並列プログラミング 1

Parallel Programming in MPI
part 1
情報ネットワーク特論
南里豪志
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1
Preparation:
Request for your account of the server
• もし、公開鍵暗号方式の鍵を作っていなければ、作成する
If you haven't created a pair of keys of public key cryptosystem,
create them.
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• メールに「公開鍵」を添付し、本文に学籍番号と名前を書いて以下
に送付
Send a mail to the following address with your public key attached
and your student ID and name are written in the body of it.
• [email protected]
• Your account information will be sent later.
2
「並列プログラミング実習」の目的
Purpose of “parallel programming tutorial”
• 「通信」 = 複数のプロセス間でのデータの送受信
“Communication”
= Data transfer among multiple processes.
• 複数のプロセスが並行してそれぞれのプログラムを実行
Each of the processes executes its own program
concurrently.
• これが並列処理
This is “parallel processing”.
• 並列処理には「並列プログラム」が必要
“Parallel program” is required for parallel processing
Learn how to write “parallel programs”.
3
どうやって、プログラムに通信を記述するか？
How to Describe Communications in a Program?
• TCP, UDP ?
• Good:
- 多くのネットワークに実装されており，可搬性が高い．
Portable: Available on many networks.
• Bad:
- 接続やデータ転送の手続きが複雑
Protocols for connections and data-transfer are complicated.
記述可能だが，プロトコル関連の記述が必要。
Possible. But require additional descriptions for protocols.
4
MPI (Message Passing Interface)
• 並列計算向けに設計された通信関数群
A set of communication functions designed for parallel
processing
• C, C++, Fortranのプログラムから呼び出し
Can be called from C/C++/Fortran programs.
• "Message Passing" = Send + Receive
• 実際には，Send, Receive 以外にも多数の関数を利用可能．
Actually, more functions other than Send and Receive are available.
• ともかく、プログラム例を見てみましょう
Let's see a sample program, first.
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#include <stdio.h>
#include "mpi.h"
int main(int argc, char *argv[])
{
int myid, procs, ierr, i;
double myval, val;
MPI_Status status;
FILE *fp;
char s[64];
Setup MPI environment
MPI_Init(&argc, &argv);
Get own ID (= rank) of the process
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
Get total number of processes
MPI_Comm_size(MPI_COMM_WORLD, &procs);
If my ID is 0
if (myid == 0) {
fp = fopen("test.dat", "r");
input data for this process and keep it in myval
fscanf(fp, "%lf", &myval);
i = １～procs－１
for (i = 1; i < procs; i++){
input data and keep it in val
fscanf(fp, "%lf", &val);
MPI_Send(&val, 1, MPI_DOUBLE, i, 0, MPI_COMM_WORLD);
}
use MPI_Send to send value in val to process i
fclose(fp);
} else
MPI_Recv(&myval, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD, &status);
processes with ID other than 0
use MPI_Recv to receive data from process 0 and keep it in myval
printf("PROCS: %d, MYID: %d, MYVAL: %e\n", procs, myid, myval);
MPI_Finalize();
print-out its own myval
end of parallel computing
return 0;
}
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プログラム例の実行の流れ
Flow of the sample program.
• 複数の"プロセス"が，自分の番号（ランク）に応じて実行
Multiple "Processes" execute the program according to their number (= rank).
rank 0
read data
from a file
read data
from a file
myval
send val
to rank 2
print myval
rank 2
receive data
from rank 0
receive data
from rank 0
val
wait for the arrival of
the data
send val
to rank 1
read data
from a file
rank 1
myval
val
print myval
wait for the arrival of
the data
myval
print myval
7
実行例
Sample of the Result of Execution
• 各プロセスがそれぞれ勝手に表示するので、表示の順番は毎回変
わる可能性がある。
The order of the output can be different,
since each process proceeds execution independently.
