Project work for the course Advanced Systems Lab, FS2021 @ETHZ

• Mark Frey
• Beat Hubmann
• Martin Tschechne
• Robin Worreby

Team 33 Final Report

Create the build directory and run cmake and then make. The optimization level can be set from the command line using

cmake -D CMAKE_CXX_FLAGS="-O3"

This will generate two files, unit_tests and hdbscan. For testing just execute unit_tests.
hdbscan takes 6 required and 6 optional command line arguments. The minimal command to run is

./hdbscan -points_file=../data/data_set_medium.csv -hierarchy_file=output/hierarchy.csv -tree_file=output/tree.csv -visualization_file=output/results.vis -partition_file=output/partition.csv -outlier_score_file=output/outlier_scores.csv -num_points 1000 -num_dimension 2

The optional arguments are

• constraints path to the constraints csv
• min_pts minimum number of points (default: 8)
• min_cl_size minimal cluster size (default: 8)
• compact Whether or not to compact the output (default: true)
• dist_function Which distance function to use (default: euclidean)
• optimization_level Which optimization level to use (default: no_optimization)

This information can also be accessed by executing

hdbscan -help

Different build variants (compiler optimizations) can be added in CMakeLists. To create a new build variant add

build_hdbscan_benchmarking("-O3")

to CMakeLists and change -O3 to whatever flag you want. All builds will be written to build/benchmarking with name hdbscan<OPTIMIZATION FLAG> (without <>). These executables can then e.g. be used by a python script to create the plots.

From the plotting folder execute

python3 plot_mst_benchmark.py --points_file=../data/unit_tests/example_high_dim_10000_32.csv --num_points=10000 --num_dimension=32 --recompute --output_name=results_10k --title_heatmap="Relative speed-up 10k points, 32 dimensions" --title_bar="Cycles by optimization, 10k points, 32 dimensions" --disable_nobitset --num_runs=2

Adapt the num_runs parameter to taste

In order to benchmark with LIKWID you need to checkout out the 82-benchmark-with-likwid-v2 branch. Depending on your setup you might have to adjust the MSR rights on your machine, which can be done the following way:

sudo modprobe msr

An example on how to run LIKWID is given in run_files/run_likwid.sh. For further information on LIKWID you can check the official documentation here.

LIKWID benchmarking results

Raw distance benchmarking results

Raw MST benchmarking results

Hierarchical Density Estimates for Data Clustering, Visualization, and Outlier Detection
Accelerated Hierarchical Density Clustering