Publications

2018

Task-parallel Analysis of Molecular Dynamics Trajectories. Ioannis Paraskevakos, Andre Luckow, Mahzad Khoshlessan, George Chantzialexiou, Thomas E. Cheatham, Oliver Beckstein, Geoffrey C. Fox and Shantenu Jha. 47th International Conference on Parallel Processing (ICPP 2018).
[Abstract] [Paper]

Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications. Balasubramanian, Vivek, Matteo Turilli, Weiming Hu, Matthieu Lefebvre, Wenjie Lei, Guido Cervone, Jeroen Tromp and Shantenu Jha. 32nd IEEE International Parallel and Distributed Processing Symposium.
[Abstract] [Paper]

2017

A Comprehensive Perspective on Pilot-Jobs. Matteo Turilli, Mark Santcroos and Shantenu Jha. ACM Computing Surveys (accepted, in press), arXiv preprint {arXiv}:1508.04180v3.
[Abstract]

Computational reproducibility for scientific workflows in large-scale environments. Line Pouchard, Sterling Baldwin, Todd Elsethaggen, Carlos Gamboa, Shantenu Jha, Bibi Raju, Eric Stephan, Li Tang and Kerstin Kleese Van Dam. Proceedings of Computational Reproducibility at Exascale 2017 (in press)Special Issue of IJHPCA, Workshop at ACM/IEEE SC'17 (CRE2017).
[Abstract]

Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library. Mahzad Khoshlessan, Ioannis Paraskevakos, Shantenu Jha and Oliver Beckstein. Proceedings of the 15th Python in Science Conference. (SCIPY 2017).
[Abstract] [Paper]

Introducing distributed dynamic data-intensive (D3) science: Understanding applications and infrastructure. Jha, Shantenu and Katz, Daniel S. and Luckow, Andre and Chue Hong , Neil and Rana, Omer and Simmhan, Yogesh. Concurrency and Computation: Practice and Experience.
[Abstract] [Paper]

Learning Neural Markers of Schizophrenia Disorder Using Recurrent Neural Networks. Jumana Dakka, Pouya Bashivan, Mina Gheiratmand, Irina Rish, Shantenu Jha and Russell Greiner. Machine Learning for Health Workshop at Neural Information Processing Systems (NIPS 2017), Long Beach, California, US.
[Abstract] [Paper]

Toward Common Components for Open Workflow Systems. Jay Jay Billings and Shantenu Jha. Proceedings of Open Source SuperComputing, Workshop at SC'17.
[Abstract] [Paper]

High-throughput Binding Affinity Calculations at Extreme Scales. Jumana Dakka, Matteo Turilli, David W Wright, Stefan J Zasada, Vivek Balasubramanian, Shunzhou Wan, Peter V Coveney and Shantenu Jha. Computational Approaches for Cancer Workshop at SuperComputing (SC 2017).
[Abstract] [Paper]

Evaluating Distributed Execution of Workloads. M. Turilli, Y. N. Babuji, A. Merzky, M. T. Ha, M. Wilde, D. S. Katz and S. Jha. 2017 IEEE 13th International Conference on e-Science (e-Science).
[Abstract]

High-Throughput Computing on High-Performance Platforms: A Case Study. D. Oleynik, S. Panitkin, M. Turilli, A. Angius, S. Oral, K. De, A. Klimentov, J. C. Wells and S. Jha. 2017 IEEE 13th International Conference on e-Science (e-Science).
[Abstract]

2016

Executing dynamic heterogeneous workloads on Blue Waters with RADICAL-Pilot. Santcroos, Mark, Castain, Ralph, Merzky, Andre, Bethune, Iain and Jha, Shantenu. Cray User Group 2016 (London).
[Abstract]

Synapse: Synthetic Application Profiler and Emulator. Andre Merzky and Shantenu Jha. 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, IPDPS Workshops 2016, Chicago, IL, USA, May 23-27, 2016.
[Abstract] [Paper]

