metomi-vms

Vagrant virtual machines with FCM + Rose + Cylc installed.

Table of contents:

• Software Requirements
• Setting up the Default Virtual Machine
• Using the Default Virtual Machine
• Disabling the Desktop Environment
• Using other Virtual Machines
• Optional Windows Software
  • Git BASH
  • Cygwin
• Ubuntu Pro
• VMware
• libvirt
• Troubleshooting
• Amazon AWS

Software Requirements

In order to use a virtual machine (VM), you must first install:

• VirtualBox, software that enables running of virtual machines (version 5.1.x or later required).
  • As an alternative, VMware Workstation Player (version 16 or later) or VMware Fusion Player (version 12 or later) can also be used to run the virtual machine. See the VMware section for further information.
• Vagrant, software that allows easy configuration of virtual machines (version 2.0.x or later required).

These applications provide point-and-click installers for Windows and can usually be installed via the package manager on Linux systems.

Setting up the Default Virtual Machine

After you have installed VirtualBox and Vagrant, download the metomi VM setup files from github:

• https://github.com/metomi/metomi-vms/archive/master.zip.

Then extract the files which will be put into a directory called metomi-vms-master.

The default VM uses Ubuntu 18.04. If necessary you can customise the VM by editing the file Vagrantfile.ubuntu-1804 as follows:

• By default the VM will be built with support for accessing the Met Office Science Repository Service. If you don't want this (or don't have access) then remove mosrs from the args in the config.vm.provision line.
• As described below, you may prefer not to install the desktop environment. To do this remove desktop from the args in the config.vm.provision line and comment out the line v.gui = true.
• By default the VM is configured with 1 GB memory and 2 CPUs. You may want to increase these if your host machine is powerful enough.

See the Vagrant documentation for more details on configuration options.

Before proceeding you need to be running a terminal with your current directory set to metomi-vms-master.

• Windows users can navigate to the directory using Windows File Explorer and then use Shift-> Right Mouse Click -> Open command window here.

Now run the command vagrant up to build and launch the VM. This involves downloading a base VM and then installing lots of additional software so it can take a long time (depending on the speed of your internet connection). Note that, although a login screen will appear in a separate window, you will not be able to login at this stage. Once the installation is complete the VM will shutdown.

Using the Default Virtual Machine

Run the command vagrant up to launch the VM. A separate window should open containing a lightweight Linux desktop environment (LXDE) with a terminal already opened.

If your VM includes support for the Met Office Science Repository Service then you will be prompted for your password (and also your user name the first time you use the VM). If you get your username or password wrong and Subversion fails to connect, just run mosrs-cache-password to try again.

The VM is configured with a local Rose suite repository and with the suite log viewer running under apache. If you want to learn more about Rose and Cylc you can follow the tutorials contained in the Rose User Guide.

To shutdown the VM you can either use the menu item available in the bottom right hand corner of the Linux desktop or you can issue the command vagrant halt from the command window where you launched the VM.

Note that the desktop environment is configured to use a UK keyboard. If you need to change this, take a look at how this is configured in the file install-desktop.sh.

Disabling the Desktop Environment

If you are using the VM on a Mac or Linux system where you already have a X server running then you may find it easier to not install the desktop environment. In order to do this, edit the file Vagrantfile.ubuntu-1804 as described above. Then run the command vagrant up to launch the VM in the normal way. Note that, unlike when installing the desktop environment, it will not shutdown after the initial installation.

Once the VM is running, run the command vagrant ssh to connect to it.

To shutdown the VM you can either run the command sudo shutdown -h now from within your ssh session or you can exit your ssh session and then issue the command vagrant halt.

Using other Virtual Machines

In addition to the default VM, additional VMs are supported in separate files named Vagrantfile.<distribution>, e.g. Vagrantfile.centos-7. These other VMs are provided primarily for the purpose of testing FCM, Rose & Cylc on other Linux distributions and providing a reference install on these platforms. Note that they are not as well tested as the default VM and may not include a desktop environment.

To use a different VM, modify the file which is loaded in the default Vagrantfile before running vagrant up. Alternatively you can set the environment variable VAGRANT_VAGRANTFILE, for example:

export VAGRANT_VAGRANTFILE=Vagrantfile.ubuntu-1604

(use set in place of export when using the command window on Windows).

