Storage quota

Frequently asked questions

  • I cannot copy files although we haven’t used up all space: You have probably exceeded the quota on the number of files.

  • I have moved files to the project folder but my home quota usage did not go down: Depending on the cluster, moving files does not change ownership of the files. You need to also change the ownership of the files in the project folder from you to the project (change the ownership from username_g to username; see also below).

What is quota and why is it needed?

Storage is a shared and limited resource and in a number of places we need to enforce quota to avoid that some script accidentally fills up the disk and the system becomes unusable for everybody.

Storage quota is specified in:

  • Number of files (or “inodes”): limits how many files you or a group may own. When this limit is reached, you or the group cannot create new files (but you might still increase the size of existing files). “Inodes” are entries in the index node table which store attributes and disk block locations for each file and folder.

  • Space limit: affects the aggregated size of all your files or files of a group. When this limit is reached you or the group cannot store more data (new data or increasing file sizes) on the system.

Quota applies to specific folders

Often it is intended that storage quota applies to a specific folder on the file system. For example, the so-called HOME quota shall apply to your home folder /cluster/home/user. A project may have dedicated quota for data stored under their project folder which is found under /cluster/projects/nnABCDk where nnABCDk is the account name of your project.

Because file systems have different features, unfortunately it is not always guaranteed that what you observe on the system matches this intention. Below, we will discuss how to detect and troubleshoot such situations.

Getting information about your usage and quota

We can get an overview with the dusage command. This is not a built-in Unix command but rather a tool which we have developed for NRIS clusters to wrap around lower-level commands and tools to get a quick overview. The actual output might be different for every user:

$ dusage

dusage v0.3.0

                     path    space used    quota (s)    quota (h)      files    quota (s)    quota (h)
-------------------------  ------------  -----------  -----------  ---------  -----------  -----------
                /cluster/      14.5 GiB                              235 068
       /cluster/home/****       5.4 GiB     20.0 GiB     20.0 GiB     39 921      100 000      100 000
 /cluster/work/users/****       7.6 GiB                              195 083
/cluster/projects/nn****k       1.7 TiB      2.0 TiB      2.0 TiB  1 036 089    2 000 000    2 000 000
/cluster/projects/nn****k       3.0 TiB     10.0 TiB     10.0 TiB  2 805 458   10 000 000   10 000 000
/cluster/projects/nn****k     134.2 MiB      1.0 TiB      1.0 TiB        168    1 000 000    1 000 000

Please report issues at: https://github.com/NordicHPC/dusage

The column “files” (number of files) actually lists inodes and we know that these are not precisely the same thing but we have chosen the name “files” since it is hopefully more intuitive to the users who may have never heard of “inodes”.

What are inodes?

Inodes are entries in the index node table which store attributes and disk block locations for each file and folder. If you want to see the inode numbers for your files and folders, try:

$ ls -li

Troubleshooting: Disk quota is full

  • This can be surprising for users and difficult to debug for staff:

    • On Saga and Fram: Depending on the state of the file system there can be a lag between going over quota and experiencing “Disk quota exceeded” errors.

    • On Saga and Fram: If you moved files and kept wrong group permissions, this can exceed quota but we have overnight scripts which fix group permissions so it can look good again next morning.

    • dusage can indicate that you are above quota although du may show that there are almost no files or data used: the reason is that moving files does not change ownership and in this case du and dusage can give a different information. Only dusage gives you reliable information about how your quota is affected.

  • Recovery on Fram and Saga:

    • Moving files to project data or $USERWORK may not be enough since mv preserves group permissions. Therefore you have the following options:

      • Copy files and then carefully delete the files in $HOME.

      • Move files and adjust group permission with chown or chgrp.

      • Move files and wait overnight for our scripts to adjust them for you.

  • Recovery on Betzy:

    • Try to move data from $HOME to project data.

    • Consider using /cluster/work/users/$USER ($USERWORK). But also mind that files older than 21 days might get automatically deleted and no recovery option exists then (auto-cleanup period is at least 21 days and up to 42 days if sufficient storage is available).

