biohpc/brms repository overview

Dockerfile:

FROM ubuntu:20.04 ARG DEBIAN_FRONTEND=noninteractive RUN apt-get update && apt-get -y upgrade
&& apt-get install -y
apt-utils
unzip
tar
curl
xz-utils
ocl-icd-libopencl1
opencl-headers
clinfo
;

RUN mkdir -p /etc/OpenCL/vendors &&
echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd ENV NVIDIA_VISIBLE_DEVICES all ENV NVIDIA_DRIVER_CAPABILITIES compute,utility

RUN apt-get install -y libopenblas-base software-properties-common RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu⁠ focal-cran40/' RUN apt update RUN apt install -y r-base

RUN update-alternatives --config libblas.so.3-x86_64-linux-gnu RUN R -e "install.packages(c('dplyr', 'mvMORPH', 'geiger', 'phytools'), repos='http://cran.rstudio.com/⁠')"

RUN apt install -y ocl-icd-opencl-dev

RUN R -e 'install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev⁠", getOption("repos")))'

RUN R -e 'cmdstanr::install_cmdstan(cores=4, overwrite=TRUE)'

RUN bash -lc 'CMDSTAN_DIR="$(Rscript -e '''cat(cmdstanr::cmdstan_path())''')" &&
mkdir -p "$CMDSTAN_DIR"/make &&
{
echo "STAN_OPENCL=true";
echo "OPENCL_PLATFORM_ID?=0";
echo "OPENCL_DEVICE_ID?=0";
} > "$CMDSTAN_DIR"/make/local'

RUN R -e 'install.packages("brms")'