Parallel Programming (3:1)
The objective of this course is to give you some level of
confidence in parallel programming techniques, algorithms and tools. At the end of the course, you would (we
hope) be in a position to deal with reallife parallel problems and to
explore new avenues of research in the area of parallel programming.
Class
Instructor
Sathish Vadhiyar
Reading Materials
 Introduction
to Parallel Computing
by
Ananth Grama, Anshul Gupta, George Karypis, Vipin Kumar Publisher:
Addison Wesley; (2003) ISBN: 0201648652
 Various publication materials, lecture slides
Additional Reading
 Petascale
Computing: Algorithms and Applications
David A. Bader (Ed.), Chapman & Hall/CRC Computational Science Series. 2007.
 The
Sourcebook of Parallel Computing
by Jack Dongarra (Editor), Ian
Foster, Geoffrey Fox (Editor), Ken Kennedy, Andy White (Editor), Linda
Torczon, Wiliiam Gropp
Publisher: Morgan Kaufmann; (November 2002) ISBN:
1558608710

Numerical
Linear Algebra for High Performance Computers
by
Jack Dongarra, Iain Duff, Danny Sorensen, Henk van der Vorst Publisher:
SIAM; (1998) ISBN: 0898714281
Meeting Hours
11:3013:00; Tuesday, Thursday; Room 202, SERC
Grading System
Syllabus
 Prerequisites 
Introduction,
MPI
 Parallel Programming
tools/languages/models  1
 MPI 
collective communication
implementations, communicator groups, process topologies

OpenMP
 Applications  Basic

Dense and Sparse Linear
Algebra

FFT

Molecular Dynamics

Population evolution or
Game of Life
 Parallel Programming
tools/languages/models  2

MPI2

Parallel I/O optimizations
 GPU programming 
CUDA review,
CUDA optimizations,
advanced CUDA
 OpenCL  class ppt,
lecture 5
from open university kit
 Charm++ 
ppt
 Applications  Advanced
 Cosmology/nbody
simulations ppt
 Mesh applications
ppt
 List algorithms with GPUs
ppt
 Parallel Programming
tools/languages/models  3
 Software Transactional memory,
Galois (Guest Lecture by Dr. Uday Reddy, CSA)
 Parallel System
Software
 Scheduling in Parallel
Systems ppt
 Checkpointing and Fault
tolerance for large systems ppt
Reading Material

Introduction: Grama et al.  2.4, 3.1, 3.5, 5.1, 5.6

MPI1: Online tutorial "MPI Complete Reference". Google for
it.

Collective Communications: Lecture slides, and Google for
paper "Optimization of Collective Communication Operations in MPICH" by Thakur, Rabenseifner and Gropp,
IJHPCA 2005

OpenMP  Lecture slides, and
OpenMP tutorial:
http://www.llnl.gov/computing/tutorials/openMP

Dense LA  lecture slides

Sparse LA
 Sources [You can get these papers from me and take photocopies]
 Parallel Algorithms for sparse linear systems  Heath, Ng and
Peyton
 Reordering sparse matrices for parallel elimination  Liu
 A parallel graph partitioning algorithm for a messagepassing
multiprocessor  Gilbert and Zmijewski
 Task scheduling for parallel sparse Cholesky factorization 
Geist and Ng
 Parallel algorithms for forward and back substitution in direct
solution of sparse linear systems  Anshul Gupta and Vipin Kumar
 Matrix computations  Golub and van Loan
 Lecture slides
 General steps of sparse matrix factorization: Heath, Ng and Peyton 
pages 420429
 Parallel ordering
 Heath, Ng and Peyton  pages 429435 till Kernighan Lin
 Liu  pages 75 and 89 (you can read other pages on reduction of
elimination tree heights if interested),
 for Kernighan Lin ordering  Gilbert and Zmijewski  pages
427433, 437440, your lecture slides
 for mapping: Heath, Ng and Peyton
 437439, figures 9 and 10; Geist and Ng  sections 3 and 4
 for numerical factorization: Heath, Ng and Peyton  442450
 FFT  FFT Chapter in "Introduction to Parallel Computing" book
 Molecular Dynamics  lecture slides, the paper ``A New Parallel Method
for Molecular Dynamics Simulation of Macromolecular Systems'' by Plimpton
and Hendrickson
 Game of Life  Lecture slides