Optional Windows Software

Git BASH

For an alternative to the normal command window, Windows users can install Git BASH (which comes with Git for Windows). As well as providing a nicer interface (more familiar for Linux users) this also means that you can use git to clone the metomi-vms repository (instead of downloading the zip file):

git clone https://github.com/metomi/metomi-vms.git

It is then easy to track any local changes, pull down updates, etc.

Cygwin

If you want to run a VM without a desktop environment on Windows then, in order to enable GUI programs to work, you will need to install Cygwin, making sure to select the xinit and xorg-server packages from the X11 section and the openssh and openssl packages from the Net section.

Then, instead of using a normal command window for launching the VM, you should use a Cygwin-X terminal, which you can find in the Start Menu as Cygwin-X > XWin Server. In Cygwin-X terminals, you can use many common Unix commands (e.g. cd, ls). Firstly run the command cd /cygdrive followed by ls and you should see your Windows drives. Then use the cd command to navigate to the directory where you have extracted the setup files (e.g. c/Users/User/metomi-vms-master).

Ubuntu Pro

While Ubuntu 18.04 LTS went end-of-life in May 2023, an Ubuntu Pro subscription can be used to get security updates for a further 5 years. This is free for personal use for up to 5 machines and the process is documented in a Tutorial. Before you run the sudo apt update && sudo apt upgrade commands, you should first

sudo apt-mark hold gpg-agent

After rebooting, you may get the error "gpg-preset-passphrase: caching passphrase failed: Not supported". Here you will need to re-install gpg-agent manually, in a similar way to how it is originally installed in the install-mosrs script:

sudo apt-get remove -q -y --auto-remove --purge gpg-agent
curl -L -s -S https://www.gnupg.org/ftp/gcrypt/gnupg/gnupg-2.0.31.tar.bz2 | tar -xj
cd gnupg-2.0.31/
./configure CFLAGS="-fcommon"
make
sudo make install

When you reboot your VM you may also get the error "Vagrant was unable to mount VirtualBox shared folders". This can be fixed by re-installing the VirtualBox guest additions, which can be done via the command-line by

sudo apt install -y virtualbox-guest-additions-iso

You may find that this is sufficient to fix the error after rebooting. If it is not, you can manually install them by

sudo mount -o loop /usr/share/virtualbox/VBoxGuestAdditions.iso /media/cdrom
sudo /media/cdrom/VBoxLinuxAdditions.run
sudo umount /media/cdrom

and then rebooting the VM.

VMware

As an alternative to VirtualBox, VMware Workstation Player (Windows, Linux) or (VMware Fusion Player (macOS) can be used to host the virtual machine. VMware Workstation Player is free for non-commercial use and VMware Fusion Player is free with a Personal Use License.

You will need to download and install

• VMware Workstation Player (version 16 or later) or VMware Fusion Player (version 12 or later)
• The Vagrant VMware utility
• The Vagrant VMware plugin by running the command vagrant plugin install vagrant-vmware-desktop

The configuration settings can be found in the Vagrantfile.vmware_ubuntu-1804 file. To bring the box up using VMware, you should set your VAGRANT_VAGRANTFILE to Vagrantfile.vmware_ubuntu-1804 before running the command

vagrant up --provider=vmware_desktop

You may have issues if both VMware and VirtualBox are installed, or if the Hyper-V hypervisor is also running. If you are using an Apple Silicon device with VMware Fusion you will need to set the following

config.vm.box = "uwbbi/bionic-arm64"

in the Vagrantfile.vmware_ubuntu-1804 file as you cannot use an amd64-based installation on Apple Silicon (ARM-based) hardware.

libvirt

Another alternative to VirtualBox and VMware is to use the libvirt virtualisation API, which also has a Vagrant plugin. You will need to install libvirt on your host system. You should set your VAGRANT_VAGRANTFILE to Vagrantfile.libvirt_ubuntu-1804 before running the command

vagrant up --provider=libvirt

to provision the VM. The current Vagrantfile has been used on a GNU/Linux host without a graphical login.

