Create an HPC container(AMREX) and run with MPI on a GEC cluster

https://tin6150.github.io/psg/blogger_container_hpc.html

One of the most important things for HPC is MPI support. Singularity container was well tested to run applications on a cluster.

Here are the basic steps:

1. Build a Singularity recipe that has dependencies installed, and build it locally. Example:

   build amrex.img using amrex.conf

2. Move it to your cloud cluster. Example for Google Cloud:

   gcloud compute scp amrex.img $usernameb@elasticluster:/home/$username/
   

3. Treat it like an executable and then run the container on the cloud with mpi with any needed binds.

   $ export I_MPI_FABRICS=shm:tcp
   $ export I_MPI_DEVICE=ssm
   $ mpirun -hostfile nodelist -n 4 -ppn 1 -genv OMP_NUM_THREADS=40 ./amrex.img