Introduzione al calcolo parallelo e al Grid computingenrico/IngegneriaDelSoftware/anno08-09/GRID... · Manycore : 8X to 16X multicore ... (A slide from D. Patterson Berkeley)

Introduzione al calcolo parallelo e al Grid computing

Introduzione al calcolo parallelo aa. 2008-2009

Andrea Clematis

IMATI – CNR

[email protected]

Ack. & riferimenti

� Il materiale di questa presentazione è tratto da:

Blaise Barney, Livermore Computing, Introduction To Parallel Computing, che a sua volta utilizza altre fonti dal web.

http://www.llnl.gov/computing/tutorials/parallel_comp/


� Molte altre informazioni possono essere reperite sul web, ad esempio a partire da:

http://www.llnl.gov/computing/hpc/training/index.html#training_materials

Sommario

� Cosa si intende e perché si usa il calcolo parallelo

� Terminologia e concetti


� Architetture parallele (memoria)

� Modelli di programmazione parallela

� Progettazione e valutazione di programmi paralleli

� Esempi

ITB-CNR Milano

COSTOpen European

Networkfor High Performance Computing on Complex Environments

Action IC0805

Research Interests – Collaborations & Projects

EUROMICRO –PDP Conference


CNR IMATI and DISTGenova

DISI

RINA

DLTM –NURCCIMA

SIRE

SIIT

SIIT Liguria Technological Districtfor Intelligent Integrated Systems – Genova

The District partners:University of Genova, Regione Liguria, Consiglio Nazionale delle Ricerche, Alcatel-Lucent Italia S.p.A., Ansaldo Energia S.p.A., Bombardier Transportation Italy S.p.A., Elsag Datamat S.p.A., Esaote S.p.A., Cetena S.p.A., Selex Communications S.p.A., Selex Sistemi Integrati S.p.A., Ericson S.p.A., Oto Melara S.p.A., Ansaldo Segnalamento Ferroviario S.p.A., Orizzonti Sistemi Navali, RINA, Consorzio SIIT PMI (around 80).


IMATI-CNR and DIST Genova are cooperating to set up the public-private Grid and High Performance Computing Lab of SIIT

A blade cluster with 256 computing core, a SAN with 4TB mm, Tesla workstation, EnginFrame (NICE) Portal, LSF scheduler

Operational fall 2009

80).

DIST - IBM SUR Grant & Teaching

� Professor Enrico Giunchiglia, of DIST- Dipartimento di Informatica, Sistemistica e Telematica, has been awarded in 2008 with a Shared University Research Grant of IBM Corporation, for joint research with IMATI-CNR on “Multi-core hybrid architectures and Cloud computing for HPC applications in industrial research”.


Cloud computing for HPC applications in industrial research”.

� The cluster is an heterogeneous blade configuration. It offers a total of 48 physical processors (42 intel / 6 cell) plus 1 HC10 visualization node with a Core 2 Duo 2.66 GHz, 8 GB RAM, 80 GB SATA, NVida Quadro FX 1600M (CUDA is supported), and has a total of 126 GB RAM about 3 TB of disk space.

Cosa si intende per calcolo parallelo

� Di solito il software è sviluppato ed utilizzato secondo un modello sequenziale (o seriale): una CPU, una lista di istruzioni eseguite in sequenza;

� Nel caso più generale il calcolo parallelo è l’utilizzo di più risorse di calcolo per risolvere un problema computazionale;


di calcolo per risolvere un problema computazionale;

� Le risorse possono comprendere: un computer con più processori, più computer collegati in rete, una combinazione dei due;

� Il problema computazionale possiede alcune caratteristiche: può essere diviso in “pezzi” di lavoro che possono essere eseguiti contemporaneamente; l’utilizzo di più risorse permette di ridurre il tempo di soluzione (wall clock)

Perché utilizzare il calcolo parallelo

� Due ragioni principali: � risparmiare tempo (wall clock time) ;

� risolvere problemi più grandi e/o complessi;

� Altre ragioniutilizzare risorse locali e/o remote inutilizzate, risparmiando tempo


� utilizzare risorse locali e/o remote inutilizzate, risparmiando tempo e soldi;

� superare i limiti di memoria di un singolo computer;

� Superare i limiti intrinseci dell’elaborazione sequenziale:� velocità della luce � tempo di trasmissione (30 cm/nanosecondo, 9

su rame);

� miniaturizzazione, anche con componenti a livello molecolare/atomico

� economici

Growth comparison

Introduzione al calcolo parallelo aa. 2008-2009 92008/01/09

Network is driving the market

16

32

6464

128

256

512

100

1000

� Multicore: 2X / 2 yrs ⇒ ≈ 64 cores in 8 years

� Manycore: 8X to 16X multicore(source David Patterson 2007 – Berkeley)

The role of manycoreand parallelism for IT industry


1

2

4

8

16

1

10

2003 2005 2007 2009 2011 2013 2015

(source David Patterson 2007 – Berkeley)

“…New Moore’s Law is 2X processors (“cores”) per chip every technology generation, but same clock rate …This shift toward increasing parallelism is not a triumphant stride forward based on breakthroughs …; instead, this … is actually a retreat from

even greater challenges that thwart efficient silicon implementation of

traditional solutions…” The Parallel Computing Landscape: A Berkeley View

Parallel Revolution May Fail (A slide from D. Patterson Berkeley)

� John Hennessy, President, Stanford University, 1/07:“…when we start talking about parallelism and ease of use of truly parallel computers, we're talking about a problem that's as hard as any that computer science has faced… I would be panicked if I were in industry.” “A Conversation with Hennessy and Patterson,” ACM Queue Magazine, 4:10, 1/07.

11

0

50

100

150

200

250

1985 1995 2005 2015

Millions of PCs / year

Queue Magazine, 4:10, 1/07.

� 100% failure rate of Parallel Computer Companies

� Convex, Encore, MasPar, NCUBE, Kendall Square Research, Sequent, (Silicon Graphics), Transputer, Thinking Machines, …

� What if IT goes from a growth industry to a replacement industry?

