Athena System Configuration

Disk Structure

• All user partitions are formatted with ext4 file systems.

Software Configuration Changes

Late Oct. 2021: Did additional installations of Open MPI and Intel oneAPI Fortran

• Steps to install Open MPI and the Intel oneAPI Fortran compiler in Ubuntu 20.04:

$ sudo apt install openmpi-bin libopenmpi-dev
$ wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
$ sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
$ rm GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
$ sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
$ sudo apt install intel-oneapi-compiler-fortran

• Ref. 1 - Install Open MPI from repository with GCC instead of Intel
• Ref. 2 - Intel releases oneAPI Toolkit, free, Fortran 2018
• Here are the required entries in .bashrc to make the above work together correctly:

source /opt/intel/oneapi/compiler/latest/env/vars.sh
export OMPI_FC=ifort

• Don't run "source /opt/intel/oneapi/setvars.sh", as this activates Intel MPI along with the compiler.

Jan. 2022: Installed OpenSSH, new NVIDIA drivers, DKMS, X2Go server, and MATE desktop environment

• The OS had "kept back" an unattended upgrade of libnvidia-common-470, leaving the machine without a graphics display.
• This issue was resolved by manually installing one of the package's X11 dependencies (see https://askubuntu.com/a/602).
• But before that, even, SSH access to the workstation had to be established by installing the OpenSSH server.

$ sudo add-apt-repository ppa:graphics-drivers/ppa   #this turned out to be unnecessary
$ sudo apt update
$ sudo apt install net-tools
$ sudo apt install openssh-server
$ sudo apt install dkms   #ensuring that the NVIDIA kernel modules will be rebuilt, for initramfs
$ sudo apt upgrade   #(among other things, this step upgraded ifort from 2021.4 to 2022.0)
$ sudo apt install xserver-xorg-video-nvidia-470
$ sudo reboot    #this is what triggers DKMS

• The system was now ready to accept the latest NVIDIA drivers:

$ sudo apt install nvidia-driver-495
$ sudo apt autoremove   #to clean up old packages
$ sudo reboot   #to trigger DKMS again

• The output of "nvidia-smi" and "lsmod | grep nvidia" gave sensible results after this, and the display started working again.
• To improve remote access, X2Go server and MATE desktop environment were then installed:

$ sudo add-apt-repository ppa:x2go/stable   #output of this gave info for subsequent steps
$ sudo apt-get install x2goserver x2goserver-xsession
$ sudo apt install mate-core mate-desktop-environment mate-notification-daemon
$ sudo apt-get install x2gomatebindings
$ sudo apt install mesa-utils   #for glxinfo diagnostics

• Ref. - Connect to Ubuntu 20.04 Remote Desktop using X2Go
• The following command was found to be necessary to get ParaView 5.10 to work properly in X2Go:

$ paraview --mesa

May 2023: Did a system refresh, made preparations for adding remote users

• Performed the usual steps for a general system upgrade in Ubuntu:

$ sudo apt update
$ sudo apt upgrade
$ sudo reboot

• The hostname was changed from cornell-SYS-740A-T to athena.lps.cornell.edu, to match the new network name in DNS.

$ sudo hostnamectl set-hostname athena.lps.cornell.edu

• Ref. - How to Change Hostname on Ubuntu 20.04
• Next, a startup file was created to automatically set up the environment for Open MPI and Intel Fortran in every new shell:

$ sudo apt install emacs
$ emacs /etc/profile.d/zzintel-openmpi.sh   #insert the desired commands...
$ cat /etc/profile.d/zzintel-openmpi.sh
if [ -z "`echo $PATH | grep intel`" ]; then
  source /opt/intel/oneapi/compiler/latest/env/vars.sh
fi
export HWLOC_COMPONENTS=-gl
export OMPI_FC=ifort

• The MATE desktop had some oddities in its appearance and behavior which needed correction.
  • After lots of messing around, it turned out that the default theme, Ambiant-MATE, was actually missing.
  • Other issues: an ugly background; heavy black borders around windows; and screen lock after a short time.
• The following changes to defaults fixed these issues, while adding a couple of launchers to the top panel:

$ sudo apt install ubuntu-mate-themes   #this also installs ubuntu-mate-icon-themes
$ sudo emacs /usr/share/glib-2.0/schemas/35_mate-ubuntu.gschema.override   #a new file, with overrides...
$ cat /usr/share/glib-2.0/schemas/35_mate-ubuntu.gschema.override
[org.mate.desktop.background]
picture-filename='/usr/share/backgrounds/mate/abstract/Waves.png'

[org.mate.Marco.general]
compositing-manager=false
 
[org.mate.screensaver]
idle-activation-enabled=false

[org.mate.panel]
default-layout='familiar-pv'
$ sudo glib-compile-schemas /usr/share/glib-2.0/schemas/
$ rm -rf ~/.config   #log out, log back in, changes were in effect

• Ref. 1 - Restore Ambiant-MATE & Themes
• Ref. 2 - How to set system-wide (for all users) defaults for MATE desktop?
• Ref. 3 - x2go MATE Compiz thick black window borders (Note, Marco should be capitalized)
• Ref. 4 - Ubuntu Mate shows no panels, but with a new user shows. How I can reset the settings?


