Res-Srv-Lin-01 notes

[rekkasa]

• sudo apt update && sudo apt upgrade -yy
• Install base packages
  • build-essential
  • git
  • tasksel:
  • sudo tasksel install ubuntu-desktop-minimal
  • sudo reboot
• timezone
  • nano /etc/netplan/<...>.yaml
• ip stuff

  • use MAC address for DHCP identification

  • nano /etc/netplan/<...>.yaml

  • in that file add for each NIC the line

  • dhcp-identifier: mac
  • optional: true

  • in that file add for each NIC the line

  • dhcp-identifier: mac
• sudo vim /etc/apt/apt.conf.d/20auto-upgrades
  • Update Package lists "0"
  • Basically set everything to "0"
• PyCharm
  • sudo snap install pycharm-educational --classic
  • configs: ~/.config/JetBrains
• Atom
  • sudo snap install atom --classic
  • configs: ~/.config/Atom
• xrdp (need to enable service on each restart)
  • download and run the script from https://c-nergy.be/blog/?p=17175
• python
  • ipython3, python3-pip/dev/tk/venv
• docker
  • docs.docker.com/engine/install/ubuntu
• nvidia drivers and cuda
• home inception
  • mount /dev/sdx on /data:
  • mkdir /data
  • edit /etc/fstab:
    • UUID=.... /data ext4 defaults 0 2
    • /data/home /home none bind (doorway to /data/home)
  • sudo useradd -m xxxx -s /bin/bash
• R and RStudio
  • R
  • instructions: cloud-.r-project.org
  • install: software-properties common dirmngr (should be already there)
  • keyring: copy /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
  • add-apt-repository... Adds to /etc/apt/sources.list a custom repository
  • RStudio
  • google Rstudio server download
  • download deb file
  • sudo snap install ./....
  • remove the deb file
  • CRAN mirror
  • Change repo name in /etc/R/Rprofile.site to "http://Shr/SRV-CRAN/CRAN"
• GNOME
  • Create user profile in /etc/dconf/profile/user:

    user-db:user
    system-db:local

  • Create keyfile in /etc/dconf/db/local.d/01-interface (name taken from last part of relevant tweak, see below)

    [org/gnome/desktop/interface]
    enable-animations=false

  • Reconfigure

    sudo dconf update

  • Log out and log back in
• JDBC drivers
  • We need rjava to be running
  • add environmental variable pointing to JDBC drivers used by DatabaseConnector
  • reate empty folder for drivers

    sudo mkdir /data/Common/jdbcDrivers

  • open environment file

    sudo nano /etc/environment

  • add environment variable pointing to new folder

    DATABASECONNECTOR_JAR_FOLDER="/data/Common/jdbcDrivers"

  • download jdbc drivers using DatabaseConnector in R, it will default download to the folder set up as environment variable

    DatabaseConnector::downloadJdbcDrivers()

[lhjohn]

install samba

sudo apt install samba

open samba config

sudo nano /etc/samba/smb.conf

add the following snippet somewhere in the beginning

netbios name = res-srv-lin-01

add the following snippet in the end

[transfer] comment = Transfer folder browseable = yes path = /data/transfer read only = no guest ok = yes public = Yes writeable = Yes

restart samba

sudo /etc/init.d/smbd restart

create the folder to be shared

sudo mkdir /data/transfer

set permission

sudo chmod 0777 /data/transfer

[lhjohn]

change temporary folder location to /data/

sudo nano /etc/environment

add the line following line

TEMP="/data/tmp"

[lhjohn]

install cifs used for backup system

sudo apt update sudo apt-get install cifs-utils sudo apt install wget

Install chrome using Internet connection

wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb sudo dpkg -i google-chrome-stable_current_amd64.deb

Started chrome for the first time and made it default browser

google-chrome

[lhjohn]

the R package sodium, which is popular in some OHDSI studies, requires the following cryptography package

sudo apt update sudo apt libsodium-dev

[lhjohn]

Install Intel oneAPI from https://www.intel.com/content/www/us/en/developer/tools/oneapi/base-toolkit.html#gs.toy4lc

sudo sh ./l_BaseKit_p_2021.4.0.3422_offline.sh # replace with correct filename