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Probabilistic Graph Query

This repository contains the source code, measurement data, and development environment that can be used to use, develop, or verify our results.

Structure

  • Devenv folder contains a directory with docker files. The provided dockerfile builds a container that has all dependencies configured for running our measurement campaign. Furthermore, it contains a web-based remote desktop to access a configured development environment.
  • Measurements contains our measurement data and post processing scrips. (Access via RDP at localhost:4100)
  • Sources contains the project source code.

Setup

Install docker

Build

Change directory to the repository. Expected location is .../ProbabilisticGraphQuery$

Build your own docker image with the following command:

docker build -t pgq-devenv devenv/dockerfile

Note that downloading eclipse takes a lot of time. Be patient, or download the eclipse instance manually and replace RUN wget 'https://www.eclipse.org/downloads ... with COPY <your file> eclipse.tar.gz

Alternatively, import the image using the following command:

docker image load -i <my image file>

Create container

Create container with the following command

docker run -d -u root \
  --name=pgq-devenv \
  --security-opt seccomp=unconfined \
  -p 4100:3389 \
  --shm-size="1gb" \
  -v $(pwd):/config/ProbabilisticGraphQuery \
  pgq-devenv

(Delayed) Don't forget to set user to abc for docker exec.

docker exec -u abc -it -w /config pgq-devenv /bin/bash

(Delayed) You can stop the container with:

docker container stop pgq-devenv

(Delayed) You can restart the container with:

docker container stop pgq-devenv

Configuring container

  • Connect to the running container from an RDP client (address: localhost:4100, username: abc, password: abc)
  • Donload jar dependencies.
    • /config/ProbabilisticGraphQuery/sources/hu.bme.mit.delta.api/libs/download.sh
    • /config/ProbabilisticGraphQuery/sources/hu.bme.mit.inf.measurement.utilities/libs/download.sh
  • Launch Eclipse from Applications -> Development -> Modeling 2024-03
  • Pick a workplace. (Any directory works, but we recommend picking /config/ProbabilisticGraphQuery/devenv/workplace)
  • Import all projects from /config/ProbabilisticGraphQuery/sources (File -> Import -> General -> Existing Projects into Workspace -> Next -> Select root directory -> /config/ProbabilisticGraphQuery/sources -> Projects -> Select All -> Finish)
  • Change missing API baseline preferences for org.eclipse.viatra.query.runtime.rete to Warning or Ignore. (Window -> Preferences -> Plug-in Development -> API Baselines -> Missing API baseline -> Ignore)
  • Import launch configurations from /config/ProbabilisticGraphQuery/devenv/launch_configs (File -> Import -> Run/Debug -> Launch Configurations -> Next -> From Directory -> /config/ProbabilisticGraphQuery/devenv/launch_configs -> tick launch_configs -> Finish)

Using the container

  • Export runnable jar for measurements: File -> Export -> Java -> Runnable JAR file -> Next -> Launch configuration (select any, e.g., SAT - Scale - hu.bme.mit.inf.measurement) -> Export destination: /config/ProbabilisticGraphQuery/measurements/pgq.jar -> select Extract required libraries into generated JAR -> Finish -> (Ignore warnings)

Running measurements

Connect to a bash terminal

docker exec -u abc -it -w /config/ProbabilisticGraphQuery/measurements pgq-devenv /bin/bash

Run measurements the following commands. (Expected runtime is a few days.)

./measure.sh

./measure-scale.sh

Post process measurement data

Connect to the container via RDP as before.

  • Stat a jupyter notebook from Applications -> Development -> Jupyter Notebook
  • Open the notebooks from ProbabilisticGraphQuery -> measurements -> diagrams[-scale].ipynb
  • Run notebook. Run -> Run All Cells

Alternatively, run the following script from the host machine.

docker exec -u abc -it -w /config/ProbabilisticGraphQuery/measurements pgq-devenv jupyter execute diagrams-scale.ipynb
docker exec -u abc -it -w /config/ProbabilisticGraphQuery/measurements pgq-devenv jupyter execute diagrams.ipynb

License