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> User Quick Start Guide
This guide will provide you with the basic information needed to get up and running on the FASRC cluster with your FARC account. If you’d like more detailed information, each section has a link to more full documentation
| LOGIN USERNAME CHEATSHEET (click to expand) Example: User John Harvard’s username is jharvard (More info About Usernames)
VPN – When connecting to our VPN you will still use your FASRC username, but you will also need to specify what VPN realm you wish to connect to. Realms provide access to different environments. For instance, the FASSE secure environment uses a special realm ‘@fasse’. Unless you have been told to use a different realm, you will want to use the ‘@fasrc’ realm. Email Address – You will not use your email address to log into any FASRC service. The only FASRC system where you will need to enter your email address is when setting or resetting your FASRC account password (see step 2 below). Harvard Key – Similarly, you will not use your Harvard Key to log into FASRC services. The single exception to this is for account approvers to log in to approve new accounts. Two-Factor – Also, Harvard Key is not your two-factor code provider. FASRC has its own two-factor authentication. When logging in to FASRC systems you will sometimes be asked for this 6-digit token code. While you can use Duo to store this token, again it is not tied to Harvard Key in any way. Please see OpenAuth below (step 3). |
PREREQUISITES
Steps to obtaining and setting up a FASRC account.
1 . Account
1. Get a FASRC account using the account request tool.
Before you can access the cluster you need to request a Research Computing account.
See How Do I Get a Research Computing Account for instructions if you do not yet have an account.
Once you have your FASRC account, move to the Step 2 tab.
2 . Password
2. Set your FASRC Password
You will be unable to login until you set your password via the RC password reset link: https://portal.rc.fas.harvard.edu/p3/pwreset/
You will need to enter the same email address you used to sign up for your account and then will receive an email with a link (this email and link expires after 15 minutes and is for one-time use – it is never needed again).
Once you’ve set your password, click Step 3 to request your OpenAuth two-factor (2FA) token.
3. OpenAuth
3. Set up OpenAuth for two-factor authentication (2FA)
NOTE: This is not your Harvard Key two-factor code. FASRC has its own two-factor system.
You will need to set up our OpenAuth two-factor authentication (2FA) either on your smartphone (using Google Authenticator, Duo, or similar OTP app) or by downloading our Java applet on your computer.
See the OpenAuth Guide for instructions if you have not yet set up OpenAuth.
For troubleshooting issues you might have, please see our troubleshooting page.
4 . FASRC VPN
4. Use the FASRC VPN when connecting to storage, VDI, or other resources
FASRC has its own VPN service which is separate from other Harvard VPNs you may use.
Harvard users: For access to most FASRC resources, you should generally be able to access them from the FAS or Harvard VPN as well as when on the campus wired network. However, for some services, such as Open OnDemand (OOD), XDMoD, dash.rc dashboards, and a handful of others will require you to use our VPN. If you cannot reach a website/service that ends in rc.fas.harvard.edu, you should connect to our VPN and try again.
External users: If you are an external, non-Harvard, user you will almost definitely need to connect to our VPN for access to anything other than SSH to login nodes.
See our FASRC VPN Setup Guide – You will use your FASRC username (plus a realm), your FASRC password, and your OpenAuth token when connecting.
5 . Training
5. Review our introductory training
Watch “Getting Started on the FASRC Cluster – Introduction”
[slides]
FASRC also provides
- Online training materials including videos
- Frequent virtual training sessions
- Weekly office hours.
Accessing the Cluster and Cluster Resources
Terminal access
Terminal access via SSH to login.rc.fas.harvard.edu
If you did not request cluster access when signing up, you will not be able to log into the cluster or login nodes as you have no home directory. You will simply be asked for your password over and over. See this doc for how to add cluster access as well as additional groups.
For command line access to the cluster, you will SSH to login.rc.fas.harvard.edu using your FASRC username, password and OpenAuth token.
