Performant version of pylmm for Genenetwork.org
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README.md

pylmm - A lightweight linear mixed-model solver

pylmm is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS). The original is derived from FaST-LMM and that code base can be found here.

This is an improved and faster version of pylmm which is part of the Genenetwork2 project.

Install

This edition of pylmm has been tested on Python 2.7.3. Dependencies for single and multi-core use are

numpy
scipy

For CUDA dependencies are (in addition to a functional NVIDIA Tesla installation)

pycuda
scikits.cuda

You may need to add something like

export CUDA_ROOT=/usr/local/cuda-7.0
export PATH=$CUDA_ROOT/bin:$PATH
export LD_LIBRARY_PATH=$CUDA_ROOT/lib64

Test CUDA support with

./bin/cuda_properties.py

Run

By default pylmm finds CUDA and runs on the GPU. If there is no CUDA support multi-core numpy is used. To avoid CUDA use --no-cuda. To force BLAS use the --blas switch.

Pjotr Prins

License

pylmm is offered under the GNU Affero GPL (https://www.gnu.org/licenses/why-affero-gpl.html). See also LICENSE.txt file that comes with the source.