Welcome to tem-docs’s documentation! ( Last updated : 2024-07-08 )

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
    • PBS job script examples
    • Job submission
    • Monitoring and 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