Workstations - BU-ISCIII/BU-ISCIII Wiki

BU-ISCIII workstations are part of our desktop infrastructure, besides several screens, internal HDDs and external HDDs.

An inventory with IPs, HOSTNAMES and item ids can be found in our shared resource bioinfo_doc, inside documentation/BUISCIII_DESKTOP_INFRASTRCUTURE.xlsx.

Software location

Common software from the OS repositories can be installed using the package manager.

Software or software versions not found in the repositories and inteded to be used by all users has to be compiled in /opt/, inside a folder named as the software and version. A symbolic link to the latest version of the software folder has to be created in /opt. This link is later added to /etc/profile.d/extrapath to make the latest version of the software available in $PATH.

Other software needed for testing, developing or one-time use can be installed in the local home folder of the user.

Mounting remote drives

See Data Structure.

Create boot start disk

Download the latest LTS version from ubuntu.com.

In your Linux server open the "startup disk Creation" tool to create a bootable USB disk.

Clean installation

  1. Boot the server using the bootable disk.

There are 2 different settings when installed the OS. It will depend if the server is used for a single user or for many people in the unit.

Installation for single user

Kubuntu

During software installation, select the following options:

  • Which applications would you like to start with?

    • Normal installation

  • Other options

    • Click on the Download updates while installing

  • Click Install third-party software for graphics and Wi-Fi hardware

  • Installation type menu.

    • Where would you like to install ?
      • Click on the "Guided - use entire disk" Create the user "bioinfoadm" with the password we all know and nobody talks about.

Named your computer as, "PC<inventoryNumber>" After finish this step continue on Steps after installation

Gnome

  1. Welcome: Select English in the left panel and install Ubuntu
  2. Keyboard layout: Spanish > Spanish
  3. Updates and other software: Select:
    • Normal installation
    • Install third-party software...
  4. Installation Type: Select:
    • Erase Ubuntu and reinstall
    • Install Now
    • Continue in the new window
  5. Where are you: Madrid
  6. Who are you?:
    • Your name: bioinfoadm
    • Your computer's name: "PC<inventoryNumber>"
    • Username same as your name
    • Password: YKWIM
    • Require my password to log in
    • Continue After finish this step continue on Steps after installation

Workstation installation for several users configuration

When server is planned for computation propose, the installation settings are different to prevent for one side that critical partitions could full by user data and for other hand to install software packets for this propose.

During software installation, select the following options:

  • Which applications would you like to start with?

    • Minimal installation

  • Other options

    • Click on the Download updates while installing

  • Click Install third-party software for graphics and Wi-Fi hardware

  • Installation type menu.

    • Where would you like to install ?
      • Click on Manual
  1. Create swap primary partition at the end of the disk (8000 MB). Select filesystem as ext4 and partition name and label as swap.
  2. Create pvolume in gparted with the rest of disk space. Select as filesystem lvm2 pv, and as partition name and label pvolume.(Remaining space)
  3. Create vgroup and lvolumes with the command line as follows, where is "vg_<your_pc_name>", and <your_pc_name> is "pc" followed by the numeric code on the isciii's label of the physical machine:
pvdisplay
vgcreate <vgroup> /dev/sda3
lvcreate -L 20G -n lv_root <vgroup>
lvcreate -L [whatever space you want to assign to your home]T -n lv_home <vgroup> # Left some space free so you can reassign this space in whatever partition you need in the future.
lvcreate -L 30G -n lv_opt <vgroup>
lvcreate -L 20G -n lv_tmp <vgroup>
lvcreate -L 20G -n lv_var <vgroup>
lvcreate -L 2G -n lv_var_log <vgroup>
lvcreate -L 20G -n lv_root_all <vgroup>
  1. Install your favourite Linux distribution on top of those partitions, assigning the following mounting points:
boot        -> boot     (ext4)
efi         -> efi      (unformated)
lv_root_all -> /        (ext4)
lv_root     -> /root    (ext4)
lv_home     -> /home    (ext4)
lv_opt      -> /opt     (ext4)
lv_tmp      -> /tmp     (ext4)
lv_var      -> /var     (ext4)
lv_var_log  -> /var/log (ext4)
swap        -> swap     (linux_swap)

Continue with the next chapter

Steps after OS installation

Users and groups

  1. Create the following groups replacing the gid values for the ones defined in axterix:
sudo addgroup bioinfo
sudo groupmod -g <gid_bioinfo> bioinfo
sudo addgroup sshaccess
sudo groupmod -g <gid_sshaccess> sshaccess
sudo addgroup bioinfoaccess
sudo groupmod -g <gid_bioinfoaccess> bioinfoaccess
  1. Add bioinfoadm user to the groups
sudo usermod -a -G bioinfoaccess bioinfoadm
sudo usermod -a -G sshaccess bioinfoadm
sudo usermod -a -G bioinfo bioinfoadm
  1. Create your user <user> and add the following groups

3.1 If your user name is already defined in asterix use the same uid and gid as in asterix

sudo adduser <user> -u <uid>
sudo usermod -a -G bioinfoaccess,sshaccess,bioinfo,sudo <user>
sudo groupmod -g <gid> <user>

3.2 If you do not have user account in asterix yet, do the following:

sudo adduser <user>
sudo usermod -a -G bioinfoaccess,sshaccess,bioinfo,sudo <user>

3.2.1 If you get your user account in asterix after some time using your server, perform the following: Use id <user> logged in asterix to know your assigned uid and gid, and change them in your local machine:

usermod -u <uid> <user>
groupmod -g <gid> <user>
  • Change ownership of your files to the new uid and gid. In this example I am assuming 1001 was the uid and gid assigned by default when creating <user> in the local machine, adapt them if needed:
find / -group 1001 -exec chgrp -h <user> {} \;
find / -user 1001 -exec chown -h <user> {} \;
  1. Reboot your server and login with your user.

