(Python) Process Manager
Table of Contents
This repository provides several python scripts that can be used as either standalone executables or as modules in python code. The common theme of this respository is process (and file) management. The following scripts/modules are provided:
- pman: a process manager;
- pfioh: a file IO manager;
- purl: a tool to transfer data using HTTP (similar to curl);
- crunner: a low-level encapsulator that runs commands (and is used by pman).
Most simply, pman manages processes, i.e. programs or applications that are run by an underlying system. Typically, these processes are command line applications (i.e. have no GUI) and usually do not interact really with a user at all. The primary purpose of pman is to provide other software agents the ability to execute processes via http. In addition, pman keeps a record of the current and historical state of processes that it has executed and is thus able to respond to queries about the processes. Some of the queries that pman can address are
- state: Is job <XYZ> still running?
- result: What is the stdout (or stderr) from job <XYZ>?
- control: Kill job <XYZ>
pman also maintains a persistent human-readable/friendly database-in-the-filesystem of jobs and states of jobs.
While pman is a service that runs other programs (and provides information about them), pfioh is a service that pushes/pulls files and directories between different locations.
Since both pman and pfioh are services that listen for messages transported via http , a companion client application called purl is provided that can be used to speak to both pman and pfioh.
crunner is the actual “shim” or “wrapper” around an underlying system process. Most users will not need nor want necessarily to use crunner directly, although in many respects pman is a thin layer above crunner.
Installation is relatively straightforward, and we recommend using either python virtual environments or docker.
On Ubuntu, install the Python virtual environment creator
sudo apt install virtualenv
Then, create a directory for your virtual environments e.g.:
You might want to add to your .bashrc file these two lines:
export WORKON_HOME=~/python-envs source /usr/local/bin/virtualenvwrapper.sh
Then you can source your .bashrc and create a new Python3 virtual environment:
source .bashrc mkvirtualenv --python=python3 python_env
To activate or “enter” the virtual env:
To deactivate virtual env:
We provide a slim docker image with python3 based off Ubuntu. If you want to play inside this dock and install pman manually, do
docker pull fnndsc/ubuntu-python3
This docker has an entry point python3. To enter the dock at a different entry and install your own stuff:
docker run -ti --entrypoint /bin/bash fnndsc/ubuntu-python3
Now, install pman and friends using pip
apt update && \ apt install -y libssl-dev libcurl4-openssl-dev librtmp-dev && \ pip install pman
If you do the above, remember to commit your changes to the docker image otherwise they’ll be lost when you remove the dock instance!
docker commit <container-ID> local/ubuntu-python3-pman where ``<container-ID>`` is the ID of the above container.
The easiest option however, is to just use the fnndsc/pman dock.
docker pull fnndsc/pman
and then run
docker run --name pman -v /home:/Users --rm -ti fnndsc/pman pman --rawmode 1 --http --port 5010 --listeners 12
For usage of the individual components, pman, pfioh, and purl, consult the relevant wiki pages.