​Research Data Backup Services​

The Computational Module of the Core Grant is providing data backup services to vision researchers and associated staff.

This backup server is available to perform backups of any and all vision research data. It is a robust and highly automated system.

The benefits of taking advantage of this include:

  • Consistency: Backups performed nightly (without you having to think about it) or initiate them
  • Redundancy: Data is stored redundantly in two separate campus locations
  • Security: Backup server is in a departmental server rack at the UCSD RCI Colocation Facility
  • Longevity: Backup data sets will be kept for 6 months. Longer term archiving can be arranged for static datasets.
  • Comprehensive: Nearly all networkable computers, devices and instruments can be included in the backup routine.

The server is being administered by Manny Acera in the HGC Computer Group. If you have any questions about how this works, or would like to request backups of your data, contact Manny Acera (VisCoreCompute@ucsd.edu )

Triton Shared Computational Cluster Access

The Computational Module of the Core Grant has arranged for interested vision researchers to have access to the UCSD Research CyberInfrastructure computational cluster: Triton Shared Computational Cluster (TSCC).

Accessing the TSCC Cluster
Core Grant access to the TSCC cluster is being administered by Dan Auerbach. If you would like to request a login account for the cluster, contact Dan at VisCoreCompute@ucsd.edu.

Log in to the cluster using ssh at the command line as follows:

ssh <UCSD_Active_Directory_Username>@tscc-login.sdsc.edu

where “<UCSD_Active_Directory_Username>” is your UCSD active directory username (your email username @ucsd.edu).

Information & Resources

The TSCC website has lots of information on the hardware specifications, software availability, how to submit jobs, and job queue characteristics. You should review the information on this website before attempting to run your jobs.

In order to stay up-to-date on cluster status, or to ask questions if you are having problems, you can subscribe and submit questions to the TSCC staff and community mailing lists.

Node Info
We have one condo node with 16 physical cores and 128GB of RAM. You can see the detailed system and cluster specs on TSCC website above.

Software Availability
Many applications and programming tools are installed on the cluster. Please see the TSCC Software page for more information. Matlab and R, as well as numerous life science and genetics packages are installed.

Submitting Jobs
Please see TSCC website for more details, here specifically: http://rci.ucsd.edu/computing/jobs/index.html

You MUST use our TSCC group name as the account name when submitting jobs. Our group name is: visres-group.

Data Storage
Each cluster user has ~100GB of local disc space on the login node, however, running jobs on the cluster should access data using the TMPDIR environment variable. This location will be accessible to the compute nodes with much higher performance. There is additional (temporary) storage available with a 90-day purge policy. You can access this at /oasis/tscc/scratch/. Access to data that is stored on the vision research file server (macula.ucsd.edu) is configured on a user by user basis. Please email Dan at viscorecompute@ucsd.edu for more information.

Detailed information on how to run different software packages will be posted as time permits.

File Server Available for Vision Researchers: Macula (macula.ucsd.edu)​

The Macula Research File Server as a secure repository for research data and documents. It provides enhanced cooperation and collaboration among vision researchers who need to share research data.

This server will provide the following:

  • User Folders
    • Public
    • Private
    • Drop Box
  • Group and Lab Folders
  • Flexible access controls on group and lab folders based on group needs
  • UCSD Active Directory (AD) authentication
  • Mac and PC compatibility


To request an account on Macula please send an email to Dan Auerbach.

Macula Connection Instructions

Mac OS XPC/Windows
Step 1 – From Finder, click on “Go” in the Menu bar
Step 2 – type in afp://macula.ucsd.edu and hit Connect
Step 3 – Enter your UCSD e-­mail username and password and hit Connect
Step 4 – Highlight the appropriate sharepoint(s) and click OK.
Step 1 – Click on the Orb/Start button on the lower left of your PC screen,
Step 2 – Type in \\macula.ucsd.edu and hit enter
Step 3 – Enter your UCSD e-­mail username and password and hit ok
Step 4 – Double-click on the desired sharepoint(s) to access the contents

Server Spe cifications

  • System: OS X Server 10.9.1; 2.3 GHz Intel Core i7
  • Storage Capacity: 12+TB of usable storage, expandable to approx 36TB

Restoration of Service
If a disruption of service occurs, a maximum effort will be made to restore service as quickly as possible. Users of the service will be notified via email.

Communications
This will be accomplished using electronic mail published to a mailing list. All server system users will automatically be subscribed to this list. The mailing list address is: oph-maculaserver@ad.ucsd.edu

System Maintenance & Downtime
Hardware, software and maintenance procedures necessary for proper system performance and function will be scheduled as needed. Any scheduled maintenance that will interrupt server availability will be announced to all system users in advance. In the event of any unforeseen technical problems that affect the availability of the server, all users will be notified using the macula mailing list.

Data Back ups, Recovery and Data Redundancy
The data on the Macula server is backed up every night to two separate campus locations. In the event of a hardware, or other system failure, data will be restored from the most recent backup. In the event of a user inadvertantly deleting individual file(s), a request can be made to for the restoration of these files from the most recent backup.

IT Support Contacts for macula.ucsd.edu:

Manny Acera
eacera@ucsd.edu
858-822-0629

Ronnie McClean
rmmclean@ucsd.edu
858-822-2556

Policies
Those using the Macula Research File Server should be guided by the principles and practices identified in the UCSD Responsible Computing Use Policy.

Database (​​​FileMaker 12+) Server Available​

The Computational Module of the Core Grant  has provided a FileMaker Database Server for use by vision researchers and associated staff.

This server will provide the following for our research data:

  • Sharing & Security: This server provides secure, multi-user access, to shared databases using UCSD Active Directory authentication
  • Accessibility: FM DBs can be accessed from both Windows and Macs, and from iOS devices: iPads and iPhones. With additional programming, FM DBs can be web-enabled and accessed from any web-browser
  • Visibility: DB access can be restricted to only those persons authorized by the appropriate PI
  • Redundancy: The server is located at the UCSD RCI facility at SDSC with redundant power, cooling and networking
  • Data Integrity: The databases are backed up nightly to two locations
  • Active Server Management: The server will be managed by HGC Computer Group in coordination with the Department IT group

If you have any questions or would like to discuss how you can take advantage of the server, contact Dan Auerbach at VisCoreCompute@ucsd.edu.