HPC2N
High Performance Computing Center North
The aim of the course is to let participants learn how to use NAMD to set up basic molecular dynamics simulations, and to understand typical NAMD input and output files.
OpenMP provides an efficient method to write parallel programs in C, C++ and Fortran. OpenMP programs are suitable for execution on shared memory architectures such as modern multi core systems or a single compute node of the HPC clusters deployed by Lunarc or HPC2N, and within SNIC.
HPC2N is offering an ONLINE introduction course to HPC2N and Kebnekaise.
We begin with a short (optional) introduction to Linux, then continue with an introduction to HPC, HPC2N, and a walkthrough of Kebnekaise, including the GPUs and the KNLs. We then look at the module system and loading the software you need, and how to submit jobs through the batch system.
There will be hands-ons as a part of the course, where the participants get the opportunity to load modules, compile programs, and submit jobs to the Kebnekaise system.
The aim of this ONLINE course is to give an intro to classical Molecular Dynamics (MD) simulations and the combined Quantum Mechanical and Molecular Mechanics (QM/MM) simulations. We will start from scratch by setting a MD simulation, in the first half-day of the course, and then use this system to setup a QM/MM simulation. Regarding the software, we will use VMD, NAMD, ORCA, and GAUSSIAN for the full QM/MM protocol. We will also provide users with a set of best practices to improve the performance of their simulations.
This four-day course will be an introduction to version control, with a focus on Git. It is a SNIC/PRACE course and will be given online, through Zoom.
Some of the main concepts, like repositories, commits, trees, branches, and merges will be covered, as will many of the basic commands, like clone, add, push, pull, commit, and fork.
Message Passing is presently the most widely deployed programming model in massively parallel high performance computing. Message passing is suitable for programming a wide range of current computer architectures, ranging from multi-core desk top equipment to the fastest HPC systems in the world, offering several hundred thousand processing elements.
Organizers: BioExcel Centre of Excellence, Sweden; STFC Daresbury Laboratory, UK; NCSA, Bulgaria; Sofia University, Bulgaria.
The school will be held virtually.
Date: 20-24 September 2021 via Zoom.
NOTE: The course will be online! We will use Zoom.
We begin with a short introduction to Linux, which is what is used on HPC2N's compute clusters, and the vast majority of HPC clusters on the planet. This part is only meant for complete beginners to the Linux operating system, and can be omitted if you are proficient already. See the schedule.
The aim of the course is to provide MD users with a set of best practices to improve the performance of their simulations. This will be accomplished by tuning the appropriate SLURM switches and flags proper to the MD packages.
This course will be two half-days. It will have lectures interspersed with some hands-on sessions where you get to try out what you have just learned.
NOTE: The course will be online!
