: Edit -> Undo').
* Click in the middle of the construction window (blue background). The selected fragment should now be displayed there (undo clicks via 'Menu: Edit -> Undo').
* Start a Gaussian calculation 'Menu: Calculate -> Gaussian Calculation Setup'. Keep all defaults and hit 'Button: Quick Launch' at the bottom.
* Start a Gaussian calculation 'Menu: Calculate -> Gaussian Calculation Setup'. Keep all defaults and hit 'Button: Quick Launch' at the bottom.
* View the results via 'Menu: Results -> Summary'.
* View the results via 'Menu: Results -> Summary'.
* Create orbital contour plots via 'Menu: Results -> Surface/Contours', 'Button: Cube Actions -> New Cube', 'Button: Surface Actions -> New Surface'. If you have accepted all defaults, you should see the HOMO orbital now.
* Create orbital contour plots via 'Menu: Results -> Surface/Contours', 'Button: Cube Actions -> New Cube', 'Button: Surface Actions -> New Surface'. If you have accepted all defaults, you should see the HOMO orbital now.


= Version-Specific Information =

For specific information about version ''VERSION'' see the information available via the module system with the command
<pre>
$ module help chem/gaussview/VERSION
</pre>
Please read the local module help documentation before using the software. The module help contains links to additional documentation and resources as well as information about support contact.
⚫
<br>

----
[[Category:Chemistry software]][[Category:bwForCluster_Chemistry]]

Latest revision as of 10:00, 23 April 2024

The main documentation is available via module help chem/gaussview on the cluster. Most software modules for applications provide working example batch scripts.


Description Content
module load chem/gaussview
License Commercial - see Pricing for Gaussian Products
Citing See section Citation of the Release Notes
Links Gaussian Homepage; GaussView Documentation
Graphical Interface Yes
Related program See Gaussian

Description

GaussView is an advanced and powerful graphical user interface for Gaussian. With the aid of GaussView you can

  • build, save or load molecular structures (advanced molecule editor)
  • prepare Gaussian calculations (create and save Gaussian input files with all parameters)
  • monitor progress of running Gaussian calculations (login to the compute node and change to the temporary job directory)
  • load, view and analyze results (e.g. visualize 3D ISO surfaces of densities and orbitals, plot IR and Raman spectra)
  • setup, visualize and analyze parameter scans
  • setup QM/MM calculations

For more information on features please visit GaussView's GaussView Documentation web page.

Usage

There are two methods to start GaussView remotely on JUSTUS 2:

  • Remote-VNC method (recommended): First set up a VNC (Virtual Network Computing) remote desktop connection to one of the JUSTUS 2 login or visualization nodes. To help you with that we have pre-installed TigerVNC on JUSTUS 2. See the TigerVNC documentation for details. Thereafter you can open a terminal window in that VNC session, load the GaussView module and start GaussView via command gaussview.
  • X-forwarding method (usually slow): First log in to the JUSTUS 2 login or visualization nodes with X-forwarding enabled (i.e. ssh -X). Then load the GaussView module and start GaussView via command gaussview. Major disadvantage: X-forwarding requires a very fast network connection with low latency. Usually home or Wi-Fi networks are too slow.


NEVER start long running large calculations interactively on login or visualization nodes. Use GaussView to prepare and save the input. Then submit a Gaussian job with the input created by GaussView.

Parallel computing

One can construct/save or start serial as well as parallel jobs with GaussView. To switch from serial to parallel one has to modify entry Shared Processors within Gaussian Calculation Setup window.

Please make sure that the speed up of the calculation is reasonable when requesting more cores. When doubling the number of cores, the speed up should be at least a factor 1.7, better 1.8.

Please keep in mind that our Gaussian version is only shared-memory parallel. Therefore requesting more than one node does not make any sense.

Loading the module and starting GaussView (within VNC session)

The best method to use GaussView is to start it within an interactive remote VNC session or a (Linux-)System with X-forwarding (e.g.: ssh -X 'your-id'@FQDN-of-cluster.de).
Details on how to start an interactive VNC session running on a compute node can be found here: TigerVNC

Within the X11 session open a terminal window (e.g. xterm) and execute: 

$ module load chem/gaussview
gaussview &

The GaussView module automatically loads the corresponding Gaussian module.

Gaussview.jpg

See GaussView example session for more infos how to work with the GUI.

It is recommended to always specify the full module name including the version of the module, e.g. specify 

$ module load chem/gaussview/6.1.1

to load version 6.1.1 of GaussView.

Starting Gaussian jobs interactively via GaussView

Within the interactive VNC session running on a compute node you may start Gaussian jobs locally via Submit or Quick Launch. These buttons are located within the Gaussian Calculation Setup window of GaussView.

If you do so you must make sure that these jobs finish before the run time of the interactive VNC session ends. Furthermore your should never occupy more cores (GaussView setting Shared Processors, default 1 core) than specified when submitting the VNC session (Slurm option --ntasks-per-node, default 1 core). Finally be aware that your job might get killed if it uses more memory than requested.

Submitting Gaussian jobs to the queueing system

First you can construct your Gaussian job interactively with GaussView. When done with setting up of the job, save the Gaussian command file to disk and submit that *.com file as described in the documentation of Gaussian. Please read the Gaussian documentation as well and make sure that you specify reasonable values for the number of cores, memory usage, disk usage and job run time when submitting the job.

Examples

GaussView example session

  • When 'gaussview' is started, the 'Builder Fragment' of the programs main window (gray background) displays the 'Carbon Tetrahedral' by default.
  • Click in the middle of the construction window (blue background). The selected fragment should now be displayed there (undo clicks via 'Menu: Edit -> Undo').
  • Start a Gaussian calculation 'Menu: Calculate -> Gaussian Calculation Setup'. Keep all defaults and hit 'Button: Quick Launch' at the bottom.
  • View the results via 'Menu: Results -> Summary'.
  • Create orbital contour plots via 'Menu: Results -> Surface/Contours', 'Button: Cube Actions -> New Cube', 'Button: Surface Actions -> New Surface'. If you have accepted all defaults, you should see the HOMO orbital now.
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