The de.NBI Cloud portal represents the central access point to the de.NBI Cloud.
An application for resources in the de.NBI Cloud must be submitted by a principal investigator of a german university or research facility. After you submitted the application, you will receive a confirmation mail. Your application will be reviewed by a scientific committee. You will be notified as soon as possible whether your application is approved or declined.
You can submit an application by login to the de.NBI Cloud portal and selecting the "New application" tab (see below).
Besides general project information like project name, project description, institution name and project lifetime, you also have to provide the information independing on the project type you choose:
The Simple VM Project type allows you to start virtual machines without configuring a project in OpenStack (e.g. network configuration).
In a Cloud Project you will have your own OpenStack project and you are free to configure your network, virtual machines and storage setup.
In a Simple VM project you just have to provide the number of virtual machines you would like to run in parallel in your project. Once your application is approved you can choose different flavors for every virtual machine.
For a Cloud Project you have to specify the following parameters:
Number of Virtual Machines
Cores per VM
Disk per VM
RAM per VM
Special Hardware (GPU/FPGA)
If you want to extend a project or adjust various parameters, you can create a modification request. You can submit a modification request by selecting the "Applications" tab and clicking on the "Request Extension/Modification" button (see below).
Then a new window opens in which the parameters of your project can be adjusted. On the left side are the current parameters and on the right side are input fields where you can enter new parameters for your project.
In the Project Overview tab you get a list of all your running projects:
The color of the text indicates whether the lifetime of your project is reached or not. Red means that the project lifetime is has beed exceeded.
The following actions are only available for a project manager:
- Show members: Shows all members of this project. Project managers are colored in blue.
Appoint another member as admin (project manager).
Remove the admin (project manager) state.
Remove a member from this project.
Add another user to this project by inserting their name, email or even ELIXIR ID and clicking on
Through invitation links users can be easily added to a de.NBI Cloud project. The process is the following:
Step 1: Send the invitation link which you can find in the "Add Member" modal to the user you want to add (see figure of the previous section).
Step 2: By using this link the user will be requested to register for an ELIXIR and de.NBI Cloud account. In the final step the user also registers for your project.
- Step 3: You will be informed by mail as soon as the user submits an application. You can then approve the application in the application modal. Once the application is approved the user will have access to your project.
The development and support of the cloud is possible above all through the funding of the cloud infrastructure by the Federal Ministry of Education and Research (BMBF)! We would highly appreciate the following citation in your next publication(s):
‘This work was supported by the BMBF-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B).
Simple VM Project¶
Start a Virtual Machine¶
If you are a member of a simple vm project you can start a virtual machine at the "New Instance" tab. You may need to reload the website if you can't see the tab. Then you can choose your project and fill the form to start a virtual machine.
Connect to your Virtual Machine¶
After the virtual machine has been started a modal with connection information is displayed. Alternatively you can find this information in the Instance Overview.
Here you can find general information about how to connect to your virtual machine and only if you chose to open UDP ports mosh-connection information is shown too.
Here you can see an example with open UDP ports. A ssh and mosh command is shown.
X2Go Images allow you to start your own desktop in the de.NBI Cloud which you can access from any operating system (Windows, Linux, MacOS).
(Windows only) Export key in OpenSSH format for X2GO¶
To connect to a machine with X2GO you have to export your private key in openssh format. To achieve this first load your private key into puttygen.
Then click Conversions and choose Export OpenSSH Key. Afterwards save this file on your computer. This file will be needed when you want to establish a connection to a machine with the X2GO client.
Connect to X2GO machine¶
You can start an X2Go image when you select an image starting with the X2Go label e.g
Once your image started, you will see a message similar to the following one:
Provide the data in the red rectangle in the settings of your x2go client:
You also have to select the session type and the private key of your public ssh key that you provided in the user information tab.
There are two ways to create a volume:
1.When starting a virtual machine you can choose to start a volume when selecting optional params.
The volume is automatically mounted this way.
2.At the Volume tab you can choose to create an volume.
In order to use the Volume you need to mount it.
Mount a volume¶
In order to mount a volume connect via ssh to your machine. You will find your volume with the command
This command will list all your block devices connected to your VM. Chose the correct device (mostly the name will be the second entry, you can orientate oneself on the SIZE parameter) and format it with a filesystem if you are using this volume for the first time. Common filesystems are ext4 or xfs.
After the formating you have to create a mountpoint
mkdir -p /mnt/volume
Check that you have the correct permissions for this directory, otherwise set them with the follwoing command
chmod 777 /mnt/volume/
And mount the Cinder Volume under the created directory
mount /dev/device_name /mnt/volume
Now you should see your device by executing the command
If you do not need you Cinder Volume you can also unmount it with
A snapshot is an exact copy of your virtual machine. A snapshot of an instance can be used as the basis of an instance and booted up at a later time.
After starting a machine you can go to instance overview and create a snapshot.
Now you can enter a name for your snapshot and confirm it by pressing Create Snapshot.
After the snapshot is successfully created you can go to the "New Instance" tab and choose the created snapshot as image to start a vm.