Short course on HPC-based Computational Bio-Medicine @ BSC

Room S208 (Barcelona BSC Campus Nord)

Room S208

Barcelona BSC Campus Nord

Vertex Building

The registration to this course is now open. Please, bring your own laptop. All the PATC courses at BSC are free of charge.

Course convener: Mariano Vazquez

Lecturers:  Mariano Vázquez (BSC), Okba Hamitou (Atos), Ricard Borrell (BSC), Diana Fernandez Velez (BSC), Carlos Teijeiro Barjas (SURFsara), Ben Czaja (UvA), Paul Melis (SURFsara), Cristobal Samaniego (BSC), David Oks (BSC), Alfonso Santiago(BSC), Alexander Heifetz (EVOTEC), Andrea Townsend-Nicholson (UCL).

Objectives:The objetive of this course is to give a panorama on the use of HPC-based computational mechanics in Engineering and Environment through the projects BSC are carrying on. This panorama includes the basics of what is behind the main tools: computational mechanics and parallelization. The training is delivered in collaboration with the center of excellence CompBioMed.

Learning outcomes: The course gives a wide perspective and the latest trends of how HPC helps in industrial, clinical and research applications allowing to achieve more realistic multiphysics simulations.  In addition, the student has the opportunity of running Jobs in Marenostrum supercomputer.

Level: INTERMEDIATE: For trainees with some theoretical and practical knowledge

Day 1 (Feb. 11)

Session 1 / 9:00am – 1:00 pm
9:00-9:15 Welcome (Mariano Vázquez, BSC)

9:15-11:00 Compilation and Optimization in the HPC environment (O. Hamitou)

11:00-11:20h Coffee Break

11:20-13:00 Parallel algorithms for Computational Mechanics (Guillaume Houzeaux - Ricard Borrell, BSC)

13:00-14:00 Lunch Break


Session 2 / 2:00pm – 4:00 pm 

14:00-16:00 Data Visulization for Researchers Crash Course (Diana Fernandez Velez, BSC)

16:00-18:00 Visit to MareNostrum


Day 2 (Feb. 12)


9:00-10:50 Introduction to HPC in Computational Modelling (Carlos Teijeiro Barjas, SURFsara)

10:50-11:10h Coffee Break

11:10-13:00 Computational Hemodynamics on HPC (UvA) (Ben Czaja, UvA)

13:00-14:00 Lunch Break


Session 4 / 2:00pm – 6:00 pm (2 h lectures, 2 h practical)

14:00-15:30 Visualization applied to 2D/3D scientific datasets (Paul Melis, SURFsara)

15:30-17:00 Cardiac Modelling (J. Aguado-Sierra)


Day 3 (Feb. 13)


Session 5 / 9:00am – 1:00 pm (4 h lectures)

9:00-11:00 Fluid-Structure Interaction methods for biomechanics (C. Samaniego, D. Oks, A. Santiago)

11:00-11:20h Coffee Break

11:20-13:00 hands-on onFluid-Structure Interaction methods for biomechanics(C. Samaniego, D. Oks)


Session 6 / 2:00pm – 6:00 pm 

14:00-15:00 Introduction to Computer-Aided Drug Design (CADD) and GPCR Modelling (Dr Alexander Heifetz, EVOTEC)

15:00-16:00 Innovations in HPC-training for medical, science and engineering students (Andrea Townsend-Nicholson, UCL)

16:00-16:15 Coffee Break

16:15-18:00 Molecular Medicine: Hands On (Andrea Townsend-Nicholson, UCL)



The agenda of this meeting is empty