� If SW can’t effectively use 8, 16, 32, ... cores per chip ⇒⇒⇒⇒ SW no faster on new computer ⇒⇒⇒⇒ Only buy if computer wears out

Perché: alcune applicazioni

� weather and climate

� chemical and nuclear reactions

� biological, human genome

� geological, seismic activity

mechanical devices - from

� parallel databases, data mining

� oil exploration

� web search engines, web based business services

� computer-aided diagnosis in


� mechanical devices - from prosthetics to spacecraft

� electronic circuits

� manufacturing processes

� Fluidodynamics

� Parameters sweep

� computer-aided diagnosis in medicine

� management of national and multi-national corporations

� advanced graphics and virtual reality, particularly in the entertainment industry

� networked video and multi-media technologies

� collaborative work environments

Sommario







� Esempi

Concetti e terminologia: l’architettura von Neumann

� Basic design:

� Memory is used to store both program and data instructions

� Program instructions are coded data which tell the computer to


data which tell the computer to do something

� Data is simply information to be used by the program

� A central processing unit (CPU) gets instructions and/or data from memory, decodes the instructions and then sequentially performs them.

Concetti e terminologia: classificazione di Flynn

Flynn's taxonomy distinguishes multi-processor computer architectures according to how they can be classified along the two independent dimensions of Instruction and Data. Each of these dimensions can have


Data. Each of these dimensions can have only one of two possible states: Single or Multiple.

S I S D

Single Instruction, Single DataS I M D

Single Instruction, Multiple Data

M I S D

Multiple Instruction, Single DataM I M D

Multiple Instruction, Multiple Data

Single Instruction Multiple Data (SIMD)

� Single instruction: All processing units execute the same instruction at any given clock cycle

� Multiple data: Each processing unit can operate on a different data element

� This type of machine typically has an


� This type of machine typically has an instruction dispatcher, a very high-bandwidth internal network, and a very large array of very small-capacity instruction units.

� Best suited for specialized problems characterized by a high degree of regularity,such as image processing.

� Synchronous (lockstep) and deterministic execution

� Two varieties: Processor Arrays (Connection Machine CM-2, Maspar MP-1, MP-2) and Vector Pipelines (IBM 9000, Cray C90, Fujitsu VP, NEC SX-2, Hitachi S820 )

Multiple Instruction Multiple Data

� Currently, the most common type of parallel computer

� Multiple Instruction: every processor may be executing a different instruction stream

Multiple Data: every processor may


� Multiple Data: every processor may be working with a different data stream

� Execution can be synchronous or asynchronous, deterministic or non-deterministic

� Examples: most current supercomputers, networked parallel computer "grids" and multi-processor SMP computers -including some types of PCs.

Terminologia

� Task A logically discrete section of computational work. A task is typically a program or program-like set of instructions that is executed by a processor.

� Parallel Task A task that can be executed by multiple processors safely (yields correct results)


(yields correct results)

� Serial Execution Execution of a program sequentially, one statement at a time. In the simplest sense, this is what happens on a one processor machine. However, virtually all parallel tasks will have sections of a parallel program that must be executed serially.

� Parallel Execution Execution of a program by more than one task, with each task being able to execute the same or different statement at the same moment in time.

Terminologia

� Shared Memory From a strictly hardware point of view, describes a computer architecture where all processors have direct (usually bus based) access to common physical memory. In a programming sense, it describes a model where parallel tasks all have the same "picture" of memory and can directly address and access the same logical memory


memory and can directly address and access the same logical memory locations regardless of where the physical memory actually exists.

� Distributed Memory In hardware, refers to network based memory access for physical memory that is not common. As a programming model, tasks can only logically "see" local machine memory and must use communications to access memory on other machines where other tasks are executing.

Terminologia

� Communications Parallel tasks typically need to exchange data. There are several ways this can be accomplished, such as through a shared memory bus or over a network, however the actual event of data exchange is commonly referred to as communications regardless of the method employed.


of the method employed.

� Synchronization The coordination of parallel tasks in real time, very often associated with communications. Often implemented by establishing a synchronization point within an application where a task may not proceed further until another task(s) reaches the same or logically equivalent point. Synchronization usually involves waiting by at least one task, and can therefore cause a parallel application's wall clock execution time to increase.

Terminologia

� Granularity In parallel computing, granularity is a qualitative measure of the ratio of computation to communication.

� Coarse: relatively large amounts of computational work are done between communication events

� Fine: relatively small amounts of computational work are done between communication events


communication events

� Observed Speedup Observed speedup of a code which has been parallelized, defined as:

wall-clock time of serial execution --------------------------------------------

wall-clock time of parallel execution

One of the simplest and most widely used indicators for a parallel program's performance.

Terminologia

� Parallel Overhead The amount of time required to coordinate parallel tasks, as opposed to doing useful work. Parallel overhead can include factors such as:

� Task start-up time

� Synchronizations


� Synchronizations

� Data communications

� Load unbalancing

� Software overhead imposed by parallel compilers, libraries, tools, operating system, etc.

� Task termination time

� Massively Parallel Refers to the hardware that comprises a given parallel system - having many processors. The meaning of many keeps increasing, but currently means more than 1000.

Terminologia

� Scalability Refers to a parallel system's (hardware and/or software) ability to demonstrate a proportionate increase in parallel speedup with the addition of more processors. Factors that contribute to scalability include:

� Hardware - particularly memory-cpu bandwidths, network communications


� Hardware - particularly memory-cpu bandwidths, network communications and I/O memory bandwidths

� Application algorithm

� Parallel overhead related Characteristics of your specific application and coding

� Data characteristics and size

Sommario



Architetture parallele (memoria - comunicazione)


� Architetture parallele (memoria - comunicazione)



� Esempi

Architetture parallele e modelli di memoria

Shared Memory General Characteristics:

� Shared memory parallel computers vary widely, but generally have in common the ability for all processors to access all memory as global address space.

Multiple processors can operate


� Multiple processors can operate independently but share the same memory resources.

� Changes in a memory location effected by one processor are visible to all other processors.

� Shared memory machines can be divided into two main classes based upon memory access times: UMA and NUMA.


� Uniform Memory Access (UMA):� Most commonly represented today by Symmetric Multiprocessor (SMP) machines

� Identical processors

� Equal access and access times to memory

� Sometimes called CC-UMA - Cache Coherent UMA. Cache coherent means if one processor updates a location in shared memory, all the other processors know about


processor updates a location in shared memory, all the other processors know about the update. Cache coherency is accomplished at the hardware level.

