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This project will relocate existing services, consolidate servers, reduce power consumption, and decommission outdated hardware to improve efficiency, enhance resiliency, and lower costs.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
Shared Containers on O2
- Gaby Rodriguez
This page provide brief information of containers available to all O2 users.
List of Containers
- 1 MaxQuant
MaxQuant
A quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
# Connect to O2
# Note: replace "PORT" by a random number in the 50000-range, e.g. 50021
ssh -Y -L PORT:127.0.0.1:PORT <your_hms_id>@o2.hms.harvard.edu
# start an interactive job (e.g., requesting 1 hour, 4 threads, and 10GB)
# Note: Replace "PORT" with the choosed number in the above step
srun -t 0-1 --x11 --pty -p interactive -c 4 --mem=10G --tunnel PORT:PORT /bin/bash
# Run the MaxQuant container
SIF_PATH="/n/app/singularity/containers/hmsrc-maxquant.sif"
singularity run -B "$TMPDIR:/tmp",/n --app MaxQuantGui.exe $SIF_PATHTo use MaxQuant from the terminal:
SIF_PATH="/n/app/singularity/containers/hmsrc-maxquant.sif"
singularity run -B "$TMPDIR:/tmp",/n --app MaxQuantCmd.exe mqpar.xml $SIF_PATHNote: the mqpar.xml file is where you specify all the information related to the data analysis.
Â