Skip to content

Latest commit

 

History

History
executable file
·
417 lines (328 loc) · 13.4 KB

16_DL4_config.md

File metadata and controls

executable file
·
417 lines (328 loc) · 13.4 KB

Configurations I've made on DL4 server for Ubuntu 20.04.

Disable sleep/suspend

Lightlocker and Xscreensaver conflicting How to Disable Suspend and Hibernation Modes In Linux How to permanently disable sleep/suspend?

Some Ubuntu 20.04 distributions have sleep/suspend mode after 20 minutes.

NOTE: not all these commands were tested.

# delete light-locker service
sudo apt purge light-locker
# disable light-locker file
sudo mv /etc/xdg/autostart/light-locker.desktop /etc/xdg/autostart/light-locker.desktop.bak
# disable services
sudo systemctl mask sleep.target suspend.target hibernate.target hybrid-sleep.target

Edit /etc/systemd/logind.conf file:

#NAutoVTs=6
#ReserveVT=6
#KillUserProcesses=no
#KillOnlyUsers=
#KillExcludeUsers=root
#InhibitDelayMaxSec=5
HandlePowerKey=ignore
HandleSuspendKey=ignore
HandleHibernateKey=ignore
HandleLidSwitch=ignore
HandleLidSwitchExternalPower=ignore
HandleLidSwitchDocked=ignore
#PowerKeyIgnoreInhibited=no
#SuspendKeyIgnoreInhibited=no
#HibernateKeyIgnoreInhibited=no
LidSwitchIgnoreInhibited=no
#HoldoffTimeoutSec=30s
IdleAction=ignore
IdleActionSec=130min
#RuntimeDirectorySize=10%
#RemoveIPC=yes
#InhibitorsMax=8192
#SessionsMax=8192

Run the following command to open the file to edit:

sudo -H gedit /var/lib/polkit-1/localauthority/10-vendor.d/com.ubuntu.desktop.pkla

Scroll to the bottom. Check to see if the following information exists, and if not add them:

[Disable suspend]
Identity=unix-user:*
Action=org.freedesktop.upower.suspend
ResultActive=no

Doing this makes suspend do nothing when you click it; it will disappear from the menu after you restart your computer.

You can run this command also to prevent computer from sleeping:

gsettings set org.gnome.desktop.session idle-delay 0

With dconf Editor, navigate to:

org.gnome.settings-daemon.plugins.power

You will find lots of options relating to sleep and suspend.

Docker installing and configuring

Links:

Install Docker from the official Docker repository.

sudo apt update
sudo apt install apt-transport-https ca-certificates curl software-properties-common
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu focal stable"
sudo apt update
apt-cache policy docker-ce
sudo apt install docker-ce

# Configure Docker to start on boot
sudo systemctl enable docker
# Check the service is running
sudo systemctl status docker

# Add username to the "docker" group
sudo usermod -aG docker ${USER}
sudo usermod -aG docker skliff13
# Log out of the server and back in, or type the following:
su - ${USER}
# Confirm that the user is now added to the docker group
id -nG ${USER}
# or
cat /etc/group | grep docker

# Check installation
docker run hello-world
docker images

Install Docker Compose tool for defining and running multi-container Docker applications.

sudo curl -L "https://github.com/docker/compose/releases/download/1.27.4/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
sudo chmod +x /usr/local/bin/docker-compose
# Check installation
docker-compose --version

Install NVIDIA Container Toolkit for Clara Train Application Framework

distribution=$(. /etc/os-release;echo $ID$VERSION_ID) \
   && curl -s -L https://nvidia.github.io/nvidia-docker/gpgkey | sudo apt-key add - \
   && curl -s -L https://nvidia.github.io/nvidia-docker/$distribution/nvidia-docker.list | sudo tee /etc/apt/sources.list.d/nvidia-docker.list
sudo apt-get update
sudo apt-get install -y nvidia-docker2
sudo systemctl restart docker

# Check installation
sudo docker run --rm --gpus all nvidia/cuda:11.0-base nvidia-smi

How-to configure TensorFlow

See virtual environment.

Install useful software

See software install.

OpenSlide

Install OpenSlide:

sudo apt install openslide-tools
# Install Python interface into virtual environment
pip install openslide-python

Snap

Unfortunately, installations via snap do not work for now. The error is:

2020/07/19 14:53:45.767662 cmd_run.go:563: WARNING: XAUTHORITY environment value is not a clean path: "/share/home/<username>/.Xauthority"
cannot perform operation: mount --rbind /home /tmp/snap.rootfs_UCBqUu//home: Permission denied

# Install Notepad++ editor
sudo apt install -y snapd            # install Snap tool
sudo apt install -y wine-stable      # install Wine tool
sudo snap install notepad-plus-plus  # install Notepad++

sudo snap install chromium  # Chromium web browser

sudo snap install pycharm-community --classic  # PyCharm IDE

# Remove possible error with Canberra Gtk.
# canberra-gtk-module translates GTK+ widgets signals to event sounds
# This module is needed for PyCharm successful start
sudo apt install -y libcanberra-gtk-module

Visual Studio

Install Visual Studio Code

sudo apt update
sudo apt install software-properties-common apt-transport-https wget
# Import the Microsoft GPG key
wget -q https://packages.microsoft.com/keys/microsoft.asc -O- | sudo apt-key add -
# Enable the Visual Studio Code repository
sudo add-apt-repository "deb [arch=amd64] https://packages.microsoft.com/repos/vscode stable main"
sudo apt install code
# Check installation
code

R and RStudio

Install latest version of R via CRAN for Ubuntu. And then install RStudio IDE.