� Non-Uniform Memory Access (NUMA):

� Often made by physically linking two or more SMPs

� One SMP can directly access memory of another SMP

� Not all processors have equal access time to all memories

� Memory access across link is slower

� If cache coherency is maintained, then may also be called CC-NUMA - Cache Coherent NUMA


� Advantages: � Global address space provides a user-friendly programming perspective to

memory

� Data sharing between tasks is both fast and uniform due to the proximity of memory to CPUs

� Disadvantages:


� Disadvantages: � Primary disadvantage is the lack of scalability between memory and CPUs.

Adding more CPUs can geometrically increases traffic on the shared memory-CPU path, and for cache coherent systems, geometrically increase traffic associated with cache/memory management.

� Programmer responsibility for synchronization constructs that insure "correct" access of global memory.

� Expense: it becomes increasingly difficult and expensive to design and produce shared memory machines with ever increasing numbers of processors.


Distributed Memory General Characteristics:

� Like shared memory systems, distributed memory systems vary widely but share a common characteristic. Distributed memory systems require a communication network to connect inter-processor memory.

� Processors have their own local memory. Memory addresses in one processor do not map to another processor, so there is no concept of global address space across all processors.


another processor, so there is no concept of global address space across all processors.

� Because each processor has its own local memory, it operates independently. Changes it makes to its local memory have no effect on the memory of other processors. Hence, the concept of cache coherency does not apply.

� When a processor needs access to data in another processor, it is usually the task of the programmer to explicitly define how and when data is communicated. Synchronization between tasks is likewise the programmer's responsibility.

� The network "fabric" used for data transfer varies widely, though it can can be as simple as Ethernet.


� Advantages:

� Memory is scalable with number of processors. Increase the number of processors and the size of memory increases proportionately.

� Each processor can rapidly access its own local memory without interference and without the overhead incurred with trying to maintain cache coherency.


cache coherency.

� Cost effectiveness: can use commodity, off-the-shelf processors and networking.

� Disadvantages:

� The programmer is responsible for many of the details associated with data communication between processors.

� It may be difficult to map existing data structures, based on global memory, to this memory organization.

� Non-uniform memory access (NUMA) times


Comparison of Shared and Distributed Memory Architectures

Architecture CC-UMA CC-NUMA Distributed

Examples

SMPs

Sun Vexx

DEC/Compaq

SGI Challenge

IBM POWER3

SGI Origin

Sequent

HP Exemplar

DEC/Compaq

IBM POWER4

Cray T3E

Maspar

IBM SP2


IBM POWER3 IBM POWER4

Communications

MPI

Threads

OpenMP

shmem

MPI

Threads

OpenMP

shmem

MPI

Scalability to 10s of

processors

to 100s of

processors to 1000s of processors

Draw Backs Memory-CPU

bandwidth

Memory-CPU

bandwidth

Non-uniform

access times

System administration

Programming is hard to

develop and maintain

Software

Availability many 1000s ISVs many 1000s ISVs 100s ISVs


� The largest and fastest computers in the world today employ both shared and distributed memory architectures.

� The shared memory component is usually a cache coherent SMP machine. Processors on a given SMP can address that machine's memory as global.

� The distributed memory component is the networking of multiple SMPs. SMPs know only about their own memory - not the memory on another SMP. Therefore, network


about their own memory - not the memory on another SMP. Therefore, network communications are required to move data from one SMP to another.

� Current trends seem to indicate that this type of memory architecture will continue to prevail and increase at the high end of computing for the foreseeable future.

� Advantages and Disadvantages: whatever is common to both shared and distributed memory architectures.

Sommario







� Esempi

Modelli di programmazione parallela

� There are several parallel programming models in common use:

� Shared Memory

� Threads

� Message Passing

� Data Parallel


� Data Parallel

� High level

� Parallel programming models exist as an abstraction above hardware and memory architectures.

� Although it might not seem apparent, these models are NOT specific to a particular type of machine or memory architecture. In fact, any of these models can (theoretically) be implemented on any underlying hardware.


Two examples:

Shared memory model on a distributed memory machine: Kendall Square Research (KSR) ALLCACHE approach.

Machine memory was physically distributed, but appeared to the user as a single shared memory (global address space). Generically, this approach is referred to as "virtual shared


memory (global address space). Generically, this approach is referred to as "virtual shared memory". Note: although KSR is no longer in business, there is no reason to suggest that a similar implementation will not be made available by another vendor in the future.

Message passing model on a shared memory machine: MPI on SGI Origin.

The SGI Origin employs the CC-NUMA type of shared memory architecture, where every task has direct access to global memory. However, the ability to send and receive messages with MPI, as is commonly done over a network of distributed memory machines, is not only implemented but is very commonly used.

Which model to use is often a combination of what is available and personal choice. There is no "best" model, although there certainly are better implementations of some models over others.


Shared Memory Model

� In the shared-memory programming model, tasks share a common address space, which they read and write asynchronously.

� Various mechanisms such as locks / semaphores may be used to control access to the shared memory.


control access to the shared memory.

� An advantage of this model from the programmer's point of view is that the notion of data "ownership" is lacking, so there is no need to specify explicitly the communication of data between tasks. Program development can often be simplified.

� An important disadvantage in terms of performance is that it becomes more difficult to understand and manage data locality.


Threads Model

� In the threads model of parallel programming, a single process can have multiple, concurrent execution paths.

� Perhaps the most simple analogy that can be used to describe threads is the concept of a single program that includes a number of


used to describe threads is the concept of a single program that includes a number of subroutines:

� The main program a.out is scheduled to run by the native operating system. a.out loads and acquires all of the necessary system and user resources to run.

� a.out performs some serial work, and then creates a number of tasks (threads) that can be scheduled and run by the operating system concurrently.


� Each thread has local data, but also, shares the entire resources of a.out. This

saves the overhead associated with replicating a program's resources for each thread. Each thread also benefits from a global memory view because it shares the memory space of a.out.

� A thread's work may best be described as a subroutine within the main program. Any thread can execute any subroutine at the same time as other


program. Any thread can execute any subroutine at the same time as other threads.

� Threads communicate with each other through global memory (updating address locations). This requires synchronization constructs to insure that more than one thread is not updating the same global address at any time.

