Download Designing Parallel Programs

Designing Parallel Programs
David Rodriguez-Velazquez
CS-6260 Spring-2009
Dr. Elise de Doncker
Manual vs. Automatic Parallelization
• Designing and developing parallel programs
has been a very MANUAL process.
• The programmer is responsible for both:
– Identifying & Implementing parallelism
• Manually developing parallel codes is a
– Time consuming
– Complex
– Error-prone
– Iterative process
Outline
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Parallelization
Partitioning
Communication
Efficiency
Synchronization
Data Dependency
Load Balancing
Granularity
I/O
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Amdhal’s Law
Complexity
Portability
Resource Requirements
Scalability
MPI demo
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Matrix Share Memory
Matrix multiplication
Alltoall
Heat Equation
Parallelizing Compiler (Pre-Processor)
• Most common type of tool used to
automatically parallelize a serial program into
parallel programs
• Parallelizing Compiler works in 2 different
ways:
– Fully Automatic
– Programmer Directed
Parallelizing Compiler (Fully Automatic)
• The compiler analyzes the source code and
identifies opportunities for parallelism
• The analysis includes:
– Identifying inhibitors to parallelism
– 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
Parallelizing Compiler (Programmer Directed)
• Using “compiler directives” or possibly
compiler flags, the programmer explicitly tell
the compiler how to parallelize the code
• May be able to be used in conjunction with
some degree of automatic parallelization also
Automatic Parallelization(Caveats)
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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 suggest there are inhibitors or the
code is too complex
Understand the Problem & the Program
• First step in developing parallel software is to:
– Understand the problem that you wish to solve in parallel (from
serial program you need to understand the existing code)
– Before spending time : determine whether or not the problem is
one that can actually be parallelized
– Identify the program’s hotspots (Know where of the real work is
being done. Performance analysis tools can help here)
– Identify bottlenecks ( I/O is usually something that slows a
program down. Change algorithms to reduce or eliminate
unnecessary slow areas)
– Investigate other algorithms
– Investigate inhibitors to parallelism . One common class of
inhibitor is data dependence
Examples (Parallelizable?)
– 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
• Each of the molecular conformation is independently
determinable. The calculation of the minimum energy
conformation is also a parallelizable problem
– Example of Non-parallelizable Problem
• Calculation of the Fibonacci series (1,1,2,3,5,8,13,21)
• F(K + 2) = F(K + 1) + F(K)
• The calculation of the Fibonacci sequences as shown would entail
dependent calculations rather than independents ones. The
calculation of the k + 2 values uses those of both k + 1 and k. These
three terms cannot be calculated independently and therefore,
not in parallel
PARTITIONING
• PARTITIONING
– Break the problem into discrete “chunks” of work
that can be distributed to multiple tasks
– Domain decomposition & Functional
decomposition
Partition
• Domain Decomposition: the data associated with
a problem is decomposed. Each parallel task then
works on a portion of of the data.
Partition
• 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.
Partition (Functional Decomposition)
Communications
• Who needs Communications :
– You don’t need :
• Some types of problems can be decomposed and
execute in parallel. Embarrassingly parallel.
• Very little inter-task communication is required
• Eg. Image processing operation, every pixel in a black
and white image needs to have its color reversed
– You do need
• Most parallel applications do require to share data with
each other. (Eg. Ecosystem)
COMMUNICATIONS (Factors to consider)
• There are a number of important factors to
consider when designing program’s inter-task
communications:
– Cost of communications
– Latency vs. Bandwidth
– Visibility of communications
– Synchronous vs. Asynchronous communication
– Scope of communications
– Efficiency of communications
Communications (Cost)
• 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.
• 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
Communications (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 or gigabytes/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.
Communications (Visibility)
• Message passing Model: communications are
explicit (under control of the programmer)
• Data Parallel Model: communications occur
transparently to the programmer, usually on
distributed memory architectures.
Communications (Synchronous vs.
Asynchronous)
• Synchronous requires some type of
“handshaking” between task that are sharing
data.
• Synchronous : Blocking communications
• Asynchronous allow tasks to transfer data
independently from one another.
• Asynchronous: Non-Blocking communications
• Interleaving computation with communication
is the greatest benefit.
Communications (Scope)
• Knowing which tasks must communicate with
each other is critical during design stage of a
parallel code.
• Two scoping can be implementing sync. Or
async.
– Point to Point: 2 task (sender/producer of data
and receiver/consumer)
– Collective: data sharing between more than two
tasks
Communications (Scope-Collective)
Efficiency of communications
• Very often, the programmer will have a choice with
regard to factors that can affect communications
performance.
• Which implementation for a given model should be
used? (Eg.MPI implementation may be faster on a
given hardware platform than another)
• What type of communication operations should be
used? (Eg. asynchronous communication operations
can improve overall program performance)
• Network media - some platforms may offer more than
one network for communications. Which one is best?
