Why use a Cluster?

Instructor note

Total: 20 min (Teaching:10 min | Discussion: 10 min | Breaks: 0 min | Exercises: 0 min)

Objectives

  • Questions

    • Why would I be interested in High Performance Computing (HPC) ?

    • What can I expect to learn from this course?

  • Objectives

    • Be able to describe what an HPC system is.

    • Identify how an HPC system could benefit you.

  • Keypoints

    • High Performance Computing (HPC) typically involves connecting to very large computing systems elsewhere in the world.

    • These other systems can be used to do work that would either be impossible or much slower on smaller systems.

    • The standard method of interacting with such systems is via a command line interface called Bash.

Welcome to HPC

Exercise

Do you have research problems that require more computing power than your laptop or desktop computer can provide?

Please take a moment to think about this and write down your answer in the collaborative document.

A standard Laptop for standard tasks

Today, people coding or analyzing data typically work with laptops.

A standard laptop


Let’s dissect what resources the programs running on a laptop require: - the keyboard and/or touch-pad is used to tell the computer what to do (Input) - the internal computing resources Central Processing Unit and Memory perform calculation - the display depicts progress and results (Output)

Schematically, this can be reduced to the following:

Schematic of how a computer works


When tasks take too long

When the task to solve becomes heavy on computations, the operations are typically out-sourced from the local laptop or desktop to elsewhere. Take for example the task to find the directions for your next vacation. The capabilities of your laptop are typically not enough to calculate that route spontaneously: finding the shortest path through a network runs on the order of (v log v) time, where v (vertices) represents the number of intersections in your map. Instead of doing this yourself, you use a website, which in turn runs on a server, that is almost definitely not in the same room as you are.

A server


Note here, that a server is mostly a noisy computer mounted into a rack cabinet which in turn resides in a data center. The internet made it possible that these data centers do not require to be nearby your laptop. What people call the cloud is mostly a web-service where you can rent such servers by providing your credit card details and requesting remote resources that satisfy your requirements. This is often handled through an online, browser-based interface listing the various machines available and their capacities in terms of processing power, memory, and storage.

The server itself has no direct display or input methods attached to it. But most importantly, it has much more storage, memory and compute capacity than your laptop will ever have. In any case, you need a local device (laptop, workstation, mobile phone or tablet) to interact with this remote machine, which people typically call ‘a server’.

When one server is not enough

If the computational task or analysis to complete is daunting for a single server, larger agglomerations of servers are used. These go by the name of “clusters” or “super computers”.

A server


The methodology of providing the input data, configuring the program options, and retrieving the results is quite different to using a plain laptop. Moreover, using a graphical interface is often discarded in favor of using the command line. This imposes a double paradigm shift for prospective users asked to

  1. work with the command line interface (CLI), rather than a graphical user interface (GUI)

  2. work with a distributed set of computers (called nodes) rather than the machine attached to their keyboard & mouse

Note

What is an HPC system?

The term HPC system is a stand-alone resource for computationally intensive workloads. They are typically comprised of a multitude of integrated processing and storage elements, designed to handle high volumes of data and/or large numbers of floating-point operations (FLOPS) with the highest possible performance. For example, all the machines on the (Top-500) list are HPC systems. To support these constraints, an HPC resource must exist in a specific, fixed location: networking cables can only stretch so far, and electrical and optical signals can travel only so fast.

The word cluster is often used for small to moderate scale HPC resources less impressive than the Top-500. Clusters are often maintained in computing centers that support several such systems, all sharing common networking and storage to support common compute intensive tasks.

Note

Difference between a HPC computing cluster and the cloud

HPC

Cloud

All computers involved are located in same location (e.g. in the same room)

Computers are located in different regions, which can be in different cities, countries, and continents

All computers are connected to each other with very fast local area network(LAN)

The computers are usually not connected with fast LAN, but some cloud solutions do offer this

All computers involved are architecturally identical and runs the same operating system

Cloud services typically offer machines of many different architecture and operating system

A set of optimised software installed and accessible from all computers

A cloud service typically offers a set of predefined software, but more is up to you to install yourself

All computers have access to shared storage, if you place a file on one machine you can access it from all the other machines

You have to set up shared storage yourself if you need that

All computers have a synchronised clock.

You have to sync the clocks yourself in you create a cluster

A scheduler is involved (see the scheduler lesson

No scheduler by default, but the service might offer you to set up a cluster with a scheduler

A cloud service could have access to a HPC cluster as part of the service as well