03_disk_areas.md

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theme: csc-eurocc-2019
lang: en

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Disk areas in CSC's HPC environment {.title}

In this section, you will learn how to work in different disk areas in CSC's HPC environment


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Overview of disk areas

• Main disk areas and their specific uses on Puhti and Mahti

  • See here for information about the disk areas on LUMI

• Moving data between supercomputers

• Understanding quotas (available space and number of files) of different disk areas

• Additional fast disk areas

Disk and storage overview

Main disk areas in Puhti/Mahti

• Home directory ($HOME)

  • Other users cannot access your home directory

• ProjAppl directory (/projappl/project_name)

  • Shared with project members

  • Possible to limit access (chmod g-rw) to subfolders

• Scratch directory (/scratch/project_name)

  • Shared with project members

  • Files older than 180 days will be automatically removed

• These directories reside on the Lustre parallel file system

• Default quotas and more info in disk areas section of Docs CSC

Moving data between and to/from supercomputers

• Puhti and Mahti have separate file systems

• Data can be moved between the supercomputers

  • directly with rsync

  • via Allas object storage

• There are many ways to transfer data between the CSC supercomputers and your local computer

Displaying current status of disk areas

• Use the csc-workspaces command to show available projects and quotas

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Disk and storage overview (revisited)

Additional fast local disk areas

• $TMPDIR on login nodes

  • Each of the login nodes have 2900 GiB of fast local storage in $TMPDIR

  • The local disk is meant for temporary storage (e.g. compiling software) and is cleaned frequently

• NVMe disks on some compute nodes on Puhti and Mahti

  • Interactive, I/O and GPU nodes have fast local disks (NVMe) in $LOCAL_SCRATCH

  • You must copy data to and from the fast disk during your batch job since the NVMe is accessible only during your job allocation

  • If your job reads and/or writes a lot of small files, using this can give a huge performance boost!

What are the different disk areas for?

• Allas -- for data which is not actively used

• $HOME -- small, only for the most important (small) files, personal access only

• /scratch -- main working area, shared with project members, only for data in active use

• /projappl -- not cleaned up, e.g. for shared binaries

• Login node $TMPDIR -- compiling, temporary storage, fast I/O

• Compute node NVMe $LOCAL_SCRATCH -- fast I/O in batch jobs

Best practices

• None of the disk areas are automatically backed up by CSC, so make sure to perform regular backups to, e.g., Allas

• Don't run databases or Conda on Lustre (/projappl, /scratch, $HOME)

  • Containerize Conda environments with Tykky and use other CSC services like Pukki, cPouta or Rahti for databases

• Don't create a lot of files, especially within a single folder

  • If you're creating 10 000+ files, you should probably rethink your workflow

• Consider using fast local disks when working with many small files

• Lustre best practices and efficient I/O in high-throughput workflows