Moving Files and Navigating SMS Lab Filesystems in Sapelo2

Quick guide for navigating Sapelo2 filesystems

Overview

This guide introduces basic command-line navigation and file movement on Sapelo2 for users working in the SMS Lab filesystem. It covers how to log in using PuTTY, move around the /home/, /work/, /scratch/, and /project/ directories, and safely copy or back up files using the transfer node.

The examples below use username as a placeholder. Replace it with your own UGA MyID.

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1. Essential Linux Commands

Command	Purpose
pwd	Prints the current directory you are in
ls -l	Lists files and directories in long format
cd	Changes directory
mkdir	Creates a new directory
mv	Moves or renames files and directories

Check your current location with pwd

After logging in, use:

pwd

Example:

username@ss-sub1 ~$ pwd
/home/username

This shows that you are currently in your home directory.

List files with ls -l

To view the files and directories in your current location:

ls -l

This shows file permissions, ownership, size, date modified, and file or directory names.

Change directories with cd

To move into another directory, use:

cd /path/to/directory

For example, to access the SMS Lab work directory:

cd /work/smslab/directory-name

After changing directories, confirm your location:

pwd

Create a directory with mkdir

To create a new directory:

mkdir new_directory_name

For example:

mkdir genome_assembly_backup

Move or rename files with mv

To move a file into another directory:

mv file.txt /work/smslab/directory-name/

To rename a file:

mv old_name.txt new_name.txt

To move a directory:

mv old_directory /work/smslab/directory-name/

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2. Logging in to Sapelo2 with PuTTY

Open PuTTY and enter the appropriate server address in the Host Name field.

Sapelo2 login node

Use this when you are working interactively, submitting jobs, checking files, or preparing scripts.

username@sapelo2.gacrc.uga.edu

Most routine work begins here.

Transfer node

Use this when moving large files between filesystems or when working with storage locations such as /project/.

username@xfer.gacrc.uga.edu

The transfer node is intended for file movement, not for running computational jobs.

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3. Starting in the Home Directory

After logging in to Sapelo2, you usually start in your home directory.

Example:

username@ss-sub1 ~$ pwd
/home/username

Your home directory is useful for small scripts, configuration files, and lightweight work. Large datasets and computational outputs should usually be stored in /work/, /scratch/, or /project/, depending on the purpose.

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4. Navigating to the SMS Lab Work Directory

To move into the SMS Lab work directory:

cd /work/smslab/directory-name

Then confirm your location:

pwd

Example:

pwd
/work/smslab/directory-name

You can also list the contents of the directory:

ls -l

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5. Navigating to Scratch

The same navigation commands apply to the /scratch/ directory.

For example:

cd /scratch/username

Then confirm your location:

pwd

Warning

The /scratch/ filesystem is intended for temporary files and active computational work. Files that have not been accessed or modified for more than 30 days, as per GACRC guidelines, may be automatically deleted. Do not treat /scratch/ as permanent storage.