Understanding of HPC Cluster and Its Component

Understanding of HPC Cluster and It's components
HPC Solutions Group © 2012, Centre for Development of Advanced Computing, Pune
Agenda
o Improving computational performance
o Introduction to cluster computing
o Components of a cluster
o Types of clusters
o Question and answer
It’s only human to “want more”
o Unhappy with the computational power at their disposal
o People wish to compress files and folders faster
o Weather forecasting quicker and broader
o Accurate predictions for financial & scientific applications
How to increase computational performance ?
o Work harder - use faster & advanced hardware
o Work smarter - optimize the software subsystem
! ! ! Still unhappy ! ! !
o Get help - processing in parallel is the way to go
Processing in Parallel
Single Processor Parallelism
o Use more pipelines
o Use more cores in same die
o Use of advanced extensions
Multi-Processor Parallelism - Shared memory
o Use of multiple processors to speed up program run-time
o By dividing up the entire computation among the processors
Processing in Parallel - mammoth style
Multi-computer systems - Distributed memory
o Uses several independent computers
o Strong interconnection network
o e.g. Cluster computers
What is a cluster ?
o Group of loosely coupled commodity computers
o Works together to achieve the same goal
o Maintains a Single System Image
o Good computational performance and reliability
o Good for compute Intensive, data or I/O, & transaction
Intensive applications
o Homogeneous cluster and Heterogeneous
o Cost-effective
Components of a cluster computer
Software
Hardware
Network
Storage
Cluster software
Software
o Cluster compatible OS
o Clustering software to generate and maintain a cluster
o Cluster-aware applications
Cluster hardware
o Uses commodity components
o Advanced processors with large cache
o High speed memory
o Advanced chipsets
o Faster I/O subsystem
Cluster network
o High speed
o Low-latency
o Scalable
o Reliable
o Data throughput
o Accelerators
Cluster storage
Scratch disk
o Linear scaling Storage disk
o Extreme bandwidth & I/O Tape storage
o Hierarchical Storage Management
o Single storage pool
o Reliable
Types of cluster computers
o LBC : Load balancing cluster
o HTC : High throughput computing cluster
o HAC : High availability computing cluster
o HPC : High performance computing cluster
Overview of Load balancing cluster
Overview of HTC cluster
o Focuses on completing more computations as possible
o Make use of all available computing platforms
o May have high latency network
o May have heterogeneous nodes
o Opportunistic type
Overview of HAC cluster
Uncertainty
o Failure to prepare is preparing to fail.
Mantra for High availability
o Always avoid Single Point Of Failures (SPOF).
o Redundancy of critical system and equipments
Availability factor
High Availability
“a system or component that is
continuously operational”
Factors affecting High Availability
o MTBF
o MTTR
o Outage
o Downtime( Planned / Unplanned).

Building a HPC Cluster HPC
Components of HPC
o Head node / Master
o Compute node / Slave
o Cluster software
o Cluster interconnect
o Cluster Storage
Software
Hardware Network Storage
Parts list for a simple 1+1 HPC Cluster
Minimum Requirements Slave Nodes

o A Master node o 1 Ethernet Port
o A Slave node o CDROM Drive
o Interconnection network o 256 MB RAM
o Instant Cluster – Live CD
Network
Master Node
o cross over network cable
o 1 Ethernet port
o CDROM Drive
o 256 MB RAM
Components of HPC - Cluster software
o Master – Slave arrangement
o Message passing libraries
o Open Mosix
o Peer to peer process migration
o Dynamic load balancing
clusterknoppix.sw.be
Steps in Building a Manual Cluster
o Identify two or more healthy machines
o Load suitable Linux & packages in to the nodes
o Name the nodes appropriately and modify /etc/hosts of all nodes
o Create a local area network and validate it
o Identify a master node
o Configure SSH and NFS daemon in master
o Configure SSH daemon and NFS mount in slaves
o Create identical user names / password and UID in all nodes
Steps in Building a Manual Cluster Cont...
o Copy ssh keys - password less authentication
o Install mpich in master(use rsh=ssh flag).
o Update 'machines' file and copy mpich to all nodes
o Install SGE, PBS etc for job scheduling
o Install ganglia to monitor the cluster
o Export a NFS partition from the master and mount it in nodes.
o Building a large manual cluster is a na na
Building an experimental cluster using Rocks
Blue print for HAC cluster
Overview of HPC cluster
o Uses advanced processors with large cache
o Uses commodity components
o High speed memory
o Advanced chipsets
o Faster I/O subsystem
o High speed network
o Distributed HPC
o Class 1 / Class 2
Blue print for HPC cluster
System Name : Tianhe-1A

