Data System

Network Filesystem /home

Each user has an area for their own private files, called their home directory. Your home directory is where you and your files live. Any data that you need to keep must be stored here. The name of your home directory is:

/home/<your_user_name>

It also has a special nickname: ~/. The string ~/ will always point to your home folder.

Each time you log in, you will be placed into your home directory. This directory is NFS-mounted across the cluster, which means that you may access the same files no matter which system you are on. If you create ~/notes.txt on the head node, you'll be able to access ~/notes.txt from any node. For example, here are some files you might see when you first log in:

[user@head ~]$ ls
Desktop  example-custom-job.sh  gromacs  hoomd-blue namd

If you then log into one of the compute nodes, you will see the exact same files:

[user@node4 ~]$ ls
Desktop  example-custom-job.sh  gromacs  hoomd-blue namd

Your home directory is the safe location to store files, but will offer lower performance. When performance is critical, use a Scratch Filesystem for temporary data that's only needed during the run.

High-Performance, Scratch Filesystem /scratch

Each system also has a high-speed data storage area for temporary data. This filesystem, often called scratch, offers temporary high-speed storage. This filesystem is wiped in between jobs, but is the best location for temporary data.

On the Compute Nodes, the /scratch directory is the scratch filesystem.

Keep in mind that data on the scratch filesystem is subject to deletion. Be sure to move data back to your /home directory.

Checking available disk space

Usually, you need to check the directories you'll be writing to (i.e., /home and /scratch):

df -h ~/

df -h /scratch

Remember that if storage quotas are in-place, you won't actually be able to use all the available disk space.

Calculating your disk usage

Summarize the size of your home directory:

du -chxs ~/*

Summarize the size of a directory (including subdirectories):

du -chxs myproject/*

List the files of a directory (sorted by size):

ls -Sho myproject/