Vipin Sachdeva
Vipin Sachdeva
IBM Research
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BioPerf: A benchmark suite to evaluate high-performance computer architecture on bioinformatics applications
DA Bader, Y Li, T Li, V Sachdeva
IEEE International. 2005 Proceedings of the IEEE Workload Characterization …, 2005
Exploring the viability of the Cell Broadband Engine for bioinformatics applications
V Sachdeva, M Kistler, E Speight, THK Tzeng
Parallel Computing 34 (11), 616-626, 2008
Enabling high-performance computing as a service
M AbdelBaky, M Parashar, H Kim, KE Jordan, V Sachdeva, J Sexton, ...
Computer 45 (10), 72-80, 2012
A Cache-Aware Parallel Implementation of the Push-Relabel Network Flow Algorithm and Experimental Evaluation of the Gap Relabeling Heuristic.
DA Bader, V Sachdeva
PDCS, 41-48, 2005
OpenRBC: A fast simulator of red blood cells at protein resolution
YH Tang, L Lu, H Li, C Evangelinos, L Grinberg, V Sachdeva, ...
Biophysical journal 112 (10), 2030-2037, 2017
Fully integrated FPGA molecular dynamics simulations
C Yang, T Geng, T Wang, R Patel, Q Xiong, A Sanaullah, C Wu, J Sheng, ...
Proceedings of the International Conference for High Performance Computing …, 2019
OpenCL for HPC with FPGAs: Case study in molecular electrostatics
C Yang, J Sheng, R Patel, A Sanaullah, V Sachdeva, MC Herbordt
2017 IEEE High Performance Extreme Computing Conference (HPEC), 1-8, 2017
Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry
T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ...
Nature communications 13 (1), 5884, 2022
K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity
CS Kim, MD Winn, V Sachdeva, KE Jordan
BMC bioinformatics 18, 1-15, 2017
Molecular dynamics range-limited force evaluation optimized for FPGAs
C Yang, T Geng, T Wang, C Lin, J Sheng, V Sachdeva, W Sherman, ...
2019 IEEE 30th International Conference on Application-specific Systems …, 2019
Mesh interface resolution and ghost exchange in a parallel mesh representation
TJ Tautges, JA Kraftcheck, N Bertram, V Sachdeva, J Magerlein
2012 IEEE 26th International Parallel and Distributed Processing Symposium …, 2012
Evaluating the jaccard-tanimoto index on multi-core architectures
V Sachdeva, DM Freimuth, C Mueller
Computational Science–ICCS 2009: 9th International Conference Baton Rouge …, 2009
Atomic-resolution prediction of degrader-mediated ternary complex structures by combining molecular simulations with hydrogen deuterium exchange
T Dixon, D MacPherson, B Mostofian, T Dauzhenka, S Lotz, D McGee, ...
Biorxiv, 2021.09. 26.461830, 2021
System-level modeling of GPU/FPGA clusters for molecular dynamics simulations
C Wu, S Bandara, T Geng, V Sachdeva, W Sherman, M Herbordt
2021 IEEE high performance extreme computing conference (HPEC), 1-8, 2021
Upgrade of fpga range-limited molecular dynamics to handle hundreds of processors
C Wu, T Geng, S Bandara, C Yang, V Sachdeva, W Sherman, M Herbordt
2021 IEEE 29th Annual International Symposium on Field-Programmable Custom …, 2021
A Communication-Efficient Multi-Chip Design for Range-Limited Molecular Dynamics
C Wu, T Geng, C Yang, V Sachdeva, W Sherman, M Herbordt
2020 IEEE High Performance extreme Computing Conference (HPEC), 1-8, 2020
Execution of complete molecular dynamics simulations on multiple FPGAs
C Pascoe, L Stewart, BW Sherman, V Sachdeva, MW Herbordt
2020 IEEE High Performance Extreme Computing Conference (HPEC), 1-2, 2020
SimBSP: Enabling RTL Simulation for Intel FPGA OpenCL Kernels
A Sanaullah, C Yang, D Crawley, M Herbordt
Proc. Heterogeneous High Performance Reconfigurable Computing, 2018
BioSPLASH: A sample workload for bioinformatics and computational biology for optimizing next-generation performance computer systems
DA Bader, V Sachdeva, V Agarwal, G Goel, AN Singh
University of New Mexico, Tech. Rep, 2005
Particle mesh ewald for molecular dynamics in opencl on an fpga cluster
LC Stewart, C Pascoe, BW Sherman, M Herbordt, V Sachdeva
arXiv preprint arXiv:2009.12617, 2020
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