HPC Admin Notes

Who this is for: lab members who maintain the shared setup on the RSPH cluster. New members can skip this page. Facts are as of 10/12/26.

Shared Spack instance

R and other tools come from the lab's Spack instance at /projects/epimodel/spack (Spack 1.3.0.dev0), owned by sjennes. Users load it as described in Using R via Spack on the HPC. We do not use Spack environments.

• Spack builds R with --without-recommended-packages, so packages such as Matrix, MASS, lattice, and survival come from each project's renv library, not from R itself.
• Configuration scopes, highest priority first: etc/spack/ in the instance, the user's ~/.spack, the site scope etc/spack/site/, system, and defaults.
• /projects/epimodel/spack/var/spack/repos/builtin is an old Spack 0.x recipe tree (742 MB, 12/4/24) that Spack 1.x does not use.

Package recipes: one clone per user

etc/spack/defaults/base/repos.yaml points the builtin package repository at GitHub with no shared destination, so every user's first Spack command clones spack/spack-packages into ~/.spack/package_repos/ (about 1.2 GB of home quota and two minutes; it also happens inside a job with a fresh home directory). A shared, read-only clone avoids this. It was tested on 10/12/26 with a user-scope repos.yaml pointing at a read-only clone: spack load r@4.6.1 took under a second with no clone, and loaded the same R prefix as before. To set it up at site scope, run as sjennes on the login node:

. /projects/epimodel/spack/share/spack/setup-env.sh
DEST=/projects/epimodel/spack/var/spack/package_repos/spack-packages
COMMIT=63d7f6f57dfce15fd1181436cd7400b1b25663b2   # the commit in use on 10/12/26
SITE=/projects/epimodel/spack/etc/spack/site/repos.yaml
if [ -e "$SITE" ]; then cp -p "$SITE" "$SITE.bak-2026-10-12"; fi
mkdir -p "$(dirname "$DEST")"
git init --quiet "$DEST"
git -C "$DEST" remote add origin https://github.com/spack/spack-packages.git
git -C "$DEST" config feature.manyFiles true
git -C "$DEST" fetch --quiet --depth=2 origin "$COMMIT"
git -C "$DEST" checkout --quiet -b develop "$COMMIT"
git -C "$DEST" config branch.develop.remote origin
git -C "$DEST" config branch.develop.merge refs/heads/develop
chmod -R g+rX,go-w "$DEST"
cat > "$SITE" <<'EOF'
# Shared clone of the builtin package recipes, so users do not each clone
# spack-packages into ~/.spack/package_repos. Owned by sjennes, read-only for
# the group. Update it as sjennes with: spack repo update builtin
repos:
  builtin:
    git: https://github.com/spack/spack-packages.git
    destination: /projects/epimodel/spack/var/spack/package_repos/spack-packages
EOF
chmod 644 "$SITE"
spack config blame repos | grep destination   # should cite etc/spack/site/repos.yaml
spack load r@4.6.1 && type -P R

To undo it, rename etc/spack/site/repos.yaml. Once it is in place, remove the "first Spack command" warning from Using R via Spack on the HPC.

What is installed in the Spack R libraries

Every Spack build of R has its own site library, owned by sjennes and readable by the whole lab. Anything installed there is visible to everyone who loads that R, and R uses it silently when a package is not in the user's or the project's library.

Build	Non-base packages	Notes
r@4.1.2	98, plus 14 stale 00LOCK-* folders	EpiModel 2.2.1
r@4.2.0	142	EpiModel 2.2.1, renv 0.15.5
r@4.2.2	146	EpiModel 2.3.1, renv 0.17.0
r@4.3.0	35	rmarkdown and its dependencies
r@4.2.1, r@4.3.1, r@4.4.0, r@4.4.1, r@4.5.1	1 to 3 each	renv only (none in 4.4.1)
r@4.0.5, r@4.1.3, r@4.3.2, r@4.6.1	0

Do not install project packages into these libraries; projects get theirs from renv.

PNG and JPEG output

capabilities() reports png, jpeg, tiff, cairo, and X11 all FALSE in r@4.6.1 and r@4.5.1, so png() fails and svg() fails, while pdf() works. Users can install ragg 1.4.0 and use ragg::agg_png() (tested); ragg 1.5 and later do not build because the nodes lack libwebp-devel. A permanent fix is to build R with the +X variant (spack install r@4.6.1+X with the same compiler), the recipe's only variant that turns on cairo, libpng, jpeg, and tiff. That build gets a new hash, so R/hpc_configs.R and these pages would need to name it.

renv cache

Each user has their own renv cache in ~/.cache/R/renv (the renv default). There is no shared lab cache.

Housekeeping

• On 10/12/26 we moved two unused items into /projects/epimodel/_retired/2026-10-12/: renv_shared_cache (owner aleguil, 339 MB), an old shared renv cache for R 4.3 only, last written 1/15/24; and the shared/ folder holding compilers.yaml (5/31/22), a Spack 0.x compilers file that Spack 1.x ignores. To restore them, move them back to /projects/epimodel/. Delete the folder after 1/12/27 if nobody has asked for them.

ARTnet example objects

The example epistats-example.rds and netstats-example.rds objects shipped in ARTnet's inst/ folder let people run EpiModelHIV without access to ARTnetData. To rebuild them, run the calls documented in the ARTnet README with network.size = 1e4 (the size of the shipped objects; the README says 1e3), trim epistats, and save both into the package:

library(ARTnet)

epistats <- build_epistats(
  geog.lvl = "city", geog.cat = "Atlanta",
  init.hiv.prev = c(0.33, 0.137, 0.084), race = TRUE, time.unit = 7
)
netparams <- build_netparams(epistats = epistats, smooth.main.dur = TRUE)
netstats <- build_netstats(
  epistats, netparams, expect.mort = 0.000478213, network.size = 1e4
)

epistats <- trim_epistats(epistats)
saveRDS(epistats, "inst/epistats-example.rds")   # from the ARTnet repo root
saveRDS(netstats, "inst/netstats-example.rds")

Do not trim netstats: trim_netstats() drops the main, casual, and one-time target statistics that the models need.