See also our SSH/Command Line access documentation for more-detailed instructions: Command line access using a terminal
Watch “Getting Started on FASRC Cluster with CLI (Command Line Interface)”
[slides]
OpenOnDemand (OOD)
Graphical Desktop Access using OpenOnDemand (OOD)
We also provide an interactive graphical desktop environment using Open OnDemand (aka OOD) from which you can launch graphical applications as well as SSH/command line jobs.
Please remember that you must be connected to the FASRC VPN to access this service.
See the following docs for more details: Virtual Desktop through Open OnDemand (OOD)
Watch “Getting Started on FASRC Cluster with Open OnDemand”
[slides]
Storage and Data Management
Research Data Management
There are many policies and procedures related to managing data at Harvard. See our Research Data Management (RDM) page for tools, resources, and guidance to help researchers manage their data effectively and prepare it for sharing, and reuse.
Watch “Research Data Management at FASRC”
[slides]
Transferring Data
See our Transferring Data on the Cluster page for best practices for moving data around on the cluster.
There are also graphical tools available. The Filezilla SFTP client is available cross-platform for Mac OSX, Linux, and Windows. See our SFTP file transfer using Filezilla document for more information. Windows users who prefer SCP can download it from WinSCP.net and follow the steps from Connecting with WinSCP to connect to Cannon.
If you are off-campus or behind a firewall and wish to connect to FASRC servers other than the login servers, you should first connect to the Research Computing VPN.
Determine where files will be stored
See our Data Storage Workflow page for an overview of storage ats FASR
Each user of the cluster are granted 100Gb of storage in their home directory. This volume has decent performance and is regularly backed up. For many, this is enough to get going. However, there are a number of other storage locations that are important to consider when running software on the FASRC cluster.
- /n/netscratch – Our global scratch (environment variable $SCRATCH) is large, high performance temporary VAST filesystem. We recommend that people use this filesystem as their primary job working area, as this area is highly optimized for cluster use. Use this for processing large files, but realize that files will be removed after 90 days and the volume is not backed up. Create your own folder inside the folder of your lab group. If that doesn’t exist, contact RCHelp.
- Local On-Node Scratch
/scratch – Local on-node scratch. When running batch jobs (see below), /scratch is a large, very fast temporary store for files created while a tool is running. This space is on the node’s local hard drive. It is a good place for temporary files created while a tool is executing because the disks are local to the node that is performing the computation making access is very fast. However, data is only accessible from that node so you cannot directly retrieve it after calculations are finished. If you use /scratch, make moving any results off and onto another storage system part of your job. - Lab Storage
Lab storage – Each lab that is doing regular work on the cluster can request an initial 4Tb of group accessible storage at no charge. Like home directories, this is a good place for general storage, but it is not high performance and should not be used during I/O intensive processing. See the global scratch above. For additional paid lab storage, see Storage Service Center.
Do NOT use your home directory or lab storage for significant computation.
This degrades performance for everyone on the cluster.
For details on different types of storage and how to obtain more, see the Cluster Storage page.
Running Jobs and Loading Software
For detailed information on running jobs on the FASRC cluster(s), partitions, workflows, and other job details, please see our Running Jobs page.
Information on using software on the cluster can be found on our Software Overview page.
Familiarize yourself with proper decorum on the cluster
The FASRC cluster is a massive system of shared resources. While much effort is made to ensure that you can do your work in relative isolation, some rules must be followed to avoid interfering with other user’s work.
The most important rule on the cluster is to avoid performing computations on the login nodes. Once you’ve logged in, you must either submit a batch processing script or start an interactive session (see Running Jobs). Any significant processing (high memory requirements, long running time, etc.) that is attempted on the login nodes will be killed.
See the full list of Cluster Customs and Responsibilities.
Getting further help
If you have any trouble with running jobs on the cluster, first check the comprehensive Running Jobs page and/or search our documentation. If your questions are not answered there or in any of our other many documentation pages, feel free to submit a help ticket to FASRC. Please include any job ID of the job in question. Also provide us with your username, what script you ran, the error and output files, and where they’re located as well. The output of module list is often helpful, too.
If you need more hands-on help, FASRC holds weekly Office Hours on Wednesdays from 12pm – 3pm.