Also try RStudio Builds or Official RStudio Desktop.

# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# add the signing key (by Michael Rutter) for these repos
# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc 
# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

# Install R
sudo apt install --no-install-recommends r-base

# Get 5000+ CRAN Packages. Add the current R 4.0 or later ‘c2d4u’ repository
sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+

#sudo apt install --no-install-recommends r-cran-rstan
#sudo apt install --no-install-recommends r-cran-tidyverse

# Check installation of r-base
R --version  # `R` command to start console and q() to exit

# After installing latest version of r-base, install RStudio IDE
# New releases: https://posit.co/download/rstudio-desktop/
wget https://download1.rstudio.org/electron/jammy/amd64/rstudio-2024.12.0-467-amd64.deb
sudo apt install -f ./rstudio-2024.12.0-467-amd64.deb
#sudo apt remove rstudio  # Uninstall RStudio IDE

# If there is an error "Could not initialize GLX", fix it with this:
export QT_XCB_GL_INTEGRATION=none
# Add this string to the end of files: ~/.bashrc and ~/.profile
# nano ~/.bashrc
# nano ~/.profile

rstudio --version  # check version
rstudio  # start RStudio

Check it through the menu: Programming --> RStudio

RStudio IDE menu

Nvidia and CUDA installation

Install Nvidia drivers and CUDA Toolkit from binary files:

# Get NVidia driver
wget https://download.nvidia.com/XFree86/Linux-x86_64/470.57.02/NVIDIA-Linux-x86_64-470.57.02.run
sudo sh NVIDIA-Linux-x86_64-470.57.02.run

# Get CUDA toolkit 11
wget https://developer.download.nvidia.com/compute/cuda/11.7.0/local_installers/cuda_11.7.0_515.43.04_linux.run
sudo sh cuda_11.7.0_515.43.04_linux.run

nvidia-smi      # verity Nvidia driver
nvcc --version  # verify CUDA version

CUDA 10 should be installed for bioinformatics department. Set no for the question: Do you want to install a symbolic link at /usr/local/cuda?

# Get CUDA toolkit 10
wget -O cuda_10.0.130_410.48_linux.run https://developer.nvidia.com/compute/cuda/10.0/Prod/local_installers/cuda_10.0.130_410.48_linux
sudo sh cuda_10.0.130_410.48_linux.run

pyenv virtual environment

Links:

System administrator must install required libraries for pyenv.

# Install required libraries
sudo apt install -y build-essential libssl-dev zlib1g-dev libbz2-dev \
libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev \
xz-utils tk-dev libffi-dev liblzma-dev python-openssl git

sudo apt install -y libedit-dev

Install pyenv into your account.

# The automatic installer
curl https://pyenv.run | bash

nano ~/.bashrc  # edit .bashrc file

# Load pyenv automatically by adding
# the following to the end of ~/.bashrc file:
export PATH="~/.pyenv/bin:$PATH"
eval "$(pyenv init -)"
eval "$(pyenv virtualenv-init -)"

exec $SHELL  # restart shell
pyenv update  # update

Configure Python virtual environment using pyenv.

pyenv install --list  # show all available versions

# Choose Python version and install it.
# This will take a while because `pyenv`
# is building Python from source.
pyenv install -v 3.8.4

# Uninstall Python version if necessary
#rm -rf ~/.pyenv/versions/3.8.4
# or
#pyenv uninstall 3.8.4

# Set Python version
pyenv versions  # show installed versions
pyenv local 3.8.4  # set an application-specific version
#pyenv global 3.8.4  # use Python 3.8.4 globally
python --version  # get current Python version
#python -m test  # run the built-in test suite
#pyenv commands  # list of pyenv commands

# Create virtual environment
# pyenv virtualenv <python_version> <environment_name>
pyenv virtualenv 3.8.4 myproject
pyenv local myproject  # activate environment

# Deactivation doesn't work without default system Python.
# Just create another virtual environment and activate it.
pyenv deactivate  # deactivate environment
#pyenv virtualenv-delete myproject  # delete venv

For example, install Anaconda:

pyenv install anaconda3-2020.02
pyenv local anaconda3-2020.02
pyenv virtualenv anaconda3-2020.02 myproject2
pyenv local myproject2  # activate environment
conda --version  # check it

Shows PIDs of NVIDIA processes

Use `nvtop` command instead

Create nvidia-show command for non-root users to view NVidia processes.

Create and edit file with visudo editor in the directory /etc/sudoers.d/.

# Create and edit file
sudo visudo -f /etc/sudoers.d/show_nvidia_pid

# Write these lines into the file /etc/sudoers.d/show_nvidia_pid

# Members of the bioimage and genomics groups
# can view NVIDIA processes
User_Alias USERS = %bioimage, %genomics

# $USER $HOST = (root) NOPASSWD: /the/absolute/path/to/your/command
USERS ALL=NOPASSWD: /bin/fuser -v /dev/nvidia*

For more information about sudoers.d see allow user permissions.

# Create alias for the command
alias nvidia-pids='sudo fuser -v /dev/nvidia*'

# Or create nvidia-show executable file
echo 'sudo fuser -v /dev/nvidia*' | sudo tee -a /usr/bin/nvidia-show
sudo chmod u=rwx,g=rx,o=rx /usr/bin/nvidia-show
ls -hal /usr/bin/nvidia-show /usr/bin/nvidia-smi  # check it

# Run it
nvidia-show