PROCS:
PROCS:
PROCS:
PROCS:
4
4
4
4
MYID:
MYID:
MYID:
MYID:
1
2
0
3
MYVAL:
MYVAL:
MYVAL:
MYVAL:
20.0000000000000000
30.0000000000000000
10.0000000000000000
40.0000000000000000
rank
rank
rank
rank
1
2
0
3
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MPIインタフェースの特徴
Characteristics of MPI Interface
• MPI プログラムは，普通の C言語プログラム
MPI programs are ordinal programs in C-language
• Not a new language
• 各プロセスが同じプログラムを実行する
Every process execute the same program
• ランク（＝プロセス番号）を使って，プロセス毎に違う仕事を実行
Each process executes its own work according to its rank(=process number)
• 他のプロセスの変数を直接見ることはできない。
A process cannot read or write variables on other process directly
Rank 0
Read file
Read file
myval
Rank 2
val
Receive
Send
Read file
Rank 1
val
Receive
myval
Print myval
Send
Print myval
myval
Print myval
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9
TCP, UDP vs MPI
• MPI:並列計算に特化したシンプルな通信インタフェースSimple
interface dedicated for parallel computing
• SPMD(Single Program Multiple Data-stream) model
• 全プロセスが同じプログラムを実行
All processes execute the same program
• TCP, UDP: 各種サーバ等，様々な用途を想定した汎用的な通信イ
ンタフェース
Generic interface for various communications,
such as internet servers
• Server/Client model
• 各プロセスが自分のプログラムを実行
Each process executes its own program.
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TCP Client
sock = socket(PF_INET, SOCK_STREAM, IPPROTO_TCP);
memset(&echoServAddr, 0, sizeof(echoServAddr));
echoServAddr.sin_family = AF_INET;
echoServAddr.sin_addr.s_addr = inet_addr(servIP);
echoServAddr.sin_port = htons(echoServPort);
connect(sock, (struct sockaddr *) &echoServAddr,
sizeof(echoServAddr));
echoStringLen = strlen(echoString);
send(sock, echoString, echoStringLen, 0);
initialize
int main(int argc, char *argv[])
{
int myid, procs, ierr, i;
double myval, val;
MPI_Status status;
FILE *fp;
char s[64];
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
MPI_Comm_size(MPI_COMM_WORLD, &procs);
if (myid == 0) {
fp = fopen("test.dat", "r");
fscanf(fp, "%lf", &myval);
for (i = 1; i < procs; i++){
fscanf(fp, "%lf", &val);
MPI_Send(&val, 1, MPI_DOUBLE, i, 0, MPI_COMM_WORLD);
}
fclose(fp);
} else
MPI_Recv(&myval, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD, &status);
totalBytesRcvd = 0;
printf("Received: ");
while (totalBytesRcvd < echoStringLen){
bytesRcvd = recv(sock, echoBuffer, RCVBUFSIZE - 1, 0);
totalBytesRcvd += bytesRcvd;
echoBuffer[bytesRcvd] = '\0' ;
printf(echoBuffer);
}
printf("\n");
close(sock);
initialize
TCP Server
servSock = socket(PF_INET, SOCK_STREAM, IPPROTO_TCP);
memset(&echoServAddr, 0, sizeof(echoServAddr));
echoServAddr.sin_family = AF_INET;
echoServAddr.sin_addr.s_addr = htonl(INADDR_ANY);
echoServAddr.sin_port = htons(echoServPort);
bind(servSock, (struct sockaddr *) &echoServAddr,
sizeof(echoServAddr));
listen(servSock, MAXPENDING);
for (;;){
clntLen = sizeof(echoClntAddr);
clntSock = accept(servSock,(struct sockaddr *)&echoClntAddr,
&clntLen);
recvMsgSize = recv(clntSock, echoBuffer, RCVBUFSIZE, 0);
while (recvMsgSize > 0){
send(clntSock, echoBuffer, recvMsgSize, 0);
recvMsgSize = recv(clntSock, echoBuffer, RCVBUFSIZE, 0);
}
close(clntSock);
}
MPI
#include <stdio.h>
#include "mpi.h"
printf("PROCS: %d, MYID: %d, MYVAL: %e\n", procs, myid, myval);
MPI_Finalize();
return 0;
}
initialize
11
MPIの位置づけ
Layer of MPI
• ネットワークの違いを、MPIが隠ぺい
Hide the differences of networks
Applications
MPI
Sockets
TCP
…
XTI
UDP
IP
Ethernet driver,
Ethernet card
…
…
High-Speed
Interconnect
(InfiniBand, etc.)
