Combating 'Disk quota exceeded'

Owned by UKY CCS RCD
Aug 08, 2024
2 min read

LCC enforces storage quotas, meaning certain directories have an upper limit on how much data you can store in them. If you exceed this limit, you'll receive a 'Disk quota exceeded' error, and your job will crash. You can review the established quotas in our /wiki/spaces/UPR/pages/7669196.

Some applications will invisibly create directories under /home and store large files there. Because /home/$USER has the most strict quotas, this is the most frequent culprit for errors. For example, when running Singularity containers, Singularity will create a /home/$USER/.singularity directory and download large image files which will quickly hit your home quota. But there is a simple solution for this problem.

The solution is to move the directory in question to your /scratch/$USER space, and provide a symlink from home to scratch. This will allow applications to look under /home/$USER but actually be directed to /scratch/$USER where the quotas are much more forgiving. Following is a two-command example of this, using .singularity as a case study.

mv /home/$USER/.singularity $SCRATCH/.singularity
ln -s $SCRATCH/.singularity /home/$USER/.singularity

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For users installing conda packages:

Please do the same as above since conda installs all the packages in your home directory in the folder $HOME/.conda. Since you need conda packages for long term use put them in your shared project space instead of your scratch folder.

Eg: If your shared group project space is /project/xxxx_uksr  then

      mkdir -p /project/xxxx_uksr/$USER/my_conda
      ln -s /project/xxxx_uksr/$USER/my_conda /home/$USER/.conda

     

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For users installing R packages:

Please do the same as above since R installs all the packages in your home directory in the folder $HOME/R. Since you need R packages for long term use put them in your shared project space instead of your scratch folder.

Eg: If your shared group project space is /project/xxxx_uksr  then

      mkdir -p /project/xxxx_uksr/$USER/my_R
      ln -s /project/xxxx_uksr/$USER/my_R /home/$USER/R

Also make sure you load the same R module (eg: module load ccs/conda/r-base-4.0.0) each time if you want to use the R packages that were installed with that version of R.

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For users installing Julia packages:

Please do the same as above since Julia installs all the packages and the registries in your home directory in the folder $HOME/.julia. Since you need Julia packages for long term use put them in your shared project space instead of your scratch folder.

Eg: If your shared group project space is /project/xxxx_uksr  then

      mkdir -p /project/xxxx_uksr/$USER/my_julia
      ln -s /project/xxxx_uksr/$USER/my_julia /home/$USER/.julia

Also make sure you load the same Julia module (eg: module load ccs/julia/1.6.1) each time if you want to use the Julia packages that were installed with that version of Julia.

     

Here are the storage quotas on LCC https://docs.ccs.uky.edu/display/HPC/LCC+storage+Quotas


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