#### Publications

- J. Enos, C. Steffen, J. Fullop, M. Showerman, G. Shi, K. Esler,
__V. Kindratenko__, J. Stone, J. Phillips,**Quantifying the Impact of GPUs on Performance and Energy Efficiency in HPC Clusters**, In Proc.*Workshop on Work in Progress in Green Computing, First International Green Computing Conference*, 2010 (paper) __V. Kindratenko__, J. Enos, G. Shi, M. Showerman, G. Arnold, J. Stone, J. Phillips, W. Hwu,**GPU Clusters for High-Performance Computing**, In Proc.*Workshop on Parallel Programming on Accelerator Clusters - PPAC'09*, 2009. (paper, slides)- G. Shi, J. Enos, M. Showerman,
__V. Kindratenko__,**On testing GPU memory for hard and soft errors**, In Proc.*Symposium on Application Accelerators in High-Performance Computing – SAAHPC'09*, 2009. (paper, slides) __V. Kindratenko__,**Novel Computing Architectures**, inaugural Novel Architectures department article,*IEEE/AIF Computing in Science and Engineering*, vol. 11, no. 3, pp. 54-57, May/June 2009 (paper)- M. Showerman, J. Enos, A. Pant,
__V. Kindratenko__, C. Steffen, R. Pennington, W. Hwu,**QP: A Heterogeneous Multi-Accelerator Cluster**, In Proc.*10th LCI International Conference on High-Performance Clustered Computing*, 2009 (paper) - A. Pant, H. Jafri,
__V. Kindratenko__,**Phoenix: A Runtime Environment for High Performance Computing on Chip Multiprocessors**, In Proc.*17th Euromicro International Conference on Parallel, Distributed and Network-Based Processing - PDP'09*, 2009, pp. 119-126 (paper) - S. Lee, D. Raila,
__V. Kindratenko__,**LLVM-CHiMPS: compilation environment for FPGAs using LLVM compiler infrastructure and CHiMPS computational model**, In Proc.*4th Annual Reconfigurable Systems Summer Institute - RSSI'08*, 2008 (paper) - T. El-Ghazawi, E. El-Araby, M. Huang, K. Gaj,
__V. Kindratenko__, D. Buell,**The Promise of High-Performance Reconfigurable Computing**,*Computer*, vol. 41, no. 2, pp. 78-85, 2008. (paper) __V. Kindratenko__, C. Steffen, R. Brunner,**Accelerating Scientific Applications with Reconfigurable Computing: Getting Started**,*Computing in Science and Engineering*, vol. 9, no. 5, pp. 70-77, 2007 (paper)- D. Buell, T. El-Ghazawi, K. Gaj,
__V. Kindratenko__,**High-Performance Reconfigurable Computing**, Guest Editors' Introduction,*Computer*, March 2007, pp. 27-31 (paper) - D. Meixner,
__V. Kindratenko__, D. Pointer,**On Using Simulink to Program SRC-6 Reconfigurable Computer**, In Proc.*9th Military and Aerospace Programmable Logic Devices International Conference - MAPLD'06*, 2006 (paper) - D. Meixner,
__V. Kindratenko__, D. Pointer,**Running Simulink-based Designs on SRC-6**, In Proc.*10th Annual Workshop on the High Performance Embedded Computing - HPEC'06*, 2006 (paper) __V. Kindratenko__,**Code Partitioning for Reconfigurable High-Performance Computing: A Case Study**, In Proc.*International Conference on Engineering of Reconfigurable Systems and Algorithms - ERSA'06*, 2006, pp. 143-149 (paper)

- J. Enos, C. Steffen, J. Fullop, M. Showerman, G. Shi, K. Esler,
#### Technical reports

