Programming Clusters using Message-Passing Interface (MPI

)

Dr. Rajkumar Buyya
Cloud Computing and Distributed Systems (CLOUDS) Laboratory

The University of Melbourne Melbourne, Australia www.cloudbus.org

Outline  



Introduction to Message Passing Environments HelloWorld MPI Program Compiling and Running MPI programs 

On interactive clusters And Batch clusters 

  

Elements of Hello World Program MPI Routines Listing Communication in MPI programs Summary

Message-Passing Programming Paradigm 

Each processor in a message-passing program runs a sub-program 
 

written in a conventional sequential language all variables are private communicate via special subroutine calls
M P M P M P Memory Processors/Node

Interconnection Network

char **argv) { if(process is assigned Master role) { /* Assign work and coordinate workers and collect results */ MasterRoutine(/*arguments*/). } else /* it is worker process */ { /* interact with master and other workers. Do the work and send results to the master*/ WorkerRoutine(/*arguments*/).SPMD: A dominant paradigm for writing data parallel applications main(int argc. } } .

Messages   Messages are packets of data moving between subprograms. The message passing system has to be told the following information        Sending processor Source location Data type Data length Receiving processor(s) Destination location Destination size .

Phone line. Fax. Collective. etc Point-to-Point. E-mail.Messages  Access:  Each sub-program needs to be connected to a message passing system Messages need to have addresses to be sent to It is important that the receiving process is capable of dealing with the messages it is sent Post-office. Synchronous (telephone)/Asynchronous (Postal)  Addressing:   Reception:   A message passing system is similar to:   Message Types:  .

0 contains over 115 routines/functions that can be grouped into 8 categories. which is derived from experience or common features/issues addressed by many message-passing libraries.mpi-forum.Message Passing Systems and MPI . often incompatible MPI Forum brought together several Vendors and users of HPC systems from US and Europe ² overcome above limitations. .www.org     Initially each manufacturer developed their own message passing interface Wide range of features.0)  MPI 1. Produced a document defining a standard. It aimed:      to provide source-code portability to allow efficient implementation it provides a high level of functionality support for heterogeneous parallel architectures parallel I/O (in MPI 2. called Message Passing Interface (MPI).

General MPI Program Structure MPI Include File Initialise MPI Environment Do work and perform message communication Terminate MPI Environment .

..h>  MPI Function Format  C: error = MPI_Xxxx(parameter...MPI programs   MPI is a library .)..). MPI_Xxxx(parameter.. .there are NO language changes Header Files  C: #include <mpi.

C #include <mpi.h> /* include other usual header files*/ main(int argc.Example . } . &argv). exit(0). char **argv) { /* initialize MPI */ MPI_Init(&argc. /* main part of program */ /* terminate MPI */ MPI_Finalize().

&rank). } .h> main(int argc.c #include <mpi.MPI helloworld. &argv). printf("Hello World from process %d of %d\n³. MPI_Comm_size(MPI_COMM_WORLD. MPI_Finalize(). rank. & numtasks). MPI_Comm_rank(MPI_COMM_WORLD. numtasks). char **argv) { int numtasks. rank. MPI_Init(&argc.

MPI Programs Compilation and Execution .

mu.cs.oz.au Internal worker nodes:     node1 node2 ....3 (Valhalla) Each of the 13 worker node consists of the following: Pentium 4 2GHz 512 MB memory 40 GB harddisk Gigabit LAN Red Hat Linux release 7.au         Dual Xeon 2GHz 512 MB memory 250 GB integrated storage Gigabit LAN CDROM & Floppy Drives Red Hat Linux release 7.cs.Manjra: GRIDS Lab Linux Cluster  Master Node: manjra. node13  Worker Nodes(node1.oz.3 (Valhalla) Master: manjra.node13)       Manjra Linux cluster ..mu.

How Manjra cluster looks  Front View  Back View .

A snapshot of Manjra cluster .

list helloworld manjra. if they had failed! .mu.au node1 node2 . node6 node13  Run:    The file machines..oz.Compile and Run Commands  Compile:  manjra> mpicc helloworld.cs.list contains nodes list:       No of processes  Some nodes may not work today.c -o helloworld manjra> mpirun -np 3 helloworld [hosts picked from configuration] manjra> mpirun -np 3 -machinefile machines.

list helloworld  Hello World from process 0 of 3  Hello World from process 1 of 3  Hello World from process 2 of 3  A Run by default  manjra> helloworld  Hello World from process 0 of 1 .Sample Run and Output  A Run with 3 Processes:  manjra> mpirun -np 3 -machinefile machines.

list helloworld       Hello World from process 0 of 6 Hello World from process 3 of 6 Hello World from process 1 of 6 Hello World from process 5 of 6 Hello World from process 4 of 6 Hello World from process 2 of 6  Note: Process execution need not be in process number order.Sample Run and Output  A Run with 6 Processes:  manjra> mpirun -np 6 -machinefile machines. .

