Watch Jennings' talk "Medical Research Computing Infrastructure on Hybrid Kubernetes" presented at Kubecon + CloudNativeCon North America 2024.

Demo of the "fetal MRI reconstruction web user interface" proof-of-concept.

https://github.com/FNNDSC/fetal-recon-ui-mvp

At this year's scientificcomputing.rs workshop, Jennings gave a presentation about the DICOM protocol and how we developed ChRIS to support it.

Dr. Rudolph Pienaar and Dr. Ellen Grant presented at Red Hat Summit 2024.

ChRIS is now available on the NERC at https://app1.chrisproject.org. This deployment is a milestone comprising many improvements to ChRIS made in 2023.

To shrink a PersistentVolumeClaim (PVC) in OpenShift or Kubernetes, we need to:

1. pause our deployments
2. copy its data to a smaller, temporary PVC
3. delete the original PVC
4. create a new PVC with the original name
5. copy the data from the temporary PVC to the new PVC
6. restart our deployments

tl;dr the container filesystem lives in-memory, so temporary files and directories which don't get deleted will eat up RAM.

1. Containers are useful for portability
2. Containerization shifts the burden of software installation to the developer/publisher, not the users
3. Containers are useful for compatibility
4. How to use Docker CLI (properly)
5. Using Apptainer as an alternative to Docker
6. Running containers locally, on E2, and on ChRIS

Link to slides: jennings_intro_to_containers.pdf

FNNDSC computer help and dev team email: Newborn_FNNDSCdev-dl@childrens.harvard.edu

Part 1​

How to run the fetal reconstruction pipeline.

Part 2​

Fetal reconstruction pipeline output files.

Recently a colleague accidentally changed their Mac system settings through /etc/synthetic.conf. This caused the collegue could not even login into the Mac with any account.

We then found the following mac recovery steps from the Apple Website:

https://support.apple.com/en-us/102603

In case this page may disappear in the future:

• With Apple Silicon:
  • Turn on your Mac and continue to press and hold the power button as your Mac starts up.
  • Release the power button when you see the startup options screen, which shows your startup disks and a gear icon labeled Options.
  • From this window you can start up from a different disk, start up in safe mode, use macOS Recovery, and more.
• With Intel-based Mac:
  • Command (⌘)-R: Start up from the built-in macOS Recovery system.
  • Option (⌥) or Alt: Start up to Startup Manager, which allows you to choose other available startup disks or volumes.
  • Option (⌥)-Command (⌘)-P-R: Reset NVRAM or PRAM.
  • Shift (⇧): Start up in safe mode.
  • T: Start up in target disk mode.

The Mac is a 2014 Intel-based Mac. We use Command (⌘)-R to get into the built-in macOS Recovery system. In addition, we connected an external-drive to the Mac. We were able to:

• Select this external-drive as the target disk.
• Install MacOS on this external-drive.
• Reboot the Mac through this external-drive.
• Found the /etc/synthetic.conf in the internal disk and rm /etc/synthetic.conf.