KernelForge - Optimized Kernels for ML

I really only care about writing optimized kernel code, so this project will be completed as I find additional time... XD

I'm reviving this project to finish an old project using random Fourier features for kernel ML.

Installation

Quick Start (Recommended)

For most users, install from PyPI:

pip install kernelforge

This installs pre-compiled wheels with optimized BLAS libraries:

• Linux: OpenBLAS
• macOS: Apple Accelerate framework

Requirements: Python 3.11+

Development Installation

Linux

# Create virtual environment with uv
uv venv
source .venv/bin/activate

# Install in editable mode with test dependencies
make install-linux

# Or manually:
CMAKE_ARGS="-DKF_USE_NATIVE=ON" uv pip install -e .[test] --verbose

macOS

macOS requires Homebrew LLVM for OpenMP support:

# Install dependencies
brew install llvm libomp

# Create virtual environment
uv venv
source .venv/bin/activate

# Install in editable mode
make install-macos

# Or manually:
CMAKE_ARGS="-DCMAKE_C_COMPILER=/opt/homebrew/opt/llvm/bin/clang -DCMAKE_CXX_COMPILER=/opt/homebrew/opt/llvm/bin/clang++ -DKF_USE_NATIVE=ON" uv pip install -e .[test] --verbose

Note: The -DKF_USE_NATIVE=ON flag enables -march=native/-mcpu=native optimizations for maximum performance on your specific CPU.

Linux with CUDA

PyPI ships a CPU kernelforge wheel plus a Linux companion kernelforge-cuda that drops cuda_*.so into site-packages/kernelforge/.

From PyPI (Linux, CPython 3.11–3.15 for CUDA):

uv pip install kernelforge                 # CPU (3.11–3.15)
uv pip install 'kernelforge[cuda]'         # + torch + kernelforge-cuda

Or install the companion explicitly:

uv pip install kernelforge kernelforge-cuda

Notes:

• The kernelforge-cuda companion wheel is Linux manylinux only (CPython 3.11–3.15, same as CPU).
• Default-index torch may be CPU-only. For GPU runs, install a CUDA build of PyTorch (e.g. from the PyTorch CUDA wheel index) and an NVIDIA driver compatible with that build.
• Release CUDA wheels are built on GHA build-wheels-cuda with manylinux_cuda (no GPU needed to compile).
• FCHL18 CUDA KRR supports --dtype float32 / float64 via kernelcli (float32 uses GPU rfp_potrf end-to-end).

Local monorepo / wheel smoke (developers):

# One editable tree with CPU+CUDA (needs CUDA toolkit + torch):
source /opt/intel/oneapi/setvars.sh
make install-linux-mkl-ilp64-cuda   # passes -DKF_WITH_CUDA=ON

# Or build the split wheels and smoke-test imports in a fresh venv:
make demo-cuda-wheels

Requires a CUDA toolkit + PyTorch for local CUDA builds.

Advanced: Custom BLAS/LAPACK Libraries

Intel MKL (Linux)

# Install Intel oneAPI Base Toolkit
sudo apt install intel-oneapi-base-toolkit

# Set up environment
source /opt/intel/oneapi/setvars.sh

# Install (MKL will be auto-detected by CMake)
uv pip install -e .[test] --verbose

# Optional: Use Intel compilers
CC=icx CXX=icpx uv pip install -e .[test] --verbose

Note: In practice, GCC/G++ with OpenBLAS performs similarly to (or better than) Intel compilers with MKL. On macOS, LLVM with Accelerate framework is highly optimized for Apple Silicon.

ASE molecular dynamics

Install the optional ASE extra:

pip install 'kernelforge[ase]'

Wrap a fitted force-capable model (for example CudaLocalKRRModel) with KernelForgeCalculator, or use run_md() / the kernelmd CLI:

kernelmd --model model.npz --structure start.xyz --steps 5000 --dt 0.5 \
         --temperature 300 --output traj.extxyz

See examples/run_md_rmd17_*.py and examples/run_opt_rmd17_*.py.

Timings

I've rewritten a few of the kernels from the original QML code completely in C++. There are performance gains in most cases. These are primarily due to better use of BLAS routines for calculating, for example, Gramian sub-matrices with chunked DGEMM/DSYRK calls, etc. In the gradient and Hessian matrices there are also some algorithmic improvements and pre-computed terms. Memory usage might be a bit higher, but this could be optimized with more fine-grained chunking if needed. More is coming as I find the time ...

Some speedups vs the original QML code are shown below:

TODO list

Tracked in GitHub issue #45 (roadmap, open items, and stretch goals).