Setup your scientific computing environment

In this series, we setup a Linux environment for scientific computing from scratch and discuss its various aspects.

Series Commands, Codes and Materials

In order to follow the videos more efficiently and reproduce the workflows, you may need the list of commands we have executed in each video. You can find the commands (and other relevant materials) in this GitHub repository.


  1. Introducing “Setup your scientific computing environment” syllabus presentation
  2. Installing Ubuntu inside a VirtualBox virtual machine presentation
  3. Introduction to Linux shell commands in bash presentation
  4. Install programs using package managers: GNU Octave presentation
  5. Install Visual Studio Code and Atom using installer packages and dpkg presentation
  6. Install ParaView, GMSH, and SALOME using precompiled (portable) binaries presentation
  7. Python package managers and Conda environments: Install meshio and Jupyter presentation
  8. Compile programs from source code using GCC, GNU Make, and CMake presentation
  9. Build GNU Scientific Library using Make presentation
  10. Build Mmg mesh generator using CMake presentation
  11. Build CGAL-based programs using CMake presentation
  12. Build OpenLB programs for lattice Boltzmann simulations presentation
  13. Build FreeFEM finite element solver presentation
  14. Build LAMMPS molecular dynamics simulation code and link it to VTK toolkit presentation
  15. Install OpenFOAM computational fluid dynamics (CFD) toolbox and run a sample presentation