Tuesday, July 10, 2018
We are a little more than halfway through the 2018 edition of our summer Data Intensive Scientific Computing REU program at the University of Notre Dame. This summer, our students are working on projects in network science, genome analysis, workflow systems, data visualization, and more. At this point in the summer, students are finalizing their results and starting to work on posters and videos to present what they have learned for our summer research symposium.
Thursday, July 5, 2018
The software may be downloaded here:
This is a major release which adds several features and bug fixes. Among them:
- [General] Catalog updates compressed, and via TCP. (Douglas Thain, Nick Hazekamp, Ben Tovar)
- [JX] Bug fixes to JX, a superset of JSON to dynamically describe workflows, see doc/jx-tutorial.html. (Tim Shaffer, Douglas Thain)
- [Makeflow] Formally define and implement hooks to workflow rules. Hooks may be used to wrap rules with containers (e.g. singularity), a monitoring tool, etc. (Nick Hazekamp, Tim Shaffer)
- [Makeflow] Rule execution as Amazon Lambda functions and S3 objects. (Kyle Sweeney, Douglas Thain)
- [Makeflow] Efficient shared file system access. (Nick Hazekamp)
- [Makeflow] Several bug fixes for rules executing in Mesos. (Chao Zheng)
- [ResourceMonitor] Several bug fixes. (Ben Tovar)
- [WorkQueue] Add user-defined features to workers and tasks. (Nate Kremer-Herman)
- [WorkQueue] Fixes for python3 support. (Ben Tovar)
Thanks goes to the contributors for many features, bug fixes, and tests:
- Nathaniel Kremer-Herman
- Nicholas Hazekamp
- Tim Shaffer
- Douglas Thain
- Ben Tovar
- Kyle Sweeney
- Chao Zheng
Please send any feedback to the CCTools discussion mailing list:
Monday, June 11, 2018
Early Experience Using Amazon Batch for Scientific Workflows gives some of practical experience using Amazon Batch for scientific workflows, comparing the performance of straight EC2 virtual machines against Amazon Batch and overlaying the WorkQueue system on top of virtual machines.
Efficient Integration of Containers into Scientific Workflows explores different methods of composing container images into complex workflows, in order to make efficient use of shared filesystems and data movement.
Monday, June 4, 2018
Tuesday, May 29, 2018
Friday, May 25, 2018
VC3 makes it easy for science groups to deploy custom software stacks across existing university clusters and national facilities. For example, if you want to run your own private Condor pool across three clusters and share it with your collaborators, then VC3 is for you.
We are now running VC3 as a "limited beta" for early adopters who would like to give it a try and send us feedback. Check out the instructions and invitation to sign up.
Tuesday, May 22, 2018
It was a busy graduation weekend here at Notre Dame! The CSE department graduated nineteen PhD students, including CCL grads Dr. Peter Ivie and Dr. James Sweet. Prof. Thain gave the graduation address at the CSE department ceremony. Congratulations and good luck to everyone!
Wednesday, April 25, 2018
In Automatic Dependency Management for Scientific workflows (paper slides) we introduce a tool for sofware environments deployments in clusters. This tool, called the vc3-builder, has minimal dependencies and a lightbootsrap, which allows it to be deployed along batch jobs. The vc3-builder then install any missing sofware using only user-priviliges (e.g., no sudo) so that the actual user payload can be executed. The vc3-builder is being developed as part of the DOE funded Virtual Clusters for Community Computation (VC3) project, in which users can construct custom short-lived virtual clusters across different computational sites.
In MAKER as a Service: Moving HPC applications to Jetstream Cloud (paper poster slides) we discussed the lessons learn in migrating MAKER, a traditional HPC application, to the cloud. This focused on issues like recreating the software stack using VC3-Bulder, addressing the lack of shared filesystems and inter-node communications with Work Queue, and building the application focused on user feedback allowing for informed decisions in the cloud. Using WQ-MAKER we were able to run MAKER not only on Jetstream, but also resources from Notre Dame's Condor cluster. Below you can see the systems architecture.
Monday, March 12, 2018
You can find the slides and tutorial at: CCL at CyVerse Container Camp
Here you can see the active participants:
Monday, January 15, 2018
If you have discovered a new result, published a paper, given a talk, or just done something cool, please take a few minutes to tell us about it on this simple form.
If we accept your submission, we will highlight your story on our website, include a mention in our annual report to the NSF, and send you some neat CCL stickers and swag as a little thank-you.
You can see what others have submitted on our community highlights page.