Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 1
in the Medical Field with Thoughts on the Applicability of CnC as a - - PowerPoint PPT Presentation
Archive # A Sketch of Data (graph) Analytic Applications in the Medical Field with Thoughts on the Applicability of CnC as a Framework for Hybrid Platforms in These Application Spaces Gary S. Delp, PhD Just a simple engineer Mayo Clinic S
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 1
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 2
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 3
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 4
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 5
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 6
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 7
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 8
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 9
Committee on the Analysis of Massive Data Committee on Applied and Theoretical Statistics Board on Mathematical Sciences and Their Applications Division on Engineering and Physical Sciences National Research Council of The National Academies
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 10
Problem Architecture View Data Source and Style View Execution View
Linear Algebra Kernels Graph Algorithms Deep Learning Classification Recommender Engine Search / Query / Index Basic Statistics Optimization Methodology Global Analytics Local Analytics Micro-benchmarks Visualization
Streaming
Alignment
9 8 7 5 4 3 2 1 14 13 12 11 10 6
Performance Metrics (PM) Flops/Byte Flops/Byte; Memory I/O Execution Environment; Core Libraries Volume Velocity Variety Veracity Communication Structure Iterative / Simple Metric = M / Non-Metric = N 𝑃 𝑂2 = NN / 𝑃(𝑂) = N Regular = R / Irregular = I Dynamic = D / Static = S Data Abstraction
1 2 3 4 5 6 7 8 9 10 11 13 14 12 15
GIS – Geographic Information System HPC Simulations IoT – Internet of Things Metadata / Provenance Shared / Dedicated / Transient / Permanent Archived / Batched / Streaming HDFS / Lustre / GPFS Files / Objects EDM – Enterprise Data Model SQL / NoSQL / NewSQL
10 9 8 7 6 5 4 3 2 1
Ogre Views and Facets
1 2 3 4 5 6 7 8 9 10 11 12
Pleasingly Parallel (PP) Classic MapReduce (MR) Map-Collective (MC) Map Point-to-Point (MP2P) Map Streaming (MS) Shared Memory (SM) Single Program Multiple Data (SPMD) Bulk Synchronous Parallel (BSP) Fusion Dataflow Agents Workflow (WF) Adapted from, Fox, G.C., et al.: “Towards a Systematic Approach to Big Data Benchmarking,” Community Grids Lab: Pervasive Technology Labs, Computer Science and Informatics, Indiana University, Bloomington, IN, Technical Report submitted for publication, 15 February 2015; http://grids.ucs.indiana.edu/ptliupages/publications/OgreFacetsv9.pdf
APR_07 / 2015 / GSD / 44838
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 11
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 12
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 13
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 14
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 15
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 16
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 17
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 18
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 19
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 20
next prev Used With Permission from, Weber, G.M., K.D. Mandl and I.S. Kohane: “Finding the Missing Link for Big Biomedical Data”, JAMA, 311(24):2479-2480, 2014; http://jama.jamanetwork.com/article.aspx?articleid=1883026.
FEB_09 / 2015 / GSD / 44765
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 21
Adapted from: Costigliola V., P. Gahan, and O. Golubnitschaja: Predictive Medicine as the New Philosophy in Health
Nova Science, 2009. (ISBN 978-1-60692-737-3)
DEC_3 / 2014 / GSD / 44687
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 22
Medical Application and Low Level Algorithmic Coverage
Dense linear algebra Sparse linear algebra Graph Algorithms Frequency Analysis Data Retrieval/ Filtering/ Sorting Stochastic processes Monte Carlo Particle methods
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 23
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 24
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 25
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 26
next prev
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 27
Simulating 23,558 Atoms comprising the Enzyme Dihydrofolate Reductase (DHFR) using Four-Femtosecond Time-Slices, in the Number, Volume, Energy (NVE) Ensemble Using Hydrogen Mass Repartitioning (HMR)
MAR_09 / 2015 / GSD / 44793r4 Adapted from data in, Walker, R. and S.L. Grand: “Amber 14 NVIDIA GPU Acceleration Support”, 2015, http://ambermd.org/gpus/ benchmarks.htm & Salomon-Ferrer, R., D.A. Case and R.C. Walker: “An Overview of the Amber Biomolecular Simulation Package,” WIREs Comput Mol Sci, Wiley-Blackwell, 2012, http://dx.doi.org/10.1002/wcms.1121.
423.69 334.05 229.29 489.68 364.67 266.07 263.85 196.99 116.09 356.48 383.32 261.82 280.54 262.39 251.43 129.79 81.26 1.92 30.21
2x K80 boards (4 GPUs) 1x K80 board (2 GPUs) 1/2x K80 board (1 GPU) 4x K40 2x K40 1x K40 2X K20 1x K20 1x K8 GTX-Titan-Z (2 GPU, full board) GTX-Titan-Z (1 GPU. 1/2 board) 2x GTX Titan Black 1x GTX Titan Black 1x GTX 980 1x GTX 780 2x C2075 1x C2075 Cray XT5 (8 cores) 2xE5-2660v2 CPU (16 Cores)
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 28
next prev
Image the Planning Volume Delineate Imaged Structures Place Sources Ready to Treat Simulate Evaluate Perturb
Placement
& Properties Simulate Simulate Sensi- tivities Insert Fibers Verify
Placement
Finished Treatment Simulate As-Placed Check Properties Deliver Light & Monitor Simulate Update
Adapted with permission from, Cassidy, J., V. Betz, and L. Lilge: “Treatment Plan Evaluation for Interstitial Photodynamic Therapy In A Mouse Model By Monte Carlo Simulation With FullMonte”. Front. Phys., 3:6 (Feb) 2015; doi:10.3389/fphy.2015.00006.
