HPC FAQ - Home and Scratch Disk

Supercomputer documentation is always a work in progress! Please email questions, corrections, or suggestions to the HPC support team at help-hpc@uky.edu as usual. Thanks!

Files in scratch are NOT backed up.

Files left in scratch more than 30 days may be deleted.

Frequently Asked Questions

1. What is my 'home' directory?

Each user has space allocated on the /home filesystem for programs, code, and modest amounts of data. The path is /home/userid and there is a quota (limit) on how much space you can use. Your home directory is backed up nightly.

2. How do I check my disk quota?

Use the quota command.

3. Why do I get the message disk quota exceeded?

If you run a large job from your /home directory, then you can easily exceed your disk quota. In order to run jobs without exceeding your disk quota, create any large files in your scratch directory (/scratch/userid).

4. What is 'scratch' space?

Scratch space is temporary disk space for actively running jobs. You have your own scratch area in /scratch/userid where your jobs won't interfere with others. There is a link to this in your home directory (/home/userid/scratch) for your convenience.

There are no quotas on the /scratch filesystem and your jobs can write data to the limit of the filesystem. However, there is a finite amount of space and that space is shared among all users. Use the command df -h /scratch to check the current usage of the scratch file system.

If scratch fills completely, then most active jobs will fail. Whenever scratch becomes dangerously full, the system administrators will take countermeasures, including canceling running jobs.

Only put files in scratch temporarily! Make sure you don't put source code or other hard to recreate files in scratch, unless you have another copy stored elsewhere. Large files that need to be stored for an extended time may be transferred to the HSM near-line storage system. See Long Term Storage for more information.

User directories in /scratch on the cluster are automounted by the file system as they are needed. When you list the subdirectories under /scratch (that is, ls /scratch), you will see only a few of them, the ones that are currently in use. However, there are hundreds of userids and each has its own scratch directory. When you cd to one (cd /scratch/userid) it will be 'automagically' mounted for you.

5. How do I check the available space on a filesystem?

Use the df -h command to list information about each available file system.

6. Is my scratch space the same on all machines in the cluster?

Yes. The global clustered file system presents the same home and scratch filesystem to the login nodes and all of the compute nodes.

7. Can two of my jobs interfere with each other? Will files from one job over-write files from the other?

Yes, but only if the files have the exact same pathname. The easiest and safest way to prevent that is to make separate scratch directories for the files for each job, either by hand or by using the mktemp command to create a unique directory name.

Note: this problem will not normally occur with Gaussian jobs. The script that sets up the job creates a unique scratch directory for each job. However, if you run two jobs from the same directory using the same Gaussian file command file name, then the output file from the first job to finish will be overwritten by the second. Don't run jobs with the same Gaussian command file name from the same directory.

8. How long can files remain in my scratch directory?

Files in the scratch filesystem are NOT backed up. Files left in scratch more than 30 days may be deleted. Once a file is deleted from a scratch directory, it is permanently gone. It is each user's responsibility to keep copies, either in the home directory or in some other location

Only put files in scratch temporarily! Make sure you don't put source code or other hard to recreate files in scratch, unless you have another copy stored elsewhere. Large files that need to be stored for an extended time may be transferred to the HSM near-line storage system. See Long Term Storage for more information.

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