Intro v 2

_episodes/00-why-hpc.md

@@ -1,30 +1,122 @@
 ---
-title: "Introducing High-Performance Computing"
+title: "Why Use a Cluster?"
+teaching: 15
+exercises: 5
 questions:
-- "Why use a large-scale computing system?"
-- "How is using a cluster different than your laptop?"
-keypoints: 
-- "A cluster or distributed system is useful when your computations require more than one computer." 
-- "Because a cluster is distributed, it is only useful for certain types of computational problems."
+- "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 or smaller systems."
+- "The standard method of interacting with such systems is via a command line interface called Bash."
 ---
 
-Topics
+## Why Use These Computers?
 
-When it is appropriate to use a cluster
-
-> ## How can you use a cluster?
-> 
-> Talk to your neighbor about your research.  How does computing 
-> help you do your research?  How could more computing help you 
+> ## What do you need?  
+>
+> Talk to your neighbor about your research.  How does computing
+> help you do your research?  How could more computing help you
 > do more or better research?  
-{: .callout}
+{: .challenge}
+
+Frequently, research problems that use computing can outgrow the desktop
+or laptop computer where they started:
+
+* A statistics student wants to do cross-validate their model.  This involves
+running the model 1000 times -- but each run takes an hour.  Running on their
+laptop will take over a month!
+
+* 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 their computer -- analyzing
+these larger datasets will probably crash it.
+
+* An engineer is using a fluid dynamics package that has an option to run
+in parallel.  So far, they haven't used this option on their desktop, but in
+going from 2D to 3D simulations, simulation time has more than tripled and it
+might be useful to take advantage of that feature.  
+
+In all these cases, what is needed is access to more computers than can be
+used at the same time.  Luckily, large scale computing systems -- shared computing
+resources with lots of computers -- are available at many universities, labs,
+or through national networks.  These resources usually have
+more central processing units(CPUs), CPUs that operate at higher speeds,
+more memory, more storage, and
+faster connections with other computer systems.  They are frequently called
+"clusters", "supercomputers" or resources for "high performance computing" or
+HPC.  In this lesson, we will usually use the terminology of HPC and HPC cluster.  
 
-How is using a cluster different than your laptop?  
+Using a cluster often has the following advantages for researchers:
+
+* **Speed.** With many more CPU cores, often with higher performance specs,
+  than a typical laptop or desktop, HPC systems can offer
+  significant speed up.
+* **Volume.** Many HPC systems have both the processing memory (RAM) and disk
+  storage to handle very large amounts of data. Terabytes of RAM and
+  petabytes of storage are available for research projects.
+* **Efficiency.** Many HPC systems operate a pool of resources that are drawn
+  on by a many users.  In most cases when the pool is large and diverse enough
+  the resources on the system are used almost constantly.
+* **Cost.** Bulk purchasing and government funding mean that the cost to the
+  research community for using these systems in significantly less that it
+  would be otherwise.
+* **Convenience.** Maybe your calculations just take a long time to run or are
+  otherwise inconvenient to run on your personal computer. There's no need to
+  tie up your own computer for hours when you can use someone else's instead.
+
+This is how a large-scale compute system like a cluster can help solve problems like
+those listed at the start of the lesson.  
 
 > ## Thinking ahead
-> How is using a large-scale computing system different 
-> from using your laptop? Talk to your neighbor about some 
-> differences you may already know about, and some 
+>
+> How do you think using a large-scale computing system will be different
+> from using your laptop? Talk to your neighbor about some
+> differences you may already know about, and some
 > differences/difficulties you imagine you may run into.
+{: .challenge}
+
+## On the Command Line
+
+Using HPC systems often involves the use of a shell through a command line
+interface (CLI) and either specialized software or programming techniques.  The
+shell is a program with the special role of having the job of running other
+programs rather than doing calculations or similar tasks itself.  What the user
+types goes into the shell, which then figures out what commands to run and
+orders the computer to execute them.  (Note that the shell is called "the
+shell" because it encloses the operating system in order to hide some of its
+complexity and make it simpler to interact with.)  The most popular Unix shell
+is Bash, the Bourne Again SHell (so-called because it's derived from a shell
+written by Stephen Bourne).  Bash is the default shell on most modern
+implementations of Unix and in most packages that provide Unix-like tools for
+Windows.
+
+Interacting with the shell is done via a command line interface (CLI) on most
+HPC systems.  In the earliest days of computers, the only way to interact with
+early computers was to rewire them.  From the 1950s to the 1980s most people
+used line printers.  These devices only allowed input and output of the
+letters, numbers, and punctuation found on a standard keyboard, so programming
+languages and software interfaces had to be designed around that constraint and
+text-based interfaces were the way to do this.  Typing-based interfaces are
+often called a **command-line interface**, or CLI, to distinguish it from a
+**graphical user interface**, or GUI, which most people now use.  The heart of
+a CLI is a **read-evaluate-print loop**, or REPL: when the user types a command
+and then presses the Enter (or Return) key, the computer reads it, executes it,
+and prints its output.  The user then types another command, and so on until
+the user logs off.
+
+Learning to use Bash or any other shell sometimes feels more like programming
+than like using a mouse.  Commands are terse (often only a couple of characters
+long), their names are frequently cryptic, and their output is lines of text
+rather than something visual like a graph.  However, using a command line
+interface can be extremely powerful, and learning how to use one will allow
+you to reap the benefits described above.  
 
+## The rest of this lesson
 
+Depending on your instructor, you may now cover some
+basic command line skills, or jump right into using a
+cluster!