IPUMA Library

Multi-purpose alignment library on the Graphcore Intelligent Processing Unit (IPU).

This project contains the ipuma-library which implements implementations of the Smith-Waterman alignment algorithm for the IPU.

Installation

Requirements

The following software are required for building and running the alignment libraries:

poplar-sdk >= 2.3.0
cmake >= 3.18.4
gcc >= 7.5.0

Python script dependencies

For some python scripts used in extracting log files numpy and pandas are required. These are not required for running the alignment binaries themselves!

Preferably execute the following commands in a venv or a conda environment:

$ pip install numpy==1.22.2 pandas==1.4.1

Building

$ mkdir -p build
$ cd build
$ cmake -DCMAKE_BUILD_TYPE=Release -GNinja ..
$ ninja

Testing

Correctness tests are contained in ipuma-tests.

$ build/test/ipuma-tests

Artificial performance test scenarios on generated data are contained in ipuma-perf. These do not fail, but should present GCUPS results that can be compared.

$ build/test/ipuma-perf

Running

The ipusw binary can be used to perform benchmark measurements on specified datasets on the IPU.

The cpusw binary is a wrapper around StripedSmithWaterman.

Running paper benchmarks

The ./scripts/run_ipusw_benchmarks_mult.sh script will execute IPU-based alignment benchmarks.

The script expects alignment benchmark datasets to be located in ./download and will output log files to ./output.

The script optionally accepts a name for the execution, otherwise ipuswrun will be used:

$ ./scripts/run_ipusw_benchmarks_mult.sh [NAME]

The StripedSmithWaterman CPU benchmark results can be obtained by the following command, the parameter is optional and defaults to cpuswrun:

$ ./scripts/run_cpusw.sh [NAME]

After executing either script, a folder containing logs will be created inside the ./output/* directory. These logs can be parsed into CSV format using the following script:

$ ./scripts/merge_results_rep.sh ./output/<NAME> out.csv

Obtaining seqan results

seqan uses an existing align_bench wrapper. The following commands will automatically build and execute the experiments for seqan:

$ ./scripts/run_seqan.sh

This will pull and build seqan inside the scripts/seqan folders and output result logs into scripts/seqan/results.

The benchmark results in a table format will be output to stdout.