UvA HPC course 2021-01-22
Part A

This is part A of the tutorial UvA HPC course 2021-01-22 and covers the following topics:

1. Accessing the user interface
2. Setting your public SSH key
3. Starting your first VM

1. Accessing the User Interface

The User Interface (UI) is the web site that allows you to manage your Virtual Machines (VMs) on the HPC Cloud.

Log in to the UI

• Open the UI page in your browser: https://ui.hpccloud.surfsara.nl/.
• Your username is wolk-NNN, replace NNN with the three-digit number assigned to you.
• You will receive the password from the workshop facilitators.
• Hit the Login button.

Switch to “user view”

The interface supports several views and for this course, you should use the “user view”.

• Locate the buddy icon with your user name at the top-right corner of the screen and click it.
• In the drop-down menu, move to Views and in that sub-menu select user.

Change your password

Once you login to the UI, it is a best practice to change the initial password.

• Locate the buddy icon with your user name at the top-right corner of the screen, click it and select Settings.
• In the Settings display, locate the Password field and click the blue edit icon .
• On the Update Password pop-up dialog fill in a new password (twice) and click the Change button to submit it.

Logout

Let’s check whether it worked.

• Click your buddy icon .
• Choose Sign Out.

From now on you can use your new password to log in to the UI. Do so now.

2. Setting your public SSH key

To complete the setup of your HPC Cloud account, you need to add a Secure Shell (SSH) public key to your profile. This is a one-time task.

First, you need an SSH private/public key pair.

• Read about SSH and public keys on the private/public keys page.
  If you are already familiar with SSH public keys, you can skip reading this page.
• You need a private/public key pair in your ~/.ssh/ directory. Create one now if needed.
• Check with the command ls ~/.ssh; you should see the files id_rsa and id_rsa.pub.

Next, you need to copy the public SSH key (id_rsa.pub) to the UI. The matching private key (id_rsa) stays safe in your laptop.

• Copy the content of your public SSH key to the clipboard (for example, by doing cat ~/.ssh/id_rsa.pub, then selecting and copying all of that text).
• Go to the UI and select Settings from the buddy icon .
• Locate the section Public SSH Key (if needed, click the Info icon) and click on the blue edit icon .
• Paste the content of your public SSH key file into the text box.
• There is no Save button; click outside the text box to complete your action (e.g.: on the words “Public SSH Key”).
• Check the contents of the text box against your public key and verify they match: it should start with ssh-rsa AAAAB…

3. Starting your first VM

Using the HPC Cloud revolves around building Virtual Machines (VM). SURF provides several Apps readily available in the HPC Cloud UI, to facilitate creating simple VMs. Apps are ready-made appliances for you to copy and use.

These are the steps to build your first VM from one of the Apps; detailed instructions follow:

• Importing a pre-made image with a Linux operating system installed.
• Reviewing the shape of the VM (so-called template).
• Instantiating the template to create your first VM.
• Accessing your VM and shutting it down.

Let’s run your first VM on the HPC Cloud!

Importing an app

• Log in to the UI.
• Choose the Storage tab on the left menu of the screen and then Apps.
• View the extended the app Ubuntu-18.04-Desktop by clicking anywhere on that line except the tick-box to the left of it.
• Carefully read the DESCRIPTION attribute (located towards the bottom of the page). In particular, pay attention to the default username mentioned there, since that is the username you will need to use to log in to your VM.
• Click on the blue OpenNebula button above the list of apps.
• A dialogue will pop up asking you for a few details. Edit as follows:
  • Name: Course Image.
  • VM Template Name: Course Template.
  • Below “Select the Datastore to store the resource”, select 147: Courses_img. It should now read “You selected the following datastore: Courses_img”
• Click the green Download button. This will copy the app to your work environment, and return to the Apps list.

Food for brain:

When you import an app, an image and a template will be created, as explained during the introductory presentation. In the UI you have an Images tab under Storage and a VMs tab under Templates on the left menu. You should see your new image and template there.

• Can you see them?
• What is the STATUS of the image just after you import it?
• Refresh the contents of the Images tab page by clicking button , next to the button until it is READY.

Reviewing the Template

A template consists of a set of attributes that defines a Virtual Machine. For example, how many cores you want your VM to have, how much RAM memory, what storage drives to attach, which network connections, etc. We will have to adapt the template to meet your requirements before you can use it to create VMs out of it.

Edit the imported template following these steps:

• Go to the VMs tab under Templates on the left menu.
• Find the template you just imported (Course Template), and click on it (anywhere except the tick-box).
• Click on the blue Update button to start editing the template.
• Browse through the different tabs there (i.e. General, Storage, Network, …) to get acquainted with their contents.
• Verify that your VM will have internet access:
  • Select the Network tab which shows the network interfaces (or nics) for your VM.
  • The feedback below tells that the internet interface NIC 0 on the left pane is mapped to internet.
    
• Check the Input/Output tab:
  • In the Graphics section, the VNC radio button must be selected.
  • In the Inputs section, make sure an USB tablet is listed. If not: select Type Tablet and Bus USB; then click the Add button next to that.
• If you made any changes to the template, click the green button Update at the top, to save your changes.

