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INSTALL-Docker-Ubuntu.md

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Install MrBayes+Beagle3 inside an Ubuntu 20.04 Docker container

  • Status (June 2020):

    • CUDA: N/A
    • OpenCL: OK
    • OpenMPI: OK
    • Beagle3: OK
    • MrBayes+MPI: OK
    • MrBayes: OK

  • This file describes a "proof-of-concept" installation of the develop branch of MrBayes with Beagle. The installation is made inside a Docker container, hence, this is not a Dockerfile.

  • Instructions for Debian are identical, but you would use a Debian container such as debian:sid instead of ubuntu:20.04.

  • We could not get beagle to work from inside MrBayes unless Beagle is configured using -rpath, or LD_LIBRARY_PATH is set before running MrBayes.

  • When configuring the beagle library, we expect to see these warning messages (since we asked for not using CUDA or Java):

    • WARNING: NVIDIA CUDA nvcc compiler not found
    • WARNING: JDK installation not found

  • We are not building the LaTeX version of the documentation for MrBayes. For building the documentation, we recommend to use the latexmk script. Using apt install latexmk texlive-latex-extra will install the script an all necessary TeX-libraries.

  • When running the MPI (parallel) version of MrBayes inside the Docker container, we need to use --allow-run-as-root (since we are starting mpirun as user root).

Install and run

$ docker run -it ubuntu:20.04 /bin/bash

# Base system
apt update -y && apt upgrade -y

DEBIAN_FRONTEND=noninteractive apt install -y tzdata

apt install -y \
    autoconf \
    g++ \
    git \
    libreadline-dev \
    libtool \
    make

# OpenCL
apt install -y \
    ocl-icd-opencl-dev \
    pocl-opencl-icd

# OpenMPI
apt install -y \
    libopenmpi-dev

# Beagle
git clone --depth=1 https://github.com/beagle-dev/beagle-lib.git
cd beagle-lib
./autogen.sh
LDFLAGS=-Wl,-rpath=/usr/local/lib ./configure --without-jdk --disable-doxygen-doc
make -j2
make install

cd /

# MrBayes
git clone --depth=1 --branch=develop https://github.com/NBISweden/MrBayes.git
cd MrBayes
./configure --with-mpi --enable-doc=no
make -j2

# Test MPI (parallel) version
mpirun --allow-run-as-root -np 1 src/mb <<< 'version;showb;quit'

make clean
./configure --enable-doc=no
make -j2

# Test serial version
src/mb <<< 'version;showb;quit'