SYNCHRONIZATION (Types)
• Barrier
– All tasks are involved
– Each task perform its work. When the last task
reaches the barrier, all task are synchronized
• Lock / semaphore
– Typically used to serialize access to global data or
section of code. Task must wait to use the code
• Synchronous communication operations
– Involves only those tasks executing a communication
operations (handshaking)
Data Dependencies
• A dependence exists between program
statements when the order of statements
execution affects the results of the program
• 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
Data Dependencies
• Loop carried data dependence (most important)
DO J = MYSTART,MYEND
A(J) = A(J-1) * 2.0
CONTINUE
• 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 is inhibited.
• If Task 2 has A(J) and task 1 has A(J-1), computing the
correct value of A(J) necessitates: 1 Calculate, 2 get value
• Loop independent data dependence
– task 1
X=2
Y = X**2
task 2
X=4
Y = X**3
• As with the previous example, parallelism is inhibited. The
value of Y is dependent on:
Data Dependencies
• How to Handle Data Dependencies:
– Distributed memory architectures - communicate
required data at synchronization points.
– Shared memory architectures -synchronize
read/write operations between tasks.
Load Balancing
• Refers to the practice of distributing work
among tasks so that all task are kept busy all
of the time.
• It can be considered a Minimization of task
idle time
• Important for performance reasons
Load Balancing
• How to achieve
– Equally partition the work each task receives
– Use dynamic work assignment
How to Achieve (Load Balancing)
• 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.
– For loop iterations where the work done in each
iteration is similar, evenly distribute the iterations
across the tasks.
How to Achieve (Load Balancing)
• Use dynamic work assignment
– 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.
• Sparse arrays:some task with zeros
• Adaptive grid methods: some task need to refine their mesh
How to Achieve (Load Balancing)
Granularity (Computation / Communication Ratio)
• 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
• Two types
– Fine-grain Parallelism
– Coarse-grain Parallelism
Granularity (Fine-grain Parallelism)
• Relatively small amounts of computational work
are done between communication events
• Low computation to communication ratio
• Implies high communication overhead
• If granularity is too fine it is possible that the
overhead required for communications and
synchronization between tasks takes longer than
the computation
Granularity (Coarse-grain Parallelism)
• Relatively large amounts of computational
work are done between
communication/synchronization events
• High computation to comunication rate
• Implies more opportunity for performance
increase
• Harder to load balance efficiently
Granularity (What is Best?)
• The most efficient granularity depend on the
algorithm and the hardware environment in
which it runs
• In most cases the overhead associated with
communication 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. Facilitates load balancing
I/O
• I/O operations are inhibitors to parallelism
• Parallel I/O systems may be inmature or not
available for all platforms
• If all of the tasks see the same file space,
WRITE operations can result in file overwriting
• Read operations can be affected by the file
server’s ability to handle multiple read
requests at the same time
• I/O over networks can cause
bottlenecks/crash file servers
Amdahl’s Law
• States that:
“Potential program speedup is defined by the
fraction of code (P) that can be parallelized”
Speedup = 1 / (1 – P)
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If P = 0 then speedup = 1
(no code parallelized)
If P = 1 then speedup is infinite
(all code parallelized)
If P = .5 then speedup is 2
(50% of the code parallelized)
meaning the code will run
twice as fast.
Amdahl’s Law
• Introducing the number of processors performing the parallel
fraction of work
Speedup = 1 / ((P / N) + S)
P = parallel fraction,
N = number of processors
S = serial fraction
Complexity
• Parallel applications are much more complex
than corresponding serial applications.
• Cost of complexity is measured in programmer
time in every aspect of the software
development cycle
– Design, Coding, Debugging, Tuning, Maintenance
Portability
• There are standardization in some API’s s.t.
MPI
– Implementations will differ in a number of details,
requiring code modifications
– Hw architectures can affect portability
– Operating systems can play a key role in code
portability issues
– All of the portability issues associated with serial
programs apply to parallel programs
Resource Requirements
• Goal of Parallel programming is decrease
execution wall clock time, more CPU time is
required. Eg. 1 parallel code that runs 1 hour on 8
processors actually use 8 hours of CPU time
• Amount of memory can be greather in parallel
• Short parallel code it is possible a decrease in
performance. (setting up the parallel
environment, task creation/termination,
communication)
Scalability
• Result of a numer of interrelated factors
• Adding more machines is rarely the answer
• At some point, adding more resources causes
performance to decrease
• Hardware factors play a significant role in
scalability.
– Communications network bandwidth
– Amount of memory available on any machine
• Parallel support libraries and subsystems (limit)
References
• Author: Blaise Barney, Livermore Computing.
• A search on the WWW for "parallel programming" or
"parallel computing" will yield a wide variety of
information.
• "Designing and Building Parallel Programs". Ian Foster.
http://www-unix.mcs.anl.gov/dbpp/
• "Introduction to Parallel Computing". Ananth Grama,
Anshul Gupta, George Karypis, Vipin Kumar.
http://www-users.cs.umn.edu/~karypis/parbook/
Question
• Mention 5 Communication factors to be
consider when you are designing a Parallel
Program
– Cost of Communication
– Latency , Bandwidth
– Visibility
– Synchronous , Asynchronous
– Scope