parallel-computation.pdf

An Overview of Parallel computing
Jayanti Prasad
Inter-University Centre for Astronomy & Astrophysics
Pune, India (411007)
May 20, 2011

Plan of the Talk
Introduction
Parallel platforms
Parallel Problems & Paradigms
Parallel Programming
Summary and conclusions

High-level view of a computer system

Why parallel computation ?
The speed with which a single processor can process data
(number of instructions per second, FLOPS) cannot be
increased indefinitely.
It is difficult to cool faster CPUs.
Faster CPUs demand smaller chip size which again creates
more heat.
Using a fast/parallel computer :
Can solve existing problems/more problems in less time.
Can solve completely new problems leading to new findings.
In Astronomy High Performance Computing is used for two
main purposes
Processing large volume of data
Dynamical simulations
References :
Ananth Grama et. al. 2003, Introduction to Parallel Computing, Addison Wesley
Kevin Dowd & Charles R. Severance, High Performance Computing, OReily

Performance
Computation time for different problems may depend on the
followings:
Input-Output:- problems which require a lot of disk
read/write.
Communication:- Problems, like dynamical simulations need
a lot of data to be communicated among processors. Fast
inter-connects (Gig-bit Ethernet, Infiniband, Myrinet etc.) are
highly recommended.
Memory:- Problems which need a large amount of data to
be available in the main memory (DRAM), demand more
memory. Latency and bandwidth are very important.
Processor:- Problems in which a large number or
computations have to be done.
Cache :- Better memory hierarchy (RAM,L1,L2,L3..) and
efficient use of that benefits all problems.

Performance measurement and benchmarking
FLOPS:- Computational power is measured in units of
Floating Point Operations Per Second or FLOPS (Mega, Giga,
Tera, Peta,.. FLOPS).
Speed UP:-
Speed Up =
T1
TN
(1)
where T1 is the time needed to solve a problem on one
processor and Tn is the time needed to solve that on N
processors.

Pipeline
If we want to add two numbers we need five computational steps:
If we have one functional unit for every step then the addition still
requires five clock cycles, however, all the units being busy at the
same time, one result is produced every cycle. Reference : Tobias Wittwer 2005,
An Introduction to Parallel Programming

Vector Processors
A processor that performs one instruction on several data sets
is called a vector processor.
The most common form of parallel computation is in the form
of Single Instruction Multiple Data (SIMD) i.e., same
computational steps are applied on different data sets.
Problems which can be broken into small problems for
parallelization are called embarrassingly parallel problems e.g.,
SIMD.

Multi-core Processors
That part of a processor which execute instructions in an
application is called a core.
Note that in a multiprocessor system we can have each
processor having one core or more than one cores.
In general the number of hardware threads are equal to the
number of cores.
In some processors one core can support more than one
software threads.
A multi-core processor presents multiple virtual CPUs to the
user and operating system which are not physically countable
but OS can give you clue (check /proc).
Reference : Darryl Gove, 2011, Multi-core Application Programming, Addison-Wesley

Distributed Memory system
Topology : Star, N-Cube, Torus ...

Parallel Problems
Scalar Product
S =
N
X
i=1
Ai Bi (2)
Linear-Algebra: Matrix multiplication
Cij =
M
X
k=1
AikBkj (3)
Integration
y = 4
Z 1
0
dx
1 + x2
(4)
Dynamical simulations
fi =
N
X
j=1
mj (~
xj − ~
xi )
(|~
xj − ~
xi |)3/2
(5)

Models of parallel programming: Fork-Join

Models of parallel programming: Master-Slave

Synchronization
More than one processors working on a single problem must
coordinate (if the problem is not embarrassingly parallel
problem).
The OpenMp CRITICAL directive specifies a region of code
that must be executed by only one thread at a time.
The BARRIER (in OpenMp, MPI etc.,) directive
synchronizes all threads in the team.
In pthreads Mutexes are used to avoid data inconsistencies
due to simultaneous operations by multiple threads upon the
same memory area at the same time.

