Skip to content

Directory Structure#

This page provides an overview of the key directories on the cluster, covering their intended use, storage capacity, and availability across login and compute nodes.

/home/<cnet_id>#

Your personal home directory, automatically assigned upon account creation. This is the default directory you land in upon logging in to the cluster.

cd $HOME

  • Filesystem: NFS
  • Total Capacity: 100G (per user)
  • Use this for: Configuration files, scripts, and small personal files.
Storage Limit

/home has a limited capacity shared across all users. Avoid storing large datasets or job output here.

/scratch/<cnet_id>#

A high-capacity local disk available exclusively on compute nodes, intended for temporary storage during job execution. A personal directory under /scratch/<cnetid> is automatically created when you start a job. The /scratch directory is only accessible during an active job — you must have a running job to read or write to this space.

  • Filesystem: Local Disk
  • Total Capacity: 6.4T
  • Available On: Compute nodes only
  • Use this for: Large temporary files, job input/output, and intermediate results during job execution.
Temporary Storage

/scratch is local to each compute node and is not shared across nodes. Copy any results you wish to keep back to /home or /share before your job ends, as data may not persist after the job completes.

Accessing /scratch/<cnet_id>
  1. Run a job via srun (see Submitting Jobs) 
    1
2
    srun <cli-options> --pty /bin/bash 
cd /scratch/<cnet_id>
  2. Create a job via sbatch and SSH into compute node (see Submitting Jobs & SSH into running jobs) 
    1
2
3
4
5
6
7
8
9
    $ sbatch first-job.sh
Submitted batch job 946393

$ squeue -u $USER -o "%.18i %.9P %.20j %.10u %.2t %.10M %.6D %R"
Get the Node name

$ ssh <nodename>

cd /scratch/<cnet_id>

/share#

A large shared NFS filesystem accessible to authorized research groups, labs, and schools connected to the cluster. Access is restricted by group membership.

  • Filesystem: NFS
  • Access: Restricted to authorized groups.
  • Use this for: Collaborative research data shared across labs or departments.

Note

Access to /share is granted based on group membership. Contact SSCS Server Support to request access for your lab or research group.

Once access is granted, your lab’s shared directory is available at: 

1
cd /share/johndoelab
Permissions note — who can read/write:

Only members of the johndoelab group have read/write access to this directory.

Filesystem Snapshots (Backup)#

The cluster storage system automatically maintains filesystem snapshots to protect against accidental file deletion or corruption. Snapshots are available for the following directories:

  • /home
  • /share/<lab_name>

These snapshots allow files and directories to be restored to a previous state if needed.

Snapshot Frequency#

Snapshots are created automatically at multiple intervals:

Frequency Purpose
Hourly Recover recent accidental changes
Daily Recover files deleted within the past several days
Monthly Long-term recovery and archival protection

Snapshots are managed automatically by the storage system and older snapshots are removed according to retention policies.

Requesting File Recovery#

If you need to recover a file or directory, please contact the cluster support team at ssc-server-support@lists.uchicago.edu, with the following information:

  • Name of file or directory
  • Full path to the file or directory
  • Approximate date and time when the file existed
  • Your username and lab/group (if applicable)

The support team will assist with restoring the data from available snapshots.

Warning

Snapshots are not a substitute for good data management practices. Users should maintain their own backups for critical data whenever possible.

Useful Commands#

Check Disk Usage#

1
2
3
4
5
6
7
8
# Check your home directory usage
du -sh ~

# Check a specific directory
du -sh /path/to/directory

# Check available space on a specific filesystem
df -h /home

Check File and Directory Sizes#

1
2
3
4
5
# List files with sizes in human-readable format
ls -lh

# List top 10 largest files/directories in current directory
du -sh * | sort -rh | head -10

1
2
3
4
5
6
7
8
# Check current directory
pwd

# Check who you are
whoami

# Check your group memberships
groups $USER