Scratch storages

Scratch storage is a storage for temporary files for running job. This storage should be used only during computations and should be freed immediately after your job ends. The location of scratch directory is defined by a system variable SCRATCHDIR. Scratch types

We offer four types of scratch storage:

scratch_local
    available on every node, located on a regular hard disc
    choose this type as a default if you have no reason to do otherwise
    integer type, submitted as scratch_local=10gb
    located in /scratch/USERNAME/job_JOBID
scratch_ssd
    located on a small SSD disc
    ultra fast (compared to local scratch) but smaller in volume
    integer type, submitted as scratch_ssd=1gb
    not available on all computational nodes!
    to check for availability on a particular node, go to https://metavo.metacentrum.cz/pbsmon2/props -> choose a node -> search for scratch_ssd in a grey table
    recommended in jobs where the bottleneck is disc-related operations (applications that create/read a lot of files)
    located in /scratch.ssd/USERNAME/job_JOBID
scratch_shared
    network volume, which is shared between all nodes in a given cluster
    read/write operation slower than on local scratch
    useful if you need to run more than one application that needs access to the same data
    integer type, submitted as scratch_shared=10gb
    not available on all computational nodes!
    to check for availability on a particular node, go to https://metavo.metacentrum.cz/pbsmon2/props -> choose a node -> search for scratch_shared in a grey table
    mounted to directory /scratch.shared/USERNAME/job_JOBID
scratch_shm
    the scratch directory is in the RAM
    fastest, but data on scratch do not survive the end/failure of the job
    use when you need ultra-fast scratch AND when you absolutely don't care about data from failed/killed/ended jobs
    boolean type, submitted as scratch_shm=true
    maximum size of scratch is defined by the mem (memory) parameter
    remember to choose memory large enough (to hold both data in scratch and the actual memory requirements for the job)
    mounted to directory /dev/shm/scratch.shm/USERNAME/job_JOBID

No default scratch

For a batch job, you must set the size and type of scratchdir! There is no default type of scratch.

Directory SCRATCHDIR is not writable, only it’s content is. Therefore, you cannot, e.g. do rm -rf $SCRATCHDIR, but you can rm -rf $SCRATCHDIR/*.

Users should always clear the content of the scratch directory after the job ends to free disc space. Otherwise, this directory will be automatically deleted after 14 days at most (earlier if there is lack of space on disks).

Examples:

Submit batch job with 100 GB scratch on local disc:

qsub -l select=1:ncpus=1:mem=4gb:scratch_local=100gb

Submit the interactive job with 20 GB memory and scratch in RAM:

qsub -I -l select=1:ncpus=1:mem=20gb:scratch_shm=true

Submit batch job with 1 GB of scratch on SSD disc:

qsub -l select=1:ncpus=1:mem=4gb:scratch_ssd=1gb

System variables

SCRATCHDIR
    location of the scratch directory
    echo $SCRATCHDIR
SCRATCH_TYPE
    type of scratch directory
    echo $SCRATCH_TYPE
SCRATCH_VOLUME
    size of the scratch directory
    echo $SCRATCH_VOLUME

Scratch storages

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