Laboratory for Scientific Computing

Remote working

Linux remote working

The following instructions assume that you have a working knowledge of ssh and have an ssh client installed on your home computer. Linux and Mac OS X will have this installed already. Windows users should install PuTTY from the official site.

Accessing the CSC network from inside the CUDN

If you are in another Department, or in University/College accommodation, then you can use ssh to access all CSC machines. You will need to append .lsc.phy.private.cam.ac.uk to the machine names first.

Accessing the CSC network from outside CUDN

The CSC desktops are on a private network within the University Data Network (CUDN). In order to access them, you therefore need to gain access to the CUDN. There are two ways to do this:

Use the University's VPN service

If you follow the instructions for your local OS at UIS VPN then your local machine will effectively be on the University network and you can access the machines via ssh as normal. If you get a message such as:

Could not resolve hostname chaos.lsc.phy.private.cam.ac.uk: Name or service not known

then try using the specific IP address for the machine instead. (See CSC Systems.)

The drawback of this approach is that all of your internet traffic (YouTube, FaceBook, etc.) then goes through Cambridge. A more nuanced approach follows.

Use Split VPN

This approach is more involved than the VPN above, but is more optimal. Following this, only Internet traffic destined for University hosts will use the VPN, and other traffic (YouTube, Facebook, etc.) will go direct as usual.

If you have a CSC laptop, then you can use the custom command

setup_vpn

which will set all of the following for you.

Manual Split VPN

These instructions require you to have root/sudo access. If you do not, the full VPN approach is easier.

Install the StrongSwan packages and all plugins:

sudo apt install strongswan-charon libcharon-extauth-plugins libcharon-extra-plugins

Create a new UIS Network Access Token by going to: UIS Tokens.

For example, pmb39+desktop@cam.ac.uk with token: mytokenis2secret.

Add the following to the file /etc/ipsec.conf: 

conn UIS
  keyexchange=ikev2
  reauth=no
  left=%any
  leftid="USERNAME"
  leftauth=eap
  leftsourceip=%config4,%config6
  leftfirewall=yes
  right="vpn.uis.cam.ac.uk"
  rightid="vpn.uis.cam.ac.uk"
  rightca="C=US, ST=New Jersey, L=Jersey City, O=The USERTRUST Network, CN=USERTrust RSA Certification Authority"
  rightsubnet=131.111.0.0/16,172.16.0.0/13,172.24.0.0/14,172.28.0.0/15,172.30.0.0/16
  rightdns=131.111.8.42, 131.111.12.20
  auto=add

ca AAA
  cacert=/etc/ssl/certs/Comodo_AAA_Services_root.pem
  auto=add

where USERNAME would be pmb39+desktop@cam.ac.uk in my case.

Now, add your username and token to /etc/ipsec.secrets:

pmb39+desktop@cam.ac.uk : EAP "mytokenis2secret"

(See above for how to create your own token.)

In order to connect to the VPN, do:

sudo service strongswan-starter restart
sudo ipsec reload

In order to connect to the VPN, do:

sudo ipsec up UIS

In order to test the connection, go to UIS IP checking site. You should see two separate IP addresses, one as your normal IP address (for servers outside the University), and one of the form 172.16.x.y for servers inside the University.

Now, you should find that ssh apollo.lsc.phy.private.cam.ac.uk connects correctly.

Split VPN on Windows/Mac OS

General instructions for VPN on Mac OS and Microsoft Windows are available from the UIS.

For a split VPN on Windows, make sure that "Use default gateway on remote network" is NOT checked (contrary to UIS's instructions). If you had already set up your VPN connection, then start from Step 10 on the above page to find the "Use default gateway" option and uncheck it (then click OK when closing the settings boxes).

If you are connected to the VPN already, then disconnect from it.

  • Open a PowerShell Terminal by going to the Windows "Start" menu, and typing "Powershell".
  • Click the "Windows PowerShell" app to run it.
  • At the terminal, type the following two commands:
    • Add-VpnConnectionRoute -ConnectionName 'Cambridge VPN' -DestinationPrefix 131.111.0.0/16
Add-VpnConnectionRoute -ConnectionName 'Cambridge VPN' -DestinationPrefix 172.24.0.0/14
  • (where 'Cambridge VPN' is whatever you called your VPN connection). This ensures that any network connection to Cambridge public IPs (131.111.*.*) and private IPs (172.24.*.*) goes via the VPN.
  • Reconnect to your VPN (on the task-bar: click the Network icon, then find the "Cambridge VPN" connection and click Connect).

Check that it's worked by going to:

  • UIS's IP checker (should show 172.16.***.***)
  • and What's My IP (should show something *not* in 172.x.x.x)
  • PuTTY or WSL connections to apollo.lsc.phy.private.cam.ac.uk should also succeed.

For a split VPN on Mac OS, please let me know appropriate instructions.

Data access

Remember that all machines have one (or more) scratch data partitions, which can be used to store large amounts of data. More details are at scratch-data.

