Workshop on High Performance Computing at Louisiana Tech University

DATE : Wednesday, October 29th,

3:00-4:30pmVENUE : Nethken Hall

(NH 142 - new Playstation3 lab)

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Agenda

• Intro to HPCI – Tech own supercomputing initiative

• A new Playstation 3 Lab – the 1st in the nation of its kind

• A series of presentations to jump start you on how to access and use our HPC facilities.– A computing cluster & MPI– PS3 & programming technique– GPU & CUDA

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HPCI – Powered by intel donations& state-of-art HPC systems

• 32-66 nodes Dual Xeon cluster• 10 nodes infiniband Dual Xeon cluster• 21 nodes Dual Itanuim cluster

– 64 bit CPUs, large cache and memory– 2 quad (Tiger 4)

• 24 nodes PS3 cluster• 3 GPU systems with quad core• 105 nodes PIII cluster• Other systems

– 56 multicore MB– 64 dual code CPUs– 2 quad core CPUs– Clearspeed accelerator boards

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National Lambda Rail

Louisiana Optical NetworkIBM P5 Supercomputers

LONI Sites

Dell 80 TF Cluster

Access Grid

Louisiana Optical Network InitiativeLONI Institute

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Intro to HPCI Supercomputing infrastructures @latechhttp://hpci.latech.edu

Chokchai Box LeangsuksunAssociate Professor, Computer Sciencebox@latech.edu

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Agenda

• Introduction to HPCI, Box Leangsuksun

• HPC hardware and infrastructure at Louisiana Tech, James Elliott

• Guide to accessing and utilizing HPC resources, Himanshu Chhetri

• Writing and Running your own HPC program, K. C. Ter

• Case studies and Unleashing the Playstation3 supercomputer, Narate Taerat

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HPCI

• High Performance Computing Initiative (HPCI) is Tech campus-wide initiative to promote HPC and enable our local R&D community & their collaborators with our own supercomputing facility.

• Provides various highly computational infrastructure and several supporting staffs. HPCI is made possible by Intel equipment donation and University Research funds.

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LONI and LONI Institute

• A consortium of Louisiana universities (LSU, Latech, ULL, Tulane, UNO, Southern etc..)

• One of the most advanced networking and most powerful supercomputing infrastructures– 100 Tflops machines, QeenBee 23th in the world– 40 Gb/s Lambda network

• World class research staffs

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Knowledge Economy & HPC

• KE - Vague term

• The use of knowledge to produce economic benefits

• Information and knowledge can be shared, and actually grow through application.

• Computing/IT helps accelerating KE. Faster & accurate computing are keys.

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What is HPC?

• High Performance Computing – Parallel , Supercomputing– Achieve the fastest possible computing outcome– Subdivide a very large job into many pieces – Enabled by multiple high speed CPUs, networking, software etc – fastest

possible solution – Technologies that help solving non-trivial tasks including scientific,

engineering, medical, business entertainment and etc.

• Time to insights, Time to discovery, Times to markets

• BTW, HPC is not GRID!!!.

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Parallel Programming Concepts

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Problem

instructionsinstructions

CPU

Conventional serial execution where the problem is represented as a series of instructions that are executed by the CPU

CPU CPU CPU CPU

instructionsinstructions

Task Task Task TaskProblemProblem

Parallel execution of a problem involves partitioning of the problem into multiple executable parts that are mutually exclusive and collectively exhaustive represented as a partially ordered set exhibiting concurrency.

Parallel computing takes advantage of concurrency to :• Solve larger problems with less

time• Save on Wall Clock Time• Overcoming memory constraints• Utilizing non-local resources

Source from Thomas Sterling’s intro to HPC

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HPC accelerates a product

• FE analysis on 1 CPU– 1,000,000 elements– Numerical processing for 1

element = .1 secs– One computer will take

100,000 secs = 27.7 hrs

• Says 100 CPUs– .27 hr ~ 16 mins

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Avian Flu Pandemic Modeled on a Supercomputer

•MIDAS (Models of Infectious Disease Agent Study) program•The large-scale, stochastic simulation model examines the nationwide spread of a pandemic influenza virus strain•A simulation starts with 2 passengers with contaminated AF arriving LAX•The simulation rolls out a city-city and census-tract-level picture of the spread of infection •a synthetic population of 281 million people over the course of 180 days•It is a very large scale and complex multi-variant

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Simulation - Avian Flu Pandemic

Source from www.lanl.gov

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Avian Flu Pandemic (90 days)

Timothy C. Germann, Kai Kadau, Catherine A. Macken (Los Alamos National Laboratory); Ira M. Longini Jr. (Emory University)

Source from www.lanl.gov

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Avian Flu Pandemic (II)

•The results show that advance preparation of a modestly effective vaccine in large quantities appears to be preferable to waiting for the development of a well-matched vaccine that may be too late.•The simulation models a synthetic population that matches U.S. census demographics and worker mobility data by randomly assigning the simulated individuals to households, workplaces, schools, and the like.•The models serve as virtual laboratories to study how infectious diseases and what intervention strategies are more effective•Run on the Los Alamos supercomputer known as Pink, a 1,024-node (2,048 processor) LinuxBIOS/Bpro with 2 GB/node.

Source from www.lanl.gov

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HPC Movie Show

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HPC Applications and Major Industries

• Finite Element Modeling – Auto/Aero

• Fluid Dynamics – Auto/Aero, Consumer Packaged Goods Mfgs,

Process Mfg, Disaster Preparedness (tsunami)

• Imaging– Seismic & Medical

• Finance – Banks, Brokerage Houses (Regression Analysis,

Risk, Options Pricing, What if, …)

• Molecular Modeling – Biotech and Pharmaceuticals

Complex Problems, Large Datasets, Long RunsComplex Problems, Large Datasets, Long Runs

This slide is from Intel presentation “Technologies for Delivering Peak Performance on HPC and Grid Applications”

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Next -

HPC hardware and infrastructure

By James Elliot