� Threads can come and go, but a.out remains present to provide the necessary shared resources until the application has completed.

� Threads are commonly associated with shared memory architectures and operating systems.


POSIX Threads

� Library based; requires parallel coding

� Specified by the IEEE POSIX 1003.1c standard (1995).

OpenMP

� Compiler directive based; can use serial code

Jointly defined and endorsed by a group

Unrelated standardization efforts have resulted in two very different implementations of threads: POSIX Threads and OpenMP.


standard (1995).

� C Language only

� Commonly referred to as Pthreads.

� Most hardware vendors now offer Pthreads in addition to their proprietary threads implementations.

� Very explicit parallelism; requires significant programmer attention to detail.

� Jointly defined and endorsed by a group of major computer hardware and software vendors. The OpenMP Fortran API was released October 28, 1997. The C/C++ API was released in late 1998.

� Portable / multi-platform, including Unix and Windows NT platforms

� Can be very easy and simple to use -provides for "incremental parallelism"

Microsoft has its own implementation for threads, which is not related to the UNIX POSIX standard or OpenMP


Message Passing Model

The message passing model demonstrates the following characteristics:

� A set of tasks that use their own local memory during computation. Multiple tasks can reside on the same physical


tasks can reside on the same physical machine as well across an arbitrary number of machines.

� Tasks exchange data through communications by sending and receiving messages.

� Data transfer usually requires cooperative operations to be performed by each process. For example, a send operation must have a matching receive operation.


� From a programming perspective, message passing implementations commonly comprise a library of subroutines that are embedded in source code. The programmer is responsible for determining all parallelism.

� Historically, a variety of message passing libraries have been available since the 1980s. These implementations differed substantially from each other making it difficult for programmers to develop portable applications.


� In 1992, the MPI Forum was formed with the primary goal of establishing a standard interface for message passing implementations.

� Part 1 of the Message Passing Interface (MPI) was released in 1994. Part 2 (MPI-2) was released in 1996. Both MPI specifications are available on the web at www.mcs.anl.gov/Projects/mpi/standard.html.

� MPI is now the "de facto" industry standard for message passing, replacing virtually all other message passing implementations used for production work. Most, if not all of the popular parallel computing platforms offer at least one implementation of MPI. Very few have a full implementation of MPI-2.

� For shared memory architectures, MPI implementations usually don't use a network for task communications. Instead, they use shared memory (memory copies) for performance reasons.


Data Parallel Model

The data parallel model demonstrates the following characteristics:

� Most of the parallel work focuses on performing operations on a data set. The data set is typically organized into a common structure, such as an


organized into a common structure, such as an array or cube.

� A set of tasks work collectively on the same data structure, however, each task works on a different partition of the same data structure.

� Tasks perform the same operation on their partition of work, for example, "add 4 to every array element".

� On shared memory architectures, all tasks may have access to the data structure through global memory. On distributed memory architectures the data structure is split up and resides as "chunks" in the local memory of each task.


� Programming with the data parallel model is usually accomplished by writing a program with data parallel constructs. The constructs can be calls to a data parallel subroutine library or, compiler directives recognized by a data parallel compiler.

� Fortran 90 (F90): ISO/ANSI standard extensions to Fortran 77. � Contains everything that is in Fortran 77

� New source code format; additions to character set

Additions to program structure and commands


� Additions to program structure and commands

� Variable additions - methods and arguments

� Pointers and dynamic memory allocation added

� Array processing (arrays treated as objects) added

� Recursive and new intrinsic functions added

� Implementations are available for most common parallel platforms.

� High Performance Fortran (HPF): Extensions to Fortran 90 to support data parallel programming. � Contains everything in Fortran 90

� Directives to tell compiler how to distribute data added

� Assertions that can improve optimization of generated code added

� Data parallel constructs added (now part of Fortran 95)

� Implementations are available for most common parallel platforms.


Single Program Multiple Data (SPMD):

� SPMD is actually a "high level" programming model that can be built upon any combination of the previously mentioned parallel programming models.

� A single program is executed by all tasks


� A single program is executed by all tasks simultaneously.

� At any moment in time, tasks can be executing the same or different instructions within the same program.

� SPMD programs usually have the necessary logic programmed into them to allow different tasks to branch or conditionally execute only those parts of the program they are designed to execute. That is, tasks do not necessarily have to execute the entire program - perhaps only a portion of it.

� All tasks may use different data

� Un programma MPI di solito è scritto secondo uno schema SPMD

Sommario







� Esempi

Parallelizzazione automatica o manuale?

� Designing and developing parallel programs has characteristically been a very manual process. The programmer is typically responsible for both identifying and actually implementing parallelism.

� Very often, manually developing parallel codes is a


� Very often, manually developing parallel codes is a time consuming, complex, error-prone and iterativeprocess.

� For a number of years now, various tools have been available to assist the programmer with converting serial programs into parallel programs. The most common type of tool used to automatically parallelize a serial program is a parallelizing compiler or pre-processor.

Parallelizzazione automatica o manuale?

� A parallelizing compiler generally works in two different ways:

� Fully Automatic � The compiler analyzes the source code and identifies opportunities for parallelism.

� The analysis includes identifying inhibitors to parallelism and possibly a cost weighting on whether or not the parallelism would actually improve performance.

� Loops (do, for) loops are the most frequent target for automatic parallelization.

� Programmer Directed � Using "compiler directives" or possibly compiler flags, the programmer explicitly tells the compiler how to

parallelize the code.


parallelize the code.

� May be able to be used in conjunction with some degree of automatic parallelization also.

� If you are beginning with an existing serial code and have time or budget constraints, then automatic parallelization may be the answer. However, there are several important caveats that apply to automaticparallelization:

� Wrong results may be produced

� Performance may actually degrade

� Much less flexible than manual parallelization

� Limited to a subset (mostly loops) of code

� May actually not parallelize code if the analysis suggests there are inhibitors or the code is too complex

� Most automatic parallelization tools are for Fortran

� The remainder of this course applies to the manual method of developing parallel codes.