Starting the VM

A template is just a description of the virtual machine that we want to build. Let’s create the actual virtual machine from it.

• Go to the VMs section below Instances on the left menu. An overview of all existing VMs that you have the right to see, are displayed. This list is (probably) empty at the moment, because you have not yet started any VM.
• Click the button to bring up a “Create Virtual Machine” screen.
• Select the Course Template by clicking once at it. Since this is your first template, there is only one item in the list. You can see the feedback:
  
• Find the input box for VM name and give your virtual machine a name: My First VM. This name is also used as the VM’s host name.
• Inspect the remaining template attributes, for the time being do not change them (leave “Number of instances” at 1).
• Click on the green Create button at the top of the screen.
• Refresh the VM status by clicking button at the top.

What happened?

Congratulations! You have just created a fresh, clean virtual machine!

Let’s summarise what you have seen so far. Click on each of the tabs on the left side menu and inspect the information provided. The most important ones at this point in time are described here:

• Dashboard: shows an overview of the project status, like the number of running machines or usage statistics.
• Instances > VMs: here you can manage your VMs (i.e.: create, start, shutdown). Click anywhere on a running VM’s row (except the tick-box). Inspect the information present in the different tabs providing you extended details.
• Templates > VMs: the template gives your VM the shape you want. A template is just a recipe; not the machine itself.
• Storage > Images: this is the equivalent of a hard drive. Your OS is stored on this image.
• Storage > Apps: a list of appliances endorsed by SURFsara HPC Cloud team that you can use.

NOTE:
Your VM will appear in the list of virtual machines. At first, it will have the state PENDING. This indicates that the HPC Cloud is looking for a place where your virtual machine can actually run. Finding the right place depends on the amount of resources (cores, memory, and disk) you requested in the associated template. Keep refreshing the list by clicking button . When the required capacity becomes available, your VM will show the status RUNNING. Only then can you actually use your VM.

Logging in to the VM

You can interact with your VM in several ways: command-line (e.g.: SSH), VNC (UI in your browser) or a remote desktop. We will use SSH in a terminal for the time being.

The way to log in to your virtual machine is making use of the SSH key pair that you stored in your profile earlier.

Commandline access - SSH

• First find your VM’s IP address. It is shown in the IPs column from the virtual machines list on the UI and also in the Network tab of the VM’s details page.

• On your laptop, start a terminal (in Mac/Linux) or GitBash (in Windows).

• Type the following command on the terminal to establish a connection with your VM:

NOTE:

Replace 145.100.5Q.RST with your IP address! And remember that we know which username to use because we read that on the Description attribute of the app when we were importing it.

ssh ubuntu@145.100.5Q.RST

First login

If everything went well, the first time you try to log in, your terminal will ask you to add the VM’s IP to the list of known hosts in your laptop. Type Yes, in that case.

NOTE:

Right after you reach the newly created VM via SSH for the first time, you may see a prompt asking you to change the default password for user ubuntu. Please, do so by typing first the current password, which is the same as the username. You can then type the password you want. When this password-changing process is finished (even successfully), you may be logged out of the VM. You will then have to submit the SSH command again, and then everything should work as expected: you are connected to a shell in the VM.

You should now see a similar line in your terminal: ubuntu@ip-145...:~$

This means that you have logged in successfully to your Virtual Machine!

• Look around a bit, make yourself familiar with the system:

ubuntu@ip-145...:~$ ls /
ubuntu@ip-145...:~$ whoami

• Create a file:

ubuntu@ip-145...:~$ echo "Some text ..." > myfile
ubuntu@ip-145...:~$ cat myfile

• Logout by typing logout or ctrl-D in your terminal (do not issue any shutdown command):

ubuntu@ip-145...:~$ logout

Food for brain:

Log in to your VM again. Is your file still there?

First shutdown

Let’s shut your first VM down. Anytime you expect your VM to be doing nothing useful, you should shut it down to stop consuming the resources that your VM is holding.

• Go to the list of running VMs in the Cloud UI (Instances > VMs).
• Tick the box to the left on the row with your VM.
• At the upper right corner of the screen, click the red button and click Terminate. A confirmation action is needed, click OK.
• Refresh the list of VMs () until your VM is gone. You can always boot the “same” VM again whenever you need it.

Food for brain:

When the VM has been shut down and disappeared from the list, check and refresh the Storage > Images and Templates > VMs tabs. Are your image and template still there?

BONUS food for brain

This section is meant to propose extra questions we thought would be nice for you to investigate. We invite you to do/think about them even after the workshop has finished.

Bonus: The HPC Cloud has hundreds of users. Many of them have common questions. In order to address these we have put together a web site with some documentation for users. We call it the HPC Cloud Documentation. Do you know the URL of this web site? Make sure you find out!

NOTE:

Your running VMs get exclusive access to their resources whether they are doing something useful or are idle. Because the HPC Cloud is offered on a fair-share basis and other users may actually be needing resources that you may be holding, before you move to the next part of this workshop, please remember to shut all your VMs down.

Next: part B

You completed part A of the Tutorial UvA HPC course 2021-01-22. Please continue with Tutorial Part B.