12
MPIプログラムのコンパイル
How to compile MPI programs
• Compile command:
mpicc
Example)
mpicc -O3 test.c -o test
optimization option
O is not 0
source file
to compile
executable file
to create
13
MPIプログラムの実行
How to execute MPI programs
• Prepare a script file
Sample:
#!/bin/sh
#PBS -l nodes=2,walltime=00:01:00
#PBS -j oe
#PBS -q p4
Number of Nodes (maximum: 4)
Maximum Execution Time
Store standard output and
error in the same file.
Name of Job Queue
Commands to be Executed
cd to the directory from where
this job is submitted
/usr/local/bin/mpiexec -f $PBS_NODEFILE -np 8 ./test-mpi
cd $PBS_O_WORKDIR
• Submit the script file
qsub test.sh
• Other commands
Run MPI program with
specified number (ex: 8) of
processes
• qstat (= check status), qdel job_number (= cancel job)
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Ex 0) MPIプログラムの実行
Execution of an MPI program
• まず、133.5.150.53 にログイン
First of all, login to 133.5.150.53
• Windows:
Use Putty
• specify your private key
• MacOS X:
Use ssh command from terminal
• specify your private key
Ex 0) MPIプログラムの実行
Execution of an MPI program
• ログイン後、以下を実行しなさい。
After login, try the following commands.
$ cp /tmp/test-mpi.c .
$ cp /tmp/test.dat .
$ cp /tmp/test.sh .
$ cat test-mpi.c
$ cat test.dat
$ mpicc test-mpi.c –o test-mpi
$ qsub test.sh
wait for a while
$ ls
(check the name of the result file (test.sh.o????))
$ less test.sh.o????
• 時間に余裕があったら，プロセス数を変えたり，
プログラムを書き換えたりしてみる．
Try changing the number of processes,
or modifying the source program.
MPIライブラリ
MPI Library
• MPI関数の実体は，MPIライブラリに格納されている
The bodies of MPI functions are in "MPI Library".
• mpicc が自動的に MPIライブラリをプログラムに結合する
mpicc links the library to the program
mpicc
main()
{
MPI_Init(...);
...
MPI_Comm_rank(...);
...
MPI_Send(...);
...
}
source program
compile
link
Executable
file
MPI_Init
MPI_Comm_rank
...
MPI Library
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MPIプログラムの基本構造
Basic Structure of MPI Programs
#include <stdio.h>
#include "mpi.h"
Crucial lines
header file
"mpi.h"
int main(int argc, char *argv[])
{
...
MPI_Init(&argc, &argv);
Function for start-up
...
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
MPI_Comm_size(MPI_COMM_WORLD, &procs);
...
MPI_Send(&val, 1, MPI_DOUBLE, i, 0, MPI_COMM_WORLD);
...
MPI_Recv(&myval, 1, MPI_DOUBLE, 0, 0, MPI_COMM_WORLD, &status);
You can call
MPI functions
in this area
...
MPI_Finalize();
Functions for finish
return 0;
}
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今日の MPI関数
MPI Functions Today
• MPI_Init
• Initialization
• MPI_Finalize
• Finalization
• MPI_Comm_size
• Get number of processes
• MPI_Comm_rank
• Get rank (= Process number) of this process
• MPI_Send & MPI_Recv
• Message Passing
• MPI_Bcast & MPI_Gather
• Collective Communication ( = Group Communication )
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MPI_Init
Usage:
int MPI_Init(int *argc, char **argv);
• MPIの並列処理開始
Start parallel execution of in MPI
• プロセスの起動やプロセス間通信路の確立等。
Start processes and establish connections
among them.
