Command Line Interface to Rivanna

Prerequisites

We assume you already know the Linux basics, such as

• Listing files (ls)
• Removing files (rm)
• Navigating directories (cd)
• Listing file contents (cat and optionally head, tail, less, more)
• Ability to use one or more standard editors (vi, vim, emacs, nano)
• Relative and absolute paths

Rivanna

Rivanna is the university’s primary resource for high-performance computation. It provides a platform for computationally-intensive research across disciplines.

Logging In

There are several ways to log in to UVA’s HPC system.

Open OnDemand: https://ood.hpc.virginia.edu/

FastX: https://ood.hpc.virginia.edu/ (OOD > Interactive Apps > FastX Web)

MobaXterm (Windows): https://www.rc.virginia.edu/userinfo/rivanna/logintools/mobaxterm/

Terminal (Mac, Linux):

ssh -Y gka6a@rivanna.hpc.virginia.edu

Transfer Files

To transfer files between computers, you can use commands like scp, rsync, or sftp in your command line interface.

scp

scp l_SOURCE jus2yw@rivanna.hpc.virginia.edu:r_TARGET
scp jus2yw@rivanna.hpc.virginia.edu:r_SOURCE l_TARGET

rsync

rsync -av ldir/ jus2yw@rivanna.hpc.virginia.edu:rdir
rsync my_file jus2yw@Rivanna.hpc.virginia.edu:/scratch/$USER

sftp

sftp jus2yw@Rivanna.hpc.virginia.edu
Sftp> put myfile    # transfer from local to Rivanna
Sftp> get myfile    # transfer from Rivanna to local

Globus Data Transfer

Globus is a simple, reliable, and fast way to access and move your research data between systems. Globus allows you to transfer data to and from systems such as:

• Laptops & personal workstations
• Rivanna HPC cluster
• Ivy Central Storage
• Lab / departmental storage
• Tape archives
• Cloud storage
• Off-campus resources (ACCESS, National Labs)

Globus can help you share research data with colleagues and co-investigators, or to move data back and forth between a lab workstation and Rivanna or your personal computer.

Is your data stored at a different institution? At a supercomputing facility? All you need is your institution’s login credentials.

For more info, visit https://www.rc.virginia.edu/userinfo/globus/

Creating & Editing Files

There are a wide variety of text editors you can use to create and edit files.

• gedit
• vi/vim
  • To enter the insert mode, press i
  • To enter the command mode, press Esc
  • To save the file, enter w filename
  • To exit without saving, press q
• nano
  • To start writing, immediately start typing
  • To stop writing, press ctrl+X
  • To save the file, type the filename and press Enter
• vscode
  • enter module load code-server/4.16.1
  • enter code-server
  • Open the browser and copy the given url from terminal (http://127.0.0.1:8080/)