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