Cryo-EM Data Processing @S3IT: 2. Start a GPU-enabled VM

Login to the ScienceCloud dashboard dashboard only works from UZH network. Either access it from campus or use UZH VPN.

Log in with your UZH webpass (the usual shortname and password).

You need to share your project ID with ZMB, in order to receive the turnkey data processing image.

You can find the project details under: Identity>Projects

Send your project ID to a cryo-EM specialist at ZMB.

Add new security group, that allows for remote connection. (not SSH)

COMPUTE > Access & Security > Security Groups > Create Security Group

Add new rules with the Manage Rules action.

UZH VPN in CIDR format: 89.206.64.0/18 and UZH Campus in CIDR format: 130.60.0.0/16

It is possible that your institute has a different IP range. You can check your IP address and add it to the rules as well.

Launch new instance from COMPUTE>Instances menu.

As source image, select ZMB Cryo-EM processing from the list.

From the flavors, select either 1xT4 GPU (16cpu-64ram-hpcv3-gpuT4) or 2xT4 GPU flavor (64cpu-256ram-hpcv3-2gpuT4).

Generally, data processing speed scales with the number of GPUs you use. Recommended is min. 2 GPU for larger datasets.

Add the UZH RDP security group, that was created in step #3.

Select preciously uploaded SSH key or create new one on-the-spot.

Launch instance.

Your new instance will spawn and boot in ca. 3 mins. You can login using RDP protocols from Windows/Mac/Linux environments. The IP address you find under COMPUTE>Instance menu.

Further more detailed information you find in the S3IT documentation

Initial Ubuntu login credentials are shared upon request to share and use the image file.

Use any Remote Desktop client to connect to your processing instance.

Remote Desktop client is built-in for almost every OS. A few visual examples are on the the images.

Make sure you use RDP protocol to connect.

Customize your instance with the startup.sh script on the Desktop. Run in Terminal: "bash startup.sh" then follow the instructions.

Attach and mount storage volumes for your cryo-EM data under the COMPUTE>Volumes menu. Detailed description can be found on the S3IT documentation website.