Progettazione e valutazione di programmi paralleli

� Understand the Problem and the Program

� Partitioning

� Communications

� Synchronization


� Synchronization

� Data Dependencies

� Load Balancing

� Granularity

� I/O

� Limits and Costs of Parallel Programming

� Performance Analysis and Tuning

Progettazione del programma parallelo –comprensione del problema e del programma

� Undoubtedly, the first step in developing parallel software is to first understand the problem that you wish to solve in parallel. If you are starting with a serial program, this necessitates understanding the existing code also.

� Before spending time in an attempt to develop a parallel solution for a problem, determine whether or not the problem is one that can


problem, determine whether or not the problem is one that can actually be parallelized.

� Example of Parallelizable Problem:

� Calculate the potential energy for each of several thousand independent conformations of a molecule. When done, find the minimum energy conformation.

� This problem is able to be solved in parallel. Each of the molecular conformations is independently determinable. The calculation of the minimum energy conformation is also a parallelizable problem.


� Example of a Non-parallelizable Problem:

� Calculation of the Fibonacci series (1,1,2,3,5,8,13,21,...) by use of the formula: F(k + 2) = F(k + 1) + F(k)


� This is a non-parallelizable problem because the calculation of the Fibonacci sequence as shown would entail dependent calculations rather than independent ones. The calculation of the k + 2 value uses those of both k + 1 and k. These three terms cannot be calculated independently and therefore, not in parallel.


� Identify the program's hotspots: � Know where most of the real work is being done. The majority of scientific and

technical programs usually accomplish most of their work in a few places.

� Profilers and performance analysis tools can help here

� Focus on parallelizing the hotspots and ignore those sections of the program that account for little CPU usage.


account for little CPU usage.

� Identify bottlenecks in the program

� Are there areas that are disproportionately slow, or cause parallelizable work to halt or be deferred? For example, I/O is usually something that slows a program down.

� May be possible to restructure the program or use a different algorithm to reduce or eliminate unnecessary slow areas

� Identify inhibitors to parallelism. One common class of inhibitor is data dependence, as demonstrated by the Fibonacci sequence above.

� Investigate other algorithms if possible. This may be the single most important consideration when designing a parallel application.

Progettazione di programmi paralleli -Partizionamento

There are two basic ways to partition computational work among parallel tasks: domain decomposition and functional decomposition.

Domain Decomposition:

� In this type of partitioning, the data associated with a problem is decomposed.


� In this type of partitioning, the data associated with a problem is decomposed. Each parallel task then works on a portion of the data.


There are different ways to partition data:



Functional Decomposition: In this approach, the focus is on the computation that is to be performed rather than on the data manipulated by the computation. The problem is decomposed according to the work that must be done. Each task then performs a portion of the overall work.



� Esempio – Signal processing An audio signal data set is passed through three distinct computational filters. Each filter is a separate process. The first segment of data must pass through the first filter before progressing to the second. When it does, the second segment of data passes through the first filter. By the time the third segment of data is in the first filter, all three tasks are busy.



Climate Modelling - Each model component can be thought of as a separate task. Arrows represent exchanges of data between components during computation: the atmosphere model generates wind velocity data that are used by the ocean model, the ocean model generates sea surface temperature data that are used by the atmosphere model, and so on.


I moduli funzionali possono essere a loro volta data parallel e/o composizione di funzioni parallele

Progettazione di programmi paralleli -Comunicazioni

Who Needs Communications?

� The need for communications between tasks depends upon your problem:

� You DON'T need communications

� Some types of problems can be decomposed and executed in parallel with virtually no need for tasks to share data. For example, imagine an image processing operation where every pixel in a black and white image needs to have its color reversed. The


where every pixel in a black and white image needs to have its color reversed. The image data can easily be distributed to multiple tasks that then act independently of each other to do their portion of the work.

� These types of problems are often called embarrassingly parallel because they are so straight-forward. Very little inter-task communication is required.

� You DO need communications

� Most parallel applications are not quite so simple, and do require tasks to share data with each other. For example, a 3-D heat diffusion problem requires a task to know the temperatures calculated by the tasks that have neighboring data. Changes to neighboring data has a direct effect on that task's data.


Factors to Consider: There are a number of important factors to consider when designing your program's inter-task communications:

� Cost of communications� Inter-task communication virtually always implies overhead.

� Machine cycles and resources that could be used for computation are instead used to package and transmit data.


package and transmit data.

� Communications frequently require some type of synchronization between tasks, which can result in tasks spending time "waiting" instead of doing work.

� Competing communication traffic can saturate the available network bandwidth, further aggravating performance problems.

� Latency vs. Bandwidth� latency is the time it takes to send a minimal (0 byte) message from point A to point

B. Commonly expressed as microseconds.

� bandwidth is the amount of data that can be communicated per unit of time. Commonly expressed as megabytes/sec.

� Sending many small messages can cause latency to dominate communication overheads. Often it is more efficient to package small messages into a larger message, thus increasing the effective communications bandwidth.


� Visibility of communications� With the Message Passing Model, communications are explicit and generally quite

visible and under the control of the programmer.

� With the Data Parallel Model, communications often occur transparently to the programmer, particularly on distributed memory architectures. The programmer may not even be able to know exactly how inter-task communications are being accomplished.

Synchronous vs. asynchronous communications


� Synchronous vs. asynchronous communications� Synchronous communications require some type of "handshaking" between tasks that

are sharing data. This can be explicitly structured in code by the programmer, or it may happen at a lower level unknown to the programmer.

� Synchronous communications are often referred to as blocking communications since other work must wait until the communications have completed.

� Asynchronous communications allow tasks to transfer data independently from one another. For example, task 1 can prepare and send a message to task 2, and then immediately begin doing other work. When task 2 actually receives the data doesn't matter.

� Asynchronous communications are often referred to as non-blockingcommunications since other work can be done while the communications are taking place.

� Interleaving computation with communication is the single greatest benefit for using asynchronous communications.


� Scope of communications� Knowing which tasks must

communicate with each other is critical during the design stage of a parallel code. Both of the two scopings described below can be implemented synchronously or asynchronously.


asynchronously.

� Point-to-point - involves two tasks with one task acting as the sender/producer of data, and the other acting as the receiver/consumer.

� Collective - involves data sharing between more than two tasks, which are often specified as being members in a common group, or collective. Some common variations (there are more):


� Efficiency of communications

� Very often, the programmer will have a choice with regard to factors that can affect communications performance. Only a few are mentioned here.