Usability tools

With remote connections, there is a risk that the connection will drop (poor connection or your own machine needs rebooting).

The GNU screen utility can be used to run several text-terminals over a single ssh connection. To start, run screen. Useful commands are:

  • Ctrl-A Ctrl-C: Create a new terminal
  • Ctrl-A 0: Go to terminal 0 (works for 0-9)
  • Ctrl-A Ctrl-D: Detach from a screen session (while keeping all terminals running).
  • Ctrl-A [: Then use PgUp/PgDown to scroll through terminal output.

If you log into a machine where a screen session is already running, screen -x -r will reconnect you to it.

Graphical access

The majority of Scientific Computing work should be possible via a simple command-line interface.

If not, then the use of ssh -X should work, although relatively slowly.

VNC Access (Remote Desktop)

For more efficient access to a desktop session on a remote machine, you can make use of VNC.

On the remote machine (e.g. apollo), create a file ~/.vnc/xstartup with contents:

#!/bin/sh

unset SESSION_MANAGER
unset DBUS_SESSION_BUS_ADDRESS

[ -x /etc/vnc/xstartup ] && exec /etc/vnc/xstartup
[ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources
xsetroot -solid grey
vncconfig -iconic &

startxfce4 &

Make it executable: chmod u+x ~/.vnc/xserver.

Now on apollo run vncserver which will ask you to create a password (different from your usual CSC password), and then launch a desktop session (invisibly).

You can have multiple desktop sessions running on multiple machines; you need to keep track of the desktop numbers, or look in ~.vnc/ for a list of desktops. This will affect the localhost:1 or 5901 ports mentioned below e.g. desktop 3 would be at localhost:3 or port 5903.

To end a remote desktop session entirely, run vncserver -kill :1 to kill desktop 1, for example.

VNC from Linux

On your local laptop/desktop, install TurboVNC:

  • Download the correct release from TurboVNC Releases where TurboVNC-*.deb should be used for Ubuntu/Debian/etc. distributions, or TurboVNC-*.rpm for Fedora/RedHat/etc.
  • Install this using: 
    	    sudo dpkg -i ./TurboVNC.deb

Now, to connect from your local Linux desktop to the remote one, set up ssh-tunnelling from your local machine:

ssh -L 5901:localhost:5901 pmb39@apollo.lsc.phy.private.cam.ac.uk

Then, connect to the VNC session:

vncviewer localhost:5901

The first command redirects port 5901 on localhost to port 5901 on apollo; the second command then connects the VNC viewer to port 5901 on localhost.

VNC from Windows

On your local laptop/desktop, install TurboVNC:

  • Download the correct release from TurboVNC Releases where TurboVNC-*-x64.exe should be used for Windows.
  • Install this by running the downloaded executable.
  • Run TurboVNC from your Windows app menu, and fill in the name and port of the remote server: For example: apollo.lsc.phy.private.cam.ac.uk::5901
  • Then, click Options, and go to the Security tab: Leave all settings as default, except for the bottom section "Gateway (SSH server)" where you should fill in your username on apollo and check the box "Use VNC server as gateway"
  • Click OK, then click Connect.
  • You will be prompted first for your ssh-password for apollo, then for your VNC password on apollo (which should be different).

3D Remote graphics

Due to the complex interaction between graphics drivers and displays, a VNC session will not work properly for 3D graphics. In this case, you can use a machine with VirtualGL installed to run a single graphical program:

  • On your laptop: download VirtualGL from: VirtualGL (it takes a few seconds to start)
  • Install VirtualGL:
    • In a terminal: 
    su
[ Enter root password ]
dpkg -i /home/username/Downloads/virtualgl_2.6.3_amd64.deb
exit [ to return to normal user ]
  • Connect to chaos (the only machine with VirtualGL installed at the moment):
    • vglconnect -s pmb39@chaos.lsc.phy.private.cam.ac.uk
[ You will need to enter your password twice ]
  • Run VisIt under VGL:
    • /opt/VirtualGL/bin/vglrun /lsc/opt/visit/bin/visit
  • You should find that the meshing window is no longer black.

VNC and VirtualGL

In theory, it should be possible to use VirtualGL from inside a VNC session. However, this does not work on any machine properly yet.

Specific visualisation tools

Many scientific computing disciplines have their own visualisation tools. If you need help with specific ones not listed below, please let me know.

VisIt

VisIt supports a wide range of operating systems by default, including Ubuntu, Mac OS X and Windows. See VisIt executables and follow the appropriate instructions for your system.

If you need to use VisIt remotely, you can set it up in client-server mode. Make sure you have installed VisIt 3.0.2 (later versions may not work), then go to Options -> Host profiles, and enter information as below, for example.

Note that this uses the IP address of apollo, not its full name, due to the system I used to generate this image.

More details are at Visualisation.

AMRvis

Anyone using AMReX-based code for visualisations can run AMRvis:

cp /lsc/opt/bin/amrvis.defaults ~/
/lsc/opt/bin/amrvis2d.gnu.ex