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Contents:

  • Change Logs
  • Accounts
    • Requesting accounts
    • Accessing GSDC TEM cluster
      • For Linux/Mac users
      • For Windows users
  • Two-factor Authentication (2FA) with One-Time-Password (OTP)
    • 2FA with One-Time-Passowrd (OTP) Guide
    • 2FA Tips and Tricks
      • How can I resolve the IPA command error?
      • How can I resolve “Unable to display QR code” error?
      • Releasing screen lock
  • Data Transfers
    • How can I use SSH/SFTP programs with 2FA?
    • How can I use FileZilla with 2FA?
    • How can I use WinSCP with 2FA?
  • GSDC Computing Cluster for TEM Users and Operators
    • 1. Service overview
    • 2. Computing and storage resources
    • 3. Cluster management softwares
    • 4. Data analysis tools
    • 5. Understanding environment modules
      • Listing available modules
      • Show module details
      • Loading modules
      • Listing loaded modules
      • Unloading modules
      • Unloading all the modules
      • Module environment help
    • 6. Batch systems (PBS job manager)
      • Resources manager and job scheduler
      • Directives in PBS job scripts
        • Resource limits
        • Job name
        • Queue name
        • Job log files
      • PBS job script examples
        • Simple sequential job
        • Serial job with OpenMP multithreading
        • Simple MPI parallel job
        • Parallel job with MPI and OpenMP
      • Job submission
      • Monitoring and managing your jobs
        • Status of queued jobs
        • Managing your jobs
    • 7. Module paths and job submission templates
      • Module paths for data analysis tools
      • Job submission templates
    • 8. Batch queues
      • Checking batch queue names and their status
      • Checking all worker nodes status
    • 9. fstat.bin : Monitoring the usage of all the worker nodes
    • 10. dynmotd : Checking storage quota limit and usage ratio
  • GSDC TEM Computing Cluster based on AlmaLinux 9.x
  • Batch System
    • Batch queue list
  • Relion
    • Executing Relion GUI tools
      • How to start Relion data analysis tool
    • PBS Strings used in Relion
    • Running data analysis jobs using CPU cores
      • Module path
      • Environment variables
      • Standard job submission script (for relion 5.0.0 CPU use)
    • Running data analysis jobs using GPGPUs
      • Environment variables
      • Standard job submission script (for relion 5.0.0 GPGPU use)
      • Specifying which GPGPUs to use
    • Examples
      • Motion Correction
      • CTF Estimation
      • 2D Classification
  • cisTEM
    • Executing cisTEM
      • How to start cisTEM data analysis tool
    • Run profiles for job submission
      • Profile templates
      • Adding a new Run Profile
    • Examples of running cisTEM jobs
      • Importing Movies and images
      • Movie Alignment
  • CryoSPARC
    • Prerequisites
    • Getting a CryoSPARC instance
      • 1. (Admin) Install and setup a CryoSPARC instance
      • 2. (User) Verifying installation
    • Launching CryoSPARC instance
      • For Linux/Mac users
      • For Windows users
    • Exploring CryoSPARC web apps
      • CryoSPARC login
      • CryoSPARC dashboard
      • CryoSPARC project
      • CryoSPARC cluster(lane)
    • Tutorial on processing T20S
    • Trouble shooting
      • 1. How to stop or start the CryoSPARC instance?
      • 2. How to reset the password of non-admin user?
      • 3. Job (or Workflow) failed caused by SSD caching
      • 4. Failed to launch!
      • 5. Binary locations of Gctf, MotionCor2
  • Topaz
    • Topaz Executables
      • Topaz binary executable with CUDA 9.2
      • Topaz binary executable with CUDA 11.2
    • Using Topaz in CryoSPARC
    • Using Topaz in Relion (v3.1.0 above)
  • UCSF PyEM
    • PyEM
    • PyEM Executables
  • Frequently Asked Questions
    • How to resolve the problems on (re)starting your own cryosparc instance?
    • How to repair cryosparc database corruption?
    • How to upgrade (or downgrade) to the specific version of cryosparc softwares?
      • 1. Checking for updates
      • 2. Before you update: complete or kill running jobs
      • 3. Back-up cryosparc databases
      • 4. Cryosparc master updates
      • 5. Cryosparc worker updates
      • 6. Running the new cryosparc instance
  • APPENDIX : Application Form & Materials
    • GSDC TEM Application Form
    • Tutorial
  • Contacts
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