Container

Container definition files for Boise State University Research Computing

Notes on specific distributions and applications

Alpine

Building from scratch

An Alpine image can be quickly build from scratch by downloading the minirootfs tarballs in the %setup section. For example, to build from Alpine 3.19.0 on x86_64:

%setup
curl -LO https://dl-cdn.alpinelinux.org/alpine/v3.19/releases/x86_64/alpine-minirootfs-3.19.0-x86_64.tar.gz
curl -LO https://dl-cdn.alpinelinux.org/alpine/v3.19/releases/x86_64/alpine-minirootfs-3.19.0-x86_64.tar.gz.sha512
sha512sum -c alpine-minirootfs-3.19.0-x86_64.tar.gz.sha512
tar -C ${APPTAINER_ROOTFS} -xf alpine-minirootfs-3.19.0-x86_64.tar.gz

Using Alpine edge and community repositories

To change the alpine repostories to use the bleeding edge packages, swap the $MAJOR.$MINOR version to edge:

sed -i 's/v3.19/edge/g' /etc/apk/repositories

To add the testing repository to apk after switching to edge:

tail -n 1 /etc/apk/repositories | sed 's/community/testing/' >> /etc/apk/repositories

R

R packages can be difficult to build, especially with dependencies on various systems. Posit (creators of RStudio) have ppa repositories to help with some of these dependencies, and handles them especially well in conjuction with RStudio server. See the r-spatial build for an example.

Another option that appears to work well is using guix to create a squashfs image directly. There is an HPC/cran channel for guix that mirrors R packages. See the peregrine build for an example.

Issues on Alpine

If you are getting iconv translation errors, set LC_ALL=en_US.UTF-8.

Other pkgconfig and text related issues may be solved by installing common text libraries:

apk add \
    fontconfig-dev \
    freetype-dev \
    fribidi-dev \
    gnu-libiconv-dev \
    harfbuzz-dev

Also, the linux-headers package is frequently needed for packages:

apk add linux-headers

GUIX

In order to use a guix based build, the user should test the environment using guix shell, then dump the channel configuration to a channels.scm file using:

guix describe --format=channels > channels.scm

Then guix time-machine to build the environment/squashfs. The full process may look like:

$ # optional
$ guix pull
$ guix shell bash go
$ # test environment...
$ guix shell --export-manifest shell bash go > manifest.scm
$ # export the current channel definition
$ guix describe --format=channels > channels.scm
$ # test
$ guix time-machine -C channels.scm -- shell -m manifest
$ # build squashfs
$ guix time-machine -C channels.scm -- pack -f squashfs -m manifest.scm

To build a container from the squashfs, simply use the squashfs as the source:

appatiner build --fakeroot x.sif /gnu/store/${guixhash}.squashfs

For simple examples of adding metadata to the container, see peregrine/Makefile