pman

pman, which once stood for process manager, is a Flask application providing an API for creating jobs with various schedulers e.g. Kubernetes, Podman, Docker Swarm, and SLURM. It basically translates its own JSON interface to requests for the various supported backends.

pman is tightly-coupled to pfcon. pman and pfcon are typically deployed as a pair, providing the pfcon service.

Running `pman`

The easiest way to see it in action is to run miniChRIS-docker. The instructions that follow are for pman hackers and developers.

Development

This section describes how to set up a local instance of pman for development.

Using Docker Compose

These instructions run pman inside a container using Docker and Docker Swarm for scheduling jobs. Hot-reloading of changes to the code is enabled.

docker swarm init --advertise-addr 127.0.0.1
docker compose up -d

Using Docker Swarm

To run a full test using docker stack deploy, run the test harness test_swarm.sh.

./test_swarm.sh

Using Podman for Development

pman must be able to schedule containers via Podman by communicating to the Podman socket.

systemctl --user start podman.service
export DOCKER_HOST="$(podman info --format '{{ .Host.RemoteSocket.Path }}')"

Install pman using Python

python -m venv venv
source venv/bin/activate
pip install -r requirements/local.txt
pip install -e .

Run pman using Python in Development Mode

python -m pman

Using Kubernetes via Kind

https://github.com/FNNDSC/pman/wiki/Development-Environment:-Kubernetes

Configuration

pman is configured by environment variables. Refer to the source code in pman/config.py for exactly how it works.

How Storage Works

pman relies on pfcon to manage data in a directory known as "storeBase." The "storeBase" is a storage space visible to every node in your cluster.

For single-machine deployments using Docker and Podman, the best solution is to use a local volume mounted by pfcon at /var/local/storeBase. pman should be configured with STORAGE_TYPE=docker_local_volume VOLUME_NAME=....

On Kubernetes, a single PersistentVolumeClaim should be used. It is mounted by pfcon at /var/local/storeBase. pman should be configured with STORAGE_TYPE=kubernetes_pvc VOLUME_NAME=....

SLURM has no concept of volumes, though SLURM clusters typically use a NFS share mounted to the same path on every node. pman should be configured with STORAGE_TYPE=host STOREBASE=..., specify the share mount point as STOREBASE.

`swarm` v.s. `docker`

Originally, pman interfaced with the Docker Swarm API for the sake of supporting multi-node clusters. However, more often than not, pman is run on a single-machine. Such is the case for developer environments, "host" compute resources for our single-machine production deployments of CUBE, and production deployments of CUBE on our Power9 supercomputers. Swarm mode is mostly an annoyance and its multi-node ability is poorly tested. Furthermore, multi-node functionality is better provided by CONTAINER_ENV=kubernetes.

In pman v4.1, CONTAINER_ENV=docker was introduced as a new feature and the default configuration. In this mode, pman uses the Docker Engine API instead of the Swarm API, which is much more convenient for single-machine use cases.

Podman Support

CONTAINER_ENV=docker is compatible with Podman.

Podman version 3 or 4 are known to work.

Rootless Podman

Configure the user to be able to set resource limits.

https://github.com/containers/podman/blob/main/troubleshooting.md#symptom-23

Environment Variables

Environment Variable	Description
`SECRET_KEY`	Flask secret key
`CONTAINER_ENV`	one of: "swarm", "kubernetes", "cromwell", "docker"
`STORAGE_TYPE`	one of: "host", "docker_local_volume", "kubernetes_pvc"
`STOREBASE`	where job data is stored, valid when `STORAGE_TYPE=host`, conflicts with `VOLUME_NAME`
`VOLUME_NAME`	name of data volume, valid when `STORAGE_TYPE=docker_local_volume` or `STORAGE_TYPE=kubernetes_pvc`
`PFCON_SELECTOR`	label on the pfcon container, may be specified for pman to self-discover `VOLUME_NAME` (default: `org.chrisproject.role=pfcon`)
`CONTAINER_USER`	Set job container user in the form `UID:GID`, may be a range for random values
`ENABLE_HOME_WORKAROUND`	If set to "yes" then set job environment variable `HOME=/tmp`
`SHM_SIZE`	Size of `/dev/shm` in mebibytes. (Supported only in Docker, Podman, and Kubernetes.)
`JOB_LABELS`	CSV list of key=value pairs, labels to apply to container jobs
`JOB_LOGS_TAIL`	(int) maximum size of job logs
`IGNORE_LIMITS`	If set to "yes" then do not set resource limits on container jobs (for making things work without effort)
`REMOVE_JOBS`	If set to "no" then pman will not delete jobs (for debugging)

`STOREAGE_TYPE=host`

When STORAGE_TYPE=host, then specify STOREBASE as a mount point path on the host(s).

`STOREAGE_TYPE=docker_local_volume`

For single-machine instances, use a Docker/Podman local volume as the "storeBase." The volume should exist prior to the start of pman. It can be identified one of two ways:

Manually, by passing the volume name to the variable VOLUME_NAME
Automatically: pman inspects a container with the label org.chrisproject.role=pfcon and selects the mountpoint of the bind to /var/local/storeBase

`STORAGE_TYPE=kubernetes_pvc`

When STORAGE_TYPE=kubernetes_pvc, then VOLUME_NAME must be the name of a PersistentVolumeClaim configured as ReadWriteMany.

In cases where the volume is only writable to a specific UNIX user, such as a NFS-backed volume, CONTAINER_USER can be used as a workaround.

Kubernetes-Specific Options

Applicable when CONTAINER_ENV=kubernetes

Environment Variable	Description
`JOB_NAMESPACE`	Kubernetes namespace for created jobs
`NODE_SELECTOR`	Pod `nodeSelector`

SLURM-Specific Options

Applicable when CONTAINER_ENV=cromwell

Environment Variable	Description
`CROMWELL_URL`	Cromwell URL
`TIMELIMIT_MINUTES`	SLURM job time limit

For how it works, see https://github.com/FNNDSC/pman/wiki/Cromwell

Container User Security

Setting an arbitrary container user, e.g. with CONTAINER_USER=123456:123456, increases security but will cause (unsafely written) ChRIS plugins to fail. In some cases, ENABLE_HOME_WORKAROUND=yes can get the plugin to work without having to change its code.

It is possible to use a random container user with CONTAINER_USER=1000000000-2147483647:1000000000-2147483647 however considering that pfcon's UID never changes, this will cause everything to break.

Missing Features

pman's configuration has gotten messy over the years because it attempts to provide an interface across vastly different systems. Some mixing-and-matching of options are unsupported:

IGNORE_LIMITS=yes only works with CONTAINER_ENV=docker (or podman).
JOB_LABELS=... only works with CONTAINER_ENV=docker (or podman) and CONTAINER_ENV=kubernetes.
CONTAINER_USER does not work with CONTAINER_ENV=cromwell
CONTAINER_ENV=cromwell does not forward environment variables.
STORAGE_TYPE=host is not supported for Kubernetes

TODO

Dev environment and testing for Kubernetes and SLURM.

FNNDSC/pman