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. However, we hope to include images from the JEOL JEM 1010 into our computational framework as soon as possible.

The JEOL JEM 3200FS writes images and spectra 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. At the end of each day, 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 Quarry, Mason and Big Red II. All users of the 3200FS will need to obtain an account on Quarry in order to access data collected using the 3200FS. We have worked with the Scientific Applications and Performance Tuning group of the IU Pervasive Technology Institute to install an assortment of image processing software on these systems. To make accessing these programs as easy as possible, we have created a Modules working environment on Quarry for our users. Setting up the Modules environment to access data and to use these programs is described elsewhere.

The following programs or packages are currently installed on Quarry and/or Mason:

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 quarry, and if you need a different version for some reason, please contact David Morgan.

We hope to have many of these programs running on Mason and BigRed II in the future and also to add the following packages:

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 manager on Quarry. 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: Users 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 an appropriate computer if necessary, setting up programs so they are as compatible as possible with the software on the clusters. etc.

Finally, we have recently begun (spring, 2014) a monthly meeting to disuss various issues that involve computational aspects of using the EMC and the campus cyber-infrastructure. This meeting occurs the second Tuesday of evey month from 11 to noon in Simon Hall 030. Contact David Morgan for further information about this discussion group.