CryoSPARC-Sapelo2: Difference between revisions

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


=== Running Program ===
=== Running Program ===
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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
Please do not run GaussView directly on
<pre class="gcommand">
head -n 6 /proc/cpuinfo
</pre>
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
 
<pre class="gcommand">
 
module load gaussian/09-AMD-SSE4a
 
. $g09root/g09/bsd/g09.profile
 
gview.csh
</pre>
 
'''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
 
<pre class="gcommand">
 
module load gaussian/09-Intel-SSE4_2
 
. $g09root/g09/bsd/g09.profile
 
gview.csh
</pre>
For more information on how to run interactive jobs, please see [https://wiki.gacrc.uga.edu/wiki/Running_Jobs_on_Sapelo2#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities 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
 
<pre class="gcommand">
 
module load gaussian/16-AVX
 
. $g16root/g16/bsd/g16.profile
 
gview.sh
</pre>
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 [https://wiki.gacrc.uga.edu/wiki/Running_Jobs_on_Sapelo2#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities 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:
<pre class="gcommand">
export USE_MESAGL=1
</pre>
 
=== 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

Revision as of 11:12, 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 [[https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25844 General Support]] 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

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