Here is a recommended method for building the container with podman and converting it to .sif with singularity
podman build -t gfdlsoftware:2024.01-gcc13 -f Dockerfile-spack202401-rocky8-gcc13.2 | & tee log.log
podman save -o gfdlsoftware_2024.01-gcc13.tar gfdlsoftware:2024.01-gcc13
singularity pull gfdlsoftware_2024.01-gcc13.sif docker-archive:gfdlsoftware_2024.01-gcc13.tar
Here are instructions for using Docker and building a singularity container from the docker daemon
sudo systemctl start docker
sudo docker build -t gfdlsoftware:2024.01-gcc13 -f Dockerfile-spack202401-rocky8-gcc13.2 .
sudo singularity build gfdlsoftware_2024.01-gcc13.sif docker-daemon:gfdlsoftware:2024.01-gcc13
Using apptainer exec requires the user to pass in a PATH and execute
the shell. Here is an example run command
apptainer exec --env PATH=/opt/views/view/bin:/opt/views/view/grace/bin:/opt/spack/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin gfdlsoftware_2024.01-gcc13.sif bash -c 'mpicc --version'
Here is an example that worked on the gaea supercomputer to execute a MPI hello world program
srun -n 256 --mpi=pmi2 apptainer exec -B $PWD --env PATH=/opt/views/view/bin:/opt/views/view/grace/bin:/opt/spack/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin gfdlsoftware_2024.01-gcc13.sif bash -c './mpi_hello.x'
We did not bind MPI, so we needed to use --mpi=pmi2