#include <stdio.h>
• 他のMPI関数を呼ぶ前に、
#include "mpi.h"
int main(int argc, char *argv[])
必ずこの関数を呼ぶ。
{
Most be called once before calling
int myid, procs, ierr;
otherMPI functions
double myval, val;
• 引数：
Parameter:
Example
MPI_Status status;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
MPI_Comm_size(MPI_COMM_WORLD, &procs);
...
• main関数の2つの引数へのポインタを渡す。
Specify pointers of both of the arguments of 'main' function.
• 各プロセス起動時に実行ファイル名やオプションを共有
するために参照。
Each process most share the name of the executable file,
and the options given to the mpirun command.
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20
MPI_Finalize
Usage:
int MPI_Finalize();
• 並列処理の終了
Finishes paralles execution
• このルーチン実行後はMPIルーチンを
呼び出せない
MPI functions cannot be called
after this function.
• プログラム終了前に全プロセスで必ずこのルーチンを実行させる。
Every process needs to call this function before exitting the program.
Example
main()
{
...
MPI_Finalize();
}
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21
MPI_Comm_rank
Usage:
int MPI_Comm_rank(MPI_Comm comm, int *rank);
• そのプロセスのランクを取得する
Get the rank(= process number) of the process
• 2番目の引数に格納
Returned in the second argument
Example
...
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
...
• 最初の引数 = “コミュニケータ”
1st argument = "communicator"
• プロセスのグループを表す識別子
An identifier for the group of processes
• 通常は，MPI_COMM_WORLD を指定
In most cases, just specify MPI_COMM_WORLD, here.
• MPI_COMM_WORLD: 実行に参加する全プロセスによるグループ
a group that consists all of the processes in this execution
• プロセスを複数のグループに分けて、それぞれ別の仕事をさせることも可能
Processes can be devided into multiple groups and attached different jobs.
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22
MPI_Comm_size
• プロセス数を取得する
Get the number of processes
• 2番目の引数に格納される
Usage:
int MPI_Comm_size(MPI_Comm comm, int *size);
Example
...
MPI_Comm_size(MPI_COMM_WORLD, &procs);
...
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23
一対一通信
Message Passing
• 送信プロセスと受信プロセスの間で行われる通信
Communication between "sender" and "receiver"
• 送信関数と受信関数を，"適切"に呼び出す．
Functions of Sending and Receiving most be called in a correct manner.
• "From" rank and "To" rank are correct
• Specified size of the data to be transferred is the same on both side
• Same "Tag" is specified on both side
Rank 0
Send
To: Rank 1
Size: 10 Integer data
Tag: 100
Rank 1
Receive
From: Rank 0
Size: 10 Integer data
Tag: 100
Wait for the
message
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MPI_Send
Usage:
int MPI_Send(void *b, int c, MPI_Datatype d,
int dest, int t, MPI_Comm comm);
• 送信内容
Information of the message to send
Example
• start address of the data 開始アドレス,
...
MPI_Send(&val, 1, MPI_DOUBLE,
number of elements 要素数,
MPI_COMM_WORLD);
data type データ型,
...
rank of the destination 送信先,
tag,
communicator (= MPI_COMM_WORLD, in most cases)
• data types:
Integer
MPI_INT
Real(Single)
MPI_FLOAT
Real(Double)
MPI_DOUBLE
Character
MPI_CHAR
i, 0,
• tag：メッセージに付ける番号（整数）
The number attached to each message
• 不特定のプロセスから届く通信を処理するタイプのプログラムで使用
Used in a kind of programs that handles anonymous messages.
• 通常は、0 を指定しておいて良い. Usually, you can specify 0.
