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README.md

File systems

Eagle has three primary file systems available for compute nodes. Understanding the usage of these is important for achieving the best performance.

NREL file systems

  • Home File System
    • Quota of 50 GB
    • Used to hold scripts, source code, executables
  • Lustre parallel file system: Accessiblle across all nodes. When using this file system please familiarize yourself with the best practices section
    • /scratch/username
    • /projects
    • /shared-projects
    • /datasets
  • Node file system: The local drive on each node, these are accessible only on a given node.
    • /tmp/scratch

For more information on the file systems available on Eagle please see: Eagle System Configuration

Lustre best practices

In some cases special care must be taken while using Lustre so as not to affect the performance of the filesystem for yourself and other users. The below Do's and Don'ts are provided as guidance.

  • Do

    • Use the lfs find
      • e.g.
      lfs find /scratch/username -type f -name "*.py"
    • Break up directories with many files into more directories if possible
    • Store small files and directories of small files on a single OST.
    • Limit the number of processes accessing a file. It may be better to read in a file once and broadcast necessary information to other processes.
    • Change your stripecount based on the filesize
    • Write many files to the node filesystem /tmp/scratch/ this is not a Lustre filesystem. The files can then be added to a tar archive and transferred to the /project/project_name

  • Don't

    • Use ls -l
    • Have a file accessed by multiple processes
    • In Python avoid using os.walk or os.scandir
    • List files instead of using wildcards
      • e.g. don't use cp * dir/
      • If you need to tar/rm/cp a large number of files use xargs or similar.
      lfs find /scratch/username/old_data/ -t f -print0 | xargs -0 rm
    • Have many small files in a single directory
    • Run binary executables from the Lustre filesystem
      • e.g. don't keep libraries or programs in /scratch/username

Useful Lustre commands

  • Check your storage usage:
    • lfs quota -h -u <username> /scratch
  • See which MDT a directory is located on
    • lfs getstripe --mdt-index /scratch/<username>
    • This will return an index 0-2 indicating the MDT
  • Create a folder on a specific MDT (admin only)
    • lfs mkdir –i <mdt_index> /dir_path

Striping

Lustre provides a way to stripe files, this spreads them across multiple OSTs. Striping a large file being accessed by many processes can greatly improve the performace. See Lustre file stripingfor more details.

lfs setstripe <file> -c <count> -s <size>
  • The stripecount determines how many OST the data is spread across
  • The stripe size is how large each of the stripes are in KB, MB, GB

References