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INSTALL-Docker-CentOS.md

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Run MrBayes+Beagle3 inside a CentOS 8 Docker container

  • Status (June 2020):

    • CUDA: N/A
    • OpenCL: FAIL
    • 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.

  • 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 OpenCL, CUDA or Java):

    • WARNING: OpenCL not found or disabled
    • 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 the commands below will install the script an all necessary TeX-libraries.

      yum install -y epel-release
  yum -y update
  yum -y install texlive latexmk texlive-wrapfig

  • 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 centos:8 /bin/bash

LC_ALL=C

# Base system
yum -y install \
    autoconf \
    gcc-c++ \
    git \
    libtool \
    make \
    readline-devel

# OpenCL
# Tue 30 Jun 2020: Beagle compiles with OpenCL, but when run in MrBayes, we get
# OpenCL error: Unknown error from file <GPUInterfaceOpenCL.cpp>, line 115.
#yum -y install \
#    'dnf-command(config-manager)'
#yum -y config-manager --set-enabled PowerTools
#yum -y update
#yum -y install \
#    ocl-icd \
#    ocl-icd-devel
#ln -s /usr/lib64/libOpenCL.so.1 /usr/lib/libOpenCL.so # https://unix.stackexchange.com/questions/292630/how-to-install-opencl-in-centos-7-using-yum

# OpenMPI
yum -y install \
    openmpi-devel
source /etc/profile
module load mpi

# 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 --without-cuda --without-opencl --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

mpirun --allow-run-as-root -np 1 src/mb <<< 'version;showb;quit'

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

src/mb <<< 'version;showb;quit'