General Software Requirements

Many of the hands-on sessions require an active connection to a supercomputer/cluster. All participants should have the following installed on their laptops prior to the hands-on sessions.


SSH and SCP client
  • Windows: we recommend PuTTY for SSH and WinSCP for SCP. Both can be downloaded from here. Alternatively, you can install MobaXterm, which provides both an ssh client and an X Windows environment.
  • Mac OS X / Linux: SSH and SCP clients should be part of the OS and can be installed using the OS's package manager.

X Windows environment

  • Windows: we recommend the following two packages to be downloaded and installed prior to the course:
  • Windows alternative: you could also install MobaXterm, which provides both an ssh client and an X Windows environment.
  • Mac OS X: X11 is no longer installed by default, but can be found here: https://www.xquartz.org; otherwise an optional install of Xcode from the Mac OS X media (CD/DVD) may be required.
  • Linux: nothing to be done if using a GUI version of Linux (e.g. Ubuntu Desktop).

Scientific Visualization

  • Download and install ParaView v5.0.0 found at http://www.paraview.org
    • Select Download tab at top of window
    • Version of ParaView: v5.0
    • Type of Download: ParaView Binary Installers
    • Operating System: <select the appropriate version for your computing environment>
    • File to Download: ParaView-5.0.0-<...>
      Note: this is not a typo, select version 5.0.0
    • Download the executable file; double click to install
  • Tutorial data files can be downloaded from https://web.ics.purdue.edu/~vbyrd/trainingData.html.
    You should download data files from the following sections:
    • ParaView (RectGrid2.vtk, headsq.vti)
    • Getting Your Data into VTK Simple file format (all files in this section).

HPC Python Programming

Although we will be working on Bridges, for the smaller examples, or in case Bridges and Comet are both not available, you will need to have Python installed on your laptop.

  • Distributions such as Anaconda by Continuum Analytics (free) and Enthought Canopy (basic version free, academic license gives access to more features) are a good starting point.
  • Your laptop python environment should have the following packages (in addition to what comes standard with python):
    • numpy
    • scipy
    • matplotlib
    • psutil
    • line_profiler
    • memory_profiler
    • numexpr
    • ipython
    • cython
    • mpi4py
    • ipyparallel (or IPython.parallel if your python version is a bit older)
  • Depending on your python distribution, you can install these from the package manager that comes with it or on the command line with commands like "pip install <packagename>" or "conda install <packagename>". Note that for mpi4py you will need an mpi library installation as well; this may prove hard on Windows machines.

Performance Analysis and Optimization

We are going to do performance measurements on Bridges (or Comet). The measurements will then be analyzed on your laptops using the tools ParaProf and Cube. We will do the analysis on your laptops and not on a remote machine because the network latency will impact responsiveness of GUIs in a way that it is just too slow.
I.e., you need to install ParaProf and Cube on your laptop. Alternatively, you can use the latest VI-HPS Linux Live ISO/OVA for execution within VirtualBox. Both options are described below.

Use Cube and ParaProf from the latest VI-HPS Linux Live ISO/OVA within VirtualBox

Either choose this option or Install Cube and ParaProf on your laptop, see below. You don't need both.

  • Install a 64bit VirtualBox. Linux distributions often provide a ready-to-use package. Packages for various operating systems can be found here.
  • Once installed, download the latest VI-HPS Linux Live ISO/OVA. The lite version will be sufficient for our purpose.
    • If you are going to download the OVA file, you need to do this prior to arriving for the summer school. Don't expect downloading the 4GB OVA via the wireless network to succeed!
    • We will provide a few USB drives containing the OVA. You can do the import using this drives. Please do this prior to the session on Thursday. The drives are exFAT formatted. exFAT is natively supported on Windows and MacOS. On Linux please install support for exFAT (e.g., for Ubuntu you need the packages exfat-fuse and exfat-utils).
  • Import the OVA file into VirtualBox.
    • Note that this requires at least 12GB of free disk space.
  • Boot into the new virtual machine.
    • login: livetau
      password: HPCLinux12!

Install Cube and TAU on your laptop
Either choose this option or Use Cube and ParaProf from the latest VI-HPS Linux Live ISO/OVA within VirtualBox, see above. You don't need both.

  • ParaProf (TAU)
    Download and install TAU, which includes ParaProf, on your laptops. There are installers for Windows and MacOS. The Linux installation from source takes a few steps, see the instructions below, but a full TAU installation is not required. Only the ParaProf analysis tool needs to be installed on laptops. After installation, please start ParaProf to verify the installation was successful.
    Note that an up-to-date version of Java is required to install and run ParaProf on laptops.
    • Java JDK for your platform
    • Windows: tau.exe
    • Mac OS: tau.dmg
    • Linux: tau.tgz
      # linux sample build/install
      cd $HOME
      wget http://tau.uoregon.edu/tau.tgz
tar xzvf tau.tgz
cd tau-2.26.2
./configure
make install
echo 'export PATH=$PATH:$HOME/tau-2.26.2/x86_64/bin' >> $HOME/.bashrc
xterm -e paraprof  # xterm launches a new shell and sources your $HOME/.bashrc
  • Cube
    Download and install Cube on your laptops. There are installers for Windows and MacOS. The Linux installation from source takes a few steps, see the instructions below. After installation, please start Cube/cube to verify the installation was successful.
    • WIndows: cube-4.3.4.exe (MD5sum: 55574082891738c136057158e9ece468)
    • Mac OS: cube-4.3.4.dmg (MD5sum: f44a8ec8cf5e5cdd5987f0285be45f75)
    • Linux: cube-4.3.5.tar.gz (MD5sum: e5dce986e3c6381ea3a5fcb66c553adc)
      # Linux build and install
# you need to have Qt's qmake (or qmake-qt4/5) in $PATH. If this is not the case,
# please install a package like qt5-qmake (depends on your distribution).
wget http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3.5.tar.gz
tar xzvf cube-4.3.5.tar.gz
cd cube-4.3.5
cube_prefix=<choose_cube_prefix>
./configure --prefix=$cube_prefix
make all install
echo 'export PATH=$cube_prefix:$PATH' >> $HOME/.bashrc
      xterm -e cube # xterm launches a new shell and sources your $HOME/.bashrc

Last modified: Tuesday, June 27, 2017, 6:20 PM