On the Complexities of Utilizing Large-Scale Lightpath-Connected Distributed Cyberinfrastructure. Jason Maassen et al . Concurrency and Computation: Practice and Experience.
[Abstract]

Hadoop on HPC: Integrating Hadoop and Pilot-Based Dynamic Resource Management. Andre Luckow, Ioannis Paraskevakos, George Chantzialexiou and Shantenu Jha. 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).
[Abstract] [Paper]

Integration Of PanDA Workload Management System with Supercomputers for ATLAS and Data-Intensive Sciences. A. Klimentov, K. De, S. Jha, T. Maeno, R. Mashinistov, P. Nilsson, A. Novikov, D. Oleynik, S. Panitkin, A.Poyda, K.F.Read, E. Ryabinkin, A. Teslyuk, J.C. Wells and T. Wenaus. Journal of Physics: Conference Series, Volume 762 (2016), 012021, 17th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2016, Valparaiso, Chile, 20160118, 20160122).
[Abstract] [Paper]

Integration of Panda Workload Management System with supercomputers. De, K., Jha, S., Klimentov, A., Maeno, T., Mashinistov, R., Nilsson, P., Novikov, A., Oleynik, D., Panitkin, S., Poyda, A., Read, K. F., Ryabinkin, E., Teslyuk, A., Velikhov, V., Wells, J. C. and Wenaus, T.. Physics of Particles and Nuclei Letters.
[Abstract] [Paper]

ExTASY: Scalable and flexible coupling of MD simulations and advanced sampling techniques. V. Balasubramanian, I. Bethune, A. Shkurti, E. Breitmoser, E. Hruska, C. Clementi, C. Laughton and S. Jha. 2016 IEEE 12th International Conference on e-Science (e-Science).
[Abstract] [Paper]

RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations. A. Treikalis, A. Merzky, H. Chen, T. S. Lee, D. M. York and S. Jha. 2016 45th International Conference on Parallel Processing (ICPP).
[Abstract]

Ensemble Toolkit: Scalable and Flexible Execution of Ensembles of Tasks. Vivekanandan Balasubramanian, Antons Treikalis, Ole Weidner, and Shantenu Jha. 45th International Conference on in Parallel Processing (ICPP), pp. 458-463. IEEE, 2016.
[Abstract] [Paper]

Application Skeleton: Generating Synthetic Applications for Infrastructure Research. Zhao Zhang and Daniel S. Katz and Andre Merzky and Matteo Turilli and Shantenu Jha and Yadu Nand. The Journal of Open Source Software.
[Abstract] [Paper]

Integrating Abstractions to Enhance the Execution of Distributed Applications. Matteo Turilli, Feng (Francis) Liu, Zhao Zhang, Andre Merzky, Michael Wilde, Jon Weissman, Daniel S. Katz and Shantenu Jha. Proceedings of 30th IEEE International Parallel and Distributed Processing Symposium (IPDPS).
[Abstract] [Paper]

2015

Characterization of the Three-Dimensional Free Energy Manifold for the Uracil Ribonucleoside from Asynchronous Replica Exchange Simulations. Brian K. Radak, Melissa Romanus, Tai-Sung Lee, Haoyuan Chen, Ming Huang, Antons Treikalis, Vivekanandan Balasubramanian, Shantenu Jha and Darrin M. York. Journal of Chemical Theory and Computation.
[Abstract] [Paper]

{SAGA}: A Standardized Access Layer to Heterogeneous Distributed Computing Infrastructure. Andre Merzky, Ole Weidner and Shantenu Jha. Software-X.
[Abstract] [Paper]

Next Generation Workload Management System For Big Data on Heterogeneous Distributed Computing. A Klimentov, P Buncic, K De, S Jha, T Maeno, R Mount, P Nilsson, D Oleynik and S Panitkin, A Petrosyan, R J Porter, K F Read, A Vaniachine, J C Wells and T Wenaus. Journal of Physics: Conference Series.
[Abstract] [Paper]

