File transfer from the CLI

Overview

The clusters support secure file transfers with SSH-based tools: rsync, scp, and sftp. All transfers require DUO two-factor authentication.

scp — simple one-off transfers

scp file1.txt file2.txt your_netid@login.seawulf.stonybrook.edu:/gpfs/home/your_netid/
scp your_netid@login.seawulf.stonybrook.edu:/gpfs/home/your_netid/output.txt ./

# wildcards and brace expansion
scp *.txt your_netid@login.seawulf.stonybrook.edu:subdir
scp your_netid@login.seawulf.stonybrook.edu:'/path/{a,b,c}.txt' ./

Quotes around the remote path ensure brace expansion happens on the remote server. Bundle multiple files into a single command when possible.

rsync — resumable, efficient

rsync myfolder/ your_netid@login.seawulf.stonybrook.edu:/gpfs/home/your_netid/myfolder/
rsync your_netid@login.seawulf.stonybrook.edu:/gpfs/projects/SmithGroup/data ./data

Use rsync for large files, interrupted transfers that need resuming, directories with many files, or when you only want to transfer changes — it sends only file differences.

sftp — interactive browsing

sftp your_netid@login.seawulf.stonybrook.edu
sftp> cd /gpfs/home/your_netid
sftp> get myfile.txt
sftp> put localfile.txt
sftp> ls
sftp> bye

Graphical options for Windows

• MobaXterm (recommended) — create a dedicated SFTP session (New Session → SFTP) and drag-and-drop between panels. Avoid the SSH-session sidebar browser: it triggers repeated authentication prompts.
• WinSCP — SFTP protocol, host login.seawulf.stonybrook.edu, your NetID; drag and drop.
• Open OnDemand — browser-based upload/download to any directory (home, scratch, project).