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
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.
Who: The course is aimed at research staff and graduate students who are interested in using cloud computing to further their research.
Contact: Please mail firstname.lastname@example.org for more information.
|08:30||Morning coffee, registration, and software setup|
|09:15||Automating tasks with the Unix shell|
|11:00||Version control with Git|
|14:30||Managing Cloud Services with ConPaaS (Presentation)|
|16:15||Managing Cloud Services with ConPaaS (Practical)|
|09:00||Building Programs with Python|
|11:00||Building Programs with Python|
|14:00||Dataflow Programming with Maxeler 1|
|16:00||Dataflow Programming with Maxeler 2|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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.
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.
nano is the editor installed by the Software
Carpentry Installer, it is a basic editor integrated into the
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.
Kate is one option for
Linux users. In a pinch, you can use
should be pre-installed.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Install Git for Windows by downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program.
It installs and configures
nano (Among other things)
This installer requires an active internet connection.
After installing Git Bash:
The default shell in all versions of Mac OS X is bash, so no
need to install anything. You access bash from the Terminal
/Applications/Utilities). You may want to keep
Terminal in your dock for this workshop.
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
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).
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.8 and higher, install Git for Mac
by downloading and running
After installing Git, there will not be anything in your
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
here. Use the Leopard installer for 10.5 and the Snow
Leopard installer for 10.6-10.7.
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 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).
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.)
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.
Download and install PuTTY, following the instructions from the website.
A command-line ssh client is installed by default on most versions of Mac OS X
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.
The Maxeler development module requires the free VMware player.
Download vmware player 6.0.6 and install from this link.
Download the MaxCompiler VMware image.
As there is no vmware player available, Mac OS X users should install VirtualBox.
Download the MaxCompiler OVA image.
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.
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.