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parsb

A parallel implementation of the SlashBurn vertex ordering algorithm using OpenMP, ips4o sort, Afforest, and Spray Block Reductions

Contents

  1. Running parsb in Docker
  2. Running parsb Locally
  3. parsb Parameters

Running parsb in Docker

Use the atrostan/parsb Docker image to run parsb.
The image is created using this Dockerfile.

Requirements

Name Version
Docker >= 24.0.6
Python >= 3.10

  1. Create a virtual environment to run the docker container
    (Required packages are listed in ./docker/requirements.txt)

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

  2. Build parsb in Docker container
    The following will:

    1. pull docker image from atrostan/parsb (if not already pulled)
    2. (re)compile parsb using the input arguments (See parsb Compile Time Parameters for a description of parameters)
    python docker/build.py --block-width 32768

  3. Run parsb
    The following will run parsb on the given edgelist

    (See parsb Runtime Parameters for a description of input parameters)

    python docker/run.py \
   --graph-path "./data/graphs/librec-ciaodvd-trust.net" \
   --output-path "./data/graphs/librec-ciaodvd-trust.sb"  \
   -p 0.005 \
   --num-threads 8 \
   --plot-verify

    If the input graph contains less than 10,000 vertices, you can verify the output of parsb by passing the optional --plot-verify flag.
    This will plot the original graph and the SlashBurn adjacency matrices side-by-side, and save the plot in the same directory as the original edgelist.
    e.g., adj-mats

Running parsb Locally

Follow these instructions if you want to configure, build, and run parsb locally.

Cloning

git clone --recurse-submodules https://github.com/ubc-systopia/parsb.git

Requirements and Dependencies

parsb was developed and tested using Ubuntu clang version 17.0.0 and Ubuntu 22.04.3.

Name Version
CMake >= 3.16
OpenMP >= 5.1
Ninja >= 1.10.1
abseil latest

Compilation and Build

Installing abseil

Intructions taken from https://abseil.io/docs/cpp/quickstart-cmake.html

$ cd <root directory for pasrb>

# clone
mkdir install && cd install
git clone https://github.com/abseil/abseil-cpp.git

# configure
cd abseil-cpp
mkdir build && cd build
cmake ..

# build
cmake --build . --target all

Building Parallel SlashBurn

Configure

  1. ensure submodules are installed

    git submodule update --init --recursive

export PARSB_ROOT_DIR=<root directory for parsb>
export BSIZE=1024
export BWIDTH=65536
export TIME=0

cmake \
    -DCMAKE_BUILD_TYPE:STRING=Release \
    -DCMAKE_C_COMPILER:STRING=/usr/bin/clang \
    -DCMAKE_CXX_COMPILER:STRING=/usr/bin/clang++ \
    -DBSIZE:STRING=${BSIZE} \
    -DBWIDTH:STRING=${BWIDTH} \
    -DTIME:STRING=${TIME} \
    -S${PARSB_ROOT_DIR} \
    -B${PARSB_ROOT_DIR}/build \
    -G Ninja

Build

cmake --build ${PARSB_ROOT_DIR}/build --config Release --target parsb --

Running Parallel SlashBurn

./build/parsb \
    -f ./data/graphs/librec-ciaodvd-trust.net \
    -s \
    -o ./data/graphs/librec-ciaodvd-trust.sb \
    -p 0.005 \
    -t 8

parsb prints the following information per iteration:

  • i: Iteration number
  • gcc: Size of the Giant Connected Component (GCC)
  • avss: Active Vertex Set Size - the number of vertices remaining in the graph
  • start: offset into beginning of the permutation array
  • end: offset into end of the permutation array
  • n_cs: number of spokes (connected components that are not the GCC)

parsb Parameters

Compile Time

BSIZE

Unused. Required by Spray compilation. Default = 1024. (Safe to Ignore)

BWIDTH

Spray Hyperparameter. Size of Spray BlockReduction - used in degree-decrement operation.
"BlockReduction privatizes the original locations lazily by dividing the array into statically sized blocks that are then privatized individually on demand."
Default: 65536, Recommended: experiment by setting to few multiples of size of L2 cache.

TIME

True or False; Default: False.
If True, time the execution of each subroutine in every iteration of parsb, namely:
Degree sort, Afforest, Spoke-Sizing, Spoke-Sorting, and Degree-Decrement.

Runtime

-f, --graph-path

Path to input edgelist.
Important
parsb assumes the input edgelist meets the following requirement:

  • Given a graph with $n$ vertices, vertex IDs are in the range $[0, n)$
    You can use the compress utility from rhubarb to ensure your input graph meets this requirement.

-s,

Required. Symmetrize the input graph.

-o, --output-path

Writes the SlashBurn vertex ordering to this path. The vertex ordering will be written using the following format:

<number of vertices in the graph>
<number of edges in the graph>
0 <vertex 0's new vertex ID>
1 <vertex 1's new vertex ID>
.
.
.
n - 1 <vertex n-1's new vertex ID>

-p, --percent

SlashBurn removes $k$ hubs per iteration from the graph,
Where $k = pn$, $p=$percent, and $n$ is the number of vertices in the graph.

-t, --num-threads

How many threads to use for parsb.
The number of threads in all omp parallel regions are set using this parameter.
e.g.

#omp parallel num_threads(num_threads)
{
   ...
}

Structure

This repository contains the following folders and files:

  • build/ - CMake build directory
  • data/graphs - Contains sample data
    • librec-ciaodvd-trust.net - a sample directed graph: librec-ciaodvd-trust from Konect
    • librec-ciaodvd-trust.net.plot.png - plot of original and SlashBurn adjacency matrices
    • librec-ciaodvd-trust.net.sb - SlashBurn ordering
  • docker/ - Dockerfile, python requirements, and scripts for running parsb in Docker
  • include/ - C++ headers (adapted from gapbs)
  • install/ - Installation directory for abseil
  • ips4o/ - ips4o submodule
  • src/ - SlashBurn class implementation
  • CMakeLists.txt
  • main.cpp

References

  1. Axtmann, M., Witt, S., Ferizovic, D. and Sanders, P., 2017. In-place Parallel Super Scalar Samplesort (IPS $^ 4$ o). arXiv preprint arXiv:1705.02257.
  2. Beamer, S., Asanović, K. and Patterson, D., 2015. The GAP benchmark suite. arXiv preprint arXiv:1508.03619.
  3. Hückelheim, J. and Doerfert, J., 2021, May. Spray: Sparse reductions of arrays in OpenMP. In 2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS) (pp. 475-484). IEEE.
  4. Lim, Y., Kang, U. and Faloutsos, C., 2014. Slashburn: Graph compression and mining beyond caveman communities. IEEE Transactions on Knowledge and Data Engineering, 26(12), pp.3077-3089.
  5. Sutton, M., Ben-Nun, T. and Barak, A., 2018, May. Optimizing parallel graph connectivity computation via subgraph sampling. In 2018 IEEE International Parallel and Distributed Processing Symposium (IPDPS) (pp. 12-21). IEEE.

Gotchas

  1. ensure that Spray block-width does not exceed the number of vertices in the graph.
    i.e. Don't use a block-width of 65,536 on a graph with 100 vertices.