Online training materials

Name	Online training materials
Description	Overview page on online training materials freely available

We provide an overview on publicly available training materials that are available on the web.

Basic use of HPC systems

Overview material about HPC systems

The HPC-Carpentry initiative has online training material for a 1-day introduction to HPC. It covers both Linux command line and SLURM.

UNIX and LINUX

Almost all current HPC system use UNIX or LINUX as their operating system. Basic UNIX/LINUX skills are essential for using such a system:

Texas Advanced Computing Center (TACC) has produced a clear and general set of slides about HPC Linux.

This video about Unix from 1982 is surprisingly relevant today, and can impart an understanding of the underlying philosophy behind the *NIX operating system.

The teaching materials on the UNIX shell of the software carpentry courses are available online. They are suitable for self study.

Job schedulers

SLURM

SLURM is currently the most widely used job scheduler by the SNIC centres. Unless you are using software, whose GUI is well integrated into the scheduler, having some knowledge about it is required when working at a SNIC installation. On the SLURM website you can access the official SLURM documentation an FAQ and (video) tutorials. In addition the SNIC centres provide their own documentation, also describing local customisation:

Programming and code development

Python programming

The teaching materials on Python programming of the software carpentry courses are available online. They are suitable for self study and provide a good introduction for novices.
SeSE course on Python for Matlab users
BioExcel webinars on computational biomolecular research. Topics include best practices for using the Gromacs and CPMD codes.

Statistic package R

The software carpentry course material on the R package provides a first introduction.

Software development tools and helpers

The teaching materials on Version Control with Git of the software carpentry courses provide a good introduction to version control and the git package.
NeIC's CodeRefinery lessons on version control with Git, automated testing, CMake, etc.
ARM provides video demos and tutorials for the DDT debugger and MAP performance profiler components of the Forge suite, for which SNIC has licenses.

Parallel programming

General HPC training material from PRACE
General HPC training material from XSEDE

Distributed memory programming with MPI

For MPI related training and documents see the resource section of our MPI page

Shared memory programming with OpenMP

For OpenMP related training materials refer to the resource section of the OpenMP page.

GPU programming

Online tutorials from Oak Ridge National Laboratory

Software

CESM (Community Earth System Model)

Link to material including practical sessions from the 2016 CESM Tutorial run by UCAR. See also Building CESM models on the NSC triolith system

CHARMM (Chemistry at HARvard Macromolecular Mechanics)

Documentation of CHARMM.
Full example of a CHARMM simulation setup for a solvated protein.

CP2K

Linkto HOWTOs

GULP

Link to online manuals

GROMACS

Tutorial section of the GROMACS website
GROMACS tutorials by Justin A. Lemkul from Virginia Tech

NAMD & VMD

collection of tutorials of TCBG website. Both NAMD and VMD tutorials are presented on this link.

OpenFOAM

Link to material from CFD course given in Chalmers.

Quantum Espresso

Link to the Quantum Espresso web page for tutorials and lectures from workshops.

VASP

Link to 3-day VASP workshop at NERSC 2016, including videos of presentations and slides.

WIEN2k

Link to material from WIEN2k workshop 2016 at McMasters University, with videos and presentation slides.

WRF ARW (Weather Research and Forecasting Model)

Link to WRF ARW online tutorial made available by UCAR. See also Building and testing WRF on Triolith.