MPI2: Online tutorial:
http://wwwunix.mcs.anl.gov/mpi/mpistandard/mpireport2.0/mpi2report.htm

Parallel
I/O Optimizations: Google for paper Rajeev Thakur, William Gropp, and Ewing
Lusk, “A Case for Using MPI's Derived Datatypes to. Improve I/O
Performance,” in Proceedings of SC98

GPU and CUDA:
 OpenCL
 Charm++
 Cosmology
 Lecture slides
 The paper "Scalable parallel formulations of the BarnesHut method
for nbody simulations" by Grama, Kumar and Sameh. In Parallel Computing
24(1998) 797822.
 The paper "Load balancing and data locality in adaptive hierarchical
Nbody methods: BarnesHut, Fast Multipole, and Dardiosity" by Singh,
Holt, Totsuka, Gupta and Hennessey. In Journal of Parallel and
Distributed Computing, 1994
 Mesh applications
 Lecture slides
 Paper: "Multilevel diffusion schemes for repartitioning of adaptive
meshes" by Schloegel et al.
 Paper: "A unified algorithm for loadbalancing adaptive scientific
simulations" by Schloegel et al.
 Paper: "Dynamic repartitioning of adaptively refined meshes" by
Schloegel et al.
 Paper: "Dynamic Octree Load Balancing Using Spacefilling curves" by
Campbell et al.  Section 2.5
 Paper: "Irregularity in Multidimensional spacefilling curves with
applications in multimedia databases" by Mokbel and Aref  Section 4
 List Ranking
 Lecture slides

Paper: Optimization of Linked List Prefix Computations
on Multithreaded GPUs Using CUDA
 Software Transactional Memory and Galois
 STM
 Compiler and runtime support for efficient software
transactional memory, AliReza AdlTabatabai, Brian T. Lewis, Vijay
Menon, Brian R. Murphy, Bratin Saha, Tatiana Shpeisman, In PLDI
2006.
 McRTSTM: A high performance software transactional memory
system for a multicore runtime. B. Saha, A.R. AdlTabatabai, R.
Hudson, C. C. Minh, and B. Hertzberg. In PPoPP 2006: Principles and
Practice of Parallel Programming.
 Galois
 How much parallelism is there in irregular applications? [Vinayak]
Milind Kulkarni, Martin Burtscher, Rajasekhar Inkulu, Keshav Pingali,
and Calin Casçaval In Proc. Symp. on Principles and practice of
parallel programming (PPoPP), pages 314, New York, NY, USA, 2009.\
 The Tao of Parallelism in Algorithms [Suraj] Keshav Pingali,
Donald Nguyen, Milind Kulkarni, Martin Burtscher, M. Amber Hassaan,
Rashid Kaleem, TsungHsien Lee, Andrew Lenharth, Roman Manevich,
Mario MéndezLojo, Dimitrios Prountzos, and Xin Sui. In ACM SIGPLAN
PLDI 2011
 Scheduling
 Paper: "Backfilling with lookahead to optimize the packing of
parallel jobs" by Shmueli and Feitelson. JPDC 2005.
 Paper: "A comparison study of eleven static mapping heuristics for a
class of metatasks on heterogeneous computing systems" by Tracy Braun
et al., HCW 1999.
 Checkpointing:
 Paper: "An overview of checkpointing in uniprocessor and distributed
systems, focusing on implementation and performance" by James Plank
 And other references given in the references slides of the lecture
slides
MidTerm Exams
Assignments

Assignment 1  Collective
Communications and Open MP

Assignment 2  Matrix
Multiplication

Assignment 3  Parallel Ordering

Assignment 4  MPI I/O and CUDA
Optimizations

Assignment 5  Load balancing using
space filling curves (SFCs)

Platform for Assignments

Important
Notes