__V. Kindratenko__, R. Brunner, G. Shi, D. Roeh, A. Martinez,**Investigating Application Analysis and Design Methodologies for Computational Accelerators**, NCSA Technical Report, 2009 (report)- M. Showerman, J. Enos, A. Pant,
__V. Kindratenko__, C. Steffen, R. Pennington, W. Hwu,**QP: A Heterogeneous Multi-Accelerator Cluster**, NCSA Technical Report, 2008 (report) __V. Kindratenko__, D. Pointer, D. Raila, C. Steffen,**Comparing CPU and FPGA Application Performance**, Short Report, 2006 (report)__V. Kindratenko__, D. Pointer, D. Caliga,**High-Performance Reconfigurable Computing Application Programming in C**, NCSA Technical Report, 2006 (report)- D. Meixner,
__V. Kindratenko__, D. Pointer,**Implementing Simulink Designs on SRC-6 System**, NCSA Technical Report, 2006 (report)

#### Tutorials

__V. Kindratenko__,**Introduction to GPU Programming**,*US-Egypt Collaboration Follow-up meeting*, December 2010, The American University in Cairo, Egypt (part I, part II, part III, part IV, source)__V. Kindratenko__,**Introduction to GPU Programming**,*High Performance Computing Course*, June 2010, Advanced Digital Sciences Center, Singapore (part I, part II, part III, part IV, source)__V. Kindratenko__,**Introduction to GPU Programming**,*CRA-W/CDC Careers in High Performance Systems (CHiPS) Mentoring Workshop*, July 2009, Urbana, IL (slides)- T. El-Ghazawi, D. Buell, K. Gaj,
__V. Kindratenko__,**Reconfigurable Supercomputing Tutorial**,*Supercomputing 2007*, November 2007, Reno, NV (slides)

#### Presentations

__V. Kindratenko__,**GPU HPC Clusters**,*Seminar*, Department of Computer Science & Computer Engineering, University of Arkansas, December 2010, Fayetteville, AR (abstract)
(presentation)
__V. Kindratenko__,**High Performance Computing with Application Accelerators**,*High Performance Computing Symposium*, June 2010, Advanced Digital Sciences Center, Singapore (presentation)__V. Kindratenko__,**Overview of Hardware Accelerators**,*NSF US/Egypt Meeting on Software Development for Multicore and Heterogeneous Processing Technologies*, June 2009, Cairo, Egypt, (slides)__V. Kindratenko__,**High Performance Computing with Accelerators**,*First workshop of the Joint Laboratory for Petascale Computing*, June 2009, Paris, France, (abstract, slides)__V. Kindratenko__,**High Performance Computing on FPGAs: challenges and opportunities**, Panel on Key Challenges presented by next generation hardware systems,*Key Challenges in Modeling and Simulation Fall Creek Falls conference*, September 2007, Nashville, TN (slides)__V. Kindratenko__,**Accelerating Scientific Applications with Reconfigurable Computing**,*Seminar*, Dept. of Computer and Information Sciences, University of Alabama at Birmingham, June 2007, Birmingham, AL (abstract)
(presentation)
__V. Kindratenko__,**First-hand experience on porting MATPHOT code to SRC platform**,*1st Annual Reconfigurable Systems Summer Institute - RSSI*, July 2005, Urbana, IL (presentation)

#### Codes

#### Publications

#### Technical reports and presentations

__V. Kindratenko__, G. Shi,**Evaluation and Exploration of Next Generation Systems for Applicability and Performance**,*Technical report 1*, October 2010 (report, presentation)__V. Kindratenko__, G. Shi,**Evaluation and Exploration of Next Generation Systems for Applicability and Performance**,*Technical report 2*, December 2010 (report, presentation)__V. Kindratenko__, G. Shi,**Evaluation and Exploration of Next Generation Systems for Applicability and Performance**,*Technical report 3*, March 2011 (report, presentation)__V. Kindratenko__, G. Shi,**Evaluation and Exploration of Next Generation Systems for Applicability and Performance**,*Technical report 4*, June 2011 (report, presentation)