.list helloworld       Hello World from process 0 of 6 Hello World from process 3 of 6 Hello World from process 1 of 6 Hello World from process 2 of 6 Hello World from process 5 of 6 Hello World from process 4 of 6  Note: Change in process output order. They may run on machines with different load.Sample Run and Output  A Run with 6 Processes:  manjra> mpirun -np 6 -machinefile machines. Hence such difference. For each run. process mapping can be different.

Running Applications using PBS (Portable Batch System) on Manjra cluster .

jobs get submitted to a queue The job is a shell script to execute your program The shell script can contain job management instructions (note that these instructions can also be in the command line) PBS will allocate your job to some other computer.deletes a job from a queue .PBS      PBS is a batch system . ie your script must contain cd's or aboslute references to access files (or globus objects) Useful PBS commands:    qsub . and execute your script.monitors status qdel . log in as you.submits a job qstat .

PBS directives  Some PBS directives to insert at the start of your shell script:       #PBS #PBS #PBS #PBS #PBS #PBS -q <queuename> -e <filename> (stderr location) -o <filename> (stdout location) -eo (combines stderr and stdout) -t <seconds> (maximum time) -l <attribute>=<value> (eg -l nodes=2) .

au> runs a batch system .-------. The batch system is PBS Queue Memory CPU Time Walltime Node Run Que Lm ---------------.mu.-------.-----.-workq -10000:00 10000:00 13 0 0 -defaultq ----0 0 ---.---.called PBS:    You submit a script telling the system how to run your job The script requests the number of nodes in DEDICATED mode.Manjra and PBS  <manjra.--.--0 State ----E R E R  Queue Details [raj@manjra mpi]$ qstat -q       .cs.--.oz.

mpich on majra  Run with qsub <jobscript>  where jobscript is #PBS ²l nodes=2 mpirun <progname> .

.2.5.sh    Give Full path of your working directory for your programs execution.bat   cd mpi /usr/local/mpich/mpich-1./helloworld > [raj@manjra mpi]$ cat hello.PBS Script > [raj@manjra mpi]$ cat hello.2/bin/mpirun -np 5 helloworld-hostname #!/bin/bash cd /home/mpi678-2010/mpi mpirun -np 5 .

mu.mu.manjra.oz.cs.Submitting to a Queue  [raj@manjra mpi]$ qsub hello.manjra.au ID Assigned to your job  [raj@manjra mpi]$ qsub ²V hello.bat  2811.cs.oz.sh  2811.au .

.-------.Q Status     [raj@manjra mpi]$ qstat Job id Name User Time Use S Queue ---------------.bat raj 0 Q workq  2813.manjra hello.---------------.---------------.bat raj 0 E workq .manjra hello.----2807.

if any   Where XXXXX is the ID assigned to your job by PBS .bat.oXXXXX hello.bat.Output ² Result/Error  Output  hello.eXXXXX  Error.

org/public/pbs .doesciencegrid.References  PBS User Guide:  http://www.

More on MPI Program Elements and Error Checking .

Handles     MPI controls its own internal data structures MPI releases ¶handles· to allow programmers to refer to these ´Cµ handles are of distinct typedef¶d types and arrays are indexed from 0 Some arguments can be of any type .in C these are declared as void * .

The C version accepts the arguments to main int MPI_Init(int *argc.Initializing MPI    The first MPI routine called in any MPI program must be MPI_Init.    MPI_Init must be called by every MPI program Making multiple MPI_Init calls is erroneous MPI_INITIALIZED is an exception to first rule . char ***argv).

A communicator contains a group which is a list of processes Each process has it·s rank within the communicator A process can have several communicators . All MPI communication calls require a communicator argument MPI processes can only communicate if they share a communicator.MPI_COMM_WORLD       MPI_INIT defines a communicator called MPI_COMM_WORLD for every process that calls it.

int *size)  Returns the size of the group in comm   . int *rank)  Returns the rank of the process in comm MPI_Comm_size(MPI_Comm comm.Communicators    MPI uses objects called Communicators that defines which collection of processes communicate with each other. Processes can request information from a communicator MPI_Comm_rank(MPI_comm comm. Every process has unique integer identifier assigned by the system when the process initialises. A rand is sometimes called process ID.