Partitioning or decomposing a problem: Divide and
conquer
Partitioning or decomposing a problem is related to the
opportunities for parallel execution.
On the basis of whether we are diving the executions or data
we can have two type of decompositions:
Functional decomposition
Domain decomposition
Load balance

Domain decomposition
Figure: The left figure shows the use of orthogonal recursive bisection
and the right one shows Peano-Hilbert space filling curve for domain
decomposition. Note that parts which have Peano-Hilbert keys close to
each other are physically also close to each other.
Examples: N-body, antenna-baselines, sky maps (l,m)

Mapping and indexing
Indexing in MPI
MPI Comm rank(MPI COMM WORLD, &id);
Indexing in OpenMP
id = omp get thread num();
Indexing in CUDA
1 tid=threadIdx.x + blockDim.x*( threadIdx.y+blockDim.y * threadIdx.z);
2 bid=blockIdx.x + gridDim.x * blockIdx.y;
3 nthreads = blockDim.x * blockDim.y * blockDim.z;
4 nblocks = gridDim.x * gridDim.y;
5 id = tid + nthreads * bid;
1 dim3 dimGrid(grszx ,grszy), dimBlock(blsz ,blsz ,blsz );
2 VecAdd $<<< dimGrid ,dimBlock >>>$ ();

Mapping
A problem of size N can be divided among NP processors in
the following ways:
A processor with identification number id get the data
between the data index istart and iend where
istart = id ×
N
Np
(6)
iend = (id + 1) ×
N
Np
(7)
Every processor can pick data skipping NP elements
for(i = 0; i < N; i+ = Np) (8)
Note that N/Np may not always an integer so keep load
balance in mind.

Shared Memory programming : Threading Building Blocks
Intel Threading building blocks (ITBB) is provided in the form
of C++ runtime library which and can run on any platform.
The main advantage of TBB is that it works at a higher level
than raw threads, yet does not require exotic languages or
compilers.
Most threading packages require you to create, join, and
manage threads. Programming directly in terms of threads
can be tedious and can lead to inefficient programs because
threads are low-level, heavy constructs that are close to the
hardware.
TBB runtime library automatically schedules tasks onto
threads in a way that makes efficient use of processor
resources. The runtime is very effective in load-balancing also.

Shared Memory programming : Pthreads
1 # include <pthread.h>
2 void * print_hello_world (void * param) {
3 long tid =( long)param;
4 printf("Hello world from %ld ! n",tid );
5 }
6
7 int main(int argc , char *argv []){
8 pthread_t mythread[NTHREADS ];
9 long i;
10 for(i=0; i < NTHREADS; i++)
11 pthread_create (& mythread[i],NULL ,& print_hello_world ,( void *)i);
12 pthread_exit (NULL );
13 return (0);
14 }
Reference : David R. Butenhof 1997, Programming with Posix threads, Addison-Wesley

Shared Memory programming : OpenMp
No need to make any change in the structure of the program.
Need only three things to be done :
#include< omp.h >
#pragma omp parallel for shared () private ()
-fopenmp when compiling
In general available on all GNU/Linux system by default
References :
Rohit Chandra et. al. 2001, Parallel Programming in OpenMP, Morgan Kaufmann
Barbara Chapman et. al. 2008, Using OpenMP, MIT Press
http://www.iucaa.ernet.in/∼jayanti/openmp.html

OpenMP: Example
1 # include <stdio.h>
2 # include <omp.h>
3 int main (int argc , char*argv []){
4 int nthreads , tid , numthrd;
5 // set the number of threads
6 omp_set_num_threads (atoi(argv [1]));
7
8 # pragma omp parallel private(tid)
9
10 {
11 tid = omp_get_thread_num (); // obtain the thread id
12
13 nthreads = omp_get_num_threads (); // find number of threads
14
15 printf("tHello World from thread %d of %dn", tid ,nthreads );
16
17 }
18 return (0);
19 }

Distributed Memory Programming : MPI
MPI is a solution for very large problems
Communication
Point to Point
Collective
Communication overhead can dominate computation and it
may be hard to get linear scaling.
Is distributed in the form of libraries e.g., libmpi,libmpich or in
the form of compilers e.g., mpicc,mpif90.
Programs have to be completely restructured.
References :
Gropp, William et. al. 1999, Using MPI 2, MIT Press
http://www.iucaa.ernet.in/∼jayanti/mpi.html

MPI : Example
1 # include <stdio.h>
2 # include <mpi.h>
3 int main(int argc , char *argv []){
4 int rank , size , len;
5 char name[ MPI_MAX_PROCESSOR_NAME ];
6 MPI_Init (&argc , &argv );
7 MPI_Comm_rank (MPI_COMM_WORLD , &rank );
8 MPI_Comm_size (MPI_COMM_WORLD , &size );
9 MPI_Get_processor_name (name , &len);
10 printf ("Hello world! I’m %d of %d on %sn", rank , size , name );
11 MPI_Finalize ();
12 return (0);
13 }

