pman

Table of Contents

• Overview
• Development and testing
  • Preconditions
  • Docker Swarm-based development environment
  • Kubernetes-based development environment
  • Example Job

Overview

This repository implements pman -- a process manager that provides a unified API over HTTP for running jobs on

• Docker Swarm
• Kubernetes
• Openshift

Development and testing

Preconditions

Install latest docker

Currently tested platforms:

• Ubuntu 18.04+ and MAC OS X 10.14+ and Fedora 31+ Additional instructions for Fedora
• Docker 18.06.0+

Note: On a Linux machine make sure to add your computer user to the docker group. Consult this page https://docs.docker.com/engine/install/linux-postinstall/

Docker Swarm-based development environment

Start a local Docker Swarm cluster if not already started

$> docker swarm init --advertise-addr 127.0.0.1

Start pman's Flask development server

$> git clone https://github.com/FNNDSC/pman.git
$> cd pman
$> ./make.sh

Remove pman's Flask development server

$> cd pman
$> ./unmake.sh

Remove the local Docker Swarm cluster if desired

$> docker swarm leave --force

Kubernetes-based development environment

Install single-node Kubernetes cluster

On MAC OS Docker Desktop includes a standalone Kubernetes server and client. Consult this page https://docs.docker.com/desktop/kubernetes/

On Linux there is a simple MicroK8s installation. Consult this page https://microk8s.io Then create the required alias:

$> snap alias microk8s.kubectl kubectl
$> microk8s.kubectl config view --raw > $HOME/.kube/config

Start pman's Flask development server

$> git clone https://github.com/FNNDSC/pman.git
$> cd pman
$> ./make.sh -O kubernetes

Remove pman's Flask development server

$> cd pman
$> ./unmake.sh -O kubernetes

Example Job

Simulate incoming data

Docker Swarm:

$> pman_dev=$(docker ps -f name=pman_dev_stack_pman.1 -q)
$> docker exec $pman_dev mkdir -p /home/localuser/storeBase/key-chris-jid-1/incoming
$> docker exec $pman_dev mkdir -p /home/localuser/storeBase/key-chris-jid-1/outgoing
$> docker exec $pman_dev touch /home/localuser/storeBase/key-chris-jid-1/incoming/test.txt

Kubernetes:

$> pman_dev=$(kubectl get pods --selector="app=pman,env=development" --output=jsonpath='{.items[*].metadata.name}')
$> kubectl exec $pman_dev -- mkdir -p /home/localuser/storeBase/key-chris-jid-1/incoming
$> kubectl exec $pman_dev -- mkdir -p /home/localuser/storeBase/key-chris-jid-1/outgoing
$> kubectl exec $pman_dev -- touch /home/localuser/storeBase/key-chris-jid-1/incoming/test.txt

Using HTTPie to run a job

$> http POST http://localhost:30010/api/v1/ cmd_args='--saveinputmeta --saveoutputmeta --dir cube/uploads' cmd_path_flags='--dir' auid=cube number_of_workers=1 cpu_limit=1000 memory_limit=200 gpu_limit=0 image=fnndsc/pl-dircopy selfexec=dircopy selfpath=/usr/local/bin execshell=/usr/local/bin/python type=fs jid=chris-jid-1

Get job status

$> http http://localhost:30010/api/v1/chris-jid-1/

Keep making the previous GET request until the "status" descriptor in the response becomes "finishedSuccessfully"

Delete the job

$> http DELETE http://localhost:30010/api/v1/chris-jid-1/