� Which implementation for a given model should be used? Using the Message Passing Model as an example, one MPI implementation may be


Message Passing Model as an example, one MPI implementation may be faster on a given hardware platform than another.

� What type of communication operations should be used? As mentioned previously, asynchronous communication operations can improve overall program performance.

� Network media - some platforms may offer more than one network for communications. Which one is best?

� Overhead and Complexity


� Overhead and Complexity� Finally, realize that this is only a partial list of things to consider!!!


Progettazione di programmi paralleli -Sincronizzazione

Types of Synchronization: � Barrier

� Usually implies that all tasks are involved

� Each task performs its work until it reaches the barrier. It then stops, or "blocks".

� When the last task reaches the barrier, all tasks are synchronized.

� What happens from here varies. Often, a serial section of work must be done. In other


� What happens from here varies. Often, a serial section of work must be done. In other cases, the tasks are automatically released to continue their work.

� Lock / semaphore

� Can involve any number of tasks

� Typically used to serialize (protect) access to global data or a section of code. Only one task at a time may use (own) the lock / semaphore / flag.

� The first task to acquire the lock "sets" it. This task can then safely (serially) access the protected data or code.

� Other tasks can attempt to acquire the lock but must wait until the task that owns the lock releases it.

� Can be blocking or non-blocking

Progettazione di programmi paralleli -Sincronizzazione

Types of Synchronization:

� Synchronous communication operations

� Involves only those tasks executing a communication operation

� When a task performs a communication operation, some form of coordination is required with the other task(s) participating in the communication. For example, before a task can perform a send operation, it must first receive an


before a task can perform a send operation, it must first receive an acknowledgment from the receiving task that it is OK to send.

� Discussed previously in the Communications section.

Progettazione di programmi paralleli –Dipendenza tra i dati

Definition:

� A dependence exists between program statements when the order of statement execution affects the results of the program.

� A data dependence results from multiple use of the same location(s) in storage by


� A data dependence results from multiple use of the same location(s) in storage by different tasks.

� Dependencies are important to parallel programming because they are one of the primary inhibitors to parallelism.


Examples:

� Loop carried data dependence� The value of A(J-1) must be

computed before the value of A(J), therefore A(J) exhibits a data dependency on A(J-1). Parallelism

DO 500 J = MYSTART,MYEND


therefore A(J) exhibits a data dependency on A(J-1). Parallelism is inhibited.

� If Task 2 has A(J) and task 1 has A(J-1), computing the correct value of A(J) necessitates:

� Distributed memory architecture -task 2 must obtain the value of A(J-1) from task 1 after task 1 finishes its computation

� Shared memory architecture - task 2 must read A(J-1) after task 1 updates it

A(J) = A(J-1) * 2.0500 CONTINUE


Examples:

� Loop independent data dependence

� As with the previous example, parallelism is inhibited. The value of Y is dependent on:

� Distributed memory architecture - if or when the value of X is communicated between the

task 1 task 2------ ------


the value of X is communicated between the tasks.

� Shared memory architecture - which task last stores the value of X.

� Although all data dependencies are important to identify when designing parallel programs, loop carried dependencies are particularly important since loops are possibly the most common target of parallelization efforts.

X = 2 X = 4. .. .Y = X**2 Y = X**3

How to Handle Data Dependencies:

� Distributed memory architectures - communicate required data at synchronization points.

� Shared memory architectures -synchronize read/write operations between tasks.

Progettazione di programmi paralleli – Load Balancing

Load Balancing

� Load balancing refers to the practice of distributing work among tasks so that all tasks are kept busy all of the


that all tasks are kept busy all of the time. It can be considered a minimization of task idle time.

� Load balancing is important to parallel programs for performance reasons. For example, if all tasks are subject to a barrier synchronization point, the slowest task will determine the overall performance.


How to Achieve Load Balance:

Equally partition the work each task receives

� For array/matrix operations where each task performs similar work, evenly distribute the data set among the tasks.


distribute the data set among the tasks.

� For loop iterations where the work done in each iteration is similar, evenly distribute the iterations across the tasks.

� If a heterogeneous mix of machines with varying performance characteristics are being used, be sure to use some type of performance analysis tool to detect any load imbalances. Adjust work accordingly.


How to Achieve Load Balance:

Use dynamic work assignment

� Certain classes of problems result in load imbalances even if data is evenly distributed among tasks:

Sparse arrays - some tasks will have actual data to work on while others have mostly


� Sparse arrays - some tasks will have actual data to work on while others have mostly "zeros".

� Adaptive grid methods - some tasks may need to refine their mesh while others don't.

� N-body simulations - where some particles may migrate to/from their original task domain to another task's; where the particles owned by some tasks require more work than those owned by other tasks.

� When the amount of work each task will perform is intentionally variable, or is unable to be predicted, it may be helpful to use a scheduler - task pool approach. As each task finishes its work, it queues to get a new piece of work.

� It may become necessary to design an algorithm which detects and handles load imbalances as they occur dynamically within the code.

Progettazione di programmi paralleli –Granularità

� Computation / Communication Ratio: � In parallel computing, granularity is a qualitative measure of the ratio of computation

to communication.

� Periods of computation are typically separated from periods of communication by synchronization events.

Fine-grain Parallelism:


� Fine-grain Parallelism: � Relatively small amounts of computational work are done between communication

events

� Low computation to communication ratio

� Facilitates load balancing

� Implies high communication overhead and less opportunity for performance enhancement

� If granularity is too fine it is possible that the overhead required for communications and synchronization between tasks takes longer than the computation.

Progettazione di programmi paralleli –Granularità

Coarse-grain Parallelism:

� Relatively large amounts of computational work are done between communication/synchronization events

� High computation to communication ratio

� Implies more opportunity for performance increase


� Harder to load balance efficiently

Which is Best?

� The most efficient granularity is dependent on the algorithm and the hardware environment in which it runs.

� In most cases the overhead associated with communications and synchronization is high relative to execution speed so it is advantageous to have coarse granularity.

� Fine-grain parallelism can help reduce overheads due to load imbalance.

