HOWTO, Kirchhausen Lab, BCH

This is an old wiki page and is out-of-date. It's been retained as some of this information may still be useful.

Site Overview:

Members of the Kirchhausen Lab at the Children’s Hospital Boston have access to a large collection of structural biology software. Research Computing support is provided by SBGrid. Please contact them here .

Data Backups:

Full and incremental backups of SBGrid file servers are conducted. This includes your home and data directories. In general, backups are kept for three months, and then are stored on physical media for archival purposes. If you need a file restored,  please contact SBGrid  here .

Networking and General IT Support:

Contact Children’s help desk at (617) 919 4357 or at help.desk@childrens.harvard.edu .

Synchronizing working directories between tklab and orchestra**

Overview

The data synchronization process is a one-way synchronization, and files and directories transfered are no longer writable. For processing, there is a two-way synchronization of the ` ~/sync ` directory between the ` tklab ` server and ` orchestra ` . Since the ` ~/sync ` directories are in the user's home directories, users have full ability to create, delete, rename, etc anything within them without effecting the raw images stored in ` /groups/kirchhausen/datasync ` .

Anything outside the ` ~/sync ` directory, including ` .cshrc ` , ` .ssh ` will not be copied to orchestra.

Suggested Working Directory Structure

Symlinks can be used to keep the processing directories linked to the raw data directories, without requiring write/delete permissions for data directories. For example, instead of nstead of creating ` /datasync/Dataset001/process1 ` , create a ` ~/sync/Dataset001 ` directory. Within ` ~/sync/Dataset001 ` , create a symlink pointing to the images ( ` cd ~/sync/Dataset001 ; ln -s /groups/kirchhausen/datasync/Dataset001 images ` ).

Step by Step

Setup passwordless ssh logins between ` tklab ` and ` orchestra ` before using two-way sync.

  1. Process within the ` ~/sync ` directory, on ` orchestra ` or ` tklab ` .
  2. When done, or at a checkpoint, initiate synchronization from ` tklab ` : ` unison -auto ` (interactive) or ` unison -batch ` (non-interactive).

More details

Nightly non-interactive synchronization runs will be run from cron.

If you're curious about unison, more detail is available from the project website .