A faster lmm for GWAS. It has multi-core and GPU support.
NOTICE: this software is under active development. YMMV.
Faster_lmm_d is a lightweight linear mixed-model solver for use in genome-wide association studies (GWAS). The original is similar to FaST-LMM (an algorithm by Lippert et al.) and that code base can be found here. Prof. Karl Broman wrote a comparison with his R/lmmlite. Faster_lmm_d and pylmm are part of the Genenetwork2 project. faster_lmm_d can parse data in R/qtl2 format as input.
Faster_lmm_d has two GPU backends:
CUDA backend which helps it directly interact with CUBLAS libraries and runs only on Nvidia Hardware. For CUDA backend, Faster_LMM_D uses cuda_d (The D bindings I wrote for CUDA libraries).
ArrayFire backend which helps it run on all major GPU vendors(Nvidia, Intel, AMD) by calling CUDA, CuBLAS, OpenCL, clBLAS libraries using the ArrayFire library. For ArrayFire backend, Faster_LMM_D uses arrayfire-d (The D bindings I wrote for ArrayFire library).
faster_lmm_d is written in the fast D language and requires a D
compiler. At the moment we also use openblas (>0.2.19), lapacke, gsl
and a bunch of D libraries.
sudo apt-get install libopenblas liblapacke libgsl2
sudo apt-get install ldc2
On GNU Guix
guix package -i ldc dub openblas gsl lapack ld-wrapper gcc glibc
Get the source
Get the source-code
git clone https://github.com/prasunanand/faster_lmm_d cd faster_lmm_d
Fetch dependencies and compile
or in the case of GNU Guix (because dub does not honour the LIBRARY_PATH):
export LIBRARY_PATH=~/.guix-profile/lib env LD_LIBRARY_PATH=$LIBRARY_PATH dub --compiler=ldc2
./faster_lmm_d --control=data/genenetwork/BXD.json --pheno=data/genenetwork/104617_at.json --geno=data/genenetwork/BXD.csv --cmd=rqtl
To run tests
If you get an error (on GNU Guix)
./build/faster_lmm_d: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
time env LD_LIBRARY_PATH=$LIBRARY_PATH ./run_tests.sh
Install google-perftools and graphviz
sudo apt-get install google-perftools libgoogle-perftools-dev graphviz
Install go and then install google-pprof.
go get github.com/google/pprof
To profile uncomment out the code import
main function in
Poster on Faster Linear Mixed Models (LMM) for online GWAS omics analysis at Complex Trait Community Conference 2017, Memphis, Tennessee, USA.
This software is distributed under the GPL3 license.
Copyright © 2016 - 2018, Prasun Anand and Pjotr Prins