panoramic image of the IUB Data Center

Computational Resources

To quote from a document describing IU's cyberinfrastructure

"The cyberinfrastructure at Indiana University is among the best at any university in the world. Its supercomputers, data storage systems, visualization environments, and access to high performance research networks are intended to help you, the researcher, achieve breakthroughs in your scholarship by making possible new calculations, analyses, and visualizations of massive amounts of data."

These resources are freely available to IU students, staff and faculty and our facility makes extensive use of them as an integral part of its operation.

At present, the vast majority of these resources are intended to be used with images acquired using the JEOL JEM 3200FS and FEI Teneo VolumeScope. However, we hope to include images from the JEOL JEM 1010 and the JEOL JEM 1400plus into our computational framework in the future.

The 3200FS and Teneo save images and other data to the WAN area of the IU Data Capacitor, a large capacity (~340 terabyte) Lustre filesystem providing high-speed and high-bandwith communication for all the IU campuses and for XSEDE users. Every few days, all the newly recorded data are backed up to the Scholarly Data Archive (SDA), a very large (~15 petabyte) redundant storage system available to IU faculty, staff and graduate students.

The Data Capacitor is also mounted on the IU supercomputing systems Karst, Carbonate and Big Red 2. All users of the 3200FS and the Teneo will need to obtain an account on Karst in order to access data collected using the 3200FS. We have worked closely with the Scientific Applications and Performance Tuning group of the IU Pervasive Technology Institute both to archive images acquired in the EMC and to install an assortment of image processing software on these systems. The archival system is described elsewhere.

To make accessing the programs on the IU cluster as easy as possible, we have created a Modules working environment on Karst for our users. Setting up the Modules environment to access data and to use these programs is described elsewhere. For use of this software on other clusters such as BigRed 2 or Carbonate, contact David Morgan.

The following programs or packages are currently installed on Karst (and some are available on either Carbonate or BigRed 2):

We attempt to keep the programs listed here up-to-date, though we are often a release or two behind with the packages that offer frequent releases. You should be able to determine the version number of any of this software if you have an account on Karst, and if you need a different version for some reason, please contact David Morgan.

We hope to have all of these programs running on Carbonate and Big Red 2 in the future and also to add other packages including:

In addition to the computational resources described here, we are also assembling a series of tutorials that use these programs. They are intended to be a way to gain hands-on experience with some of this image processing software.

We are also attempting to make it as simple as possible for users to access these computational resources. Towards this end, we have created a series of GUI's that will launch certain types of image processing jobs to the queue managers on Karst, Carbonate and BigRed2. This is all described elsewhere.

Please send suggestions for additional software and any questions about things described on this page to the David Morgan.

Note about lab and personal PC's: Individual users and/or labs may also want to have these image processing programs running on computers in their labs (and visualization tools available on personal laptops). Please contact David about the details involved in purchasing appropriate computers if necessary, setting up programs so they are as compatible as possible with the software on the clusters. etc.

Finally, we have held infrequent meetings to disuss various issues that involve computational aspects of using the EMC and the campus cyber-infrastructure. Contact David Morgan for further information about this such meetings.