May 15, 2020

Public workspaceInstallation instructions for BEAST and BEAGLE on Avell G1550 RTX MUV/A65 RTX MUV V.1

DOI
dx.doi.org/10.17504/protocols.io.bgfnjtme
  • 1Fundação Oswaldo Cruz / Instituto Gonçalo Moniz
Laise Moraes
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DOI: dx.doi.org/10.17504/protocols.io.bgfnjtme
Protocol Citation: Laise Moraes 2020. Installation instructions for BEAST and BEAGLE on Avell G1550 RTX MUV/A65 RTX MUV. protocols.io https://dx.doi.org/10.17504/protocols.io.bgfnjtme
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
Created: May 15, 2020
Last Modified: May 15, 2020
Protocol Integer ID: 37070
Installing dependency packages
Installing dependency packages
Open a terminal (Ctrl + Alt + T).
Update the package list and install the dependency packages for the BEAST and BEAGLE.
Command
sudo apt-get update
sudo apt-get install -y autoconf automake build-essential g++-8 gcc-8 git libcanberra-gtk-module libcanberra-gtk3-module libfreetype6-dev libgl1-mesa-dev libglew-dev libglm-dev libsdl2-dev libsdl2-image-dev libtool mesa-utils ocl-icd-opencl-dev ocl-icd-libopencl1 openjdk-8-jdk openjdk-8-jre pkg-config
sudo apt-get update

Installing Intel OpenCL implementations
Installing Intel OpenCL implementations
Create a directory called softwares to your HOME directory, switch to it and then download the Intel OpenCL implementations installer.
Unpack the compressed .tar.gz file, switch to installer directory and install the Intel OpenCL implementations, accepting defaults.
After installation, remove the Intel OpenCL implementations installer directory and installer.
Command
mkdir $HOME/softwares
cd $HOME/softwares
wget http://registrationcenter-download.intel.com/akdlm/irc_nas/vcp/16284/intel_sdk_for_opencl_applications_2020.0.270.tar.gz
tar -zxvf intel_sdk_for_opencl_applications_2020.0.270.tar.gz
cd intel_sdk_for_opencl_applications_2020.0.270
bash install.sh
cd ..
rm -rf intel_sdk_for_opencl_applications_2020.0.270*

Installing NVIDIA CUDA drivers
Installing NVIDIA CUDA drivers
Get the PPA repository and install the NVIDIA CUDA driver.
Command
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
sudo mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
wget http://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb
sudo dpkg -i cuda-repo-ubuntu1804-10-2-local-10.2.89-440.33.01_1.0-1_amd64.deb
sudo apt-key add /var/cuda-repo-10-2-local-10.2.89-440.33.01/7fa2af80.pub
sudo apt-get update
sudo apt-get -y install cuda

Installing BEAGLE
Installing BEAGLE
Build the BEAGLE from the source repository.
Command
git clone --depth=1 https://github.com/beagle-dev/beagle-lib.git
cd beagle-lib
./autogen.sh
./configure --prefix=$HOME/softwares/beagle --with-opencl=/opt/intel/system_studio_2020/opencl/SDK --with-cuda=/usr/local/cuda
make install
make check
cd ..

Installing BEAST
Installing BEAST
Download the BEAST installer and unpack the compressed .tgz file.
After install, remove the compressed .tgz file.
Command
cd $HOME/softwares
wget https://github.com/beast-dev/beast-mcmc/releases/download/v1.10.5pre1/BEASTv1.10.5pre.tgz
tar -zxvf BEASTv1.10.5pre.tgz
rm BEASTv1.10.5pre.tgz