Starting MPI
This commit is contained in:
parent
69ca8512da
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7037335bff
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@ -17,6 +17,7 @@
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#+LaTeX_HEADER: \definecolor{darkblue}{rgb}{0.,0.2,0.7}
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#+LaTeX_HEADER: \definecolor{darkred}{rgb}{0.6,0.1,0.1}
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#+LaTeX_HEADER: \definecolor{darkpink}{rgb}{0.7,0.0,0.7}
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#+PROPERTY: header-args :exports code
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#+EXPORT_EXCLUDE_TAGS: noexport
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#+startup: beamer
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@ -645,7 +646,7 @@ user 0m3.359s
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sys 0m3.172s
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#+end_src
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* Inter-process communication
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* Inter-process communication :noexport:
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** Processes /vs/ threads
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@ -862,9 +863,10 @@ if __name__ == "__main__":
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#+ATTR_LATEX: :height 0.6\textheight
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[[./pi_convergence.png]]
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** Computation of $\pi$ with pipes in Python
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** Computation of \pi with pipes in Python
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#+begin_src python :tangle Codes/pi_python.py
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#!/usr/bin/env python
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import os, sys
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from random import random, seed
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from math import sqrt
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@ -885,7 +887,7 @@ def compute_pi():
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return 4.* float(result)/float(NMAX) # Estimate of pi
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#+end_src
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** Computation of $\pi$ with pipes in Python
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** Computation of \pi with pipes in Python
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#+begin_src python :tangle Codes/pi_python.py
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def main():
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@ -911,7 +913,7 @@ def main():
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sys.exit(0)
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#+end_src
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** Computation of $\pi$ with pipes in Python
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** Computation of \pi with pipes in Python
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#+begin_src python :tangle Codes/pi_python.py
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data = []
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@ -926,7 +928,7 @@ def main():
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else:
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variance = 0.
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error = sqrt(variance)/sqrt(N) # Compute error
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print(f"%{average} +/- %{error} %{N}")
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print("%f +/- %f %d"%(average, error, N))
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if N > 2 and error < error_threshold: # Stopping condition
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for i in range(NPROC): # Kill all children
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@ -937,8 +939,372 @@ def main():
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if __name__ == '__main__': main()
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#+end_src
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** Computation of \pi with pipes in Python
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#+begin_src text
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$ python pi_python.py
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3.141974 +/- 0.000000 1
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3.142569 +/- 0.000000 2
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3.142168 +/- 0.000528 3
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3.141938 +/- 0.000439 4
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3.141947 +/- 0.000340 5
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[...]
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3.141625 +/- 0.000107 33
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3.141614 +/- 0.000104 34
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3.141617 +/- 0.000101 35
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3.141606 +/- 0.000099 36
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#+end_src
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** Sockets
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Sockets are analogous to pipes, but they allow both ends of the pipe to be
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on different machines connected by a network interface.
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An Internet socket is characterized by a unique combination of:
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- A transport protocol: TCP, UDP, raw IP, ...
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- A local socket address: Local IP address and port number, for example 192.168.2.2:22
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- A remote socket address: Optional (TCP)
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** Sockets
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#+ATTR_LATEX: :height 0.9\textheight
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[[./socket.png]]
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** Sockets: server code in Python
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#+begin_src python :tangle Codes/socket_server.py
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#!/usr/bin/env python
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import sys, os, socket, datetime
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now = datetime.datetime.now
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def main():
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HOSTNAME = socket.gethostname()
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PORT = 11279
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print(now(), "I am the server : %s:%d"%(HOSTNAME,PORT))
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s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) # Create an INET socket
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s.bind( (HOSTNAME, PORT) ) # Bind the socket to the address and port
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s.listen(5) # Wait for incoming connections
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conn, addr = s.accept() # Accept connection
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print(now(), "Connected by", addr)
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#+end_src
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** Sockets: server code in Python
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#+begin_src python :tangle Codes/socket_server.py
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data = ""
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while True: # Buffered read of the socket
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message = conn.recv(8).decode('utf-8')
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print(now(), "Buffer : "+message)
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data += message
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if len(message) < 8: break
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print(now(), "Received data : ", data)
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print(now(), "Sending thank you...")
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conn.send("Thank you".encode())
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conn.close()
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if __name__ == "__main__":
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main()
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#+end_src
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** Sockets: client code in Python
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#+begin_src python :tangle Codes/socket_client.py
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#!/usr/bin/env python
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import sys, os, socket, datetime
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now = datetime.datetime.now
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def main():
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HOSTNAME = sys.argv[1] # Get host name from command line
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PORT = int(sys.argv[2]) # Get port from command line
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print(now(), "The target server is : %s:%d"%(HOSTNAME,PORT))
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s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) # Create an INET socket
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s.connect( (HOSTNAME, PORT) ) # Connect the socket to the address and port
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# of the server
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message = "Hello, world!!!!!!!"
