Overview

At DFCI SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers. Supported labs include Eck, Dhe-Paganon, Wang, Fischer, and Arthanari. All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI.

To reach this network from an external location please ssh to crystal.harvard.edu, and access your local resources from there.

Get Help

To request support please contact help@sbgrid.org. For support with software installation please email bugs@sbgrid.org.

New members joining the lab should contact help@sbgrid.org as well to complete the initial setup.

Email Access

Lab members have access to a Crystal email through Google Apps. If one is not already setup for you, please contact help@sbgrid.org to request one and CC your PI in the request.

SBGrid maintains a google mailing list for the labs on the Crystal Google domain. If your lab actively uses it and you need to be added to it, please contact help@sbgrid.org.

#Lab Wiki An instance of standalone Confluence server is running on a virtual machine on a SBGrid hosted VM cluster. The current version is Confluence 5.8.

Access is available to users at the PI’s request. Users must have a crystal email account to be able to use the wiki.

To access the lab wiki go to http://wiki.sbgrid.org and login with your crystal email.

Computers

Linux

Setup on Linux Computers: Linux computers share authentication and data directories and can be only accessed locally from within the lab. Home directories are located at /nfs// (example: /nfs/mje/eck). A comprehensive collections of SBGrid applications is located at the /programs directory. All systems are configured with Stereo 3D. In addition, ivory which is a 48 cores workstation can be accessed remotely and is typically used for docking computations and data processing. Please note that your home directories are only visible to your labmates and PI by default. Permissions vary depending on the nature of the directory or files in questions. PI’s should discuss file permissions with SBGrid to suit their needs.

Mac OS X

Setup on OS X Computers: The Mac computers all have local administrative accounts and are specific to the lab members. Your home directory is located at /Users/ (example /Users/eck). This allows users to install and update software without requesting help from SBGrid. Every local account is backed up to CrashPlan. Any network share, including home directories, are mounted via Samba, and require user authentication. Please contact [help@sbgrid.org](mailto:help@sbgrid.org) to request an account. These computers are also connected to the lab printers on the 3rd and 4th floors of Longwood Center.

Windows

Windows Computers: Some lab members use Windows systems as their main computers. These computers are not maintained by SBGrid, except for making them available on the network.

#Data collection and Instrument Control Computers The scanner room has two linux systems (aqua and plum) that control the x-ray scanner. Windows computers are also on the same network are used for instrument control and data collection. These include the RockImager and FPLC systems.

Accessing your Samba shares

Macs have local accounts with local home directories. You can access your linux network home directory using Samba (SMB) as follows:

• Open Finder, click Go then click 'Go to Server'
• Type in server address: smb://blacker.in.hwlab
  • Click ‘Connect’.
• Enter your Samba username and password. (contact SBGrid for SMB account issues)

Data Backups

Hourly and daily snapshots are taken on the file server Z file system. Data is replicated to another server at the C buildings on the HMS Quad. For supported Mac, local home directories are backed up to a Crashplan server, located at the SGM building also on the HMS Quad.

Printing

A Xerox Phaser 8860 is located in the third floor near the kitchen area. Another inkJet printer is located directly above on the fourth floor. If you are having issues with printing, or need it installed, please email help@sbgrid.org.

RockImager Setup

There are two types of data generated by the imager:

• Images: These are regular “jpg” image files and are stored directly in the file system on the main file server.
• Experiment data: As experiments are created, the data is stored on a “Microsoft SQL Server 2014” database, currently running on a Windows 2012 server.

The data is accessible on the RockImager PCs and also through the RockMaker software. Formulatrix provides technical support on the instrument and has remote access for troubleshooting purposes. SBGrid maintains the servers configuration.

Networking and General IT Support

There are HMS network switches on each floor (3rd and 4th), that connect the labs to the SBGrid infrastructure. For new SBGrid systems, new port must be activated before using the computers. SBGrid can work with DFCI/LC IT support to get them activated. Please provide the port number you need activated. To report problems regarding the network at DFCI, or general computing support, contact the Partners Healthcare Help desk at:

• http://helpdesk.partners.org/

Note: this link only works from within the Partners network.