Application skeletons: Construction and use in eScience . Daniel S. Katz, Andre Merzky, Zhao Zhang and Shantenu Jha. Future Generation Computer Systems.
[Abstract] [Paper]

2014

Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors. David W. Wright, Benjamin A. Hall, Owain A. Kenway, Shantenu Jha and Peter V. Coveney. Chemical Theory and Computation.
[Abstract]

Developing eThread Pipeline Using SAGA- Pilot Abstraction for Large-Scale Structural Bioinformatics. Anjani Ragothaman, Sairam Chowdary Boddu, Nayong Kim, Wei Feinstein, Michal Brylinski, Shantenu Jha and Joohyun Kim. BioMed Research International.
[Abstract]

Numerical Experiments of Solving Moderate-velocity Flow Field Using a Hybrid Computational Fluid Dynamics Molecular Dynamics Approach. Soon-Heum Ko, Nayong Kim, Shantenu Jha, Dimitris E. Nikitopoulos, Dorel Moldovan. Mechanical Science and Technology.
[Abstract]

A Tale of Two Data-Intensive Paradigms: Applications, Abstractions, and Architectures. Shantenu Jha, Judy Qiu, Andre Luckow, Pradeep Mantha and Geoffrey C.Fox. 2014 IEEE International Congress on Big Data (BigData Congress).
[Abstract] [Paper]

Pilot-Data: An Abstraction for Distributed Data. Andre Luckow, Mark Santcroos, Ashley Zebrowski and Shantenu Jha. Journal Parallel and Distributed Computing.
[Abstract]

Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force. Hugh S. C. Martin and Shantenu Jha and Peter V.Coveney. Computational Chemistry.
[Abstract] [Paper]

Towards Standardized Job Submission and Control in Infrastructure Clouds. Peter Troger and Andre Merzky. Journal of Grid Computing.
[Abstract] [Paper]

2013

Scalable Online Comparative Genomics of Mononucleosomes: A BigJob. Jack Smith, Melissa Romanus, James Solow, Pradeep Kumar Mantha, Yaakoub El Khamra, Thomas C. Bishop and Shantenu Jha. Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery.
[Abstract] [Paper]

Exploring Dynamic Enactment of Scientific Workflows using Pilot-Abstractions. Mark Santcroos, Barbera DC van Schaik, Shayan Shahand, Silvia Delgado Olabarriaga, Andre Luckow and Shantenu Jha. 13th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing.
[Abstract]

A Framework for Flexible and Scalable Replica-Exchange on Production Distributed CI. Brian K. Radak, Melissa Romanus, Emilio Gallicchio, Tai-Sung Lee, Ole Weidner, Nan-Jie Deng, Peng He, Wei Dai, Darrin M. York, Ronald M. Levy and Shantenu Jha. Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery.
[Abstract] [Paper]

Advancing next-generation sequencing data analytics with scalable distributed infrastructure. Kim, Joohyun and Maddineni, Sharath and Jha, Shantenu. Concurrency and Computation: Practice and Experience.
[Abstract] [Paper]

Distributed computing practice for large-scale science and engineering applications. Jha, Shantenu and Cole, Murray and Katz, Daniel S. and Parashar, Manish and Rana, Omer and Weissman, Jon. Concurrency and Computation: Practice and Experience.
[Abstract] [Paper]

2012

Pilot abstractions for compute, data, and network. Mark Santcroos, Silvia Delgado Olabarriaga, Daniel S. Katz and Shantenu Jha. 2012 IEEE 8th International Conference on E-Science.
[Abstract] [Paper]

