Avizo

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#

sgees001_vgl.svg There are several issues with running software remotely on HPC

  1. 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.
  2. VirtualGL is not supported by x2Go yet. Thought, VNC works fine (TigerVNC, in particular).
  3. 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#

  1. Connect to server via SSH

ssh snowjo@sgees001.geo.vuw.ac.nz

  1. 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
touch ~/.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.