Using GPUs

PopPUNK can use GPU acceleration of sketching (only when using sequence reads), distance calculation, network construction and some aspects of visualisation. Installing and configuring the required packages necessitates some extra steps, outlined below.

Installing GPU packages

To use GPU acceleration, PopPUNK uses cupy, numba and packages from RAPIDS. Both cupy and numba can be installed as standard packages using conda. To install RAPIDS, see the guide. We would recommend installing into a clean conda environment with a command such as:

conda create -n poppunk_gpu -c rapidsai -c nvidia -c conda-forge \
-c bioconda -c defaults rapids=0.17 python=3.8 cudatoolkit=11.0 \
pp-sketchlib>=1.6.2 poppunk>=2.3.0 networkx cupy numba
conda activate poppunk_gpu

The version of pp-sketchlib on conda only supports some GPUs. If this doesn’t work for you, it is possible to install from source. Add the build dependencies to your conda environment:

conda install cmake pybind11 highfive Eigen armadillo openblas libgomp libgfortran-ng


On OSX replace libgomp libgfortan-ng with llvm-openmp gfortran_impl_osx-64, and remove libgomp from environment.yml.

Clone the sketchlib repository:

git clone
cd pp-sketchlib

Edit the CMakeLists.txt if necessary to change the compute version used by your GPU. See the CMAKE_CUDA_COMPILER_VERSION section.

GPU compute versions
GPU Compute version
20xx series 75
30xx series 86
V100 70
A100 80

Make sure you have CUDA toolkit installed (this is available via conda as cudatoolkit) and nvcc is on your PATH:

export PATH=/usr/local/cuda-11.1/bin${PATH:+:${PATH}}
export LD_LIBRARY_PATH=/usr/local/cuda-11.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}

Then run:

python install

You should see a message that the CUDA compiler is found, in which case the compilation and installation of sketchlib will include GPU components:

-- Looking for a CUDA compiler
-- Looking for a CUDA compiler - /usr/local/cuda-11.1/bin/nvcc
-- CUDA found, compiling both GPU and CPU code
-- The CUDA compiler identification is NVIDIA 11.1.105
-- Detecting CUDA compiler ABI info
-- Detecting CUDA compiler ABI info - done
-- Check for working CUDA compiler: /usr/local/cuda-11.1/bin/nvcc - skipped
-- Detecting CUDA compile features
-- Detecting CUDA compile features - done

You can confirm that your custom installation of sketchlib is being used by checking the location of sketchlib library reported by popppunk points to your python site-packages, rather than the conda version.

Selecting a GPU

A single GPU will be selected on systems where multiple devices are available. For sketching and distance calculations, this can be specified by the --deviceid flag. Alternatively, all GPU-enabled functions will used device 0 by default. Any GPU can be set to device 0 using the system CUDA_VISIBLE_DEVICES variable, which can be set before running PopPUNK; e.g. to use GPU device 1:


Using a GPU

By default, PopPUNK will use not use GPUs. To use them, you will need to add the flag --gpu-sketch (when constructing or querying a database using reads), --gpu-dist (when constructing or querying a database from assemblies or reads), or --gpu-graph (when querying or visualising a database, or fitting a model).