CryoSPARC-Sapelo2: Difference between revisions

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[[Category:Sapelo2]][[Category:Software]][[Category:Chemistry]]   
[[Category:Sapelo2]][[Category:Software]][[Category:Engineering]]   
=== Category ===
=== Category ===


Chemistry
Engineering


=== Program On ===
=== Program On ===
Line 10: Line 10:
=== Version ===
=== Version ===
   
   
5, 6.1
3.3.1


=== Author / Distributor ===
=== Author / Distributor ===
   
   
See http://www.gaussian.com
See https://guide.cryosparc.com/
   
   
=== Description ===
=== Description ===
   
   
From http://www.gaussian.com/g_tech/gv5ref/intro.htm: "GaussView is a graphical user interface designed to help you prepare input for submission to Gaussian and to examine graphically the output that Gaussian produces. GaussView is not integrated with the computational module of Gaussian, but rather is a front-end/back-end processor to aid in the use of Gaussian." For more information, please see http://www.gaussian.com/g_prod/gv5.htm.
"CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state of the art HPC software solution for complete processing of single-particle cryo-electron microscopy (cryo-EM) data. CryoSPARC is useful for solving cryo-EM structures of membrane proteins, viruses, complexes, flexible molecules, small particles, phase plate data and negative stain data." For more information, please see https://guide.cryosparc.com/.


'''NOTE''': Users are required to sign a license agreement form before being allowed to run this software. Please fill out the [http://help.gacrc.uga.edu/ GACRC Support Form] to check if you have permission to use this software.
'''NOTE''': Users are required to be added into GACRC cryosparc group before being allowed to run this software. Please fill out the GACRC [General Support https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25844] form to request.  


=== Running Program ===
=== Running Program ===

Revision as of 10:10, 16 December 2021

Category

Engineering

Program On

Sapelo2

Version

3.3.1

Author / Distributor

See https://guide.cryosparc.com/

Description

"CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state of the art HPC software solution for complete processing of single-particle cryo-electron microscopy (cryo-EM) data. CryoSPARC is useful for solving cryo-EM structures of membrane proteins, viruses, complexes, flexible molecules, small particles, phase plate data and negative stain data." For more information, please see https://guide.cryosparc.com/.

NOTE: Users are required to be added into GACRC cryosparc group before being allowed to run this software. Please fill out the GACRC [General Support https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25844] form to request.

Running Program

Also refer to Running Jobs on Sapelo2.

Version 5 GaussView 5 is installed with Gaussian 09, in /apps/eb/gaussian/09-Intel-SSE4_2/gv and /apps/eb/gaussian/09-AMD-SSE4a/gv.

Version 6.1 GaussView 6.1 is installed with Gaussian 16, in /apps/eb/gaussian/16-AVX2/gv, /apps/eb/gaussian/16-AVX/gv, and /apps/eb/gaussian/16-SSE4/gv.


Please do not run GaussView directly on the login node. To run GaussView, please first start an interactive session using the xqlogin command, once the prompt on an interactive node is returned, you can check the processor type with the command 

head -n 6 /proc/cpuinfo

and then load the appropriate gaussian module, source g09.profile (for gaussian 09) or g16.profile (for gaussian 16), and then start GaussView, as described below.

Note that you will need to have your SSH configured to export X to your local machine. For more information on how to run remote X-windows applications, please see Connecting and our Frequently Asked Questions. Note for Windows users: If you are using Xming, you will also need to have Xming-mesa installed.


GAUSSVIEW 5 for GAUSSIAN 09

For AMD processors:

If your xqlogin session landed on an AMD processor, please note that Gaussian binaries optimized for AMD processors are installed in /apps/eb/gaussian/09-AMD-SSE4a/g09. To use GaussView with this version of Gaussian, please first load the gaussian/09-AMD-SSE4a module and source g09.profile with 


module load gaussian/09-AMD-SSE4a 

. $g09root/g09/bsd/g09.profile

gview.csh

For Intel processors:

If your xqlogin session landed on an Intel processor, please note that Gaussian binaries optimized for Intel processors are installed in /apps/eb/gaussian/09-Intel-SSE4_2/g09. To use GaussView with this version of Gaussian, please first load the gaussian/09-Intel-SSE4_2 module and source g09.profile with 


module load gaussian/09-Intel-SSE4_2

. $g09root/g09/bsd/g09.profile

gview.csh

For more information on how to run interactive jobs, please see How to run an interactive job with Graphical User Interface.


GAUSSVIEW 6.1 for GAUSSIAN 16


We suggest using the version with AVX optimization that are installed in /apps/eb/gaussian/16-AVX/. To use GaussView with this version of Gaussian, please first load the gaussian/16-AVX module and source g16.profile with 


module load gaussian/16-AVX

. $g16root/g16/bsd/g16.profile

gview.sh

To use AVX2 or SSE4 optimized code, please load gaussian/16-AVX and gaussian/16-SSE4, respectively, instead of gaussian/16-AVX2. But note that some xqlogin nodes do not support AVX2 optimization.

For more information on how to run interactive jobs, please see How to run an interactive job with Graphical User Interface.


If you are having trouble with GaussView starting, with errors about X11 or "OpenGL is not available", or if you are on a Mac and the GaussView window does not display properly, please try to type the command below before invoking GaussView on the interactive node: 

export USE_MESAGL=1

Documentation

http://www.gaussian.com

Installation

  • Version 5 installed for Gaussian09 in /apps/eb/gaussian/09-Intel-SSE4_2/gv and /apps/eb/gaussian/09-AMD-SSE4a/gv.
  • Version 6.1 is installed with Gaussian 16, in /apps/eb/gaussian/16-AVX2/gv, /apps/eb/gaussian/16-AVX/gv, and /apps/eb/gaussian/16-SSE4/gv.

System

64-bit Linux

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