Overview

SBGrid provides comprehensive system administration support for all Linux computers in the Gaudet and D’Souza labs.

All computers are connected to a private section of the Harvard network.

To reach this network for access to local resources from an external location, please ssh to galactica.mcb.harvard.edu.

Get Help

For general questions, email SBGrid at help@sbgrid.org and include your name and the name of your lab. Email questions about your software installation to bugs@sbgrid.org.

New lab members should contact help@sbgrid.org to complete their initial setup.

Networking is supported by FAS Research Computing on the Cambridge campus.

Computers

Linux Computers

Linux computers share authentication and data directories and can only be accessed locally from within the lab. Home directories are located at /labdata/<lab initials>/<username> (example: /labdata/vdg/testname). SBGrid's comprehensive collection of structural biology applications is located in the /programs directory. Some systems are configured with Stereo 3D.

The cerberus cluster, a 64-core, 2-node compute cluster, runs OpenLava, can be accessed remotely, and is typically used for docking computations and data processing. To access cerberus, ssh to galactica.mcb.harvard.edu.

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 question. PIs can request modifications to file permissions to suit the lab's needs.

Printing

There are 2 printers available, one located in the hallway near room 305 (carmen), the other in the wet lab (vger). For printer problems, please contact help@sbgrid.org.

Data Backups

Snapshots of the Linux filesystems are taken every hour and kept for 24 hours on the file server. Additionally, 7 daily snapshots are kept, 8 weeks, and up to 12 months. Data is also replicated to a secondary server. If you need a file restored, please contact help@sbgrid.org.

Software

NMRViewJ for D’Souza Lab

To use nmrviewj you need the NMRViewj configuration files that Victoria created.

These are in ~vdtest/NMRVIEWJ_CONFIG_FILES .

Do the following to copy the files to your home directory:

cp ~vdtest/NMRVIEWJ_CONFIG_FILES/.nvjrc ~/

cp -r ~vdtest/NMRVIEWJ_CONFIG_FILES/HHMI-tclJ ~/

Then start nmrviewj.

Custom Software

HKL2000

Licenses for HKL2000 are limited to one specific system per lab.

D'Souza LAB

D'Souza Lab members can use the following system to run HKL2000:

• rufus

Gaudet LAB

Gaudet Lab members can use the following system to run HKL2000:

• pioneer

Networking and General IT Support

To report Harvard University network problems or for general computing support, contact the Harvard University help desk. If you need to activate a port in the lab for a new SBGrid-supported system, please contact Harvard research computing and cc SBGrid.