PDC/PRACE workshop “HPC Tools for the Modern Era”¶
This page contains useful information and links to course material for the PDC/PRACE workshop “HPC Tools for the Modern Era”.
Account and login¶
Please see instructions for acquiring a PDC account and logging in to PDC clusters in the General instructions for PDC courses.
Course material and installation instructions¶
All software needed to participate in the workshop will be provided to course participants as a virtual machine on USB sticks which will be handed out when the workshop starts. However, most of the tools can also be installed directly on your laptop.
Links to the course material and optional installation instructions for all workshop modules (for those who want to install some of the software on their own laptops) are provided here. Note that we strongly recommend all workshop participants to install VirtualBox, see below.
USB sticks containing a virtual machine with Ubuntu 18.04 will be handed out to participants when the workshop starts. The Ubuntu image contains:
Kerberos and SSH configuration to enable login to PDC
Singularity version 2.5.2
A Python environment containing Jupyter Notebooks and other packages
The VM is also available for download on KTH Box.
In order to use this virtual machine (VM) you need to have virtualization software installed on your laptop. We recommend VirtualBox which can be installed on Windows, MacOS and Linux and is available for download here.
The USB sticks with the workshop VM have been formatted with exFAT file system. exFAT is supported on MacOS and Windows, but on some Linux distributions one needs to install additional packages to add exFAT file system support. On Ubuntu, you need to install these two packages to be able to mount the exFAT USB sticks:
$ sudo apt-get install exfat-utils exfat-fuse
In order to import the workshop VM into your VirtualBox application, do the following:
Click the little symbol on the right of the text box and navigate to the USB device.
Continue, and then click
VirtualBox should now start importing the VM, which might take a couple of minutes.
PRACE_Coursein the left menu in order to start the VM.
Kerberos, SSH and Jupyter can be installed on all operating systems, but Singularity requires CentOS or Ubuntu Linux distributions. If you are have MacOS or Windows on your laptop, you will therefore need to install VirtualBox. If you have CentOS or Ubuntu, you may choose to install Singularity directly on your laptop (see below), but we still strongly recommend that Linux users also install VirtualBox as a fallback option if anything doesn’t work as expected.
HPC Tips and Tricks¶
The lesson material can be found at https://pdc-support.github.io/hpc-intro/.
For this lesson you only need a PDC account, a Kerberos installation and SSH configuration to be able to log in to PDC. Further details are provided in the section General instructions for PDC courses.
Jupyter Notebooks on the cluster¶
All lesson material can be found on GitHub: https://github.com/PDC-support/jupyter-notebook. You will be asked to clone it to your home directory at PDC by using the command:
(or by downloading the zip file by clicking the green “Clone or download” button). You can also clone the material to your own laptop if you wish to play around with the notebooks.
It is not essential to install Jupyter Notebooks on your laptop since Jupyter will be run on PDC systems in the workshop. You will however need to set up a Jupyter configuration on the Tegner cluster, set a Jupyter password and generate a self-signed certificate for safe usage of Jupyter on Tegner. Instructions for doing this can be found on this software documentation page.
If you’re interested in using Jupyter outside PDC you can follow these official instructions for installing Jupyter.
All lesson material can be found in a GitHub repository: https://github.com/PDC-support/singularity-introduction. The slides are served on https://gitpitch.com/PDC-support/singularity-introduction#/.
To install Singularity on a CentOS or Ubuntu Linux distribution, follow the instructions in the Singularity documentation.
If you have a MacOS, Windows or a non-CentOS/non-Ubuntu Linux distribution, you will be instructed to use the workshop virtual machine for the Singularity exercises.
Arm Forge will be installed on the workshop virtual machine and no additional software needs to be installed on your laptop.
However, if you prefer you can install the Arm Forge Client on your laptop as well. Ubuntu users are recommended to install the full Arm Forge suite, which also functions as a remote client. Click here to download the Arm Forge installer for Ubuntu, and click here to download the Arm Forge Client installer for Windows. MacOS users are recommended to use the workshop VM.