README_DOCKER.md

Working within a Container: Docker/Shifter

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To build the docker image -- called cctbx:latest -- run:

./build_docker.sh

Pre-built docker images can be downloaded form docker hub [here][1], using:

docker pull jblaschke/cctbx:latest

Note: more instructions on using docker here.

Running Docker Containers

Running is easy:

docker run cctbx:latest <args>

and <args> are runtime arguments.

Running within Docker/Shifter Containers

To run the benchmark using Docker, run

docker run cctbx:latest mpirun -n <N MPI> /img/run/index_lite.sh <args>

where <N MPI> is the number of MPI ranks to be used. Note that <N MPI> can either be 1, or it must be greater than 3 as psana2 reserves the first 2 ranks for file IO. <args> are the arguments of index_lite.sh.

Considerations for Shifter

For HPC container runners, like shifter, we should use the host's job runner (instead of just mpirun) to deploy shifter -- i.e. it needs to be invoked outside of the container. In this case, the command above becomes:

srun -n <N MPI> shifter --image=docker:<account>/cctbx:latest /img/run/index_lite.sh <args>

where <account> is the docker-hub account hosting the shifter image. Note that shifter treats images as read-only, hence the command needs to be invoked from the working directory (just like the usual jobscrip).