The Anatomy of Successful ECSS Projects: Lessons of supporting High-Throughput High-Performance Ensembles on XSEDE. Melissa Romanus, Pradeep Kumar Mantha, Matt McKenzie, Thomas C. Bishop, Emilio Gallichio, Andre Merzky, Yaakoub El Khamra and Shantenu Jha. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the Campus and Beyond.
[Abstract] [Paper]

Running many Molecular Dynamics Simulations on many Supercomputers. Rajib Mukherjee, Abhinav Thota, Hideki Fujioka, Thomas C. Bishop and Shantenu Jha. Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the Campus and Beyond.
[Abstract]

Pilot-MapReduce: an extensible and flexible MapReduce implementation for distributed data. Pradeep Kumar Mantha, Andre Luckow and Shantenu Jha. Proceedings of third international workshop on MapReduce and its Applications.
[Abstract] [Paper]

Distributed Application Runtime Environment (DARE): A Standards-based Middleware Framework for Science-Gateways. Maddineni, Sharath, Kim, Joohyun, El-Khamra, Yaakoub and Jha, Shantenu. J. Grid Comput..
[Abstract] [Paper]

P*: A model of pilot-abstractions. Andre Luckow, Mark Santcroos, Andre Merzky, Ole Weidner, Pradeep Mantha and Shantenu Jha. IEEE 8th International Conference on e-Science.
[Abstract] [Paper]

Conformational Heterogeneity of the SAM-I Riboswitch Transcriptional ON State: A Chaperone-Like Role for S-Adenosyl Methionine. Wei Huang, Joohyun Kim, Shantenu Jha and Fareed Aboul-ela. Journal of Molecular Biology.
[Abstract] [Paper]

Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity. Benjamin A. Hall, David W. Wright, Shantenu Jha and Peter V. Coveney. Biochemistry.
[Abstract]

Understanding MapReduce-based Next-Generation Sequencing Alignment on Distributed Cyberinfrastructure. Pradeep Mantha, Nayong Kim, Joohyun Kim, Andre Luckow and Shantenu Jha. 3rd International Workshop on Emerging Methods in Computational Life Sciences, Proceedings of the 21st International Symposium on High-Performance Parallel and Distributed Computing, HPDC'12.
[Abstract]

Towards a common model for pilot-jobs. Andre Luckow, Mark Santcroos, Ole Weidner, Andre Merzky, Sharath Maddineni and Shantenu Jha. Proceedings of the 21st International Symposium on High-Performance Parallel and Distributed Computing, HPDC'12.
[Abstract] [Paper]

2011

Efficient large-scale Replica-Exchange Simulations on Production Infrastructure. Abhinav Thota and Andre Luckow and Shantenu Jha. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
[Abstract] [Paper]

Understanding Application-Level Interoperability: Scaling-Out MapReduce over High-Performance Grids and Clouds. Saurabh Sehgal, Miklos Erdelyi, Andre Merzky and Shantenu Jha. Future Generation Computer Systems.
[Abstract] [Paper]

Using the TeraGrid to teach Scientific Computing. Frank Loffler, Gabrielle Allen, Werner Benger, Andrei Hutanu, Shantenu Jha and Erik Schnetter. Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery.
[Abstract] [Paper]

Energy Landscape Analysis for Regulatory RNA Finding using Scalable Distributed Cyberinfrastructure. Joohyun Kim, Wei Huang, Sharath Maddineni, Fareed Aboul-ela and Shantenu Jha. Concurrency and Computation: Practice and Experience.
[Abstract] [Paper]

Characterizing deep sequencing analytics using BFAST: towards a scalable distributed architecture for next-generation sequencing data. Joohyun Kim and Sharath Maddineni and Shantenu Jha. Proceedings of the second international workshop on Emerging computational methods for the life sciences.
[Abstract] [Paper]

Building Gateways for Life-Science Applications using the Dynamic Application Runtime Environment (DARE) Framework. Joohyun Kim, Sharath Maddineni and Shantenu Jha. Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery.
[Abstract] [Paper]