The advantage of this method is that it allows for PCI passthrough, allowing the guest OS to directly access hardware on the host, for instance allowing the guest to access a GPU on the host machine. On a GNU/Linux system you can use the lspci -v command to determine the device information, and then include a block such as this within the config.vm.provider section of the Vagrantfile.libvirt_ubuntu-1804 file:

    # VGA controller on 65:00.0
    v.pci :domain => '0x0000', :bus => '0x65', :slot => '0x00', :function => '0x0'
    # Audio controller on 65:00.1
    v.pci :domain => '0x0000', :bus => '0x65', :slot => '0x00', :function => '0x1'
    # USB controller on 65:00.2
    v.pci :domain => '0x0000', :bus => '0x65', :slot => '0x00', :function => '0x2'
    # Serial bus controller on 65:00.3
    v.pci :domain => '0x0000', :bus => '0x65', :slot => '0x00', :function => '0x3'

This step needs to be done on the initial creation of the VM. The GPU would also need to be isolated from the host system.

Troubleshooting

Guest display resolution

When you resize the VirtualBox window (e.g. to mazimise it) the display resolution of your Linux VM should adjust to match. If this doesn't work it may be due to the Guest Additions installed in your VM not matching the version of VirtualBox you have installed. The easiest way to fix this is to install the vagrant-vbguest Vagrant plugin. Note that, if the plugin does update your Guest Additions then you will need to shutdown and restart your VM (using vagrant up) in order for them to take effect.

Amazon AWS

It is possible to run using Vagrant on an Amazon AWS EC2 virtual machine. To do this you will need to install the vagrant-aws plugin. You do not need VirtualBox. You should ensure that you are using a recent version of Vagrant to enable the AWS plugin to work, and you will first need to run the command

vagrant box add dummy https://github.com/mitchellh/vagrant-aws/raw/master/dummy.box

in a different directory to your metomi-vms directory.

Some set-up is required within the AWS console. You will first need to:

1. Generate a key to allow you to connect to the VM
2. Create a security group and restrict incoming access to the IP address of your computer
3. Create a user and make a note of the required information

The information in points 1 & 2 will need to be saved to a file called aws-credentials - an example one is provided which looks like

export VAGRANT_VAGRANTFILE=Vagrantfile.aws_ubuntu-1804
export AWS_KEY='AAAAAAAAAAAAAAAAAAAA'
export AWS_SECRET='BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'
export AWS_KEYNAME='CCCCCCCCC'
export AWS_KEYPATH='/full/path/to/CCCCCCCCC'

If you are using Windows you may want to replace the options in the Vagrantfile directly, but be careful not to commit this information back to a public repository.

Note that because the default username for EC2 Ubuntu VMs is ubuntu the /home/ubuntu directory has also been symbolically linked to /home/vagrant. You should continue to work under the ubuntu user as normal.

VM size

There are many different sizes of VM to choose from (known as instance types), some of which will be eligible for the free tier, e.g. t2.micro that has 1 CPU and 1GB of memory. To be able to run the UM you will need to select a larger type, such as t2.medium(2 CPUs and 4GB of memory) or t2.large(2 CPUs and 8GB of memory). This is changed in the aws.instance_type setting in the Vagrantfile. You can also select faster hardware, e.g. the m5 hardware uses faster Intel Xeon processors with a greater network and storage bandwidth, and may give better performance. Larger and faster options are available, but these will all come with an associated cost.

The hard disk size of the VM is set to 30GB in the Vagrantfile in the aws.block_device_mapping setting. This can be changed as required. The default t2.micro size is 8GB if nothing is set.

It is possible to resize your VM by changing the instance type once it has been created. To do this you need to first stop it using

vagrant halt

and then follow the instructions for changing the instance using the AWS console.

Chose your region

On the AWS console you should change your region to the one where you want the VM to be provisioned by using the drop-down menu on the top right of the page. The default settings may put you in us-east-2 (US East (Ohio)), but you may want to change this to, e.g., London (or eu-west-2).

From here you should click the All services drop-down menu, and then click EC2 to enter the EC2 Dashboard.

