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HMS IT RC O2

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  • Get information about current and past jobs
  • Scratch Storage
  • Filesystem Quotas
  • User Training
  • Submitting data to GEO
  • Published Papers That Used O2, Orchestra, or Research Computing
  • Report CPU/Mem usage in slurm job standard output
  • Text for Grants Referring to the HMS Research Cluster
  • Troubleshooting Slurm Jobs
  • Filesystems
  • Security on O2
  • Moving from Orchestra to O2
  • Using Mathematica on O2
  • The O2 Open OnDemand Pilot
  • sratoolkit/2.10.7 to download NCBI SRA data
  • Using O2 GPU resources
  • Scratch_gpu Storage
  • 766 Open Source Applications on O2 [BioGrids]
  • Using Slurm Basic
  • File Transfer
  • Get more informative slurm email notification
  • Local Software Installs
  • Batch small jobs together as a big job
  • UNIX Permissions Tutorial
  • Using X11 Applications Remotely
  • Public Databases
  • Over Efficient Jobs
  • sratoolkit/2.10.7 to download dbGAP data
  • Jupyter on O2
  • spp (1.15.2) for Chip-Seq
  • O2 cron service
  • How To Submit Parallel Jobs in O2
  • Personal Perl Packages
  • Using Aspera to Download Data
  • Get more informative slurm email notification and logs through rcbio/1.3.3
  • Understanding O2 Slurm Accounts/Associations and Unix Accounts/Groups
  • Juicer
  • Using AlphaFold on O2
  • Using MATLAB
  • Frequently Asked Questions and Answers
  • tmux: Keep Linux Sessions Alive (so you can go back to the same terminal window from anywhere, anytime)
  • Two Factor Authentication FAQ
  • How to troubleshoot the sratoolkit/2.10.7 module
  • RC workflows
  • UCSC Genome Browser and IGV access for data on O2
  • Running Singularity Containers in O2
  • Using Java on O2
  • GATK4 Mutect2 using Singularity Container
  • Job Priority
  • O2 HPC Cluster and Computing Nodes Hardware
  • Currently Available Software on O2
  • How to login to O2
  • Personal R Packages