Towards high-throughput, high-performance computational estimation of binding affinities for patient specific HIV-1 protease sequences. Owain Kenway, David W. Wright, Helmut Heller, Andre Merzky, Gavin Pringle, Jules Wolfrat, Peter Coveney and Shantenu Jha. Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery.
[Abstract] [Paper]

A Practical and Comprehensive Graduate Course preparing Students for Research involving Scientific Computing. Gabrielle Allen, Werner Benger, Andrei Hutanu, Shantenu Jha, Frank Loffler and Erik Schnetter. Procedia Computer Science.
[Abstract] [Paper]

Understanding Scientific Applications for Cloud Environments. Shantenu Jha and Daniel S. Katz and Andre Luckow and Andre Merzky and Katerina Stamou. Cloud Computing: Principles and Paradigms.
[Abstract] [Paper]

2010

SAGA BigJob: An Extensible and Interoperable Pilot-Job Abstraction for Distributed Applications and Systems. Andre Luckow, Lukas Lacinski and Shantenu Jha. The 10th IEEE/ACM International Symposium on Cluster,Cloud and Grid Computing.
[Abstract]

Abstractions for Loosely-Coupled and Ensemble-Based Simulations on Azure. Andre Luckow and Shantenu Jha. International IEEE Conference on Cloud Computing Technology and Science.
[Abstract] [Paper]

Efficient Runtime Environment for Coupled Multi-physics Simulations: Dynamic Resource Allocation and Load-Balancing. Soon-Heum Ko, Nayong Kim, Joohyun Kim, Abhinav Thota and Shantenu Jha. Proceedings of the 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing.
[Abstract] [Paper]

Exploring the {RNA} folding energy landscape using scalable distributed cyberinfrastructure. Joohyun Kim, Wei Huang, Sharath Maddineni, Fareed Aboul-Ela and Shantenu Jha. Emerging Computational Methods in the Life Sciences, Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing.
[Abstract]

Modelling data-driven CO2 sequestration using distributed HPC cyberinfrastructure. Yaakoub El-Khamra, Shantenu Jha and Christopher D. White. {Proceedings of the 2010 TeraGrid Conference}.
[Abstract] [Paper]

What Is the Price of Simplicity? -- A Cross-Platform Evaluation of the SAGA API. Mathijs Den Burger, Ceriel Jacobs, Thilo Kielmann, Andre Merzky, Ole Weidner and Hartmut Kaiser. Proceedings of the 16th international Euro-Par conference on Parallel processing: Part I.
[Abstract] [Paper]

Understanding Performance of Distributed Data-Intensive Applications. Chris Miceli, Michael Miceli, Bety Rodriguez-Milla and Shantenu Jha. Royal Society of London Philosophical Transactions Series A.
[Abstract] [Paper]

2009

A Fresh Perspective on Developing and Executing DAG-Based Distributed Applications: A Case-Study of SAGA-Based Montage. Andre Merzky, Katerina Stamou, Shantenu Jha and Daniel S. Katz. Proceedings of the 2009 Fifth IEEE International Conference on e-Science.
[Abstract]

Application Level Interoperability between Clouds and Grids. Andre Merzky, Katerina Stamou and Shantenu Jha. Proceedings of the IEEE Grid and Pervasive Computing Conference '09.
[Abstract] [Paper]

Adaptive Distributed Replica--Exchange Simulations. Andre Luckow, Shantenu Jha, Joohyun Kim, Andre Merzky and Bettina Schnor. Theme Issue of the Philosophical Transactions of the Royal Society A: Crossing Boundaries: Computational Science, E-Science and Global E-Infrastructure Proceedings of the UK e-Science All Hands Meeting.
[Abstract] [Paper]