Progettazione di programmi paralleli – I/O

The Bad News:

� I/O operations are generally regarded as inhibitors to parallelism

� Parallel I/O systems are immature or not available for all platforms

� In an environment where all tasks see the same filespace, write operations will result in file overwriting

� Read operations will be affected by the fileserver's ability to handle multiple read requests at the same time


same time

� I/O that must be conducted over the network (NFS, non-local) can cause severe bottlenecks

The Good News:

� Some parallel file systems are available. For example:

� GPFS: General Parallel File System for AIX (IBM)

� Lustre: for Linux clusters (Cluster File Systems, Inc.)

� PVFS/PVFS2: Parallel Virtual File System for Linux clusters (Clemson/Argonne/Ohio State/others)

� PanFS: Panasas ActiveScale File System for Linux clusters (Panasas, Inc.)

� HP SFS: HP StorageWorks Scalable File Share. Lustre based parallel file system (Global File System for Linux) product from HP

� The parallel I/O programming interface specification for MPI has been available since 1996 as part of MPI-2. Vendor and "free" implementations are now commonly available.

Progettazione di programmi paralleli – I/O

Some options:

� If you have access to a parallel file system, investigate using it. If you don't, keep reading...

� Rule #1: Reduce overall I/O as much as possible

Confine I/O to specific serial portions of the job, and then use parallel communications


� Confine I/O to specific serial portions of the job, and then use parallel communications to distribute data to parallel tasks. For example, Task 1 could read an input file and then communicate required data to other tasks. Likewise, Task 1 could perform write operation after receiving required data from all other tasks.

� For distributed memory systems with shared filespace, perform I/O in local, non-shared filespace. For example, each processor may have /tmp filespace which can used. This is usually much more efficient than performing I/O over the network to one's home directory.

� Create unique filenames for each tasks' input/output file(s)

Structured parallel programming paradigms


Progettazione di programmi paralleli – Costi e limiti

Amdahl's Law:

� Amdahl's Law states that potential program speedup is defined by the fraction of code (P) that can be parallelized

� If none of the code can be parallelized, P = 0 and the speedup = 1 (no speedup). If all

1

speedup = --------


0 and the speedup = 1 (no speedup). If all of the code is parallelized, P = 1 and the speedup is infinite (in theory).

� If 50% of the code can be parallelized, maximum speedup = 2, meaning the code will run twice as fast.

speedup = --------

1 - P


� Introducing the number of processors N, performing the parallel fraction of work, the relationship can be modeled by (S=1 - P):

1

speedup = ------------

P + S

---

N

speedup

--------------------------------


--------------------------------

N P = .50 P = .90 P = .99

----- ------- ------- -------

10 1.82 5.26 9.17

100 1.98 9.17 50.25

1000 1.99 9.91 90.99

10000 1.99 9.91 99.02

�However, certain problems demonstrate increased performance by increasing the problem size. For example: • 2D Grid Calculations 85 seconds 85% 2D Grid Calculations 85 seconds 85% 2D Grid Calculations 85 seconds 85% 2D Grid Calculations 85 seconds 85% • Serial fraction 15 seconds 15%Serial fraction 15 seconds 15%Serial fraction 15 seconds 15%Serial fraction 15 seconds 15%�We can increase the problem size by doubling the grid dimensions and halving the time step. This results in four times the number of grid points and twice the number of time steps. The timings then

look like 2D Grid Calculations 680 seconds 97.84% Serial fraction 15 seconds 2.16%2D Grid Calculations 680 seconds 97.84% Serial fraction 15 seconds 2.16%2D Grid Calculations 680 seconds 97.84% Serial fraction 15 seconds 2.16%2D Grid Calculations 680 seconds 97.84% Serial fraction 15 seconds 2.16%


Complexity:� In general, parallel applications are much more complex than

corresponding serial applications, perhaps an order of magnitude. Not only do you have multiple instruction streams executing at the same time, but you also have data flowing between them.


between them. � The costs of complexity are measured in programmer time in

virtually every aspect of the software development cycle: � Design � Coding � Debugging � Tuning � Maintenance

� Adhering to "good" software development practices is essential when working with parallel applications - especially if somebody besides you will have to work with the software.


Portability:� Thanks to standardization in several APIs, such as MPI, POSIX threads,

HPF and OpenMP, portability issues with parallel programs are not as serious as in years past. However...

� All of the usual portability issues associated with serial programs apply to parallel programs. For example, if you use vendor "enhancements" to Fortran, C or C++, portability will be a problem.


to Fortran, C or C++, portability will be a problem. � Even though standards exist for several APIs, implementations will

differ in a number of details, sometimes to the point of requiring code modifications in order to effect portability.

� Operating systems can play a key role in code portability issues. � Hardware architectures are characteristically highly variable and can

affect portability.


Resource Requirements:� The primary intent of parallel programming is to decrease execution

wall clock time, however in order to accomplish this, more CPU time is required. For example, a parallel code that runs in 1 hour on 8 processors actually uses 8 hours of CPU time.

� The amount of memory required can be greater for parallel codes than


� The amount of memory required can be greater for parallel codes than serial codes, due to the need to replicate data and for overheads associated with parallel support libraries and subsystems.

� For short running parallel programs, there can actually be a decrease in performance compared to a similar serial implementation. The overhead costs associated with setting up the parallel environment, task creation, communications and task termination can comprise a significant portion of the total execution time for short runs.


Scalability: � The ability of a parallel program's performance to scale is a result of a

number of interrelated factors. Simply adding more machines is rarely the answer.

� The algorithm may have inherent limits to scalability. At some point, adding more resources causes performance to decrease. Most parallel solutions demonstrate this characteristic at some point.


solutions demonstrate this characteristic at some point. � Hardware factors play a significant role in scalability. Examples:

� Memory-cpu bus bandwidth on an SMP machine � Communications network bandwidth � Amount of memory available on any given machine or set of machines � Processor clock speed

� Parallel support libraries and subsystems software can limit scalability independent of your application.

