Create a Singularity container from a Singularity script using a remote build from Rackham¶
There are multiple ways how to create a Singularity container.
This page shows how to do so using a remote build from Rackham.
Building images on Rackham¶
On Rackham, the singularity capabilities are instead provided by Apptainer. The differences are beyond the scope of this material, but you can safely assume you are working with Singularity. Apptainer, also allows you to build containers without sudo/administrative rights. In most of the cases, you can simply start building directly without sudo i.e. singularity build myimage.img examples/ubuntu.def. Here are some precautions that will allow you to safely build images on Rackham.
# Change to fit your account
PRJ_DIR=/crex/uppmax2022-0-00
# Singularity
export SINGULARITY_CACHEDIR=${PRJ_DIR}/nobackup/SINGULARITY_CACHEDIR
export SINGULARITY_TMPDIR=${PRJ_DIR}/nobackup/SINGULARITY_TMPDIR
mkdir -p $SINGULARITY_CACHEDIR $SINGULARITY_TMPDIR
# Apptainer
export APPTAINER_CACHEDIR=${PRJ_DIR}/nobackup/SINGULARITY_CACHEDIR
export APPTAINER_TMPDIR=${PRJ_DIR}/nobackup/SINGULARITY_TMPDIR
mkdir -p $APPTAINER_CACHEDIR $APPTAINER_TMPDIR
# Disabling cache completelly - perfect when you only need to pull containers
# export SINGULARITY_DISABLE_CACHE=true
# export APPTAINER_DISABLE_CACHE=true
Procedure¶
The remote builder service provided by Sylabs also supports remote builds through an API. This means you can call on it from the shell at UPPMAX.
Using this service also requires you to register/log in to the Sylabs cloud service. To use this, simply run
and you should see
if you visit that link and give a name, a text-token will be created for you. Copy and paste this to the prompt at UPPMAX. You should see
once you've done this, you can go on and build images almost as normal, using commands like
which will build the container from testdefinition.def remotely and transfer it to your directory, storing it as testcontainer.sif.
Could you give an example script?
A sample job script for running a tool provided in a container may look like
#!/bin/bash -l
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 0:30:00
#SBATCH -A your-project
#SBATCH -p core
cd /proj/something/containers
singularity exec ./ubuntu.img echo "Hey, I'm running ubuntu"
singularity exec ./ubuntu.img lsb_release -a
singularity run ./anotherimage some parameters here
./yetanotherimage parameters