APR_08 / 2015 / GSD / 44847
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 29
Functional block Fmax MHz ALM FF DSP M20k BRAM Point source 290 1792 2014 2 2 Henyey-Greenstein 364 1740 2857 4 Scatter 302 280 546 19 TT800 RNG 590 804 800 Intersection test 329 510 799 20 Boundary 340 1707 2713 5 2 Step finish * 3 Mesh storage * 1034 Fluence accumulation * 211 Total 280 16271 29154 59 1265 % of Available 7% 6% 23% 49% * Not synthesized individually; no isolated Fmax available Relative Platform Power (W) Speed Energy/op CPU 76 1 67.5 Single-instance Stratix V 4.5 4 1 Estimated 4 instances 13.9 16 0.77
Table 27. Resources and Fmax for Single Instance on Stratix V A7 (From [147])
67.5 1400 16 0.77
While this problem may also experience significant speedup with the dense floating point resources of a Xeon Phi™ or a GPU, Jeffery Cassidy shared in his SPPDG ROLEX presentation that this is a cache unfriendly computation (Xeon thrashes), and the a GPU’s local memory does not come close to scaling with its processing capability (GPU non-starter). Given these limitations, this FPGA 14-bit fixed point solution remains an example where the reputation of “power-hungry” that FPGA solutions have had in the past is no longer true when solving problems that suit the FPGA’s capabilities. Evaluating the power and performance, the quad FPGA solution shows a 1400 improvement
[147] Cassidy, J., V. Betz, and L. Lilge : “Treatment Plan Evaluation for Interstitial Photodynamic Therapy In A Mouse Model By Monte Carlo Simulation With FullMonte”. Front. Phys., 3:6 (Feb) 2015; doi:10.3389/fphy.2015.00006 .
Table 28. Performance and Energy-Efficiency Comparison (FPGA VS CPU) (From [147])
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 30
prev
Adapted with permission from: Pradip Bose, Energy Efficiency and Resilience Tradeoffs: Architecture and Modeling Challenges, Supercomputing 2013.
DEC_11 / 2014 / GSD / 44725
FLOPS: Floating Point Operations IOPS: Integer Operations
next
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 31
Linear Algebra Kernels Graph Algorithms Deep Learning Classification Recommender Engine Search / Query / Index Basic Statistics Optimization Methodology Global Analytics Local Analytics Micro-benchmarks Visualization Streaming Alignment
9 8 7 5 4 3 2 1 14 13 12 11 10 6
Performance Metrics (PM) Flops/Byte Flops/Byte; Memory I/O Execution Environment; Core Libraries Volume Velocity Variety Veracity Communication Structure Iterative / Simple Metric = M / Non-Metric = N 𝑃 𝑂2 = NN / 𝑃(𝑂) = N Regular = R / Irregular = I Dynamic = D / Static = S Data Abstraction
1 2 3 4 5 6 7 8 9 10 11 13 14 12 15
GIS – Geographic Information System HPC Simulations IoT – Internet of Things Metadata / Provenance Shared / Dedicated / Transient / Permanent Archived / Batched / Streaming HDFS / Lustre / GPFS Files / Objects EDM – Enterprise Data Model SQL / NoSQL / NewSQL
10 9 8 7 6 5 4 3 2 1
Ogre Views and Facets
1 2 3 4 5 6 7 8 9 10 11 12
Pleasingly Parallel (PP) Classic MapReduce (MR) Map-Collective (MC) Map Point-to-Point (MP2P) Map Streaming (MS) Shared Memory (SM) Single Program Multiple Data (SPMD) Bulk Synchronous Parallel (BSP) Fusion Dataflow Agents Workflow (WF) Adapted from, Fox, G.C., et al.: “Towards a Systematic Approach to Big Data Benchmarking,” Community Grids Lab: Pervasive Technology Labs, Computer Science and Informatics, Indiana University, Bloomington, IN, Technical Report submitted for publication, 15 February 2015; http://grids.ucs.indiana.edu/ptliupages/publications/OgreFacetsv9.pdf
APR_07 / 2015 / GSD / 44838
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 32 Adopted from, Pang, Y.-P., et al.: “Potent New Small-Molecule Inhibitor of Botulinum Neurotoxin Serotype a Endopeptidase Developed by Synthesis-Based Computer-Aided Molecular Design”. PLoS ONE, 4(11):e7730 (2009); DOI: 10.1371/journal.pone.0007730; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771286/.
MAR_17 / 2015 / GSD / 44809
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 33
Adapted from, Pang, Y., S. Brimijoin, D. Ragsdale, K. Zhu and R. Suranyi: “Novel and Viable Acetylcholinesterase Target Site for Developing Effective and Environmentally Safe Insecticides”. Curr Drug Targets, 3(4):471-482 (2012); http://www.ncbi.nlm.nih.gov/pubmed/22280344.
MAR_17 / 2015 / GSD / 44808
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 34
Archive #
SPPDG
SEP_07 / 2015 / GSD / 45067 – 35