Best Practices on HPC Storage
User Quota Limits and the myquota command
All users have quote limits set on HPC fie systems. There are several types of quota limits, such as limits on the amount of disk space (disk quota), number of files (inode quota) etc. The default user quota limits on HPC file systems are listed on our Data Management page.
One of the common issues users report is running out of inodes in their home directory. This usually occurs during software installation, for example installing conda environment under their home directory. Running out of quota causes a variety of issues such as running user jobs being interrupted or users being unable to finish the installation of packages under their home directory.
Users can check their current utilization of quota using the myquota command. The myquota command provides a report of the current quota limits on mounted file systems, the user's quota utilization, as well as the percentage of quota utilization.
In the following example the user who executes the myquota command is out of inodes in their home directory. The user inode quota limit on the /home file system 30.0K inodes and the user has 33000 inodes, thus 110% of the inode quota limit.
$ myquota
Quota Information for NetID
Hostname: torch-login-2 at 2025-12-09 17:18:24
Filesystem Environment Backed up? Allocation Current Usage
Space Variable /Flushed? Space / Files Space(%) / Files(%)
/home $HOME YES/NO 0.05TB/0.03M 0.0TB(0.0%)/54(0%)
/scratch $SCRATCH NO/YES 5.0TB/5.0M 0.0TB(0.0%)/1(0%)
/archive $ARCHIVE YES/NO 2.0TB/0.02M 0.0TB(0.0%)/1(0%)
You can use the following command to print the list of files within each sub-folder for a given directory:
$cd $HOME
$du --inodes -h --max-depth=1
6 ./.ssh
88 ./.config
2 ./.vnc
2 ./.aws
3 ./.lmod.d
5.3K ./.local
3 ./.dbus
408 ./ondemand
2 ./.virtual_documents
6 ./.nv
6.7K ./.pixi
33 ./workshop_scripts
5 ./.cupy
6 ./.gnupg
1 ./.emacs.d
194 ./.nextflow
6 ./.terminfo
2 ./.conda
2 ./.singularity
3 ./.vast-dev
1 ./custom
185 ./genai-workshop
6 ./.atuin
1 ./.apptainer
9 ./.subversion
4 ./packages
1.4K ./.cache
15K .
Large number of small files
In case your dataset or workflow requires to use large number of small files, this can create a bottleneck due to read/write rates. Please refer to our page on working with a large number of files to learn about some of the options we recommend to consider.
Installing Python packages
Your home directory is limited to a relatively small number of inodes (30,000). Creating conda/python environments in you home directory, this can eat easily exhaust your inode quota.
Please review the Package Management section of the Torch Software Page.