Finishing up    An MPI program should call MPI_Finalize when all communications have completed. Once called no other MPI calls can be made Aborting: MPI_Abort(comm)  Attempts to abort all processes listed in comm if comm = MPI_COMM_WORLD the whole program terminates .

Hello World with Error Check .

h> main(int argc. static char mpi_hostname[MPI_MAX_PROCESSOR_NAME]. MPI_Comm_size(MPI_COMM_WORLD. rank. &rank). mpi_hostname).Display Hostname of MPI Process #include <mpi. MPI_Comm_rank(MPI_COMM_WORLD. &argv). &numtasks). MPI_Init(&argc. rank. char **argv) { int numtasks. int resultlen. &resultlen ). MPI_Get_processor_name( mpi_hostname. } . printf("Hello World from process %d of %d running on %s\n". MPI_Finalize(). numtasks.

MPI Routines .

MPI Routines ² C and Fortran         Environment Management Point-to-Point Communication Collective Communication Process Group Management Communicators Derived Type Virtual Topologies Miscellaneous Routines .

Environment Management Routines .

Point-to-Point Communication    A simplest form of message passing One process sends a message to another Several variations on how sending a message can interact with execution of the subprogram .

can test/wait later for completion  Asynchronous Sends    Blocking operations   Non-blocking operations  . fax machines Only know when the message has left e.Point-to-Point variations  Synchronous Sends   provide information about the completion of the message e.g.g. post cards only return from the call when operation has completed return straight away .

Point-to-Point Communication .

Collective Communications    Collective communication routines are higher level routines involving several processes at a time Can be built out of point-to-point communications Barriers  synchronise processes one-to-many communication combine data from several processes to produce a single (usually) result  Broadcast   Reduction operations  .

Collective Communication Routines .

Process Group Management Routines .

Communicators Routines .

Derived Type Routines .

Virtual Topologies Routines .

Miscellaneous Routines .

MPI Communication Routines and Examples .

MPI Messages   A message contains a number of elements of some particular data type MPI data types   Basic Types Derived types   Derived types can be built up from basic types ´Cµ types are different from Fortran types .

MPI Basic Data types .C MPI datat ype MPI_CHAR MPI_SHORT MPI_INT MPI_LONG MPI_UNSIGNED_CHAR MPI_UNSIGNED_SHORT MPI_UNSIGNED MPI_UNSIGNED_LONG MPI_FLOAT MPI_DOUBLE MPI_LONG_DOUBLE MPI_BYTE MPI_PACKED C datat ype signed char signed short int signed int signed long int unsigned char unsigned short int unsigned int unsigned long int float double long double .

buffered. synchronous. and ready  Only one mode for receiving .Point-to-Point Communication      Communication between two processes Source process sends message to destination process Communication takes place within a communicator Destination process is identified by its rank in the communicator MPI provides four communication modes for sending messages  standard.

can lead to non-determinism processes should be eager readers .else network overload  Programs should obey the following rules:     Can be implemented as either a buffered send or synchronous send .Standard Send  Completes once the message has been sent  Note: it may or may not have been received It should not assume the send will complete before the receive begins .they should guarantee to receive all messages sent to them .can lead to deadlock It should not assume the send will complete after the receive begins .

int dest. MPI_Comm comm) buf count datatype dest tag comm ierror the address of the data to be sent the number of elements of datatype buf contains the MPI datatype rank of destination in communicator comm a marker used to distinguish different message types the communicator shared by sender and receiver the fortran return value of the send .Standard Send (cont.) MPI_Send(void *buf. int count. MPI_Datatype datatype. int tag.

status)  Synchronous Blocking Message-Passing    processes synchronise sender process specifies the synchronous mode blocking . source.Standard Blocking Receive   Note: all sends so far have been blocking (but this only makes a difference for synchronous sends) Completes when message received source . tag.returns information about message MPI_Recv(buf. comm. count.rank of source process in communicator comm status .both processes wait until transaction completed . datatype.