Un primo schema per l’analisi quantitativa di un

programma SPMD (con calcolo bilanciato)

Tcalc = Ocalc(n) t calc

Tcomm =Ocomm(n) t comm

fc= Tcomm / Tcalc fractional communication overehead


n = numero di elementi per nodo

N = numero di nodi

n*N = numero totale di elementi

S(N)= Tseq/Tconc(N) Speed_up

E=S/N Efficienza

Caso ideale Tconc(N) = Tseq/N

Caso reale (approssimato) Tconc(N) = (1+ fc) * Tseq/N

⇒S(N)= N/ (1+ fc)

⇒ e se fc è abbastanza piccolo rispetto a 1 allora E = 1- fc

Schema per l’analisi quantitativa di un programma Farm

Tcalc


Some considerations about Tpar

Refining the goale.g. for huge dataset

Tpar =feasible T

Tpar = min T


looking for max speed up

Tpar = Predictable (adaptive) T

critical task with time deadline

t deadlineevent

Some considerations about Tpar

Refining the goal any of the previous

and a full cost approach


Some considerations about TparEvaluating Tpar: Amdhal Law (revisited)

Tpar = Tpf / NP + Tsf + Tovhp+ Tovhsh

Sequential fraction Reduction of the

Resource sharing is a


size…)

Reduction of the sequential fraction (parallel I/O, algorithm design improvements, increasing in data size…)

Different sources of parallel overhead: comp/comm; load unbalancing; heterogeneity; multilevel parallelism and distributed computation; complex multi-component applications (MxN and parallel coupling)

main issue in a distributed environment: local scheduling policies; meta scheduling and co-scheduling; SLA management and QoS

Emerging HP scientific activities

� As an example we may consider multiphysics multiscale researches

� New computing architectures and software tools permitted to design and implement new


tools permitted to design and implement new sophisticated methodologies based on the coupling of many mathematical simulation techniques and experimental data. This dramatically improves modelling accuracy.

Community Climate System Model (CCSM) http://www.ccsm.ucar.edu/

Coupler

P0P0

P1

P2

P3P0

P1

P2

P3

P0

P1 P2 P3

Ocean


CCSM models are general-circulation models

(parallel but the inter-model communication is serial)

CouplerP3

P4

Ice

P3

P4

AtmosphereP0

P1 P2 P3

Land

Emerging HP scientific applications Considering different activities:

� Free ridingExplore the

Grid

experimenting

and looking for

models, tools Perform a


� Production

� Critical

models, tools

and resources

models, tools

and resources

infrastructure

Perform a

complex scientific

workflow using a

production

infrastructure

infrastructure

Perform a time

constrained

scientific task

using a reliable

(QoS)

infrastructure

Emerging HPC multilevel heterogeneous infrastrucures

� The Grid EGEE DEISA

� The HPC cluster or node


� The HPC cluster or node

� The computing node � recent evolution at the node level: multi-many core systems

A (partial) list of problems in parallel – Grid sw design

� Hide parallelism and the Grid

� Design for efficiency, portability and adaptivity

� Software reuse and legacy code encapsulation

� Heterogeneous architectures exploitation


� Heterogeneous architectures exploitation

� Non functional interfaces for matchmaking

� Effective and efficient composition of large multicomponent applications

� Parallel Coupling

� MxN problem

Developing Parallel Software

� 2 types of programmers � 2 layers

� Efficiency Layer (10% of today’s programmers)

� Expert programmers build Frameworks & libraries, Hypervisors, …

� “Bare metal” efficiency possible at Efficiency Layer


91

� “Bare metal” efficiency possible at Efficiency Layer

� Productivity Layer (90% of today’s programmers)

� Domain experts / Naïve programmers productively build parallel apps using frameworks & libraries

� Frameworks & libraries composed to form app frameworks

� Effective composition techniques allows the efficiency programmers to be highly leveraged ⇒ Create language for Composition and Coordination (C&C)

Available tools and methodologies at the efficiency layer

� Communications paradigms and libraries

� Message passing and shared (virtual) memory


� MPI2 , OpenMP, Linda and generative models, Tuple spaces…

� Parallel file systems and their API

� Debugging and parallel performance tools

Available tools and methodologies at the efficiency layer Structured parallel programming paradigms


Available tools and methodologies at the efficiency layer domain oriented parallel libraries


Efficiency layer open problems

� Many…mentions a few

� Adaptive autotuning components


� Evolve the concept of non functional interface

� Develop practical approach to define a sw component quantitative requirements

Productivity Layer

� Most parallelism is hidden within libraries and frameworks

� Productivity layer is about:� Serial programming support

� Composition of parallel components


� Composition of parallel components

� Ensuring correctness through static analysis: prohibit certain find of bugs

� Coordination and composition language� Express independence rather than parallelism:

� Provide rich type system to allow data partitioning

� Check for independence

� Language features map to programming frameworks

Productivity Layer – Coordination and composition

� Component Based Models: Common Component Architecture (CCA) – SIDL , Babel, CCaffeine, XCAT

� Service orientations: Grid Services, SOA


� Service orientations: Grid Services, SOA

� Workflow composition and orchestration tools

� Emerging paradigms and unifying approaches: Google MapReduce

Resource management aspects

� Resource discovery � a critical aspect in very large Grid (p2p –Super peer – Voronoi - smallworld)

� Resource selection: resource ranking, and resources � sw


Resource selection: resource ranking, and resources � sw components matchmaking

� Resource allocation is complex:

� Resources belong to different domains

� Resources are subject to different policies

� Resources are geographically distributed.

Best effort is a reasonable starting point

Resource Management Layer

� Grid Resource Management System consists of :� Local resource management system (Resource Layer)

� Basic resource management unit

� Provide a standard interface for using remote resources

� e.g. GRAM, etc. e.g. GRAM, etc.

� Global resource management system (Collective Layer)� Coordinate all Local resource management system within multiple or

distributed Virtual Organizations (VOs)

� Provide high-level functionalities to efficiently use all of resources

� Job Submission

� Resource Discovery and Selection

� Scheduling

� Co-allocation

� Job Monitoring, etc.

� e.g. Meta-scheduler, Resource Broker, etc.

Towards a Grid Economy

� Cooperative Scenarios:

� Charity: Seti project

� Sharing of resource among institutions.

� Competitive Scenarios:


� Competitive Scenarios:

� Buying and selling of resources in a Market

� Keynesian Scenario:

� Investment in Hardware/Software that is used by different users

� Emerging applications will drive the evolution (the Internet experience)

Towards IT as a service


The future Cloud architecture


Present Cloud platforms features


Documents

Introduzione al calcolo parallelo e al Grid computingenrico/IngegneriaDelSoftware/anno08-09/GRID... · Manycore : 8X to 16X multicore ... (A slide from D. Patterson Berkeley)