11-hpc-intro.md

title	teaching	exercises	questions	objectives	keypoints
Why use an HPC System?	15	5	Why would I be interested in High Performance Computing (HPC)? What can I expect to learn from this course?	Be able to describe what an HPC system is Identify how an HPC system could benefit you.	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.

Frequently, research problems that use computing can outgrow the capabilities of the desktop or laptop computer where they started:

• A statistics student wants to cross-validate a model. This involves running the model 1000 times — but each run takes an hour. Running the model on a laptop will take over a month! In this research problem, final results are calculated after all 1000 models have run, but typically only one model is run at a time (in serial) on the laptop. Since each of the 1000 runs is independent of all others, and given enough computers, it's theoretically possible to run them all at once (in parallel).
• A genomics researcher has been using small datasets of sequence data, but soon will be receiving a new type of sequencing data that is 10 times as large. It's already challenging to open the datasets on a computer — analyzing these larger datasets will probably crash it. In this research problem, the calculations required might be impossible to parallelize, but a computer with more memory would be required to analyze the much larger future data set.
• An engineer is using a fluid dynamics package that has an option to run in parallel. So far, this option was not utilized on a desktop. In going from 2D to 3D simulations, the simulation time has more than tripled. It might be useful to take advantage of that option or feature. In this research problem, the calculations in each region of the simulation are largely independent of calculations in other regions of the simulation. It's possible to run each region's calculations simultaneously (in parallel), communicate selected results to adjacent regions as needed, and repeat the calculations to converge on a final set of results. In moving from a 2D to a 3D model, both the amount of data and the amount of calculations increases greatly, and it's theoretically possible to distribute the calculations across multiple computers communicating over a shared network.

In all these cases, access to more (and larger) computers is needed. Those computers should be usable at the same time, solving many researchers' problems in parallel.

Break the Ice

Talk to your neighbour, office mate or rubber duck about your research.

• How does computing help you do your research?
• How could more computing help you do more or better research? {: .discussion }

A Standard Laptop for Standard Tasks

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

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Let's dissect what resources programs running on a laptop require:

• the keyboard and/or touchpad 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:

{% include figure.html url="" max-width="30%" file="/fig/Simple_Von_Neumann_Architecture.svg" alt="Schematic of how a computer works" caption="" %}

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.

{% include figure.html url="" max-width="20%" file="/fig/servers-openclipartorg-ericlemerdy.svg" alt="A rack half full with servers" caption="" %}

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".

{% include figure.html url="" max-width="20%" file="/fig/serverrack-openclipartorg-psteinb-basedon-ericlemerdy.svg" alt="A rack with servers" caption="" %}

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

I've Never Used a Server, Have I?

Take a minute and think about which of your daily interactions with a computer may require a remote server or even cluster to provide you with results.

Some Ideas

• Checking email: your computer (possibly in your pocket) contacts a remote machine, authenticates, and downloads a list of new messages; it also uploads changes to message status, such as whether you read, marked as junk, or deleted the message. Since yours is not the only account, the mail server is probably one of many in a data center.
• Searching for a phrase online involves comparing your search term against a massive database of all known sites, looking for matches. This "query" operation can be straightforward, but building that database is a monumental task! Servers are involved at every step.
• Searching for directions on a mapping website involves connecting your (A) starting and (B) end points by traversing a graph in search of the "shortest" path by distance, time, expense, or another metric. Converting a map into the right form is relatively simple, but calculating all the possible routes between A and B is expensive.

Checking email could be serial: your machine connects to one server and exchanges data. Searching by querying the database for your search term (or endpoints) could also be serial, in that one machine receives your query and returns the result. However, assembling and storing the full database is far beyond the capability of any one machine. Therefore, these functions are served in parallel by a large, "hyperscale" collection of servers working together. {: .solution} {: .challenge }

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