NOTICE: FULL O2 Cluster Outage, January 3 - January 10th

O2 will be completely offline for a planned HMS IT data center relocation from Friday, Jan 3, 6:00 PM, through Friday, Jan 10

  • on Jan 3 (5:30-6:00 PM): O2 login access will be turned off.
  • on Jan 3 (6:00 PM): O2 systems will start being powered off.

This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.

Specifically:

  • The O2 Cluster will be completely offline, including O2 Portal.
  • All data on O2 will be inaccessible.
  • Any jobs still pending when the outage begins will need to be resubmitted after O2 is back online.
  • Websites on O2 will be completely offline, including all web content.

More details at: https://harvardmed.atlassian.net/l/cp/1BVpyGqm & https://it.hms.harvard.edu/news/upcoming-data-center-relocation

Install and run Cellpose

Owned by Lingsheng Dong
Last updated: Feb 06, 2024
1 min read

Software page:

https://github.com/MouseLand/cellpose

To install:

Importantly, if you have your own anaconda installation - make sure this is not active.

 

srun -p interactive --pty --mem 10G -c 1 -t 12:00:0 bash module purge module load miniconda3/23.1.0 git clone https://github.com/MouseLand/cellpose.git cd cellpose mamba env create -f environment.yml source activate cellpose mamba install -y -c anaconda -c conda-forge libxcb xcb-util-wm xcb-util-image xcb-util-keysyms xcb-util-renderutil-cos7-x86_64 qt pyqt python==3.11 pip install PyQt5==5.14.1 pip install .[gui]

 

Once that finishes, you should be able to request a Desktop Mate session from O2Portal (https://o2portal.rc.hms.harvard.edu). At the top, click on HMS-RC Applications, and navigate to Desktop Mate. Fill out the form, requesting as many resources as you need (or think you need), then start the session. Once it starts, enter the session, then open a terminal at the top left (it's the black box icon), then do the following:

module load miniconda3/23.1.0 source activate cellpose cellpose

 

and after a few seconds, the GUI should pop up.

Please let us know if anything does not work: rchelp@hms.harvard.edu

 

Note: the above commands are based on Alex’s notes.

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