High Performance Computing using MPI

High
Performance
Computing
Ankit Mahato
amahato@iitk.ac.in
fb.com/ankitmahato
IIT Kanpur

Note: These are not the actual lecture slides but the ones you may
find useful for IHPC, Techkriti’13.

What is HPC?

It is the art of developing supercomputers and software to run on
supercomputers. A main area of this discipline is developing parallel
processing algorithms and software: programs that can be divided into
little pieces so that each piece can be executed simultaneously by separate
processors.

Why HPC?

To simulate a bio-molecule of 10000 atoms
Non-bond energy term ~ 10^8 operations
For 1 microsecond simulation ~ 10^9 steps ~ 10^17 operations
On a 1 GFLOPS machine (10^9 operations per second) it takes 10^8 secs
(About 3 years 2 months)
Need to do large no of simulations for even larger molecules

PARAM Yuva – 5 x 10^14 – 3 min 20 sec
Titan – 5.7 seconds

Amdahl's Law

Code = Serial Part + Part which can be parallelized
The potential program speedup is defined by the fraction of
code that can be parallelized

Amdahl's Law

Can you get a speed up of 5 times using quad core processor?

HPC Architecture
HPC architecture typically consist of massive number of computing
nodes (typically 1000s) highly interconnected by a specialized low
latency network fabric which use MPI for data exchange.
Nodes = cores + memory
Computation is divided into tasks distributing these tasks across the
nodes and they need to synchronize and exchange information several
times a second.

Communication Overheads

Latency
Startup time for each message transaction 1 μs

Bandwidth
The rate at which the messages are transmitted across the nodes /
processors 10 Gbits /sec.

You can’t go faster than these limits.

MPI

M P I = Message Passing Interface

It is an industry-wide standard protocol for passing messages between parallel
processors.

MPI is a specification for the developers and users of message passing
libraries. By itself, it is NOT a library - but rather the specification of what
such a library should be.

Small: Require only six library functions to write any parallel code
Large: There are more than 200 functions in MPI-2

MPI

Programming Model

Originally, MPI was designed for distributed memory architectures, which
were becoming increasingly popular at that time.

As architecture trends changed, shared memory SMPs were combined over
networks creating hybrid distributed memory / shared memory systems. MPI
implementors adapted their libraries to handle both types of underlying
memory architectures seamlessly.

It means you can use MPI even on your laptops.

Why MPI ?

Today, MPI runs on virtually any hardware platform:
• Distributed Memory
• Shared Memory
• Hybrid

A MPI program is basically a C, fortran or Python program that uses
the MPI library, SO DON’T BE SCARED.

MPI

Communicator: a set of
processes that have a valid rank
of source or destination fields.
The predefined communicator is
MPI_COMM_WORLD, and we
will be using this communicator
all the time.

MPI_COMM_WORLD is a
default communicator consisting
all processes. Furthermore, a
programmer can also define a
new communicator, which has a
smaller number of processes
than MPI_COMM_WORLD
does.

MPI

Processes: For this module, we
just need to know that
processes belong to the
MPI_COMM_WORLD. If there
are p processes, then each
process is defined by its rank,
which starts from 0 to p - 1. The
master has the rank 0.

For example, in this process
there are 10 processes

MPI

Use SSH client (Putty) to login into any of these
Multi - Processor Compute Servers with processors
varying from 4 to 15.

akash1.cc.iitk.ac.in
akash2.cc.iitk.ac.in
aatish.cc.iitk.ac.in
falaq.cc.iitk.ac.in

On your PC you can download mpich2 or openmpi.

MPI

Include Header File

C:
#include "mpi.h"

Fortran:
include 'mpif.h'

Python:
from mpi4py import MPI
(not available in CC server you can set it up on your lab workstation)

MPI

Smallest MPI library should provide these 6 functions:

MPI_Init - Initialize the MPI execution environment
MPI_Comm_size - Determines the size of the group associated with a
communictor
MPI_Comm_rank - Determines the rank of the calling process in the
communicator
MPI_Send - Performs a basic send
MPI_Recv - Basic receive
MPI_Finalize - Terminates MPI execution environment

MPI

Format of MPI Calls:
C and Python names are case sensitive.

Fortran names are not.
Example:
CALL MPI_XXXXX(parameter,..., ierr) is equivalent to
call mpi_xxxxx(parameter,..., ierr)

Programs must not declare variables or functions with names
beginning with the prefix MPI_ or PMPI_ for C & Fortran.
.
For Python ‘from mpi4py import MPI’ already ensures that you don’t
make the above mistake.

MPI

C:
rc = MPI_Xxxxx(parameter, ... )
Returned as "rc“. MPI_SUCCESS if successful

Fortran:
CALL MPI_XXXXX(parameter,..., ierr)
Returned as "ierr" parameter. MPI_SUCCESS if successful

Python:
rc = MPI.COMM_WORLD.xxxx(parameter,…)

MPI

MPI_Init
Initializes the MPI execution environment. This function must
be called in every MPI program, must be called before any
other MPI functions and must be called only once in an MPI
program.
For C programs, MPI_Init may be used to pass the command
line arguments to all processes, although this is not required
by the standard and is implementation dependent.