GPU Programming : CUDA
Programming language similar to C with few extra constructs.
Parallel section is written in the form of kernel which is
executed on GPU.
Two different memory spaces : one for CPU and another of
GPU. Data has to be explicitly copied back and forth.
A very large number of threads can be used. Note that GPU
cannot match the complexity of CPU. It is mostly used for
SIMD programming.
References :
David B. Kirk and Wen-mei W. Hwu 2010, Programming Massively Parallel Processors, Morgan Kaufmann
Jason Sanders & Edward Kandrot 2011, Cuda By examples, Addison-Wesley
http://www.iucaa.ernet.in/∼jayanti/cuda.html

CUDA : Example
1 __global__ void force_pp(float *pos_d , float *acc_d ,int n){
2
3 int tidx = threadIdx.x;
4 int tidy = threadIdx.y;
5 int tidz = threadIdx.z;
6
7 int myid = (blockDim.z * (tidy+blockDim.y *tidx )) + tidz;
8 int nthreads = blockDim.z * blockDim.y * blockDim.x;
9
10 for(int i = myid; i < n; i+= nthreads ){
11 for(int l=0; l < ndim; l++)
12 acc_d[l+ndim*i] = ...;
13
14 }//
15 __syncthreads ();
16 }
17 // this was the device part
1 dim3 dimGrid (1);
2 dim3 dimBlock(BLOCK_SIZE , BLOCK_SIZE ,BLOCK_SIZE );
3 cudaMemcpy(pos_d , pos ,npart*ndim*sizeof(float), cudaMemcpyHostToDevice );
4 force_pp <<< dimGrid ,dimBlock >>>( pos_d ,acc_d ,npart );
5 cudaMemcpy(acc ,acc_d ,npart*ndim*sizeof(float), cudaMemcpyDeviceToHost );

Nvidia Quadro FX 3700
— General Information for device 0 —
Name: Quadro FX 3700
Compute capability: 1.1
Clock rate: 1242000
Device copy overlap: Enabled
Kernel execition timeout : Disabled
— Memory Information for device 0 —
Total global mem: 536150016
Total constant Mem: 65536
Max mem pitch: 262144
Texture Alignment: 256
— MP Information for device 0 —
Multiprocessor count: 14
Shared mem per mp: 16384
Registers per mp: 8192
Threads in warp: 32
Max threads per block: 512
Max thread dimensions: (512, 512, 64)
Max grid dimensions: (65535, 65535, 1)

Dynamic & static libraries
Most of the open source software are distributed in the form of
source codes and from which libraries are created for the use.
In general libraries are not portable.
One of the most common problems which a user face is due
to not linking libraries.
The most common way to create libraries is: source code −→
object code −→ library.
gcc -c first.c
gcc -c second.c
ar rc libtest.a first.o second.o
gcc -shared -Wl,-soname, libtest.so.0 -o libtest.so.0 first.o second.o -lc
The above library can be used in the following way
gcc program.c -L/LIBPATH -ltest
Dynamic library gets preference over static one.

Hyper threading
Hyper-Threading Technology used in Intel R
Xeon
TM
and
Intel R
Pentium
TM
4 processors, makes a single physical
processor appear as two logical processors to the operating
system.
Hyper-Threading duplicates the architectural state on each
processor, while sharing one set of execution resources.
sharing system resources, such as cache or memory bus, may
degrade system performance and Hyper-Threading can
improve the performance of some applications, but not all.

Summary
It is not easy to make a super-fast single processor so
multi-processor computing is the only way to get more
computing power.
When more than one processors (cores) share the same
memory shared memory programming is uded e.g.,
pthread,OpenMp, itbb etc.
Shared memory programming is fast and it easy to get linear
scaling since communication is not an issue.
When processors having their own memory are used for
parallel computation, distributed memory programming is
used e.g., MPI, PVM.
Distributed memory programming is the main way to solve
large problems (when thousands of processors are needed).
General Purpose Graphical Processing Units (GPGPU) can
provide very high performance at very low cost, however,
programming is somewhat complicated and parallelism is
limited to only SIMD.

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