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25
Example of MPI_Send
• 整数変数 d の値を送信（整数1個）
Send the value of an integer variable 'd'
MPI_Send(&d, 1, MPI_INT, 1, 0, MPI_COMM_WORLD);
• 実数配列 mat の最初の要素から100番目の要素までを送信
Send first 100 elements of array 'mat' (with MPI_DOUBLE type)
MPI_Send(mat, 100, MPI_DOUBLE, 1, 0, MPI_COMM_WORLD);
• 整数配列 data の10番目の要素から50個を送信
Send elements of an integer array 'data' from 10th to 59th element
MPI_Send(&(data[10]), 50, MPI_INT, 1, 0, MPI_COMM_WORLD);
26
MPI_Recv
Usage:
int MPI_Recv(void *b, int c, MPI_Datatype d, int src,
int t, MPI_Comm comm, MPI_Status *st);
• Information of the message to receive
• start address for storing data 受信データ格納用の開始アドレス,
Example
number of elements 要素数,
...
data type データ型,
MPI_Recv(&myval, 1, MPI_DOUBLE, 0, 0,
rank of the source 送信元,
MPI_COMM_WORLD &status);
...
tag (= 0, in most cases),
communicator (= MPI_COMM_WORLD, in most cases),
status
• status: メッセージの情報を格納する整数配列
An integer array for storing the information of arrived message
• 送信元ランクやタグの値を参照可能（通常は、あまり使わない）
Consists the information about the source rank and the tag.
( Not be used in most case )
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27
集団通信
Collective Communications
• グループ内の全プロセスで行う通信
Communications among all of the processes in the group
• Examples)
Rank 0
Rank 1
Rank 2
• MPI_Bcast
• copy a data to other
processes
• MPI_Gather
• Gather data from
other processes
to an array
• MPI_Reduce
• Apply a 'Reduction'
operation to the
distributed data
to produce one
array
3 1 8 2
3 1 8 2
Rank 0
3 1 8 2
Rank 1
7
5
Rank 2
9
7 5 9
Rank 0
Rank 1
1 2 3
12
15
4 5 6
Rank 2
7 8 9
18
28
MPI_Bcast
Usage:
int MPI_Bcast(void *b, int c, MPI_Datatype d,
int root, MPI_Comm comm);
• あるプロセスのデータを全プロセスにコピー
copy a data on a process to all of the processes
• Parameters:
• start address, number of elements, data type,
root rank, communicator
• root rank: コピー元のデータを所有するプロセスのランク
rank of the process that has the original data
• Example:
MPI_Bcast(a, 3, MPI_DOUBLE, 0, MPI_COMM_WORLD);
Rank 0
a
Rank 1
a
Rank 2
a
Rank 3
a
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29
MPI_Gather
Usage:
int MPI_Gather(void *sb, int sc MPI_Datatype st, void *rb, int rc,
MPI_Datatype rt, int root, MPI_Comm comm);
• 全プロセスからデータを集めて一つの配列を構成
Gather data from other processes to construct an array
• Parameters:
• send data: start address, number of elements, data type,
receive data: start address, number of elements, data type,
(means only on the root rank)
root rank, communicator
• root rank: 結果の配列を格納するプロセスのランク
rank of the process that stores the result array
• Example:
MPI_Gather(a, 3, MPI_DOUBLE, b, 3, MPI_DOUBLE, 0, MPI_COMM_WORLD);
Rank 0
a
Rank 1
a
Rank 2
a
Rank 3
a
b
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30
集団通信の利用に当たって
Usage of Collective Communications
• 同じ関数を全プロセスが実行するよう、記述する。
Every process must call the same function
• 例えば MPI_Bcastは，root rankだけでなく全プロセスで実行
For example, MPI_Bcast must be called not only by the root rank but also
all of the other ranks
• 送信データと受信データの場所を別々に指定するタイプの集団通信で
は、送信データの範囲と受信データの範囲が重ならないように指定す
る。
On functions that require information of both send and receive, the
specified ranges of the addresses for sending and receiving cannot
be overlapped.
