HPC File Systems and Storage

Irena Johnson University of Notre Dame

Center for Research Computing

HPC (High Performance Computing)• Aggregating computer power for higher performance than

that of a typical desktop computer/workstation for solving large problems in science, engineering, business

• Large systems perform calculations • Data access is critical

HPC: • Compute node • Head node • File System • Storage • Networking

File

Collection of data/information: • Document • Picture • Audio or video stream • Application • Other collection of data

Metadata The information that describes the data

contained in files:

• Size • Date created • Date modified • Location on disk • Permissions (who can view/modify your file)

File SystemDefinition from TLDP (The Linux Documentation Project): "On a UNIX system, everything is a file; if something is not a file, it is a process*.”

Many Types of File Systems • Not all file systems are equal • Designed for different uses • Data is organized in different ways • Some are faster than others • Some are more robust/reliable • Some support large storage drives

*Process - a task (a process is started when a program is initiated)

UNIX/Linux File System • Hierarchical file structure

• Tree-structured file system (upside down tree)

• Everything starts from the root directory / and expands into sub-directories and so forth

• Unlike Windows which uses ‘drives’

UNIX/Linux File System

/

/boot//bin/ /dev/ /etc/ /home/ /lib/ /media/ /mnt/ /opt/ /proc/

/bea/ /ed/ /jen/

UNIX/Linux File System

Serial File System (Traditional) • A single server controls the users and data • Can be faster for one user • No redundancy • Simple

UNIX/Linux File SystemDistributed / Parallel File System • Data is spread out across many systems on a network • Single shared global namespace • Supports multiple users (can be distributed) • Supports high bandwidth • More storage than on a single system • Fault tolerant • Reliable • Scalable • Complex

Parallel File SystemClientsClientsClients

Metadata serversMetadata servers

Metadata

Storage Devices

Parallel Read/Write

Management

Parallel File System• Breaks up a data set and distributes (stripes), the blocks to

multiple storage drives (local and/or remote servers). • Users do not need to know the physical location of the data

blocks to retrieve a file. • Data access is done via a global namespace. • A metadata server stores the file name, location, owner,

access permissions. • Reads and writes data to distributed storage devices using

multiple I/O paths concurrently. • Capacity and bandwidth can be scaled. • Storage - high availability, mirroring, replication, snapshots.

File Systems at CRCAFS (Andrew File System) • Developed in 1982, part of the Andrew project at Carnegie

Mellon University. • Named after Andrew Carnegie and Andrew Mellon • Client-server architecture • Federated file sharing • Provides location independence • Scalable • Secure (Kerberos for authentication and ACL - access control

lists on directories for users and groups) • Available for a wide range of heterogeneous systems - UNIX/

Linux,  MacOS X, and Microsoft Windows

File Systems at CRCPanasas - High Performance Parallel scratch File System

/scratch365

• Parallel access to data • Data is striped across multiple storage nodes, providing

increased capacity and/or performance • Concurrent reading and writing (scalable performance to

individual files) • Global Namespace - all compute nodes accessing the storage

see the same namespace (same name and pathname); management is done through one system only

Overview CRC File SystemsPurpose File System Type, Full Name File Access Space Available Aggregated bandwidth (approx.)

Globally accessible home and project directories

User’s Home Directories

AFS - crc.nd.edu/afs/crc.nd.edu/user/first/netid

Directly using OpenAFS client (open source)$HOME

100GB - 2TB volume

up to 70-85  MB/sec per node - Approximately 200 MB/sec aggregated using multiple nodes

Group Directories AFS crc.nd.edu/afs/crc.nd.edu/group/

Directly using OpenAFS client

100GB - 2TB volume

Pseudo-temporary File System

Panasas High Performance Parallel scratch file system

/scratch365/netid Directly using Panasas proprietary pants client

500GB - 1TB 70-90 MB/sec per node with 1 Gb network

Local File Systems

Node local temporary scratch file system

Local disks /scratch (link to /tmp)

Directly - shared with other users on node

R815 - 500GB

HP DL160 -d6copt - 100GB

IBM/Lenovo nx360M4 -400GB

Daccssfe - 5TB

R815-H700 RAIDctrl -250-300 MB/sec

HP DL160 -d6copt 50-60 MB/sec

IBM/Lenovo 90-100 MB/sec

daccssfe - 800-1,000 MB/sec

RAIDRedundant Array(s) of Inexpensive/Independent Disks

• Physical disks bound together with hardware or software • Used to create larger filesystems out of standard drive technology • Configurations optimize cost vs capability

RAID Levels: 0, 1, 3, 4, 5, 6, 0+1, 1+0

• RAID 0 - striped (performance and capacity) • RAID 1 - mirrored (read performance, fault tolerance FT) • RAID 5 - striped with distributed parity (performance, capacity, FT N+1) • RAID 6 - striped with distributed parity (performance, capacity, FT N+2)

https://searchstorage.techtarget.com/definition/RAID

Data Storage

• How information is kept in a digital format that may be retrieved later

• Computers/Laptops/Tablets/Smartphones/other devices - all store data

• Hard drive/disk/flash drive/SSD (solid state data)/cloud • Is not the same as RAM memory

