Calendário Nacional

Molecular Dynamic (MD) simulations are fundamental to understand the mechanism of biological systems. This workshop aims to provide an introduction on the use and on the features of a well-established and highly used package in the field GROMACS.

The workshop covers an introduction to MD simulation, to accelerated weight histogram methods and to GraphicsGraphical Processing Units (GPU) performance. At the end the participants will be familiar with the features of GROMACS code, and they will be able to set up and perform molecular simulation on the covered topic.
More information: https://www.eventbrite.pt/e/bilhetes-gromacs-workshop-162032753327
https://indico.eurocc.fccn.pt/event/16/

Introduction (Terminology; Parallelization, load balancing; Evaluating program performance; Architectures (Distributed memory, Shared memory, Hybrid systems); Parallel programming (Message passing, MPI; Multithreading, OpenMP; Accelerators, OpenACC); Debugging and Parallel program performance analysis.
https://indico.eurocc.fccn.pt/event/13/

https://www.oblivion.uevora.pt/parallel-i-o-and-data-formats/

Syllabus: Storage filesystems; I/O strategies (one process, task-localfiles, shared files) and workflow; Parallel I/O software
stack; MPI I/O; Portable data formats (HDF5, parallel NetCDF4).

https://indico.eurocc.fccn.pt/event/7/

Syllabus: Fundamental issues; Agents; Search Strategies for single agent problems. Advanced Search Strategies. Knowledge and Reasoning. Natural computing
https://indico.eurocc.fccn.pt/event/14/

https://www.oblivion.uevora.pt/using-supercomputers-for-scientific-computing/

Syllabus: Introduction to code profiling and refactoring; Profiling tools;Refactoring tools and software; Refactoring analysis;Acceleration techniques; Practical examples using Scalasca, Score-P, Vampir.

https://indico.eurocc.fccn.pt/event/6/