For a communication to succeed  

    

Sender must specify a valid destination rank Receiver must specify a valid source rank The communicator must be the same Tags must match Message types must match Receivers buffer must be large enough Receiver can use wildcards 


MPI_ANY_SOURCE MPI_ANY_TAG 

actual source and tag are returned in status parameter

Standard/Blocked Send/Receive

MPI Send/Receive a Character (cont...)
// mpi_com.c #include <mpi.h> #include <stdio.h> int main(int argc, char *argv[]) { int numtasks, rank, dest, source, rc, tag=1; char inmsg, outmsg='X'; MPI_Status Stat; MPI_Init(&argc,&argv); MPI_Comm_size(MPI_COMM_WORLD, &numtasks); MPI_Comm_rank(MPI_COMM_WORLD, &rank); if (rank == 0) { dest = 1; rc = MPI_Send(&outmsg, 1, MPI_CHAR, dest, tag, MPI_COMM_WORLD); printf("Rank0 sent: %c\n", outmsg); source = 1; rc = MPI_Recv(&inmsg, 1, MPI_CHAR, source, tag, MPI_COMM_WORLD, &Stat); }

inmsg). tag. } . MPI_COMM_WORLD. rc = MPI_Recv(&inmsg.MPI Send/Receive a Character else if (rank == 1) { source = 0. source. printf("Rank1 received: %c\n". 1. MPI_CHAR. &Stat). MPI_CHAR. dest = 0. 1. tag. } MPI_Finalize(). dest. rc = MPI_Send(&outmsg. MPI_COMM_WORLD).

Execution Demo   mpicc mpi_com.out Rank0 sent: X Rank0 recv: Y Rank1 received: X .c [raj@manjra mpi]$ mpirun -np 2 a.

Non Blocking Message Passing .

Insert timing calls to measure the time taken for one message. Write a program in which two processes repeatedly pass a message back and forth. . 2.Exercise: Ping Pong 1. 3. Investigate how the time taken to exchange messages varies with the size of the message.

tag=1. outmsg='X'. dest. &Stat). MPI_CHAR. strlen(pingmsg)+1. char *argv[]) { int numtasks. "ping"). Receive Pong */ dest = 1. char buff[100].&argv). dest. Why + 1 ? if (rank == 0) { /* Send Ping. rc.. } . MPI_Comm_size(MPI_COMM_WORLD. char pingmsg[10].c (cont. MPI_Comm_rank(MPI_COMM_WORLD.h> int main(int argc. MPI_CHAR. char pongmsg[10]. rc = MPI_Send(pingmsg. source. "pong"). rc = MPI_Recv(buff. MPI_Init(&argc. &rank). strcpy(pingmsg. &numtasks). char inmsg. tag. strlen(pongmsg)+1. pingmsg. strcpy(pongmsg. printf("Rank0 Sent: %d & Received: %s\n". MPI_COMM_WORLD. tag. buff).) #include <mpi. source. rank. source = 1. MPI_Status Stat.A simple Ping Pong.h> #include <stdio. MPI_COMM_WORLD).

dest. MPI_COMM_WORLD). } MPI_Finalize(). buff. tag. rc = MPI_Send(pongmsg.A simple Ping Pong. MPI_COMM_WORLD. source = 0. pongmsg). MPI_CHAR. } . source. Send Pong */ dest = 0. printf("Rank1 received: %s & Sending: %s\n". MPI_CHAR. strlen(pingmsg)+1. &Stat). strlen(pongmsg)+1. rc = MPI_Recv(buff.c else if (rank == 1) { /* Receive Ping. tag.

Time to perform a task is measured by consulting the time before and after  Time is measured in seconds  .  Returns an elapsed wall clock time in seconds (double precision) on the calling processor.Timers  C: double MPI_Wtime(void).

Upcoming Evaluations  Mid term exam: ´peerµ evaluation    Review your understanding of topics covered so far. Date: April 27 (Monday).  Time: 20 min (exam). 15min (for peer marking)   Microsoft Guest Lecture (May?) Assignment 2:   Implementation of ´parallelµ Matrix multiplication (using MPI) Deadline: April 30 from G1: 10-12. G2: 2-4pm . No official marking ² ´How you are going testµ.

PPT Slides MPI Notes.unimelb.edu.hpc.Acknowledgements: MPI Slides are Derived from   Dirk van der Knijff. High Performance Parallel Programming.com/csc433/MPITut.pdf  Melbourne Advanced Research Computing Center  http://www.au .buyya. Maui HPC Centre:  http://www.

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