Singularity (since 2021 split into two forks, SingularityCE and Apptainer) is the preferred method for running containers on HPC systems. For laptop and desktop Linux machines, it is often a more user-friendly way of running containers than Docker. Singularity can use existing Docker images.
On Debian and Ubuntu, Singularity is available in the default
repository in the singularity-container package. So installing
Singularity should be as simple as running
sudo apt-get install singularity-container
On Redhat and Centos, Singularity is available through EPEL. The Singularity website has detailed installation instructions.
On HPC systems, if Singularity is available, it is probably installed as a module. Run
module av
and look for singularity.
Once Singularity is installed, the next step is to download and convert the image
singularity pull docker://bootstrapcollaboration/sdpb:master
Depending on your version of Singularity, this will create a file
named sdpb-master.simg or sdpb_master.sif.
If you want to build Singularity image from current sources, you should build Docker image first and push it to local registry:
# Build Docker image
docker build . --tag sdpb
# Run local registry
docker run -d -p 5000:5000 --name registry registry:2.8
# Push to local regisrty
docker image tag sdpb localhost:5000/sdpb:master
docker push localhost:5000/sdpb:master
# Pull from local registry and convert to Singularity image
singularity pull --no-https docker://localhost:5000/sdpb:master
# Stop local registry and remove all data
docker container stop registry && docker container rm -v registry
Singularity should automatically mount your home directory. If your
Singularity image is named sdpb-3.0.0.sif, you can invoke the SDPB
programs by prepending the command with
singularity exec sdpb-3.0.0.sif
So to convert the JSON input file at /home/user/input.json, run the command
singularity exec sdpb-3.0.0.sif mpirun -n 4 pmp2sdp --precision 1024 -i /home/user/input.json -o /home/user/input
This uses 4 cores when running pmp2sdp. You can change that number to match your own machine.
To find a primal-dual solution,
singularity exec sdpb-3.0.0.sif mpirun -n 4 sdpb --precision=1024 -s /home/user/input
In theory, Singularity can be used to run jobs across multiple nodes. We have not been able to make that work yet. So for large, multi-node jobs, it is still recommended to build from source using the instructions in Install.md.