Louisiana: a model for advancing regional e-Research through cyberinfrastructure. Daniel S. Katz, Gabrielle Allen, R. Cortez, C. Cruz-Neira, R. Gottumukkala, Z. D. Greenwood, L. Guice, Shantenu Jha, R. Kolluru, Tevfik Kosar and others. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
[Abstract] [Paper]

Using Clouds to Provide Grids with Higher Levels of Abstraction and Explicit Support for Usage Modes. Shantenu Jha, Andre Merzky and Geoffrey Fox. Concurrency and Computation: Practice and Experience.
[Abstract] [Paper]

Developing Scientific Applications with Loosely-Coupled Sub-tasks. Shantenu Jha and Yaakoub El-Khamra and Joohyun Kim. Proceedings of the 9th International Conference on Computational Science: Part I.
[Abstract] [Paper]

Critical Perspectives on Large-Scale Distributed Applications and Production Grids. Shantenu Jha, Daniel S. Katz, Manish Parashar, Omer Rana and Jon B. Weissman. The 10th IEEE/ACM Conference on Grid Computing 2009, (Best Paper Award).
[Abstract] [Paper]

Modelling Data-Driven CO_2 Sequestration Using Distributed HPC CyberInfrastructure. Yaakoub El-Khamra and Shantenu Jha. Microsoft Research eScience Workshop, Pittsburgh.
[Abstract] [Paper]

Developing Autonomic Distributed Scientific Applications: A Case Study From History Matching Using Ensemble Kalman-Filters. Yaakoub El-Khamra and Shantenu Jha. GMAC '09: Proceedings of the 6th International Conference Industry Session on Grids meets Autonomic Computing.
[Abstract] [Paper]

Adaptive Replica-Exchange Simulations. Andre Luckow, Shantenu Jha, Joohyun Kim, Andre Merzky and Bettina Schnor. Royal Society Philosophical Transactions A.
[Abstract] [Paper]

Programming Abstractions for Data Intensive Computing on Clouds and Grids. Chris Miceli and Michael Miceli and Shantenu Jha and Hartmut Kaiser and Andre Merzky. 9th IEEE/ACM International Symposium on Cluster Computing and the Grid, 2009..
[Abstract]

2008

Distributed Replica-Exchange Simulations on Production Environments Using SAGA and Migol. Andre Luckow, Shantenu Jha, Joohyun Kim, Andre Merzky and Bettina Schnor. Proceedings of the 2008 Fourth IEEE International Conference on eScience.
[Abstract] [Paper]

Developing Large-Scale Adaptive Scientific Applications with Hard to Predict Runtime Resource Requirements. Shantenu Jha, Yaakoub El-Khamra, Hartmut Kaiser, Ole Weidner and Andre Merzky. Proceedings of TeraGrid08.
[Abstract]

2007

Grid Interoperability at the Application Level Using SAGA. Shantenu Jha, Hartmut Kaiser, Andre Merzky and Ole Weidner. E-SCIENCE '07: Proceedings of the Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007).
[Abstract] [Paper]

Design and Implementation of Network Performance Aware Applications Using SAGA and Cactus. Shantenu Jha, Hartmut Kaiser, Yaakoub El-Khamra and Ole Weidner. Proceedings of the Third IEEE International Conference on e-Science and Grid Computing.
[Abstract] [Paper]

2006

SAGA: A Simple API for Grid applications, High-Level Application Programming on the Grid. Tom Goodale, Shantenu Jha, Harmut Kaiser, Thilo Kielmann, Pascal Kleijer, Gregor von Laszewski, Craig Lee, Andre Merzky, Hrabri Rajic and John Shalf. Computational Methods in Science and Technology.
[Abstract] [Paper]

2005

GRID SuperScalar and SAGA: forming a high-level and platform-independent Grid Programming Environment. Raoul Sirvent, Andre Merzky, Rosa M. Badia and Thilo Kielmann. CoreGRID Integration WorkShop.
[Abstract] [Paper]


Standards, White Papers, Technical Reports


Draft