#### Codes

- image analysis

#### Publications

- S. Gottlieb, G. Shi, A. Torok,
__V. Kindratenko__,**QUDA programming for staggered quarks**, In Proc.*The XXVIII International Symposium on Lattice Field Theory - Lattice'10*, 2010 (paper) - G. Shi, S. Gottlieb, A. Totok,
__V. Kindratenko__,**Accelerating Quantum Chromodynamics Calculations with GPUs**, In Proc.*Symposium on Application Accelerators in High-Performance Computing - SAAHPC'10*, 2010 (paper) - G. Shi,
__V. Kindratenko__, F. Pratas, P. Trancoso, M. Gschwind,**Application Acceleration with the Cell Broadband Engine**,*IEEE/AIF Computing in Science and Engineering*, vol. 12, no. 1, pp. 76-81, Jan./Feb. 2010 (paper) - G. Shi,
__V. Kindratenko__, S. Gottlieb,**The bottom-up implementation of one MILC lattice QCD application on the Cell blade**,*International Journal of Parallel Programming*, vol. 37, no. 5, pp. 488-507, 2009 (paper) - G. Shi,
__V. Kindratenko__, S. Gottlieb,**Cell processor implementation of a MILC lattice QCD application**, In Proc.*The XXVI International Symposium on Lattice Field Theory - Lattice'08*, 2008 (paper)

- S. Gottlieb, G. Shi, A. Torok,
#### Technical reports and presentations

- G. Shi, S. Gottlieb, A. Torok,
__V. Kindratenko__,**Multi-GPU Implementation of MILC using QUDA Framework**, SC10 poster, November 2010 (poster) - G. Shi, S. Gottlieb,
__V. Kindratenko__,**MILC on GPUs**, NCSA Technical Report, January 2010 (report) - G. Shi,
**GPU Implementation of CG solver for MILC**, Internal presentation, November 2009 (presentation) - D. Roeh, J. Troup, G. Shi,
__V. Kindratenko__,**Porting MILC to GPU: Lessons learned**,*Workshop on using GPUs for LQCD*, August 19-21 2009, Thomas Jefferson National Accelerator Facility, Newport News, Virginia (presentation)

- G. Shi, S. Gottlieb, A. Torok,
#### Codes

#### Publications

__V. Kindratenko__, A. Myers, R. Brunner,**Implementation of the two-point angular correlation function on a high-performance reconfigurable computer**,*Scientific Programming*, vol. 17, no. 3, pp. 247-259, 2009 (paper)__V. Kindratenko__, R. Brunner, A. Myers,**Dynamic load-balancing on multi-FPGA systems: a case study**, In Proc.*3rd Annual Reconfigurable Systems Summer Institute - RSSI'07*, 2007 (paper, presentation)- R. Brunner,
__V. Kindratenko__, and A. Myers,**Developing and Deploying Advanced Algorithms to Novel Supercomputing Hardware**, In Proc.*NASA Science Technology Conference - NSTC'07*, 2007 (paper, presentation) __V. Kindratenko__, R. Brunner, A. Myers,**Mitrion-C Application Development on SGI Altix 350/RC100**, In Proc.*IEEE Symposium on Field-Programmable Custom Computing Machines - FCCM'07*, 2007 (paper, presentation)

#### Technical reports and presentations

__V. Kindratenko__,**Accelerating Cosmology Applications: from 80 MFLOPS to 8 GFLOPS in 4 steps**,*13th SIAM Conference on Parallel Processing for Scientific Computing*, 2008 (presentation)- R. Brunner,
**Year Two Progress Report for NASA Grant NNG06GH15G**, 2007 (report, presentation) **Preliminary investigation of NVIDIA G80 GPU suitability for computing TPACF**,*ECE498AL class exercise*, 2007 (problem statement, report, presentation)- R. Brunner,
**Year One Progress Report for NASA Grant NNG06GH15G**, 2006 (report) __V. Kindratenko__,**Exploring Coarse-grain and Fine-grain Parallelism on SRC-6 Reconfigurable Computer**,*2nd Annual Reconfigurable Systems Summer Institute - RSSI'06*, 2006 (poster)

#### Codes

- TPACF 1.0 reference implementation
- TPACF 1.0 SRC-6 implementation
- TPACF 1.0 SGI RC100 implementation
- ANN PDFs SRC-7 implementation

