tem-docs
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
tem-docs
GSDC TEM Computing Cluster based on AlmaLinux 9.x
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GSDC TEM Computing Cluster based on AlmaLinux 9.x
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