The course is over. Thanks a lot to everyone who has participated and helped to make it successful!

Scientific Computing in Practice: kickstart 2015 course

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

Audience: Aalto employees and students looking for extensive intro into scientific computing facilities at Aalto.

About the course: kickstart for Aalto researchers to get started with the available computational resources at Aalto. During the course we will go through introductions to Aalto, CSC and FGI resources. Course is given in the hands-on style tutorial, there will be lot of practical things that you end up trying on your own on the live HPC cluster Triton. We give you hints, ready solutions and copy/paste ready examples on how to compile and run available software, how to optimize, debug and profile your code. Leaving the course you expect to know where and how to run your calculations. In addition to traditional introduction to HPC, this year kickstart will focus on optimizing, profiling and debuging the code as well as on OpenMP programming.

Time, date: Mon 1.6 — Wed 3.6.2015, from 9:00 – 17:00 all days

Place: Otaniemi, Otakaari 3, F239a (that hall next to Kvarkki student restaurant)

Days’ time schedule is flexible, here is the tentative plan. 45 minutes break around 12:15-13:00, plus short 10 minutes breaks in between.

Day #1:

  • HPC resources available to Aalto researcher (jointly with Kimmo Mattila and Tomasz Malkiewicz, CSC)

Will cover HPC fundamentals: terminology, architectures, interconnects, infrastructure behind. We will introduce  CSC resources, Grid facilities and traditionally will stay focus on Science-IT@Aalto and Triton. Optionally, if we are on the schedule, will let you know what is Condor about.

Slides: HPC_introduction (PDF), CSC_resources (PDF), FGI (PDF)

45 minutes break

  • Linux cluster at School of Science: Triton hands-on tutorial

On the second part of the Day #1 we will focus on Triton practicalities. Will be covered environment modules, running jobs with SLURM, filesystems usage, MATLAB runs and GPU computing. Lots of things to try.

Materials: Triton_practicalities (PDF), Triton_Filesystems (PDF), examples and templates for exercises available at

Day #2:

full day, break in between; lots of examples in Python and C, Fortran

  • Advanced practicalities: optimizing, profiling, debugging on Triton (jointly with Richard K Darst)

There will be Scientific Computing related topics like Git, debugging with GDB, profiling Python code, working with Makefiles, optimizition techniques, debugging and profiling parallel apps

Materials: (HTML), (HTML), MPI_profile (PDF)

Day #3:

full day, break in between

  • OpenMP programming (full day by Pekka Manninen, CSC)

The third day tutorial introduces the basics of parallel programming with the OpenMP paradigm. The tutorial consists of lectures and hands-on exercises. After the tutorial the participants should be able to write simple parallel programs and parallelize existing programs with the basic features of OpenMP. No prior knowledge on parallel programming is required, but the participants are assumed to have working knowledge of either Fortran or C programming languages.

Materials: OpenMP_lectures (PDF), OpenMP_exercises (PDF), OpenMP_labs (ZIP)

Lectures: Janne Blomqvist (D. Sc.), Mikko Hakala (D. Sc.), Ivan Degtyarenko (D. Sc.), Simo Tuomisto

Invited Lectures: Richard K Darst, SCI/NBE (D. Sc.), Kimmo Mattila, CSC, Tomasz Malkiewicz, CSC (D. Sc.), Pekka Manninen, CSC (D. Sc.)

Registration: The course is over.

Cost: Free of charge for Aalto employees and students.

Credits (opintopisteet): Course certificate available on request, to be shared at very end of the course. Full course hours correspond roughly to 1 ECTS. Requires all three days attendance.

Other comments: All parts will include live examples, demos and tutotials (!). 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