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Storage

Karolina cluster provides two main shared filesystems, HOME filesystem and SCRATCH filesystem, and has access to IT4Innovations' central PROJECT storage, as well. All login and compute nodes may access the same data on shared file systems. Compute nodes are also equipped with local (non-shared) scratch, RAM disk, and TMP file systems.

Archiving

Do not use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use the CESNET storage service, which is available via SSHFS. For more information, see the CESNET storage section.

HOME File System

The HOME filesystem is an HA cluster of two active-passive NFS servers. This filesystem contains users' home directories /home/username. Accessible capacity is 31 TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 25 GB per user. Should 25 GB prove insufficient, contact support, the quota may be increased upon request.

Note

The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.

The files on HOME filesystem will not be deleted until the end of the user's lifecycle.

The filesystem is backed up, so that it can be restored in case of a catastrophic failure resulting in significant data loss. However, this backup is not intended to restore old versions of user data or to restore deleted files.

HOME filesystem
Accesspoint /home/username
Capacity 31 TB
Throughput 1.93 GB/s write, 3.1 GB/s read
User space quota 25 GB
User inodes quota 500 k
Protocol NFS

Configuration of the storage:

2x NFS server HPE ProLiant DL325 Gen10 Plus

  • 1x AMD EPYC 7302P (3.0GHz/16-core/155W)
  • 8x 16GB (1x16GB) Dual Rank x8 DDR4-3200 CAS-22-22-22
  • 2x 240GB SATA 6G Read Intensive SFF (2.5in) SC SSD – (HW RAID1)
  • 1x Smart Array E208i-a SR Gen10 (No Cache) 12G SAS Modular LH Controller
  • 1x HPE SN1100Q 16Gb Dual Port Fibre Channel Host Bus Adapter
  • 1x Intel I350-T4 Ethernet 1Gb 4-port BASE-T OCP3 Adapter
  • ILO5
  • 1x InfiniBand HDR100/Ethernet 100Gb 2-port QSFP56 PCIe4 x16 MCX653106A-ECAT Adapter
  • 2x 500W Flex Slot Platinum Hot Plug Low Halogen Power Supply Kit
  • OS: Red Hat Enterprise Linux Server

1x Storage array HPE MSA 2060 16Gb Fibre Channel SFF Storage

  • 1x Base MSA 2060 SFF Storage Drive Enclosure
  • 22x MSA 1.92TB SAS 12G SFF (2.5in) M2 SSD
  • 1x MSA 16Gb Short Wave Fibre Channel SFP+ 4-pack Transceiver
  • Dual-controller, 4x 16Gb FC host interface
  • LAN connectivity 2x 1Gb/s
  • Redundant, hot-swap power supplies

SCRATCH File System

The SCRATCH filesystem is realized as a parallel Lustre filesystem. It is accessible via the Infiniband network and is available from all login and computational nodes. Extended ACLs are provided on the Lustre filesystems for sharing data with other users using fine-grained control. For basic information about Lustre, see the Understanding the Lustre Filesystem subsection of the Barbora's storage documentation.*

The SCRATCH filesystem is mounted in directory /scratch. Users may freely create subdirectories and files on the filesystem. Accessible capacity is 1000 TB, shared among all users. Users are restricted by PROJECT quotas set to 20 TB. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. Should 20 TB prove insufficient, contact support, the quota may be increased upon request.

To find out current SCRATCH quotas, use:

[usr0123@login1.karolina ~]$ getent group OPEN-XX-XX
open-xx-xx:*:1234:user1,...,usern

[usr0123@login1.karolina ~]$ lfs quota -p 1234 /scratch/
Disk quotas for prj 1234 (pid 1234):
Filesystem kbytes quota limit grace files quota limit grace
/scratch/ 14356700796 0 19531250000 - 82841 0 20000000 -

Note

The Scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high-performance access to input and output files. All I/O intensive jobs must use the SCRATCH filesystem as their working directory.

Users are advised to save the necessary data from the SCRATCH filesystem to HOME filesystem after the calculations and clean up the scratch files.

Warning

Files on the SCRATCH filesystem that are not accessed for more than 90 days will be automatically deleted.

SCRATCH filesystem
Mountpoint /scratch
Capacity 1361 TB
Throughput 730.9 GB/s write, 1198.3 GB/s read
PROJECT quota 20 TB
PROJECT inodes quota 20 M
Default stripe size 1 MB
Default stripe count 1
Protocol Lustre

Configuration of the storage:

1x SMU - ClusterStor 2U/24 System Management Unit Storage Controller

  • 5x Cray ClusterStor 1.6TB NVMe x4 Lanes Mixed Use SFF (2.5in) U.2 with Carrier
  • 2x Cray ClusterStor InfiniBand HDR/Ethernet 200Gb 1-port QSFP PCIe4 Adapter (Mellanox ConnectX-6)

1x MDU - ClusterStor 2U/24 Metadata Unit Storage Controller

  • 24x Cray ClusterStor 1.6TB NVMe x4 Lanes Mixed Use SFF (2.5in) U.2 with Carrier
  • 2x Cray ClusterStor InfiniBand HDR/Ethernet 200Gb 1-port QSFP PCIe4 Adapter (Mellanox ConnectX-6)

24x SSU-F - ClusterStor 2U24 Scalable Storage Unit Flash Storage Controller

  • 24x Cray ClusterStor 3.2TB NVMe x4 Lanes Mixed Use SFF (2.5in) U.2 with Carrier
  • 4x Cray ClusterStor InfiniBand HDR/Ethernet 200Gb 1-port QSFP PCIe4 Adapter (Mellanox ConnectX-6)

2x LMN - Aruba 6300M 48-port 1GbE

  • Aruba X371 12VDC 250W 100-240VAC Power-to-Port Power Supply

PROJECT File System

The PROJECT data storage is a central storage for projects'/users' data on IT4Innovations that is accessible from all clusters. For more information, see the PROJECT storage section.

Disk Usage and Quota Commands

For more information about Disk usage and user quotas, see the Barbora's storage section.

Extended ACLs

Extended ACLs provide another security mechanism beside the standard POSIX ACLs, which are defined by three entries (for owner/group/others). Extended ACLs have more than the three basic entries. In addition, they also contain a mask entry and may contain any number of named user and named group entries.

ACLs on a Lustre file system work exactly like ACLs on any Linux file system. They are manipulated with the standard tools in the standard manner.

For more information, see the Access Control List section of the documentation.

Local Filesystems

TMP

Each node is equipped with local /tmp directory of few GB capacity. The /tmp directory should be used to work with small temporary files. Old files in /tmp directory are automatically purged.

Summary

Mountpoint Usage Protocol Net Capacity Throughput Limitations Access Services
/home home directory NFS 31 TB 1.93 GB/s write, 3.1 GB/s read Quota 25 GB Compute and login nodes backed up
/scratch cluster shared jobs' data Lustre 1361 TB 730.9 GB/s write, 1198.3 GB/s read Quota 20 TB Compute and login nodes files older 90 days removed
/tmp local temporary files local ------ ------- none Compute / login nodes auto purged

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