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Getting Started

• > User Quick Start Guide
• > How Do I Get a FAS Research Computing Account?
• FASSE Cluster - FAS Secure Environment
• > Running Jobs
• Introduction to the FASRC Cluster -- Online
• Reset Password
• OpenAuth
• Command line access using a terminal
• Proxy Settings
• Lab groups, sponsors, and PIs - How does it all work?
• Other Institutions
• Glossary
• About Usernames
• Can I share my account?
• Using Duo Mobile to display your RC two-factor code
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Accounts

• > How Do I Get a FAS Research Computing Account?
• Account Qualifications and Affiliations
• Other Institutions
• What happens to my FASRC account when I leave Harvard, graduate, or become an external collaborator?
• Reset Password
• OpenAuth
• Cluster Account Signup - More details
• Account confirmation email contents
• How do I change lab groups?
• Lab groups, sponsors, and PIs - How does it all work?
• Editing your .bashrc
• About Usernames
• I am a PI. How can I see if I have account approvals pending?
• How do I fairly manage dual/multiple lab affiliations for work on the FASRC cluster?
• OpenAuth token on a new device
• Temporary Class Accounts
• Adding additional lab groups or cluster access
• Account is locked
• Can I share my account?
• Using Duo Mobile to display your RC two-factor code
• Manual OpenAuth Token Setup (advanced)
• VPN Proxy Settings instructions
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Login & Authentication

• > User Quick Start Guide
• FASSE Cluster - FAS Secure Environment
• Reset Password
• OpenAuth
• VPN Setup
• Access and Login FAQ
• OpenAuth token on a new device
• OpenAuth Troubleshooting
• Account is locked
• Home directory full but cannot remove files
• Command line access using a terminal
• Connecting to the FAS RC VPN from Linux clients
• 2022 NCF migration to FASSE
• My VPN client needs updating
• SSH key error, DNS spoofing message
• Using Duo Mobile to display your RC two-factor code
• Synchronizing clocks
• Using SSH ControlMaster for Single Sign-On
• X11 forwarding for lightweight graphical applications
• VPN Proxy Settings instructions
• GNU Screen
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FAQs

• > How Do I Get a FAS Research Computing Account?
• Frequently Asked Questions (FAQ)
• Glossary
• Cluster Customs and Responsibilities
• Common Cluster Pitfalls
• Other Institutions
• Center for Education Policy Research (CEPR) FAQs
• Harvard T.H. Chan School of Public Health - FAS Research Computing Overview
• Harvard T.H. Chan School of Public Health
• Harvard T.H. Chan School of Public Health + FAS Research Computing Q&A
• How do I fairly manage dual/multiple lab affiliations for work on the FASRC cluster?
• Lab groups, sponsors, and PIs - How does it all work?
• Hardware, Software, and Storage Purchasing
• Reset Password
• Account is locked
• How do I figure out how efficient my job is?
• 2022 NCF migration to FASSE
• SSH key error, DNS spoofing message
• CentOS 7 Transition FAQ
• Publications Acknowledging the FASRC Cluster
• Grant Support
• SPINAL Expense Code Guide for Laboratory Financial Administrators
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Running Jobs

• > Running Jobs
• FASSE Cluster - FAS Secure Environment
• Convenient SLURM Commands
• GPU Computing on the FASRC cluster
• How do I figure out how efficient my job is?
• Submitting Large Numbers of Jobs to the FASRC cluster
• Fairshare and Job Accounting
• Cluster Customs and Responsibilities
• Command line access using a terminal
• Slurm memory limits
• SLURM Memory Limits
• Editing your .bashrc
• MATLAB Parallel - PCT and DCS
• MATLAB Parallel Computing Toolbox simultaneous job problem
• Common Cluster Pitfalls
• Adding additional lab groups or cluster access
• How do I fairly manage dual/multiple lab affiliations for work on the FASRC cluster?
• MPI Software on the FASRC cluster
• Hybrid (MPI+OpenMP) Codes on the FASRC cluster
• BHI Partitions
• Geophysics Partitions
• HUCE Partitions
• SEAS Compute Resources
• scrontab
• SBGrid Software for Structural Biologists
• X11 forwarding for lightweight graphical applications
• Sequencing
• Format of Output File
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Software

