If the user reaches the quota limit, the filesystem that carries home directory of users on High Performance Computing (HPC) servers (called ZFS) does not let users delete files. So the following command would not work:

rm my_file.dat
rm: cannot remove file `my_file.dat': Disk quota exceeded

The reason is that the system needs to transiently write metadata to the system before performing the deletion process. The solution is the following commands:

# Copy a null file, and replace with the file you want to delete
cp /dev/null my_file.dat

# remove the file that is already changed
rm -r my_file.dat

The first line overwrite a null file on the file you would like to delete. The second line deletes that file. Now you should have enough quota to perform more deletions at your user directory.