Site : National Supercomputing center in Tianzin
Cores 186368
Memory 229376 GB
R Max GFlops 2566000
R Peak Gflops 4701000
Operating System Linux
Processor : Intel EM64T Xeon X56xx (Westmere-EP) 2930 MHz (11.72
Gflops)
List Rank Rmax (GFlops)
11/2010 1 2.566e+06
K computer, SPARC64 VIIIfx 2.0GHz, Tofu interconnect - Japan
Site: RIKEN Advanced Institute for Computational Science (AICS)
List Rank System Vendor Total Cores Rmax(GFs) Rpeak(GFs) Power (Kw)
11/2011 1 K computer, SPARC64 VIIIfx 2.0GHz, Tofu interconnect Fujitsu 705024 10510000.00 11280384.00
12659.89
06/2011 1 K computer, SPARC64 VIIIfx 2.0GHz, Tofu interconnect Fujitsu 548352 8162000.00 8773632.00 9898.56

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Understanding of HPC Cluster and It's components

o Improving computational performance

o Introduction to cluster computing

o Question and answer

o Unhappy with the computational power at their disposal

o People wish to compress files and folders faster

o Weather forecasting quicker and broader

o Accurate predictions for financial & scientific applications

o Work harder - use faster & advanced hardware

o Work smarter - optimize the software subsystem

o Get help - processing in parallel is the way to go

Single Processor Parallelism

o Use more pipelines

o Use more cores in same die

o Use of advanced extensions

Multi-Processor Parallelism - Shared memory

o Use of multiple processors to speed up program run-time

o By dividing up the entire computation among the processors

Multi-computer systems - Distributed memory

o Uses several independent computers

o Strong interconnection network

o e.g. Cluster computers

o Group of loosely coupled commodity computers

o Works together to achieve the same goal

o Maintains a Single System Image

o Good computational performance and reliability

o Good for compute Intensive, data or I/O, & transaction

o Homogeneous cluster and Heterogeneous

o Clustering software to generate and maintain a cluster

o Uses commodity components

o Advanced processors with large cache

o High speed memory

o Faster I/O subsystem

o Linear scaling Storage disk

o Extreme bandwidth & I/O Tape storage

o Hierarchical Storage Management

o Single storage pool

o LBC : Load balancing cluster

o HTC : High throughput computing cluster

o HAC : High availability computing cluster

o HPC : High performance computing cluster

o Focuses on completing more computations as possible

o Make use of all available computing platforms

o May have high latency network

o May have heterogeneous nodes

o Failure to prepare is preparing to fail.

Mantra for High availability

o Always avoid Single Point Of Failures (SPOF).

o Redundancy of critical system and equipments

“a system or component that is

Factors affecting High Availability

o Downtime( Planned / Unplanned).

o Head node / Master

o Compute node / Slave

Hardware Network Storage

Minimum Requirements Slave Nodes

o Master – Slave arrangement

o Message passing libraries

o Peer to peer process migration

o Dynamic load balancing

o Identify two or more healthy machines

o Load suitable Linux & packages in to the nodes

o Name the nodes appropriately and modify /etc/hosts of all nodes

o Create a local area network and validate it