Crash course for the computational scientists

Scientific Computing in Practice: Summer Kickstart 2018

Part of Scientific Computing in Practice lecture series at Aalto University.

Audience: Aalto employees and students looking for an extensive intro into computational resources available to Aalto people.

About the course: three days kickstart for Aalto researchers to get started with the available HPC computational resources at Aalto and CSC. The course is modular, we cover one by one several aspects. First day dedicated to the computational resources in general: one will get whole picture what computational resources are available in particular what is HTCondor, what CSC has to offer and how to access a Triton cluster at Aalto. The day two is focused on Triton usage practicalities, given in the hands-on style tutorial, there will be lot of practical things on how to get started on Triton. The third day, the last one, will cover Triton advances, like running in parallel, troubleshooting, building your code etc. During the course there will be particular use cases like examples in Matlab, R, Python.

Overall we give you hints, ready solutions and copy/paste examples on how to compile, run and monitor your applications. In addition to how to optimize your workflow in terms of filesystem traffic, memory usage etc.

The course is obligatory for all new Triton users and recommended to all interested in the field.

Time, date: Mon 11.6 — Wed 13.6, from 10:00 – 15:30 all days

Place: U1, Main building, Otakaari 1M

Days’ time schedule is flexible, here is the tentative plan. 30 minutes break around 12:00, plus short 10 minutes breaks in between. You will be given time to try and ask, it’s more like an informal help session to get you started with computing resources.

BTW, HPC stands for High Performance Computing

Day #1:

  • Module #1.1 (1.5h): HPC crash course: what is behind the front-end // lecture

HPC fundamentals: terminology, architectures, interconnects, infrastructure behind, as well as MPI vs shared memory // Ivan Degtyarenko

HPC crash course 2018 (PDF)

  • Module #1.2 (2h): CSC resources overview // lecture with demos

An overview of CSC computing environment and services including Sisu/Taito, storage, Cloud services, notebooks, containers, etc // Atte Sillanpää, Shubham Kapoor

CSC overview (external link, PDF)

  • Module #1.3 (1h): HTCondor setup at Aalto // lecture with demos

Did you know that department workstations around could be accessible for computing? It is were HTCondor comes in game // Jari Varje

HTCondor (PDF), HTCondor examples (ZIP)

  • Module #1.4 (.5h): Connecting to Triton // tutorial

Get connected to Triton in preparation for day 2 // Science-IT staff

See the Connecting to Triton tutorial – if you can ssh to Triton and run “hostname”, you are ready for tomorrow.

Day #2:

  • Module #2.1 (3h): Getting started on Triton, SLURM basics, module // tutorial

Triton’s workflow, running and monitoring serial jobs on Triton. Interactively and in batch mode. module and toolchains, special resources like GPU // Ivan Degtyarenko and Richard Darst

See the Triton tutorials (“connecting” to “running in the queue”)

  • Module #2.2 (2h): SLURM advances // tutorial

Running in parallel with MPI and OpenMP, array jobs, advances with –gres, local drives, constrains // Richard Darst and Ivan Degtyarenko

See the same Triton tutorials (“array jobs” to “GPU computing”)

Day #3:

  • Module #3.0 (2h): Use cases: Matlab, R, Deep Learning, Singularity // live demos

Matlab, R, Deep Learning, containers with Singularity as use cases. Live examples from the real project running on Triton // Simo Tuomisto

Slides (HTML)

Slides (PDF)

  • Module #3.1 (0.5h): Troubleshooting: solving running jobs issues.

Possible issues on Triton and how to resolve them. The session will include hands-on tutorial from the “SLURM advances” // Janne Blomqvist

  • Module #3.2 (1.5h): Code building on Triton // tutorial

Building your software on Triton // Janne Blomqvist

  • Module #3.3 (1h): Profiling and debugging tools on Triton // tutorial

Several tools for code profiling and debugging  // Janne Blomqvist

Homework: SCIP 2018 homework (external link, PDF)

Lectures:

Aalto: Janne Blomqvist (D. Sc.),  Ivan Degtyarenko (D. Sc.), Simo Tuomisto, Richard Darst (D. Sc.), Jari Varje (doctoral candidate)

CSC: Atte Sillanpää (D. Sc.),  Shubham Kapoor (D. Sc.)

Cost: Free of charge for Aalto employees and students.

Registration: closed

Course certificate: Full course correspond roughly to 27 hours (1 ECTS). Course organizers provide a certificate which requires all three days attendance plus homework assignment.

Other comments: Day 2 and 3 parts will include live examples, demos and hands-on tutorials. Participants will be provided with access to Triton for running examples. Participants are expected to bring their laptops with the pre-installed SSH client, configured for using WiFi (preferably Eduroam, otherwise Aalto or Aalto Open).

Additional course info at: Ivan Degtyarenko, ivan.degtyarenko at aalto.fi