* Hard drive - think long term memory * RAM - think short term memory

Data Storage Types

•File-based storage •Block-based storage •Object-based storage

File Storage• Also called file-level or file-based storage • You use file storage when you access documents/pictures

saved in files on your computer • Data is stored as a single piece of information inside a file, inside

a directory • A single path to data • Hierarchical in nature (called tree-structured system) • Oldest type of storage • Inexpensive • Simple

Block Storage• Breaks a file into individual blocks of data • The blocks are stored as separate pieces of data • No need for file-folder structure because each block of data has

a unique address • The smaller blocks of data spread out to where is most efficient • The storage system software pulls all the blocks back together

to assemble the file when accessed • The more data you need to store, the better

Block Storage• Used in storage-area network (SAN) environments where data is

stored in volumes (blocks) • Data is divided into blocks (can be different sizes) which are

stored separately on hard drive(s) • Consistent I/O performance, low latency connectivity • More expensive, complex • Good for data that has to be frequently accessed and updated • Usage examples: database storage; applications like Java

Object Storage• Also called object-based storage • Files are broken into units called objects and spread out among

hardware • The objects are kept in a single repository, instead of being kept

as files in directories or as blocks on servers • The blocks of data that make up a file, the metadata is kept into

a storage pool • Unique identifier assigned to the object • Cost efficient: you only pay for what you use • Usage examples: big data, web applications, backup archives • Good for data that doesn’t need to be modified (just READ)

File/Block/Object Storage ComparisonFile-based storage Block-based

storageObject-based storage

Transaction units Files Blocks Objects

Protocols CIFS, NFS SCSI, FiberChannel, SATA

Web services (XML-based messaging)

Metadata File-system attributes

File-system attributes

Custom metadata

Recommended for Shared file data Transactional data, frequently changing data

Static file data, cloud storage

Strength Simplified access and management of shared files

High performance Scalable, distributed access

SAN (Storage Area Network)• dedicated high-speed network that interconnects and shares

pools of storage devices to multiple servers • each server accesses the shared storage as if it were directly

attached to it • raw storage is treated as a pool of resources which can be

centrally managed and allocated • highly scalable - capacity can be added as needed • disadvantages: cost and complexity

ClientsClientsClients

Metadata server

Storage

Network

Network

NAS (Network Attached Storage)• dedicated file storage device that provides nodes within same

network file-based storage via Ethernet connection • storage appliance, connected to a network switch • reliable, flexible • highly scalable network storage • speed

ClientsClientsClients NAS Storage

Network Network

Panasas - object-based storage cluster• Performance

improves with scale - linear scalability

• Data protection improves with scale

• Scalable storage - easy to access, deploy and manage

Panasas - ActiveStor• Parallel scale-out NAS storage appliance • Complete hardware and software storage solution

• Implements: • Parallel, object-based filesystem • Global namespace • Strict client cache coherency

• Network Attached Storage (NAS) - Panasas DirectFlow (pNFS, CIFS, NFS) - rpm package for Linux (also MAC OS supported)

• Scale-out NAS - serving parallel access to data (data is striped across multiple storage nodes, providing increased capacity and/or performance)

• Parallel File System - concurrent reading and writing (data for a single file is striped across multiple storage nodes to provide scalable performance to individual files)

• Global Namespace - all compute nodes accessing the storage see the same namespace (same name and pathname); management is done through 1 system only

Panasas1 node of Panasas architecture ActiveStor16

Hybrid - Storage media is a combination of HDD and SDD: - Hard Drives - for larger files - SSD (Flash) - for small files or metadata (no moving parts - “solid” state)

Scalable data solution Redundant power modules - two Redundant battery module (power backup) Redundant switch modules (connected to the network, provide access to storage)

Storage blade: 2 HDD, 1 Flash, CPU, RAM Mem Director blade: serves File system metadata, legacy protocol (NFS, CIFS) 1 shelf = 1 Director Blade + 10 Storage Blades

Panasas

Storage blade: 2 HDD, 1 Flash, CPU, RAM Mem Director blade

1. Serves File System metadata (file’s location, owner, permissions, size of file)

2. The gateway to the storage for standard legacy protocols (NFS, CIFS)

DirectFlow - direct access between compute clients and storage

Panasas at CRCActiveStor16 - 7 Shelves: - 2 Director Blade per shelf - 9 Storage Blades per shelf

Total Director Blades: 14 Total Storage Blades: 63

Total Capacity 771.12 TB Data space Used 296.02 TB Metadata Used 8.59 TB Free Space 437.04 TB