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Heterogeneous Cloud Computing for Research
Software Carpentry Bootcamp

SAP Headquarters near London Heathrow


Jul 15-17, 2015

9:00 am - 5:30 pm

Keynote Speaker: Prof. Alexander Wolf

Instructors: Mark Stillwell, Guillaume Pierre, Peter Sanders, Christoph Kleineweber, Diego Scardaci, Enol Fernandez, Gergely Sipos, Alistair Grant

Helpers: Jose Gabriel de F. Coutinho

General Information

This is an open event for researchers from any organisation, public or private.

The FP7 HARNESS project will be hosting a cloud computing focused Software Carpentry bootcamp at the SAP headquarters in Feltham, near London Heathrow. Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing.

This free hands-on workshop is open to researchers from any institution, public or private, and will include task automation, modular programming, and version control, as well as additional modules on cloud computing, including deployment, configuration, and management of virtual machines, programming Maxeler Dataflow Engines, and how to use the EGI Federated Cloud infrastructure for research.

  • Participation is free and open to students and researchers from every organisation, so sign up now!
  • Coffee, lunch, beverages, and snacks will be arranged by SAP and provided to attendees free of charge.
  • Please feel free to pass on this information to anyone who might be able to benefit by attending this bootcamp/workshop.
  • This open event is being hosted by the FP7 HARNESS project as part of its dissemination activity.

Who: The course is aimed at research staff and graduate students who are interested in using cloud computing to further their research.

Where: Clockhouse Place, Bedfont Road, Feltham, Middlesex TW14 8HD. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail m.stillwell@imperial.ac.uk for more information.

Schedule

Day 1

08:30Morning coffee, registration, and software setup
09:00Welcome
09:15Automating tasks with the Unix shell
10:30Coffee Break
11:00Version control with Git
13:00Lunch
14:00HARNESS keynote
14:30Managing Cloud Services with ConPaaS (Presentation)
15:45Coffee Break
16:15Managing Cloud Services with ConPaaS (Practical)
17:45Close

Day 2

09:00Building Programs with Python
10:30Coffee Break
11:00Building Programs with Python
13:00Lunch
14:00Dataflow Programming with Maxeler 1
15:30Coffee Break
16:00Dataflow Programming with Maxeler 2
17:30Close

Day 3

09:00EGI Federated Cloud For Open Science
10:30Coffee Break
09:00EGI Federated Cloud For Open Science
13:00Lunch
14:00Distributed Filesystems with XtreemFS
15:30HARNESS Demo Presentation
15:45HARNESS Videos
16:00Close

Etherpad: https://etherpad.mozilla.org/2015-07-15-feltham.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

The Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Dataflow Programming with Maxeler

  • Introduction to Maxeler Technologies
  • Dataflow engines (DFE) -- What are they and why use them
  • Programming paradigm and workflow
  • Application execution using FPGA-based hardware acceleration
  • Scientific application case studies
  • Creating a DFE kernel
  • Working with streams
  • Debugging

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference...

EGI Federated Cloud For Open Science

  • Introduction to the EGI Federated Cloud
  • Cloud standards
  • Access federated resources
  • Deploying Virtual Machine
  • Contextualise Virtual Machine
  • Attach block storage to Virtual Machine
  • Object Storage
  • PaaS in the EGI Federated Cloud
  • SaaS in the EGI Federated Cloud
  • Reference...

Managing Cloud Services with ConPaaS

  • Deploying and managing cloud services with ConPaaS
  • Reference...

Distributed Filesystems with XtreemFS

  • Introduction to distributed file systems
  • Data distribution and file layouts
  • Replication and snapshots
  • XtreemFS use-cases
  • Setting up an an XtreemFS cluster
  • Reference...

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line
  • Reference...

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser. Once you are done installing the software listed below, please go to this page, which has instructions on how to test that everything was installed correctly. We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by ':q!' (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

nano is the editor installed by the Software Carpentry Installer, it is a basic editor integrated into the lesson material.

Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this.

Mac OS X

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Linux

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Install Git for Windows by downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program.

Software Carpentry Windows Installer

It installs and configures nano (Among other things)

This installer requires an active internet connection.

After installing Git Bash:

Mac OS X

The default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Linux

The default shell is usually bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.8 and higher, install Git for Mac by downloading and running the installer. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.7) use the most recent available installer for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.

Linux

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

Python

Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 2.x and not version 3.x (e.g., 2.7 is fine but not 3.4). Python 3 introduced changes that will break some of the code we teach during the workshop.

We will teach Python using the IPython notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

  • Download and install Anaconda.
  • Download the default Python 2 installer (do not follow the link to version 3). Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

  • Download and install Anaconda.
  • Download the default Python 2 installer (do not follow the link to version 3). Use all of the defaults for installation.

Linux

We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)

  • Download the installer that matches your operating system and save it in your home folder. Download the default Python 2 installer (do not follow the link to version 3).

SSH

SSH stands for Secure Shell; it is a way of accessing remote machines and running commands on them. Some of the exercises will use SSH to access machines with software or hardware resources that cannot be made available locally. Temporary accounts will be provided.

Windows

Download and install PuTTY, following the instructions from the website.

Mac OS X

A command-line ssh client is installed by default on most versions of Mac OS X

Linux

Most distributions use OpenSSH and install the command-line client by default. If the ssh command is not available, then it should be fairly straightforward to install OpenSSH using the operating system's package manager.

MaxCompiler

The Maxeler development module requires the free VMware player.

Windows

Download vmware player 6.0.6 and install from this link.

Download the MaxCompiler VMware image.

Mac OS X

As there is no vmware player available, Mac OS X users should install VirtualBox.

Download the MaxCompiler OVA image.

Linux

Download vmware player 5.0.4 and install from this link.

run the following command to install the bundle:

sudo sh VMware-Player-6.0.6-2700073.x86_64.bundle
Not that you do not need a license key for this free version and this field can be skipped.

Download the MaxCompiler VMware image.

XtreemFS

XtreemFS is a distributed file system consisting of a directory server (DIR), metadata and replica catalogues (MRCs) and object storage devices (OSDs). We will setup an XtreemFS cluster in a virtualised environment using Vagrant and VirtualBox during the workshop.

Windows

Download and install VirtualBox from the VirtualBox website. In the next step install Vagrant using the Windows installer.

Mac OS X

Download and install VirtualBox from the VirtualBox website. In the next step install Vagrant using the Mac OS X installer.

Linux

You can try to install Vagrant and VirtualBox via the package manager of your Linux distribution. E.g. for Debian/Ubuntu run sudo apt-get install vagrant virtualbox. For distributions that do not ship Vagrant and VirtualBox, you find installation instructions on the VirtualBox download page and the Vagrant download page.

After installing VirtualBox and Vagrant you have to download our Vagrantfile. This can also be done by cloning the Git repository: git clone https://github.com/chrkl/xtreemfs-software-carpentry.git. You can initialise the environment by calling vagrant up in the download directory or cloned repository. This step pulls a virtual machine image, starts multiple instances and installs the necessary XtreemFS packages. As this step might take a while and will generate a certain amount of network traffic, we recommend to prepare your environment prior to the workshop. Call vagrant halt to shutdown the VMs again.

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