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print(now(), "Sending : "+message)
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s.send(message.encode()) # Send the data
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data = s.recv(1024) # Read the reply of the server
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s.close()
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print(now(), 'Received: ', data.decode('utf-8'))
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if __name__ == "__main__": main()
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#+end_src
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** Sockets: Execution
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#+begin_src text
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$ python Codes/socket_client.py lpqdh82 11279
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2021-11-20 21:20:32.258632 The target server is : lpqdh82:11279
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2021-11-20 21:20:32.258959 Sending : Hello, world!!!!!!!
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2021-11-20 21:20:32.259042 Connected by ('127.0.0.1', 36798)
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2021-11-20 21:20:32.259068 Buffer : Hello, w
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2021-11-20 21:20:32.259076 Buffer : orld!!!!
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2021-11-20 21:20:32.259083 Buffer : !!!
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2021-11-20 21:20:32.259088 Received data : Hello, world!!!!!!!
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2021-11-20 21:20:32.259093 Sending thank you...
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2021-11-20 21:20:32.259133 Received: Thank you
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#+end_src
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Note that the client and server can be written in different languages.
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** Server for \pi with sockets in Python
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#+begin_src python :tangle Codes/pi_server_python.py
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#!/usr/bin/env python
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import sys, os, socket
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from math import sqrt
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HOSTNAME = "localhost"
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PORT = 1666
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error_threshold = 1.e-4 # Stopping criterion
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def main():
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data = []
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s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) # Create an INET socket
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s.bind( (HOSTNAME, PORT) ) # Bind the socket to the address and port
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while True:
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s.listen(5) # Wait for incoming connections
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conn, addr = s.accept() # Accept connection
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X = ""
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while True: # Buffered read of the socket
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message = conn.recv(128)
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X += message.decode('utf-8')
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if len(message) < 128: break
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data.append( float(X) )
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N = len(data)
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#+end_src
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** Server for \pi with sockets in Python
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#+begin_src python :tangle Codes/pi_server_python.py
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average = sum(data)/N # Compute average
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if N > 2: # Compute variance
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l = [ (x-average)*(x-average) for x in data ]
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variance = sum(l)/(N-1.)
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else:
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variance = 0.
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error = sqrt(variance)/sqrt(N) # Compute error
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print('%f +/- %f'%(average,error))
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# Stopping condition
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if N > 2 and error < error_threshold:
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conn.send("STOP".encode())
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break
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else:
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conn.send("OK".encode())
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conn.close()
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if __name__ == "__main__":
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main()
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#+end_src
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** Client for \pi with sockets in Python
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#+begin_src python :tangle Codes/pi_client_python.py
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#!/usr/bin/env python
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import os, sys, socket
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from random import random, seed
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from math import sqrt
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HOSTNAME = "localhost"
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PORT = 1666
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NMAX = 10000000 # Nb of MC steps/process
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error_threshold = 1.0e-4 # Stopping criterion
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NPROC=4 # Use 4 processes
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def compute_pi():
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"""Local Monte Carlo calculation of pi"""
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seed(None) # Initialize random number generator
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result = 0.
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for i in range(NMAX): # Loop NMAX times
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x,y = random(), random() # Draw 2 random numbers x and y
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if x*x + y*y <= 1.: # Check if (x,y) is in the circle
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result += 1
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return 4.* float(result)/float(NMAX) # Estimate of pi
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#+end_src
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** Client for \pi with sockets in Python
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#+begin_src python :tangle Codes/pi_client_python.py
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def main():
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while True:
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X = compute_pi()
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s = socket.socket(socket.AF_INET, socket.SOCK_STREAM) # Create an INET socket
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try: # Connect the socket to the address and port of the server
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s.connect( (HOSTNAME, PORT) )
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except socket.error:
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break
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message = str(X)
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s.send(message.encode()) # Send the data
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reply = s.recv(128).decode('utf-8') # Read the reply of the server
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s.close()
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if reply == "STOP": break
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if __name__ == '__main__':
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main()
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#+end_src
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** Execution of \pi with sockets in Python
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#+begin_src text
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$ python pi_server_python.py &
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> for i in {1..8} ; do
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> python pi_client_python.py &
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> done ; wait
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3.142136 +/- 0.000000
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3.141783 +/- 0.000000
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3.141992 +/- 0.000291
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3.141804 +/- 0.000279
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[...]
