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JHPCE

Overview

JHPCE

Home
Home
- About Us
  About Us
- Getting Started
  Getting Started
  - New user form
  - New PI information and form
    New PI information and form
    
    New PI Information
    
    New PI Form
  - Orientation/Logging In
    Orientation/Logging In
    
    Overview
    
    JHPCE Orientation (PDF download)
    
    C-SUB Orientation (PDF)
  - Leaving JHPCE as a User or PI
  - New C-SUB PI or user?
  - Policies
  - HIPAA on JHPCE
- Getting Help
  Getting Help
  - Password Reset/Google Auth
  - Basics
  - Submitting Good Queries
  - Support Email List Archives
  - External Guides
  - Glossary
  - How to read a manual page (pdf)
  - Tools For Site Developers
    Tools For Site Developers
    
    Handy Features
    
    Tips & Conventions
    
    Wishlist
- FAQ
- Accessing the cluster
  Accessing the cluster
  - Overview
  - SSH
  - X11
  - MobaXterm
  - Transferring files in or out
    Transferring files in or out
    
    Overview
    
    Globus
    
    OneDrive via rclone
- Managing Files
  Managing Files
  - Files Overview
  - Sharing Files
  - ACL
  - Copying within cluster
  - Rsync: A Key File Mgmt Tool
    Rsync: A Key File Mgmt Tool
    
    Using Rsync
    
    Itemize Output Key
    
    Itemize Manual Page
  - Archive Files
  - Navigating Deep Directory Trees
  - Data Security
  - Encrypting filesystems with ENCFS
  - Storage Tips
  - Copying within cluster
- Storage Policies and Practices
  Storage Policies and Practices
- Software
  Software
  - Overview
  - Local Software
    Local Software
    
    Matlab
    
    Python
    
    R and RStudio
    
    SAS
    
    Stata
  - Modules
  - Installing Your Own
    Installing Your Own
    
    Compile from Source
    
    Conda Environment
    
    Python Packages
    
    R Packages
  - JHPCE-created
  - Helpful GUI Programs
- Job scheduler (SLURM)
  Job scheduler (SLURM)
  - Getting Started
  - About Jobs
  - Partitions
  - Memory Usage
  - Time Limits
  - Command tips and reference
    Command tips and reference
    
    Cmd tips and reference
    
    sacct tips
    
    sacctmgr tips
    
    scontrol tips
    
    squeue tips
    
    reportseff tips
  - Interactive Jobs
  - Crafting Batch Jobs
  - Monitoring Your Jobs
  - When Will My Job Start?
  - Quality of Service (QOS)
  - Job Environment
  - Node Features
  - Example User Guides
  - SLURM FAQ
- User Guides/Tutorials
  User Guides/Tutorials
  - GPU
    GPU
    
    Using GPUs on JHPCE
    
    Alphafold
  - VS Code
  - Cost Calculator
- Web Portal
  Web Portal
- C-SUB
  C-SUB
- JADE
  JADE
  - About
  - Transitioning to JADE
    Transitioning to JADE
    
    CMS Users
    CMS Users
    
    Overview
    
    Change details
    
    Path Changes chart (pdf)
    
    Path Changes doc (pdf)
    
    dbGaP Users
    dbGaP Users
    
    Overview
  - Accessing JADE
    Accessing JADE
    
    Overview
    
    SSH
    
    X11
    
    MobaXterm
    
    Transferring files in or out
    Transferring files in or out
    
    Overview Overview
    Table of contents
    
    Overview
    
    SFTP
    
    Globus
    
    SFTP
    
    Globus

Data Transfers Into and Out of JADE¶

Overview¶

SFTP¶

Globus¶