Podman in HPC environments

By Adrian Reber GitHub Twitter

A High-Performance Computing (HPC) environment can mean a lot of things, but in this article I want to focus on running Message Passing Interface (MPI) parallelized programs with the help of Podman.

The following is a simple MPI based example taken from Open MPI: ring.c

To use it on a Fedora 30 system I first installed Open MPI and then I compiled the example:

$ sudo dnf install openmpi-devel
$ module load mpi/openmpi-x86_64
$ echo "module load mpi/openmpi-x86_64" >> .bashrc
$ mpicc -o ring ring.c

Running this on my test system (Fedora 30) with 4 CPUs gives me this:

$ mpirun ./ring
Rank 3 has cleared MPI_Init
Rank 1 has cleared MPI_Init
Rank 2 has cleared MPI_Init
Rank 0 has cleared MPI_Init
Rank 1 has completed ring
Rank 2 has completed ring
Rank 3 has completed ring
Rank 0 has completed ring
Rank 3 has completed MPI_Barrier
Rank 1 has completed MPI_Barrier
Rank 0 has completed MPI_Barrier
Rank 2 has completed MPI_Barrier

To be able to use Podman in combination with mpirun I created a container with the following definition:

$ cat Dockerfile
FROM registry.fedoraproject.org/fedora:30

RUN dnf -y install openmpi && \
    dnf clean all

COPY ring /home/ring

After building the container (podman build --tag=mpi-test:31 .) I pushed the container to the quay.io container registry (podman push mpi-test:31 quay.io/adrianreber/mpi-test:31) and can now pull it like this:

$ podman pull quay.io/adrianreber/mpi-test:30

And then I can run mpirun to start multiple containers. In my case 4 containers are started as each of the two involved systems has 2 CPUs:

$ mpirun --hostfile hostfile \
   --mca orte_tmpdir_base /tmp/podman-mpirun \
   podman run --env-host \
     -v /tmp/podman-mpirun:/tmp/podman-mpirun \
     --userns=keep-id \
     --net=host --pid=host --ipc=host \
     quay.io/adrianreber/mpi-test:30 /home/ring
Rank 2 has cleared MPI_Init
Rank 2 has completed ring
Rank 2 has completed MPI_Barrier
Rank 3 has cleared MPI_Init
Rank 3 has completed ring
Rank 3 has completed MPI_Barrier
Rank 1 has cleared MPI_Init
Rank 1 has completed ring
Rank 1 has completed MPI_Barrier
Rank 0 has cleared MPI_Init
Rank 0 has completed ring
Rank 0 has completed MPI_Barrier

Now mpirun starts up 4 Podman containers and each container is running one instance of ring. All 4 processes are communicating over MPI with each other.

The following mpirun options are used:

• --hostfile hostfile

  The hostfile tells Open MPI on which systems to run how many processes. In the case of this example it contained:

  host1 slots=2
host2 slots=2

  This means to run two processes on host1 and two processes on host2.

• --mca orte_tmpdir_base /tmp/podman-mpirun

  This tells Open MPI to create all its temporary files in /tmp/podman-mpirun and not in /tmp. If this is not specified Open MPI will create its temporary files in a directory with a host name in it in /tmp and if using more than one node this directory will be named differently on other nodes. This requires mounting the complete /tmp directory into the container which is a bit more complicated due to not being able to change SELinux labels of /tmp.

This is it for all the necessary parameters for mpirun, now the command is specified that mpirun should start; podman in this case.

• run

  This just tells Podman to run a container.

• --env-host

  This copies all environment variables from the host into the container. This is necessary to make Open MPI work at all. When mpirun is started it creates a daemon with which all other processes in this MPI job are communicating, it also tells all the MPI processes how to communicate with each other. All this is passed from mpirun to the actual MPI processes using environment variables.

  Options passed from the user to mpirun are also communicated through environment variables. Now that the MPI process in the container has all the environment variables it can communicate with the master process (Head Node Process (HNP)) and all the other involved processes.

• -v /tmp/podman-mpirun:/tmp/podman-mpirun

  This tells Podman to mount the directory where Open MPI creates its temporary directories and files to be available in the container. Through the environment variables from above the MPI process knows where to look for this directory.

• --userns=keep-id

  The user ID in the container should be mapped to the same ID on the outside of the container. This is necessary as all processes are communicating with each other over shared memory and this fails if the processes have different user IDs. Also the access of the temporary files in /tmp/podman-mpirun breaks without this.

• --net=host --pid=host --ipc=host

  Do not use separate namespace for network, PID and IPC. Without this nothing works, as all processes are also communicating via TCP on 127.0.0.1 which fails with separate network namespaces. Shared memory communication will also not work if the processes are not in the same PID and IPC namespace.

• quay.io/adrianreber/mpi-testmpi-test:30

  This is the name of the container as downloaded previously with podman pull. If mpirun will spawn processes on a host which has not yet downloaded this container image, Podman will do it before launching this container.

• /home/ring

  The MPI program in the container which should be started.

Thanks to Podman’s fork-exec model it is really simple to use it in combination with Open MPI as Open MPI will start Podman just as it would start the actual MPI application.