#### Publications

- A. Titov,
__V. Kindratenko__, I. Ufimtsev, T. Martinez,**Generation of Kernels to Calculate Electron Repulsion Integrals of High Angular Momentum Functions on GPUs – Preliminary Results**, in Proc.*Symposium on Application Accelerators in High-Performance Computing - SAAHPC'10*, 2010 (paper) - G. Shi, I. Ufimtsev,
__V. Kindratenko__, T. Martinez,**Direct Self-Consistent Field Computations on GPU Clusters**, in Proc.*IEEE International Parallel and Distributed Processing Symposium – IPDPS*, 2010 (paper) - G. Shi,
__V. Kindratenko__, I. Ufimtsev, T. Martinez, J. Phillips, S. Gottlieb,**Implementation of scientific computing applications on the Cell Broadband Engine**,*Scientific Programming*, vol. 17, no. 1-2, pp. 135-152, 2009 (paper) __V. Kindratenko__, I. Ufimtsev, T. Martínez,**Evaluation of two-electron repulsion integrals over Gaussian basis functions on SRC-6 reconfigurable computer**, In Proc.*4th Annual Reconfigurable Systems Summer Institute - RSSI'08*, 2008 (paper, poster)- G. Shi,
__V. Kindratenko__,**Implementation of NAMD molecular dynamics non-bonded force-field on the Cell Broadband Engine processor**, In Proc.*9th IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing - PDSEC*, 2008 (paper, presentation) __V. Kindratenko__, and D. Pointer,**A case study in porting a production scientific supercomputing application to a reconfigurable computer**, In Proc.*IEEE Symposium on Field-Programmable Custom Computing Machines - FCCM’06*, 2006, pp. 13-22 (paper, presentation)

- A. Titov,
#### Technical reports and presentations

__V. Kindratenko__,**Computational Chemistry Applications at NCSA/UIUC**,*US-China Workshop on High Performance Computing Application Acceleration*, 2010 (presentation)- G. Shi,
__V. Kindratenko__, I. Ufimtsev, T. Martinez,**Two-Electron Integral Evaluation on FPGA, Cell and GPU accelerators**,*Path to Petascale: Adapting GEO/CHEM/ASTRO Applications for Accelerators and Accelerator Clusters*workshop, April 2009 (poster) - G. Shi,
__V. Kindratenko__,**Implementation of Scientific Computing Applications on the Cell Broadband Engine processor**,*2nd Annual Georgia Tech, Sony/Toshiba/IBM Workshop on Software and Applications for the Cell/B.E. processor*, 2008 (presentation) - G. Shi,
__V. Kindratenko__,**Implementation of NAMD molecular dynamics non-bonded force-field on the Cell Broadband Engine processor**,*Supercomuting*, 2007 (poster) __V. Kindratenko__,**Summary of Current and Future CyberChemActivities at ISL/NCSA**,*Internal project meeting*, 2007 (presentation)

#### Codes

- NAMD SCR-6 implementation
- NAMD Cell/B.E. implementation
- ERIs reference implementation
- ERIs SCR-6 implementation
- ERIs Cell/B.E. implementation

#### Publications

__V. Kindratenko__, R. Brunner,**Accelerating Cosmological Data Analysis with FPGAs**, In Proc.*IEEE Symposium on Field-Programmable Custom Computing Machines - FCCM'09*, 2009 (paper, presentation)- D. Roeh,
__V. Kindratenko__, R. Brunner,**Accelerating Cosmological Data Analysis with Graphics Processors**, in Proc.*2nd Workshop on General-Purpose Computation on Graphics Processing Units workshop - GPGPU-2*, 2009 (paper, presentation)

#### Technical reports and presentations

__V. Kindratenko__, D. Roeh, G. Shi, R. Brunner,**Accelerating Cosmology Codes**,*Path to Petascale: Adapting GEO/CHEM/ASTRO Applications for Accelerators and Accelerator Clusters*workshop, April 2009 (poster)__V. Kindratenko__, R. Brunner, G. Shi, D. Roeh, A. Martinez,**Investigating Application Analysis and Design Methodologies for Computational Accelerators**, NCSA Technical Report, 2009 (report)__V. Kindratenko__, D. Roeh,**Internal NCSA GPU programming tutorial**, December 2008 (part 1, part 2)__V. Kindratenko__, C. Steffen,**Introduction to reconfigurable computing**, July 2008 (tutorial)

#### Codes