• Steps for creating launchers in the top panel were informed by what was done for configuring Hermes in 2017.
• Positions for launchers were determined by adding them manually with mate-tweak, then saving the configuration.
  • ParaView 5.10 already existed as a main menu entry under "Other", so mate-tweak could select it for the panel.
  • Saved info was found (via "grep -r panel") to be in ~/.config/dconf/user, suggesting a way to view the settings.
  • Ref. - How to save Mate desktop panel configs

$ sudo apt install mate-tweak
$ mate-tweak
$ dconf dump /org/mate/ | less   #note positions, use them later for editing the layout
$ gsettings get org.mate.panel default-layout
'familiar'
$ sudo cp /usr/share/mate-panel/layouts/familiar.layout /usr/share/mate-panel/layouts/familiar-pv.layout
$ sudo emacs !$   #edited the familiar-pv.layout file to add the MATE Terminal and ParaView launchers...
$ diff /usr/share/mate-panel/layouts/familiar*.layout
25a26,39
> [Object mate-terminal]
> locked=true
> position=122
> launcher-location=/usr/share/applications/mate-terminal.desktop
> toplevel-id=top
> object-type=launcher
> 
> [Object launcher]
> locked=true
> position=158
> launcher-location=/usr/share/applications/paraview-mesa.desktop
> toplevel-id=top
> object-type=launcher
> 
$ sudo cp /usr/share/applications/paraview.desktop /usr/share/applications/paraview-mesa.desktop
$ sudo emacs !$   #edited the paraview-mesa file so it would start properly in MATE desktop...
$ gsettings set org.mate.panel default-layout 'familiar-pv'
$ gsettings get org.mate.panel default-layout
'familiar-pv'
$ mate-panel --reset
$ sudo glib-compile-schemas /usr/share/glib-2.0/schemas/
$ rm -rf ~/.config   #log out, log back in, changes were in effect

• Note that the new paraview-mesa.desktop had to be created from the preexisting paraview.desktop.
  • This needed to be done because ParaView must be started with "paraview --mesa" in X2Go.
  • Also, the preexisting paraview.desktop presumably works fine on Prof. Seyler's office desktop.
  • The contents of paraview-mesa.desktop follow...

$ cat /usr/share/applications/paraview-mesa.desktop
[Desktop Entry]
Version=1.0
Name=ParaView 5.10 (Mesa)
Comment=Create 3d visualizations of data
Exec=/opt/ParaView-5.10/bin/paraview --mesa
Terminal=false
Icon=/opt/ParaView-5.10/share/icons/hicolor/96x96/apps/paraview.png
Type=Application
x-Ayatana-Desktop-Shortcuts=NewWindows

[NewWindow Shortcut Group]
Name=New Window
TargetEnvironment=Unity

• In the midst of fixing the desktop, the ssh metapackage (client and server) was upgraded to 1:8.2p1-4ubuntu0.7.

Nov. 2023: Updated ParaView to 5.11.2

• The file ParaView-5.11.2-MPI-Linux-Python3.9-x86_64.tar.gz was downloaded from the Download ParaView website.
• The contents of the uncompressed tar file were ultimately moved to /opt/ParaView-5.11.2.
• Owner and group for this folder were then changed, recursively, to the main owner name.
• However, for the new version, launching "paraview --mesa" in X2Go resulted in an error like the following:

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized.
Reinstalling the application may fix this problem.

• A few suggestions for how to fix such an error could be found online...
  • Ref. - solved: Could not load the Qt platform plugin "xcb"
  • The second command below is the one that worked:

$ sudo apt-get install libxcb-xinerama0
$ sudo apt-get install '^libxcb.*-dev' libx11-xcb-dev libglu1-mesa-dev libxrender-dev libxi-dev \
  libxkbcommon-dev libxkbcommon-x11-dev

• All occurrences of 5.10 were then changed to 5.11.2 in /usr/share/applications/paraview.desktop and paraview-mesa.desktop.
• The softlink in /usr/bin was likewise updated:

$ sudo rm /usr/bin/paraview
$ sudo ln -s /opt/ParaView-5.11.2/bin/paraview /usr/bin/paraview