MPI_Init (&argc,&argv)
MPI_INIT (ierr)

For python no initialization is required.

MPI

MPI_Comm_size
Returns the total number of MPI processes in the specified
communicator, such as MPI_COMM_WORLD. If the
communicator is MPI_COMM_WORLD, then it represents the
number of MPI tasks available to your application.

MPI_Comm_size (comm,&size)
MPI_COMM_SIZE (comm,size,ierr)
Where comm is MPI_COMM_WORLD

For python
MPI.COMM_WORLD.size is the total number of MPI
processes. MPI.COMM_WORLD.Get_size() also returns the
same.

MPI
MPI_Comm_rank
Returns the rank of the calling MPI process within the specified
communicator. Initially, each process will be assigned a unique integer
rank between 0 and number of tasks - 1 within the communicator
MPI_COMM_WORLD. This rank is often referred to as a task ID. If a
process becomes associated with other communicators, it will have a
unique rank within each of these as well.

MPI_Comm_rank (comm,&rank)
MPI_COMM_RANK (comm,rank,ierr)
Where comm is MPI_COMM_WORLD

For python
MPI.COMM_WORLD.rank is the total number of MPI processes.
MPI.COMM_WORLD.Get_rank() also returns the same.

MPI

MPI Hello World Program

https://gist.github.com/4459911

MPI

In MPI blocking message passing routines are more commonly used.

A blocking MPI call means that the program execution will be
suspended until the message buffer is safe to use. The MPI standards
specify that a blocking SEND or RECV does not return until the send
buffer is safe to reuse (for MPI_SEND), or the receive buffer is ready to
use (for PI_RECV).

The statement after MPI_SEND can safely modify the memory location
of the array a because the return from MPI_SEND indicates either a
successful completion of the SEND process, or that the buffer
containing a has been copied to a safe place. In either case, a's buffer
can be safely reused.
Also, the return of MPI_RECV indicates that the buffer containing the
array b is full and is ready to use, so the code segment after
MPI_RECV can safely use b.

MPI

MPI_Send
Basic blocking send operation. Routine returns only after the application
buffer in the sending task is free for reuse.
Note that this routine may be implemented differently on different
systems. The MPI standard permits the use of a system buffer but does
not require it.

MPI_Send (&buf,count,datatype,dest,tag,comm)
MPI_SEND (buf,count,datatype,dest,tag,comm,ierr)
comm.send(buf,dest,tag)

MPI

MPI_Send
MPI_Send(void* message, int count, MPI_Datatype datatype,
int destination, int tag, MPI_Comm comm)

- message: initial address of the message
- count: number of entries to send
- datatype: type of each entry
- destination: rank of the receiving process
- tag: message tag is a way to identify the type of a message
- comm: communicator (MPI_COMM_WORLD)

MPI

MPI_Recv
Receive a message and block until the requested data is available in the
application buffer in the receiving task.
MPI_Recv (&buf,count,datatype,source,tag,comm,&status)
MPI_RECV (buf,count,datatype,source,tag,comm,status,ierr)

MPI_Recv(void* message, int count, MPI_Datatype datatype, int source,
int tag, MPI_Comm comm, MPI_Status *status)

- source: rank of the sending process
- status: return status

MPI

MPI_Finalize

Terminates MPI execution environment

Note: All processes must call this routine before exit. The number of
processes running after this routine is called is undefined; it is
best not to perform anything more than a return after calling
MPI_Finalize.

MPI

MPI Hello World 2:

This MPI program illustrates the use of MPI_Send and MPI_Recv
functions. Basically, the master sends a message, “Hello, world”, to
the process whose rank is 1, and then after having received the
message, the process prints the message along with its rank.


MPI

Collective communication
Collective communication is a communication that must have all
processes involved in the scope of a communicator. We will be
using MPI_COMM_WORLD as our communicator; therefore, the
collective communication will include all processes.

MPI

MPI_Barrier(comm)

This function creates a barrier synchronization in a
commmunicator(MPI_COMM_WORLD). Each task waits at
MPI_Barrier call until all other tasks in the communicator reach the
same MPI_Barrier call.

MPI

MPI_Bcast(&message, int count, MPI_Datatype datatype,
int root, comm)

This function displays the message to all other processes in
MPI_COMM_WORLD from the process whose rank is root.

MPI

MPI_Reduce(&message,
&receivemessage,
int count,
MPI_Datatype datatype,
MPI_Op op, int root, comm)

This function applies a reduction
operation on all tasks in
MPI_COMM_WORLD and reduces
results from each process into one
value. MPI_Op includes for example,
MPI_MAX, MPI_MIN, MPI_PROD,
and MPI_SUM, etc.

MPI
MPI_Scatter(&message, int count, MPI_Datatype,
&receivemessage, int count, MPI_Datatype, int root, comm)

MPI_Gather(&message, int count, MPI_Datatype,
&receivemessage, int count, MPI_Datatype, int root, comm)

MPI

Pi Code


Thank You

Ankit Mahato
amahato@iitk.ac.in
fb.com/ankitmahato
IIT Kanpur

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High Performance Computing using MPI

High Performance Computing using MPI

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