The following steps illustrate the process of building NAMD 3.0 from the source code. This version is not yet built as a module on Kebnekaise. We will compile NAMD so that has supports for multi-node multi-GPU simulations. The stmv benchmark with 1M atoms performed ~1.3x faster when running it on 2 nodes w.r.t. 1 node case.

Anaconda is a Python distribution. We ask our users to not install Anaconda on our clusters. We recommand that you consider other options like a virtual environment or a Singularity container, for the most complicated cases.

Cluster upgrade to Ubuntu Focal 20.04

This is a description of the upgrade to Ubuntu Focal 20.04 of our cluster and what users may have to do to take advantage of it.

When does it start?

The upgrade will start 2021-04-19.

When is it done?

The upgrade was finished 2021-04-27.

R/RStudio/R packages install on macOS without root permission

We will extract the files from the .pkg and install those

FAQ (Setup/installation problems for the "Scientific Computing in R" course)

Problems related to access rights

Windows

• I am not allowed to install R due to lack of admin rights
  • You may have to do a an additional work-around step to install in a different location than the default.
  • Pick "R for Windows" from the nearest download mirror: UmU | Pick different mirror

Setup and installation of R for the "Scientific Computing in R" course

The purpuse of this documentation is mainly for setting up R, RStudio, and some R package in preparation for the "Scientific Computing in R" course that is given at HPC2N on 27 May 2020.

Before the course, please