• Lmod modules -- introduction and instructions
• Application Types
• HeLmod
• HELMOD FAQ
• All modules - Module Search
• Software - Overview
• Virtual Desktop (VDI) through Open OnDemand
• VDI Apps
• FASSE VDI Apps
• How to build and install an app
• Installing Software Yourself
• Singularity on the cluster
• EasyBuild
• Parallel Computing on the cluster
• MPI Software on the FASRC cluster
• OpenMP Software on the FASRC cluster
• Hybrid (MPI+OpenMP) Codes on the FASRC cluster
• Using Spyder
• Abaqus
• Citrix
• Comsol
• Concaterpillar
• Fortran and Mixed Language Codes on the FASRC cluster
• Git and Github on the FASRC cluster
• Git - Apple license requirement message
• GNU Science Library
• Gnuplot
• GraphViz
• iPython Notebook
• Julia with Jupyter notebooks on the cluster
• Jupyter notebook server on the cluster without VDI
• Lumerical
• Mathematica GUI Fonts
• MATLAB
• MATLAB Parallel - PCT and DCS
• MATLAB Figures in a Batch Mode
• MATLAB Parallel Computing Toolbox simultaneous job problem
• Using KNITRO with MATLAB
• NGS Analysis with R
• OpenFoam
• Perl
• Python (Anaconda)
• MPI for Python (mpi4py) on the FASRC cluster
• R - Basics
• R - Packages
• R - Packages with Singularity
• Ruby
• Schrodinger Suite
• Stata on the FASRC clusters
• TensorFlow on the cluster
• TOTALVIEW: Debugging Parallel Applications
• Trinity
• License Server
• X11 forwarding for lightweight graphical applications
• Desktop Software via HMS RC
• FAS Licensed Software for Local Use
• Optimization
• Format of Output File
• Summary.htm Details
• Alignment
• Migrate
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Instrument

• Scientific Instrument Reservations and Billing (SPINAL)
• SPINAL Usage Guide for Laboratory Administrators
• SPINAL Usage Guide for Researchers
• Instrument Sign-up
• Sequencing

Storage

• Connecting with WinSCP
• SFTP file transfer using Filezilla (Mac/Windows/Linux)
• Storage Service Center
• Home directory full but cannot remove files
• rsync
• Home / Lab directories and Scratch
• Mounting Storage on Desktop or Laptop
• rdiff-backup
• Transferring Data on the Cluster
• Tape Globus Access
• Storage Types - Tier 3
• Storage Types - Tier 1
• Storage Types – Tier 2
• Storage Types - Tier 0
• Globus File Transfer
• Starfish - Data Management
• Coldfront - Allocation management
• Policy: scratch space
• Data Security – Information on Storage and Use of Confidential Data (HRCI)
• rclone - transfer files to/from cloud storage
• Copying Data to & from the FASRC cluster using SCP or SFTP
• Sequencing
• Transferring Data Externally
• Unix permissions
• SFTP file transfer using Filezilla - Filtering
• Transferring files to DATA.RC
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Security

• FASSE Cluster - FAS Secure Environment
• Data and Data Use Agreements (DUA)
• Data Security – Information on Storage and Use of Confidential Data (HRCI)
• Proxy Settings
• Nielsen Dataset
• 2022 NCF migration to FASSE
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Other

• New England Research Cloud (NERC)
• Support
• Publications Acknowledging the FASRC Cluster
• RSpace/ResearchSpace
• Hardware, Software, and Storage Purchasing
• SPINAL Expense Code Guide for Laboratory Financial Administrators
• Instrument Sign-up
• Other Resources
• Unix permissions
• Grant Support
• Find-n-Replace
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Policy

• Web Scraping Policy
• Account Qualifications and Affiliations
• Data and Data Use Agreements (DUA)
• Publications Acknowledging the FASRC Cluster
• Cluster Customs and Responsibilities
• Submitting Large Numbers of Jobs to the FASRC cluster
• License Server
• Policy: scratch space
• Data Security Levels
• Data Security – Information on Storage and Use of Confidential Data (HRCI)
• Can I share my account?
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Training

• Training Materials
• Glossary
• Training Links

IQSS Sid

• IQSS FASSE Sid Quickstart Guide
• IQSS Cannon Quickstart Guide
• Getting Help with Sid
• Get a FASSE Account and Project Group
• IQSS: Differences between the RCE and FASRC Clusters
• Sid Interface Guide
• > Sid documentation
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VDI

• Using Spyder
• Developing your own app using Open OnDemand
• 2022 NCF migration to FASSE
• FASSE VDI Apps

IQSS

• IQSS: Getting started on CANNON and FASSE
• IQSS: Differences between the RCE and FASRC Clusters
• IQSS: How to Specify Resources and Choose a Cluster Partition
• IQSS: Specify Resources for Containerized FAS-RC Remote Desktop on CANNON or FASSE
• IQSS: Specify Resources for Jupyter Notebook / JupyterLab on CANNON or FASSE
• IQSS: Specify Resources for MATLAB on CANNON or FASSE
• IQSS: Specify Resources for PostgreSQL on CANNON or FASSE
• IQSS: Specify Resources for RStudio on CANNON or FASSE
• IQSS: Specify Resources for SAS on CANNON or FASSE
• IQSS: Specify Resources for Stata on CANNON or FASSE
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