The California Institute for Telecommunications and Information Technology

Supercomputing Your Inner MicrobiomeSeminarDepartment of BioengineeringUniversity of California, San DiegoFebruary 12, 2016Dr. Larry SmarrDirector, California Institute for Telecommunications and Information TechnologyHarry E. Gruber Professor, Dept. of Computer Science and EngineeringJacobs School of Engineering, UCSDhttp://lsmarr.calit2.net1

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The human body is host to 100 trillion microorganisms, ten times the number of DNA-bearing cells in the human body, and these microbes contain 300 times the number of DNA genes that our human DNA does. The microbial component of our "superorganism" is comprised of hundreds of species with immense biodiversity. To put a more personal face on the "patient of the future," I have been collecting massive amounts of data from my own body over the last seven years, which reveals detailed examples of the episodic evolution of this coupled immune-microbial system. An elaborate software pipeline, running on high performance computers, reveals the details of the microbial ecology and its genetic components, in health as well as in disease. Not only can we compare a person with a disease to a healthy population, but we can also follow the dynamics of the diseased patient. We can look forward to revolutionary changes in medical practice over the next decade.

Forty Years of Computing Gravitational Waves From Colliding Black Holes

1977L. Smarr and K. EppleyGravitational Radiation Computed from an Axisymmetric Black Hole Collision

2016LIGO ConsortiumSpiral Black Hole Collision

40 Years

Complexity of Computing First Gut Microbiome DynamicsVersus First Dynamics of Colliding Black HolesMy 1975 PhD DissertationSolving Einsteins Equations of General Relativity for Colliding Black Holes and Grav WavesCDC 6600 Megaflop/sHundreds of Hours

Rob Knight and Smarr Gut Microbiome MapMapping From Illumina Sequencing to Taxonomy and Gene Abundance DynamicsComet Petaflop/s Comet Core is 40,000x CDC6600 SpeedMillion Core-Hours10,000x Supercomputer Time

Gut Microbiome Takes ~ Billion Times the Compute Power of Early Solutions of Dynamic General Relativity

Building a UC San Diego Cyberinfrastructureto Support Integrative Omics

FIONA12 Cores/GPU128 GB RAM3.5 TB SSD48TB Disk10Gbps NICKnight Lab 10Gbps

Gordon

Prism@UCSD

Data Oasis7.5PB, 200GB/s

Knight 1024 ClusterIn SDSC Co-Lo

CHERuB100GbpsEmperor & Other Vis Tools64Mpixel Data Analysis Wall120Gbps

40Gbps

1.3TbpsPRP/

The Pacific Wave PlatformCreates a Regional Science-Driven Big Data Freeway System

Source: John Hess, CENIC

Funded by NSF $5M Oct 2015-2020

Flash Disk to Flash Disk File Transfer RatePI: Larry Smarr, UC San Diego Calit2Co-PIs: Camille Crittenden, UC Berkeley CITRIS, Tom DeFanti, UC San Diego Calit2, Philip Papadopoulos, UC San Diego SDSC, Frank Wuerthwein, UC San Diego Physics and SDSC

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Calit2s Qualcomm Institute Has Established a Pattern Recognition Lab On the PRP, For Machine Learning on non-von Neumann Processors

On the drawing board are collections of 64, 256, 1024, and 4096 chips. Its only limited by money, not imagination, Modha says.

Source: Dr. Dharmendra ModhaFounding Director, IBM Cognitive Computing GroupAugust 8, 2014

UCSD ECE Professor Ken Kreutz-Delgado Brings the IBM TrueNorth Chip to Start Calit2s Qualcomm Institute Pattern Recognition LaboratorySeptember 16, 2015

From One to a Trillion Data Points Defining Me in 15 Years:The Exponential Rise in Body DataWeightBlood BiomarkerTime SeriesHuman Genome SNPsMicrobial GenomeTime SeriesImproving BodyDiscovering DiseaseHuman Genome

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I Decided to Track My Internal BiomarkersTo Understand My Bodys Dynamics

My Blood DrawYesterdayCalit2 64 Megapixel VROOM

Only One of My Blood Measurements Was Far Out of Range--Indicating Chronic InflammationNormal Range