How do you set up Ubuntu 16.04 rigs for deep bio-molecular reinforcement learning?
A battle-tested guide to install Nvidia drivers, CUDA, cuDNN, conda, Tensorflow-GPU, PyMol, and OpenAI Gym on Linux!
install ubuntu 16.04
get a usb stick and plug it in (needs >2gb space)
download http://releases.ubuntu.com/xenial/ubuntu-16.04.5-desktop-amd64.iso
use startup disk creator to burn the iso to the usb
put the usb into the computer and restart it
press ESC, F1, F2, F8 or F10 to boot from usb
use the gui to install ubuntu
set files explorer to default as list
gsettings set org.gnome.nautilus.preferences default-folder-viewer ‘list-view’
install nvidia drivers
sudo apt-get purge nvidia* (might be unnecessary on fresh install 16.04)
sudo add-apt-repository ppa:graphics-drivers/ppa
sudo apt-get update && sudo apt-get install nvidia-396
nvidia-smi
install cuda 9.0
link http://developer.nvidia.com/cuda-downloads
avoid the runfile because it doesn’t work due to X server issues unless you switch to a text-only mode of ubuntu and deactivate stuff
sudo dpkg -i cuda-repo-ubuntu1604–9–0-local_9.0.176–1_amd64.deb
sudo apt-key add /var/cuda-repo-9–0-local/7fa2af80.pub
sudo apt-get update
sudo apt-get install nvidia-cuda-toolkit (*install cuda overwrites nvidia-396*)
install patches by double clicking in files
nvcc — version
install cudnn
guide https://docs.nvidia.com/deeplearning/sdk/cudnn-install/index.html
link https://developer.nvidia.com/rdp/cudnn-download (get 7.0)
sudo dpkg -i libcudnn7*
install with ubuntu installer
cat /usr/include/cudnn.h | grep CUDNN_MAJOR -A 2
install conda and configure the environment
link https://repo.continuum.io/archive/Anaconda3-5.1.0-Linux-x86_64.sh
cd ~/Downloads
bash Anaconda3–5.1.0-Linux-x86_64.sh
follow the prompts
close the terminal (alt-f4)
open a new terminal (ctrl-alt-t)
conda create -n tfg tensorflow-gpu=1.11
source activate tfg
install dependencies
conda install -c conda-forge slackclient
conda install -c schrodinger pymol
conda install -c anaconda pillow
conda install imageio
pip install gym
clone the repo and run neuromax
cd && mkdir hax && cd hax
git clone https://bionicle1337@bitbucket.org/bitpharma1337/neuromax.git
cd neuromax && git checkout kamelbranch
python neuromax.py (edited)
never underestimate what nerds can do in 15 hours of deep work
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