CryoSPARC-Sapelo2

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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 form to request. We will reach out to you after we get your request.

Running Program

Also refer to Running Jobs on Sapelo2.

3.3.1 CryoSPARC 3.3.1 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

Documentation

About cryoSPARC: https://guide.cryosparc.com/ User Interface and Usage Guide: https://guide.cryosparc.com/processing-data/user-interface-and-usage-guide All Job Types in cryoSPARC: https://guide.cryosparc.com/processing-data/all-job-types-in-cryosparc Management and Monitoring: https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring Introductory Tutorial: https://guide.cryosparc.com/processing-data/cryo-em-data-processing-in-cryosparc-introductory-tutorial Tutorials and Usage Guides: https://guide.cryosparc.com/processing-data/tutorials-and-case-studies

Installation

  • Version 3.3.1 master is installed on the master node (ss-cryo.gacrc.uga.edu). Source codes are downloaded in /work/cryosparc/cryosparc_master on the master node.
  • Version 3.3.1 workers are installed on two worker nodes (NVIDIA Tesla K40m GPU nodes rb6-[3-4]). Source codes are downloaded in /work/cryosparc/cryosparc_worker on the master ndoe.

System

64-bit Linux

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