High Performance Computing: Concepts, Methods & Means Final Exam Review Chirag Dekate Department of Computer Science Louisiana State University May 1st, 2007

Topics Survey by Daniel Eiland Key Announcements Final Review Slides Graduate Students fill out evaluation forms.

Topics Survey by Daniel Eiland Key Announcements Final Review Slides Graduate Students fill out evaluation forms.

Announcements Assignment 5 (Hard Copies) FINAL EXAM Due Thursday May 3rd class time (3:30 NO LATER) 320 Johnston Hall. FINAL EXAM 331 JOHNSTON HALL Tuesday May 8th 8:00 PM – 10:00 PM BRING CALCULATORS Closed book/notes exam

Topics Survey by Daniel Eiland Key Announcements Final Review Slides Graduate Students fill out evaluation forms.

S1 L3 Benchmarking Basic metrics and modifiers that define application performance (slide 4) Purposes of a benchmark and properties of a good benchmark (slide 6,7) What is linpack?(slide 15) What is HPL and what benchmark does it provide(slide 21, 24)? List at least 8 common mistakes in Benchmarking (slide 49) List the 8 ways performance results can be misrepresented & misinterpreted on parallel computers (slide 50)

S1 L4 Capacity (throughput) Computing Numerical Problem Alert! : Be able to solve Speedup, Efficiency related numerical problem (slide 5, 17, 18). Define Capacity, Capability, Cooperative computing (slide 7,8) 3 conventional models of parallel processing and list alternative models of parallel processing (slide 10, 11, 12, 15) Numerical Problem Alert! : Overhead (slides 19-23) What are Condor ClassAds (slide 30)? List the 4 steps in condor Matchmaking (slide 32)

S2 L1 Parallel Computer Architecture List and describe the 4 sources of performance degradation (slide 9) Numerical Problem Alert! : Pipeline concepts (slides 27, 28) Numerical Problem Alert! : Vector processing concepts (slides 29, 30)

S2 L2 SMP Node Architecture Numerical Problem Alert! : Amdahl’s law (slides 11, 12, 13)

S2 L3 PThreads Numerical Problem Alert! : CPI calculation problem (slides 8-10) Anatomy of a Thread (slide 13) Race Conditions & Critical Sections (slide 15, 16) Thread synchronization (slide 17) Spinlocks (slide 18) Mutexes (slide 19, 20) Semaphores (slide 21) 3 pitfalls in multithreaded programming (slide 29)

S2 L4 OpenMP OpenMP and its key components (slides 5,6) 3 main data scoping clauses (shared, private, reduction (slide 19) Temporal and Spatial Locality (slide 42) Understand synchronization fundamentals (slides 31-35) Programming Problem Alert! (Midterm exam)

S2 L5 Performance 2 gprof and the information it provides. (slide 21) PAPI , counter interfaces, features (32-34) TAU, features (56, 57)

S3 L1 CSP Strict Scaling and Weak Scaling (slide 7) Cooperative computing (slide 9) Characteristics of CSP model based computation: data decomposition (slide 12) distributed concurrent processes (slide 13) data exchange (slide 14) synchronization (slide 15) Performance implications of the above 4 (slide 16)

S3 L2 MPI mechanics of Blocking & Non-blocking calls in MPI (slides 24-26) Programming Problem Alert! (Midterm exam) API Elements : MPI_Init(), MPI_Finalize() MPI_Comm_size(), MPI_Comm_rank() MPI_COMM_WORLD Error checking using MPI_SUCCESS MPI basic data types (slide 27) Blocking : MPI_Send(), MPI_Recv() Non-Blocking : MPI_Isend(), MPI_Irecv(), MPI_Wait() Collective Calls : MPI_Barrier(), MPI_Bcast(), MPI_Gather(), MPI_Scatter(), MPI_Reduce()

S3 L3 Performance 3 Various features of SMP, MPP (slide 12) Performance factors that affect message passing systems (slides 15, 16) Be able to list and discuss performance models. No numerical problems related to performance models!

S3 L4 Parallel Algorithms 1 Parallel programming Goals and Objectives (slide 6) Array decomposition (slides 14) Mandelbrot set (slide 28) PI calculation (slide 39) Matrix Multiplication (slide 60) C Source code provided (be able to understand source code, decompose to pseudocode, be able to make small changes to algorithms)

S3 L5 Parallel Algorithms 2 N-Body problem (slide 61) C Source code provided (be able to understand source code, decompose to pseudocode, be able to make small changes to algorithms) Given a problem be able to write a short pseudocode solution.

S4 L1 Enabling Technologies Memory Bandwidth, Latency (slide 12) Microprocessor overview (slide 26, 27) I/O Channels (slides 31, 32, 33)

S4 L2 Networks Network latency, throughput (slide 3) Network Layers & mechanics (slide 4, 5) Important features of Gigabit Ethernet (slides 10 -15) CSMA-CD (slides 11-13, 16) 10 GigE (slide 17) Myrinet, features (slides 19-28, 30) Infiniband, features (slides 33-36, 40) Six low latency message concepts (slides 43 – 50 ) Numerical Problem Alert! : Calculation of buffer size for STOP and GO protocol (as seen in assignment 4)

S5 L1 Scheduling Scheduling concepts : time sharing, space sharing (slide 5) FCFS/FIFO scheduling (slides 7-10) Backfill, Easy backfill, Conservative backfill (slides 11-25) WMS and its activities (slides 32-39)

S5 L2 Operating Systems Definition, services provided (slides 6,7) OS concepts : process management (slide 14) Multitasking & multiprogramming (slide 16) OS concepts : memory management (slide 18, 19) OS concepts : protection & security (slide 23) Benefits of microkernel (slide 27) Unix concurrency mechanisms (slide 39)

S5 L3 Parallel File I/O RAID concepts (slides 8-10) Distributed File System Concepts NFS (slides 12, 13) Why NFS is bad for parallel I/O (slide 14) Parallel File System Concepts (slides 16-19) PVFS (slides 20-24) MPI-IO concepts & features (slides 29-32)

S6 L2 Visualization Challenges in visualization : (Slides 29-33) GNUplot : (Slides 40-47) OpenGL : (Slides 56,57) OpenDX : (Slides 63-65) Other tools : (Slides 69-73)

S6 L3 Libraries Why Libraries: (Slides 4, 5) What is a Library: (Slides 16-18) Library (by locality) : (Slides 19) Library (by domain): (Slides 20) Application domains: (Slides 21) Creating a library: (Slides 27, 28)

S6 L4 Libraries 2 High performance libraries 5,6,7 Linear algebra libraries: BLAS: 9, 11, 12 Linear algebra libraries: LaPACK: 18 PDE Solvers: 23, 24, 26, 27 Mesh decomposition & load balancing: 31, 34, 35, 37, 44, 45, 46, 48, 49 FFTW: 53, 54

REMEMBER : Bonus question from Beyond and Beyond… Watch video!! S6 L5 Frameworks Component based Software Engineering: slide 29 CCA Concepts: slides 34-50 What is Cactus: slides 54,55,57 Cactus Architecture: slides 58-65 Cactus, current capabilities: slides 66,67 REMEMBER : Bonus question from Beyond and Beyond… Watch video!!

THANK YOU and GOOD LUCK FOR YOUR EXAM(s) Topics Survey by Daniel Eiland Key Announcements Final Review Slides Graduate Students fill out evaluation forms. THANK YOU and GOOD LUCK FOR YOUR EXAM(s)