Additional Useful Information

Ubuntu Server

You can also set up the nodes of the virtual cluster using Ubuntu Server 18.04.

Before following the same steps as with the Ubuntu Desktop, you need to:

• Install unzip by entering the command sudo apt install unzip
• Configure the Internal Network interface to use a static IP address sudo nano /etc/netplan/00-installer-config.yaml by entering the following text:

  network:
      ethernets:
          enp0s3:
              addresses: []
              dhcp4: true
              optional: true
          enp0s8:
              addresses: [192.168.1.1/24]
              dhcp4: no
              dhcp6: no
              nameservers:
                addresses: [8.8.8.8, 8.8.4.4]
      version: 2
  

• sudo netplan apply apply the new settings.
• Repeat for each virtual machine in the virtual cluster with the correct address as mentioned in the network setup section.

Clone a virtual machine

Provided you are using Oracle VirtualBox, to save time during installation you can clone the virtual machine. To do this, follow the steps:

• Start VirtualBox.
• Right-click the fiji-vm1 virtual machine and select the clone menu item.
• In the new form, change the value of the Name field to fiji-vm2.
• Change selected option of the MAC Address Policy to the Generate new MAC addresses for all network adapters value.
• Leave the selection boxes unselected.
• Press the Next button.
• Select the "Full clone" radio button.
• Press the Clone button.

Permanently change the hostname of the virtual machine:

• sudo hostnamectl set-hostname fiji-vm2.
• sudo nano /etc/hostname change hostname to fiji-vm2.
• sudo nano /etc/hosts change hostname to fiji-vm2.
• sudo reboot restart the virtual machine.

You can repeat this process for fiji-vm3 after you have followed all steps necessary to set up a compute node.

Accessing the Virtual Machine in Host

This section will show you how to configure Oracle VirtualBox in order to:

• use HPC Workflow Manager from the host and connect to the virtual cluster.
• connect to the virtual machine using terminal from the host. On Microsoft Windows, PuTTY can be used. This way it is easy to copy and paste while following this guide, without the need to install VirtualBox Guest Additions, or in the case a GUI is not available on the virtual cluster (Ubuntu Server).

Follow the steps:

• From the main menu of Oracle VirtualBox select File > Preferences to open the Preferences window.
• Select the Network tab from the left side of the window.
• Select the green plus button from the right side of the window.
• Double click the newly created item on the NAT Networks list.
• Set the Enable Network select box.
• Set the text value of the field Network Name to "TheNatNetwork".
• Set the text value of the field Network CIDR to "10.0.2.0/24".
• Click on the Port Forwarding button, a new window will appear.
  • Press the green plus button from the right side.
  • Double-click the fields and enter the following values.
  • Name set to "Login Node of Virtual Ubuntu Cluster".
  • Protocol set to "TPC".
  • Host IP set to "127.0.0.1".
  • Host Port set "4444".
  • Guest IP set to "10.0.2.5", this may be different. Find out the IP by entering ip addr show in fiji-vm1.
  • Guest Port set to "22".
• Click the OK button on all three windows consequently.

Turn off the fiji-vm1 virtual machine, and set the new NAT Network with the following steps:

• Now you can right-click the fiji-vm1 virtual machine on the Oracle VirtualBox Manager window (the main window).
• Select the Network tab from the left.
• Set Enable Network Adapter checkbox.
• Set the Attached to option to "NAT Network" option.
• Set the Name to the "TheNatNetwork" option.
• Click the OK button.

Start fiji-vm1, now you should be able to connect using the fiji username and password you set to connect though SSH.

SSH Paradigm Manager Settings

These settings should work if you followed the worksheet's instructions step by step without any modification to the instructions.

Settings	Value	Your Action
Host name	localhost	Copy-paste the value.
Port number	4444	Copy-paste the value.
Username	fiji	Copy-paste the value.
Authentication method	Password	Select the "Password" radio button.
Key File	-	Do nothing.
Key file password	-	Do nothing.
Password	123pass	Replace with the password you chose during installation of ubuntu.
Remote directory with Fiji	/home/user/Fiji.app	Copy-paste the value.
Remote working directory	/mnt/shared/work	Copy-paste the value.
Working directory	C:\Documents\WD	Create a directory in you local machine and browse to it.
Advanced settings	Selected	Do nothing, selected by default.

main hub:house: parent worksheet ☝️