Install additional software

Once installation is complete, you will need to add the following packages:

  1. sudo apt update
  2. sudo apt upgrade
  3. sudo apt install tmux git git-flow vim vim-gtk zsh nfs-common cifs-utils filezilla docker.io openjdk-11-jdk openjdk-8-jdk net-tools desktop-file-utils openssh-server graphviz sshfs build-essential
  4. To install Google Chrome, download the .deb package and install it using (double click and install inside Ubuntu Software).
  5. Optional software, according to your needs select the ones that apply to you.
sudo apt install synaptic gnome-tweak-tool  gimp inkscape okular

Basic bioinformatics software

Install miniconda. Download latest miniconda bundle in Miniconda download page.

bash Miniconda3-latest-Linux-x86_64.sh

Write "yes" when asking for "Do you wish the installer to initialize Miniconda3"

Mount internal disk at startup

  1. Get the uuid of your disk
ls -al /dev/disk/by-uuid/
  1. Copy the resultant UUID (for your disk) and then open fstab for editing
sudo vim /etc/fstab
  1. Write the following lines at the end of the file by replacing the example value of the UUID by the one your disk
# data drive
UUID=19fa40a3-fd17-412f-9063-a29ca0e75f93 /media/data   ext4    rw,nosuid,nodev,relatime,stripe=8191 0 0
  1. Test the fstab before rebooting (an incorrect fstab can render a disk unbootable). To test do:
findmnt --verify

Check the last line for errors. Warnings can help in improving your fstab.

Set up BackUps plan

Install BackInTime:

sudo add-apt-repository ppa:bit-team/stable
sudo apt-get update
sudo apt-get install backintime-qt4

You can learn more about BackInTime at documentation site.

Backup schedule are running weekly, using BackInTime. to backup our home folder in a remote disk. We are mostly worried about our users data, software can always be reinstalled and containers redownloaded. In order to set up the backup of your home folder of your workstation, follow these steps:

  1. Create your user in the machine containing the backup disks. At this point, the machine is pc046614.
  2. Create a new rsa key and copy it to the repository:
ssh-keygen
ssh-copy-id <user>@10.15.60.49
  1. ssh into pc046614 and create your backup folder (if it does not exists already):
mkdir -p /media/backup
  1. Open BackInTime in your machine and create the following backup plan:
  2. Select your home folder in the include tab, and whatever you want to exclude in the correspondent tab.
  3. In autoremove, set it to this:
  4. Click ok and done! Create your first one on demand to check if everything works.

Configure printers

The printer network in ISCIII is connected via samba, so first we need to install the samba client package:

sudo apt install smbclient

Also, you will need to download and extract the PPD files for the printer models we have.

Now we can start configuring them:

  1. Open ubuntu settings manager
  2. Go to "Devices" -> Printers, scroll down to the bottom of the list of printers and click on "Additional Printer Settings"
  3. Click on "Add", and in the new window select "Network Printer" -> "Windows Printer via SAMBA"
  4. Set SMB Printer Address to:
smb://eunapio/IMVirtual
  1. Set Authentication to "Set authorization details now" and fill the details with your domain password and isciii/<your_domain_username>
  2. Click on "Forward" and now select the option to use your PPD file. Download the PPD file from the manufacturer, for Kyocera are here. You will need to select the right PPD file in "/wherever_you_extracted_PDP_folder/Linux_8.1301_TA...3051_x5x1ci/EU/Spanish/Kyocera_CS_3051ci.PPD".
  3. Finish the configuration setting the alias of the printer if you want and you are ready to go!

WARNING!

Due to internal configuration, if you are not allowed to print in colour you will not be able to print whatever you desire. You can only print word documents by opening them with libreoffice and printing with the advanced option "Colour: print text in black".

Monitoring tools

Additional to htop you can install "btop+" tool to get more information about the process running, memory usage, and some other useful information about your workstation.

To install btop execute these steps

  1. Install compiler version 10 and configure settings
sudo apt install coreutils sed gcc-10 g++-10

 # Select the g++-10 compiler instead of version 9
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-9 40
sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-10 60
sudo update-alternatives --config g++
 # Select in the menu the option for g++-10
  1. Create a temporary directory under Downloads folder
mkdir ~/Downloads/tmp
cd ~/Downloads/tmp
  1. Clone the github respitory located at https://github.com/aristocratos/btop 
git clone https://github.com/aristocratos/btop.git .

  1. Edit the Makefile and search by -std=c++20’ and replace by -std=c++2a'

  2. Then compile and install

sudo make
sudo make install
  1. open the tool with "btop"
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