Avizo Software#
Materials characterization and quality control software for imaging data analysis and quality assurance. More detailed information can be found here
One copy is installed on sgees001.
Connection Configuration#
There are several issues with running software remotely on HPC
- Headless GPU. As the graphics card has no display connection, Avizo won’t detect it. It can be resolved by running of virtual GL server.
- VirtualGL is not supported by x2Go yet. Thought, VNC works fine (TigerVNC, in particular).
- VNC protocol is unsecure and ports are blocked by university firewall. So you you need to pass it through SSH tunnel.
Preparation#
Set up VPN client#
If you’re out of campus, download, install and run VPN client
Set up VNC Server#
- Connect to server via SSH
ssh snowjo@sgees001.geo.vuw.ac.nz
- Set up VNC server on sgees001:
- run
vncserver
and set up password. Then it will crash due to conflict with XFCE desktop environment. We’ll fix it on the next step.
snowjo@sgees001:~$ vncserver
You will require a password to access your desktops.
Password:
Verify:
Would you like to enter a view-only password (y/n)? n
New 'sgees001.geo.vuw.ac.nz:1 (snowjo)' desktop at :1 on machine sgees001.geo.vuw.ac.nz
Starting applications specified in /etc/X11/Xvnc-session
Log file is /Users/home/snowjo/.vnc/sgees001.geo.vuw.ac.nz:1.log
Use xtigervncviewer -SecurityTypes VncAuth -passwd /Users/home/snowjo/.vnc/passwd :1 to connect to the VNC server.
tigervncserver: Failed command '/etc/X11/Xvnc-session': 256!
=================== tail -15 /Users/home/snowjo/.vnc/sgees001.geo.vuw.ac.nz:1.log ===================
See https://www.tigervnc.org for information on TigerVNC.
Underlying X server release 12008000, The X.Org Foundation
Wed Sep 15 15:06:51 2021
vncext: VNC extension running!
vncext: Listening for VNC connections on local interface(s), port 5901
vncext: created VNC server for screen 0
You are using 21 GB (172788 files) of 150 GB.
X connection to :1 broken (explicit kill or server shutdown).
Wed Sep 15 15:06:52 2021
ComparingUpdateTracker: 0 pixels in / 0 pixels out
ComparingUpdateTracker: (1:-nan ratio)
Killing Xtigervnc process ID 4049134... which seems to be deadlocked. Using SIGKILL!
=======================================================================================================
Starting applications specified in /etc/X11/Xvnc-session has failed.
Maybe try something simple first, e.g.,
tigervncserver -xstartup /usr/bin/xterm
- Now create a new custom startup file as
~/.vnc/xstartup
, make it executable
touch ~/.vnc/xstartup
chmod +x ~/.vnc/xstartup
and paste the following:
#!/bin/sh
# Uncomment the following two lines for normal desktop:
# unset SESSION_MANAGER
# exec /etc/X11/xinit/xinitrc
[ -x /etc/vnc/xstartup ] && exec /etc/vnc/xstartup
[ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources
xsetroot -solid grey
vncconfig -iconic &
x-terminal-emulator -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" &
x-window-manager &
- Then start server again:
snowjo@sgees001:~$ vncserver
New 'sgees001.geo.vuw.ac.nz:1 (snowjo)' desktop at :1 on machine sgees001.geo.vuw.ac.nz
Starting applications specified in /Users/home/snowjo/.vnc/xstartup
Log file is /Users/home/snowjo/.vnc/sgees001.geo.vuw.ac.nz:1.log
Use xtigervncviewer -SecurityTypes VncAuth -passwd /Users/home/snowjo/.vnc/passwd :1 to connect to the VNC server.
Set up SSH Tunnel#
Note the port VNC server is running on
snowjo@sgees001:~$ vncserver -list
TigerVNC server sessions:
X DISPLAY # RFB PORT # PROCESS ID
:1 5901 138974
In our case it’s 5901, so we forward it via another SSH session. Start from your home computer:
ssh -L 5901:localhost:5901 snowjo@sgees001.geo.vuw.ac.nz
If in Windows, follow the https://linuxize.com/post/how-to-setup-ssh-tunneling/#set-up-ssh-tunneling-in-windows
To protect your tunnel from disconnect after idle timeout, add the following lines to the top of your local ~/.ssh/config (Linux or MacOS)
Host *
ServerAliveInterval 100
In Windows find the relevant settings in PuTTY configuration.
Run Avizo#
Start VPN#
Start VPN client and connect to vpn.vuw.ac.nz
Start VNC Client#
You need a TigerVNC client installed on your local computer (https://tigervnc.org/
, https://github.com/TigerVNC/tigervnc/releases
, https://sourceforge.net/projects/tigervnc/files/stable/)
.
Start it and connect to localhost:port
, where port is the port number from above, e.g. localhost:5901
. Type your VNC password when prompted. You should see a grey window with a single terminal application.
Start Avizo#
Run vglAvizo
in terminal. That’s all.
After you finish#
Exit Avizo#
Close Avizo window, then close VNC client on your local computer.
Stop VNC server#
Check if any VNC sessions are still running:
snowjo@sgees001:~$ vncserver -list
TigerVNC server sessions:
X DISPLAY # RFB PORT # PROCESS ID
:1 5901 138974
And kill them all:
snowjo@sgees001:~$ vncserver -kill
Killing Xtigervnc process ID 138974... success!
Stop SSH tunnel#
Exit from second SSH session (where you started ssh -L
)
Stop VPN#
It’s better to keep it off (unless you need to connect to campus network) for avoiding of various connectivity issues.