We received an allocation on Azure Cloud to carry out computational drug design targeting COVID Main Protease. How do we get Q-Chem installed and deployed on Azure? Simple instructions like this http://www.q-chem.com/Cloud.html would be very helpful!
Q-Chem in the Cloud: Azure
These are the steps to follow in order to:
- Create virtual machines
- Capture images of virtual machines
- Deploy new virtual machines from images
on the cloud platform Azure.
1) Create New Virtual Machines (VM)
• Login to your Azure account;
• Click on “Virtual Machines”;
• Click on “Add” > “Virtual Machine”
Now we begin to customize the properties of our virtual machine in the tab “Basics”.
• The field “Subscription” refers to the sponsorship under which you are using Azure resources.
• “Resource group” is simply a name for organizing all the resources you create. Multiple groups can be created and shared with collaborators.
• The name of your VM is arbitrary.
• Choose the “Region” according to users’ locations.
• Choose an OS “Image” from the list (Linux, Windows…)
• The “Size” of the VM defines its cost. Azure provides a list of available sizes depending on quantity/quality of CPUs, RAM, Hard Disk, GPUs. Choose according to the computational resources you need for your future calculations.
• “Username” is arbitrary.
• Make sure to generate new SSH key pair. Assign a name to it.
• Choose the “Inbound ports” for connecting to the VM. You can select all of them for testing purposes. In most cases though, the SSH port will be enough.
• Now you can continue your personal customization by pressing “Next : Disks >” and providing all the information required in each field of each tab until reaching “Review + Create”. If the default settings suffice then move directly to the “Networking” tab and give a name to your “Virtual network”. Finally, move to “Review + Create”.
• IMPORTANT: Make sure pop-ups are allowed on the browser (or give clearance to Azure).
• Click on “Create”. Azure will ask you to download the private key for your VM. Once this is done, your VM will be created and Deployed! (The machine is running, careful with billing).
2) Install Q-Chem on your VM
From your Home Page click again on “Virtual Machines”, now you should be able to see your newly created VM. Click on its name.
You are now able to see the characteristics and status of your VM. Since we want to install Q-Chem in it, we need to run the machine and connect to it. If it is not already running, click “Start” on the top panel to allocate your VM. Once your VM is operative, copy its “Public IP address” and from your ssh client, type:
ssh -i <private_key_path> username@(Public IP address)
Make sure you (and you only) have just reading permission to your private key.
Once logged into your VM, install Q-Chem following the instructions from the Q-Chem web site:
Once Q-Chem is installed, logout from the VM (from your ssh client) and deallocate your machine by pressing “Stop” on Azure site (Virtual Machine Page).
Note: Stopping a VM will make it lose the current “Public IP address” unless you explicitly opt-in to preserve it. If you don’t, just remember to use the newly generated IP address when starting the machine again.
Always remember to stop your machine when not used for running jobs, otherwise you will be billed for unused resources!!!
Up to now, these are the steps necessary to install and run Q-Chem for the first time on Azure.
Below, there are instructions that are useful to those who want to:
• Allow new Azure users to use Q-Chem on the platform without wasting time installing the software (saves time to get the license)
• Deploy multiple VM where to run several Q-Chem jobs at the same time. Currently, you can run maximum 20 VMs simultaneously on Azure.
3) Create an image from VM
We now have a VM on Azure where we can run Q-Chem for calculations. Our next step is to generalize this VM to create an image of it. This procedure will make the current VM unusable, but the image so created can be used to create and deploy multiple VMs where Q-Chem is already installed.
• Once again, click on your VM from the Virtual Machines page on Azure;
• Make sure your VM is not running;
• On the top panel, click on “Capture”;
• Give a name to the image you want to create and fill in mandatory fields;
• Click on “Create”.
That should be it. You now have an image of a VM with Q-Chem installed in it.
4) Deploy a VM from an Image
Follow the same procedure as in “1) Create New Virtual Machines (VM)” above. The main difference is that now in the field “Image” you will use your personal Image created before.
Click on “Browse all public and private images”, then click on “My Items” and select your personal image. Your VM settings will now be set to the ones used in the image, feel free to change them (e.g. the size, if you need more or less computational power) as you need.
The VM created in this way should already have Q-Chem installed.
I hope this helps!