JuliaCon24 Workshop: Hands-on with Julia for HPC on GPUs and CPUs

Instructors: Carsten Bauer, Ludovic Räss, Ivan Utkin, and Johannes Blaschke (remote).

Where: TU-Eindhoven 0.244

When: July 9th, 1:30 PM (CEST)

More: https://pretalx.com/juliacon2024/talk/NTQZJJ/

Schedule

• Onboarding

  • Introduction
  • NERSC overview
  • Julia + VS Code on Perlmutter

• Introducing the example

  • 2D linear diffusion solver

• Parallelization on Perlmutter

  • Multithreading

    (short break)

  • MPI parallelization

  • GPU acceleration

Prepare for the workshop

To begin with, make sure that you have VS Code installed on your laptop.

VS Code → Perlmutter (via SSH)

1. In VS Code, press F1 and run the Remote-SSH: Open SSH Host... command.
   • If the command isn't available, make sure that Remote - SSH extension is installed (but it should be available out of the box).
2. Enter trainXY@perlmutter.nersc.gov (with trainXY replaced by your training account) and press enter.
3. In the popup input box, enter your password and press enter.

After a second or two, you should have VS Code running on a Perlmutter login node! 🎉

On Perlmutter

1. Clone the workshop materials into $SCRATCH/juliacon24-hpcworkshopby running the following command.

   git clone https://github.com/JuliaHPC/juliacon24-hpcworkshop $SCRATCH/juliacon24-hpcworkshop
   

   • You will always work in this folder ($SCRATCH/juliacon24-hpcworkshop) during the workshop.

2. Run the following commands:

   cd $SCRATCH/juliacon24-hpcworkshop
   ./setup.sh
   

   What does this do? (click me if you're curious)

   • The setup script
     • modifies your $HOME/.bashrc to
       • permanently put your Julia depot onto the parallel file system ($SCRATCH/.julia)
       • auto-load the Julia module when you login (such that the julia command is available)
       • make mpiexecjl available (i.e. modify $PATH)
     • instantiates the Julia environment
     • installs MPI.jl's mpiexecjl wrapper
     • installs a Jupyter kernel (for NERSC's Jupyter hub)

3. !! Before you proceed, restart VS Code !!

   • Close it fully, open it again, and connect to Perlmutter again (see above). Otherwise the .bashrc changes won't be in effect.

4. Let's now turn to the Julia VS Code extension.

   1. Installing the extension
      • Open the extensions view (press CTRL/CMD + SHIFT + X).
      • Search for julia.
      • Click on install.
   2. Pointing it to julia_wrapper.sh
      • Open the VS Code Settings (press CTRL/CMD + ,).
      • Click on the tab Remote [SSH: perlmutter.nersc.gov].
      • Search for Julia executable.
      • Insert /pscratch/sd/t/trainXY/juliacon24-hpcworkshop/julia_wrapper.sh - with trainXY replaced by you training account name - into the text field under Julia: Executable Path.
   3. If ALT/OPTION + J followed by ALT/OPTION + O (or pressing F1 and executing the Julia: Start REPL command) successfully spins up the integrated Julia REPL, you know that the setup is working! 🎉

5. Finally, you should open the workshop directory in VS Code.

   • In the VS Code terminal, run cd $SCRATCH/juliacon24-hpcworkshop followed by code -r .
   • Manual alternative: Click on the green button "Open Folder" (or press CTRL/CMD + O) and enter /pscratch/sd/t/trainXY/juliacon24-hpcworkshop - with trainXY replaced by you training account name.

Help?

Cheatsheets

• Perlmutter cheatsheet
• VS Code cheatsheet

VS Code isn't working for me, what should I do?

As a fallback, you can also try to use Jupyter under https://jupyter.nersc.gov. Just make sure to use the JuliaCon24 HPC Workshop 1.10.4 kernel (open a notebook and select the kernel in the top right corner).

Applying for NERSC Training Account

To get the most out of the workshop, you need to apply for a NERSC training account before the workshop (as early as possible)! The reason for this is that everyone who applies for an account has to be checked, which can take some time (between a few minutes and a week) depending on their personal background (e.g. nationality and affiliation).

Please only apply for an account if you 1) have a workshop ticket and 2) really plan to participate in the JuliaCon 2024 workshop on Tuesday, July 9 in person!

Sign up for an account

To apply for an account:

1. Go to https://iris.nersc.gov/train
2. Fill out the application form with your details and use the training code that you've received by email.
3. Iris will display your training account's login credials only once. Take a screenshot of your login credials, you will not be able to change or recover these after you close this tab!
4. You can already start experimenting once your account has been approved. Your training account will be availabe until July 14th (end of JuliaCon). Accounts get deleted afterwards, so remember to backup your data before July 14th.

If your institution is not listed in the drop down menu at https://iris.nersc.gov/train: Please choose "Training Account Only - Org Not Listed", and put your organization name in the "Department" field next.