    • If the above are not enough or not suitable, contact support and discuss whether it can make sense to increase project or user quota.

  • Recommendations:

    • If you tend to fill up quota in your job scripts, add a dusage at the beginning and at the end of the job script. Having the output will make diagnostics easier. If you don’t dusage right when you run the job, then a job crash and a later dusage may tell different stories.

    • rsync users: Please be careful adjusting the group ownership on Saga and Fram.

Troubleshooting: Too many files/inodes on Fram

Fram has a default 1 million inode quota for each user under /cluster filesystem regardless of project and group inode quota :

                     path    space used    quota (s)    quota (h)    files    quota (s)    quota (h)
-------------------------  ------------  -----------  -----------  -------  -----------  -----------
                /cluster/     247.4 GiB                             70 225    1 000 000    3 000 000
       /cluster/home/****       1.8 GiB     20.0 GiB     30.0 GiB   44 395      100 000      120 000
 /cluster/work/users/****     243.8 GiB                              3 763
/cluster/projects/nn****k     927.4 GiB      1.0 TiB      1.1 TiB  434 697    1 048 576    1 150 976
/cluster/projects/nn****k       2.3 TiB     10.0 TiB     11.0 TiB  665 879   10 000 000   11 000 000
/cluster/projects/nn****k       4.0 KiB      1.0 TiB      1.0 TiB        1    1 000 000    1 000 000

We can think of “inodes” as files or file chunks.

This means that on Fram it is possible to fill the “files”/inode quota by putting more than 1 M files in /cluster/work/users/user although the latter is not size-quota controlled.

To check the number of inodes in a directory and subsequent subdirectories, use the following command:

$ find . -maxdepth 1 -type d -exec sh -c 'echo -n "{}: "; find "{}" -type f | wc -l' \; | sort -n -k2 -r

/cluster/home/user: 75719
/cluster/home/user/.conda: 39222
/cluster/home/user/.rustup: 20526
/cluster/home/user/work: 11983
/cluster/home/user/project: 1134
/cluster/home/user/something: 602

The above command counts the number of files in each directory and lists them sorted with the most numerous directory on top.

Please contact support if you are in this situation and we can then together evaluate whether it makes sense to increase the inode quota for you.

Troubleshooting: Too many files in a Conda installation

  • A Conda installation can fill your storage quota because it can install thousands of files.

  • Recommendation: Do not install a Conda environment into $HOME.

  • Recovery from a $HOME-installed Conda environment:

    • Install a new environment into project data or $USERWORK and then delete the $HOME-installed Conda environment. But also mind that files older than 21 days might get automatically deleted and no recovery option exists then (auto-cleanup period is at least 21 days and up to 42 days if sufficient storage is available).

    • Advanced alternative: Use a Singularity container for the Conda environment.

Changing file ownership on Fram or Saga

Note

This section is not relevant for Betzy as disk quotas on Betzy are based on directories instead of groups.

Since file permissions are persistent across the file system, it might be necessary to manually change the ownership of one or more files. This page will show an example of how to change ownership on a file that was moved from $HOME to $USERWORK in order to update the disk quotas.

In this example we have a file in our $HOME called “myfile.txt” which is 1 GiB in size that we’re moving to $USERWORK for use in a job:

$ ls -l

total 1048576
-rw-rw-r-- 1 username username_g 1073741824 Nov 13 13:11 myfile.txt

$ mv myfile.txt /cluster/work/users/username

By checking our disk usage with dusage we could confirm that the file is still counted towards the $HOME quota. The reason for this is that the file is still owned by the username_g group, which is used for the $HOME quota.:

Files in $USERWORK should be owned by the default user group, in this - the group named username. To change the file group ownership we can use the command chgrp:

$ chgrp username myfile.txt

$ ls -l

total 1048576
-rw-rw-r-- 1 username username 1073741824 Nov 13 13:11 myfile.txt

The file is now owned by the correct group and we can verify that the disk quotas have been updated by running dusage again.