• MPI_Gather, MPI_Allgather, MPI_Gatherv, MPI_Allgatherv, MPI_Recude,
MPI_Allreduce, MPI_Alltoall, MPI_Alltoallv, etc.
31
まとめ
Summary
• MPIでは、一つのプログラムを複数のプロセスが実行する
On MPI, multiple processes run the same program
• 各プロセスには、そのランク（番号）に応じて仕事を割り当てる
Jobs are attached according to the rank(the number) of each process
• 各プロセスはそれぞれ自分だけの記憶空間で動作する
Each process runs on its own memory space
• 他のプロセスが持っているデータを参照するには、通信する
Accesses to the data on other processes can be made only by explicit
communication among processes
• MPI functions
• MPI_Init, MPI_Finalize, MPI_Comm_rank
• MPI_Send, MPI_Recv
• MPI_Bcast, MPI_Gather
32
References
• MPI Forum
http://www.mpi-forum.org/
• specification of "MPI standard"
• MPI仕様（日本語訳）
http://phase.hpcc.jp/phase/mpi-j/ml/
• 理化学研究所の講習会資料
http://accc.riken.jp/HPC/training/mpi/mpi_all_2007-02-07.pdf
33
33
Ex 1) 乱数を表示するプログラム
A program that displays random numbers
• 「各プロセスがそれぞれ自分のランクと整数乱数を一つ表示するプログ
ラム」を作成しなさい。
Make a program in which each process displays its own rank with one
integer random number
• Sample:
#include <stdio.h>
#include <stdlib.h>
#include <sys/time.h>
int main(int argc, char *argv[])
{
int r;
struct timeval tv;
gettimeofday(&tv, NULL);
srand(tv.tv_usec);
r = rand();
printf("%d¥n", r);
}
Ex 1) (cont.)
• Example of the result of execution
1:
0:
3:
2:
4:
5:
6:
7:
520391
947896500
1797525940
565917780
1618651506
274032293
1248787350
828046128
Ex 1) Sample of the answer
#include
#include
#include
#include
<stdio.h>
<stdlib.h>
<sys/time.h>
"mpi.h"
int main(int argc, char *argv[])
{
int r, myid, procs;
struct timeval tv;
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &myid);
MPI_Comm_size(MPI_COMM_WORLD, &procs);
gettimeofday(&tv, NULL);
srand(tv.tv_usec);
r = rand();
printf("%d: %d¥n", myid, r);
MPI_Finalize();
}
表示されるデータの順番がランクと一致しない
The data is not printed out in the order of ranks.
課題：順番をそろえて表示する
Report: Display in order
• Ex 1) で作成したプログラムについて、以下の条件を満たすように修正
しなさい。
「ランク０からランクの順に、それぞれのプロセスで生成した乱数を表
示する。」
Modify the program in Ex1), so that:
Messages are printed out in the order of the rank
of each process
• Example of the result of the execution
0:
1:
2:
3:
4:
5:
6:
7:
1524394631
999094501
941763604
526956378
152374643
1138154117
1926814754
156004811
来週の講義で、2～3名の学生を指名し、
自分の回答を説明してもらいます。
2~3 students will be designated to
show and explain their answer at the next class.
Hint
• 少なくとも 2つの方法が考えられる
At least, two methods are possible.
• Method 1) (Easy)
• Gather the data to rank 0, first.
• Then, let rank 0 to print data in order.
• Method 2) (Little hard)
• Before rank i prints its data, receive a message from rank i-1 (i > 0)
• After rank i prints its data, send a message to rank i+1 (i<P-1)
• P is the total number of processes.
ともかく、講義資料のプログラム例を実行し、各行の意味を理解しましょう。
First of all, try sample programs in this material and understand
the meanings, line by line.
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