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3.141687 +/- 0.000104
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3.141666 +/- 0.000102
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3.141651 +/- 0.000098
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#+end_src
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* Message Passing Interface (MPI)
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** Message Passing Interface
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- Application Programming Interface for inter-process communication
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- Takes advantage of HPC hardware:
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- TCP/IP: 50 $\mu \text{s}$ latency
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- Remote Direct Memory Access (RDMA): <2 $\mu \text{s}$
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(low-latency network)
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- Portable
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- Each vendor has its own implementation adapted to the hardware
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- Standard in HPC
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- Initially designed for fixed number of processes:
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- No problem for the discovery of peers
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- Fast collective communications
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- Single Program Multiple Data (SPMD) paradigm
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** Communicators
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- Group of processes that can communicate together
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- Each process has an ID in the communicator: no need for IP
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adresses and port numbers
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- ~MPI_COMM_WORLD~: Global communicator, default
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- ~size~: number of processes in the communicator
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- ~rank~: ID of the process in the communicator
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** Point-to-point communication
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*** Python
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- Send:
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~comm.send(data, dest, tag)~
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- Receive:
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~comm.recv(source, tag)~
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*** Fortran
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- Send:
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~MPI_SEND(buffer, count, datatype, destination, tag, communicator, ierror)~
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- Receive:
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~MPI_RECV(buffer, count, datatype, source, tag, communicator,
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status, ierror)~
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** Point-to-point communication (Python)
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#+begin_src python :tangle Codes/mpi_rank.py
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from mpi4py import MPI
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def main():
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comm = MPI.COMM_WORLD
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rank = comm.Get_rank()
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size = comm.Get_size()
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if rank == 0:
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data = 42
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print("Before: Rank: %d Size: %d Data: %d"%(rank, size, data))
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comm.send(data, dest=1, tag=11)
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print("After : Rank: %d Size: %d Data: %d"%(rank, size, data))
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elif rank == 1:
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data = 0
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print("Before: Rank: %d Size: %d Data: %d"%(rank, size, data))
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data = comm.recv(source=0, tag=11)
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print("After : Rank: %d Size: %d Data: %d"%(rank, size, data))
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if __name__ == "__main__": main()
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#+end_src
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** Point-to-point communication (Python)
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#+begin_src text
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$ mpiexec -n 4 python mpi_rank.py
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Before: Rank: 0 Size: 4 Data: 42
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Before: Rank: 1 Size: 4 Data: 0
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After : Rank: 0 Size: 4 Data: 42
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After : Rank: 1 Size: 4 Data: 42
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#+end_src
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In Fortran, compile using =mpif90= and execute using =mpiexec= (or =mpirun=).
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** Point-to-point communication (Fortran)
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#+begin_src fortran :tangle Codes/mpi_rank.f90
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program test_rank
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use mpi
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implicit none
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integer :: rank, size, data, ierr, status(mpi_status_size)
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call MPI_INIT(ierr) ! Initialize library (required)
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if (ierr /= MPI_SUCCESS) then
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call MPI_ABORT(MPI_COMM_WORLD, 1, ierr)
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end if
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call MPI_COMM_SIZE(MPI_COMM_WORLD, size, ierr)
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if (ierr /= MPI_SUCCESS) then
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call MPI_ABORT(MPI_COMM_WORLD, 2, ierr)
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end if
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call MPI_COMM_RANK(MPI_COMM_WORLD, rank, ierr)
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if (ierr /= MPI_SUCCESS) then
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call MPI_ABORT(MPI_COMM_WORLD, 3, ierr)
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end if
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#+end_src
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** Point-to-point communication (Fortran)
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#+begin_src fortran :tangle Codes/mpi_rank.f90
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if (rank == 0) then
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data = 42
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print *, "Before: Rank:", rank, "Size:", size, "Data: ", data
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call MPI_SEND(data, 1, MPI_INTEGER, 1, 11, MPI_COMM_WORLD, ierr)
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print *, "After : Rank:", rank, "Size:", size, "Data: ", data
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else if (rank == 1) then
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data = 0
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print *, "Before: Rank:", rank, "Size:", size, "Data: ", data
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call MPI_RECV(data, 1, MPI_INTEGER, 0, 11, MPI_COMM_WORLD, &
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status, ierr)
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print *, "After : Rank:", rank, "Size:", size, "Data: ", data
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end if
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call MPI_FINALIZE(ierr) ! De-initialize library (required)
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end program
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#+end_src
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** Collective communications
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*** One-to-all
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- Broadcast: send same data to all
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- Scatter: distribute an array
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*** All-to-one
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- Reduction: Sum/product/... of data coming from all ranks
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- Gather: collect a distributed array
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*** All-to-all
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- Reduction and broadcast
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** Deadlocks
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* OpenMP
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* Exercises
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@ -1246,3 +1612,4 @@ digraph G {
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#+RESULTS:
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: /home/scemama/MEGA/TEX/Cours/TCCM/TCCM2022/Parallelism/parallelism_scemama.pdf
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