Miscellaneous HPC administration infos - EpiModel/EpiModeling GitHub Wiki

Issues with libiconv

The igraph package requires libiconv which is not available on some HPC (Klone at least). It can be loaded with slack load libiconv/zdosouk before running R to install igraph. Not necessary later though.

Run spack load libiconv to get the list of available versions.

Renv Shared Cache

On the HPC we use a shared renv cache to reduce the space used by the packages on the user home directory.

To work this environment variable must be set: export RENV_PATHS_ROOT="/projects/epimodel/renv/", usually in ~/.bashrc

Admin: this folder must exist and be rwx by the whole team

mkdir -p /projects/epimodel/renv
chown -R :epimodel /projects/epimodel/renv
chmod -R g+rwx /projects/epimodel/renv

Updating ARTnet examples

  1. run the script R/A-networks/initialize.R
  2. run epistats <- ARTnet::trim_epistats(epistats)
  3. run `saveRDS(epistats, fs::path(path_to_artnet, "inst", "epistats-example.rds"))
  4. run `saveRDS(netstats, fs::path(path_to_artnet, "inst", "netstats-example.rds"))

Do not trim netstats