There are many different types of EC2 VMs (e.g. Ubuntu, Amazon Linux etc.), which are identified by their unique ami- identifier. This identifier is also unique to a particular region. The setting for Ubuntu 18.04 LTS in the London (eu-west-2) region has already been set in the aws.ami setting in the provided Vagrantfile. If you wish to use a different region you will need to search for the correct ami- identifier from the Launch instance option within the EC2 Dashboard and then set this in the Vagrantfile accordingly.

Create your key pair

In the EC2 Dashboard scroll down the left-hand menu until you find Network & Security and click Key Pairs, and then click Create key pair on the top right.

Here you should give your key a name, e.g. "vagrant" or "metomi-vms" etc. You should keep the pem file format, and then click Create key pair. Save this file to your local machine, and ensure it has the correct permissions so that it is only readable by you.

You should add the name of and full path to your key to your aws-credentials file. Note that the name should not include any extension (e.g. .pem), but the full path should.

Create a security group to limit IP access to your VM

In the EC2 Dashboard scroll down the left-hand menu until you find Network & Security and click Security Groups, and then click Create security group on the top right.

You should give it a name, e.g. MyIP as is used in the Vagrantfile, and a description (e.g. "limit access to my IP"). Scroll down to the Inbound rule section and click Add rule.

Here, use the drop-down menus to change the Type to All traffic and the Source to My IP (your current IP address will be automatically added). Scroll down to the bottom of the page and click Create security group.

If you used a name other than "MyIP" for the name of the group you will need to update the aws.security_groups setting in the AWS Vagrantfile.

Create a user

You will need to create a user with the correct permissions to access your EC2 VM, which again is done via the console. This is not done within the EC2 Dashboard, but is instead done within the IAM Dashboard (Identity and Access Management). To get to this from the EC2 Dashboard first click the AWS logo on the top left of the page to bring you back to the console front page, and then click the All services drop-down menu, and then click IAM under the "Security, Identity, & Compliance" section.

Under Access Management click Users and then click Add user. You should give them a name, e.g. vagrant or metomi-vms etc.. Tick the box for Programmatic access and then click the Next: Permissions button.

Here you should click the tab labelled Attach existing policies directly and search for AmazonEC2FullAccess and then tick the check-box next to this option. Now click the Next: Tags button. You can then click the Next: Review button.

Now click Create user. This will bring you to a page listing the username, the Access key ID and the Secret access key. THE SECRET ACCESS KEY INFORMATION WILL BE DISPLAYED ONLY ONCE.

You should copy this information into your aws-credentials file and download and save the .csv file containing this information. Again, do not upload this information (either the aws-credentials file or the csv file) to a public repository.

Provision your AWS VM

Once you have all the information for your aws-credentials file, you should first source this file

source aws-credentials

Once you have created (& potentially added) the security group to your AWS Vagrantfile, you should then provision the VM by

vagrant up --provider=aws

If this hangs on the line

Waiting for SSH to become available...

then you should check the security group settings above. You may also recieve an email saying "You recently requested an AWS Service that required additional validation", which may have also caused a delay. It will take several minutes to provision the VM for the first time.

Once the required packages have been installed you will need to run

vagrant up

again, before being able to connect via

vagrant ssh

If the VM becomes unresponsive you many need to force-stop it via the EC2 Dashboard and run

vagrant up

again. In the instance list it will be called metomi-vms.

Connecting via X2Go

To be able to connect to a full desktop, you can use X2Go. You should install the X2Go client.

1. Fill out the settings details on the new session popup as in the table below, then press OK.

2. Click on your new session on the right hand side of the x2goclient window.

3. It should automatically login after asking you if you wish to allow the connection.

If you stop the instance and then later restart it, the IP address may change. You can find the IP address of your EC2 instance on the EC2 Dashboard. You will need to change this in your X2Go settings and allow the connection when prompted.

X2Go settings for AWS EC2 instance

Option	Setting
Session name	e.g. AWS
Host	IP address for the VM, e.g. 3.8.24.92
Login	ubuntu
Use RSA/DSA key for ssh connection	The full path to the key file you created earlier (navigate via button)
Session type	Select LXDE from drop-down menu