An Introduction to Parallel Programming with MPI

1
An Introduction to Parallel Programming with MPI

• March 22, 24, 29, 31
• 2005
• David Adams
• daadams3_at_vt.edu
• http//research.cs.vt.edu/lasca/schedule

2
Outline

• Disclaimers
• Overview of basic parallel programming on a
  cluster with the goals of MPI
• Batch system interaction
• Startup procedures
• Quick review
• Blocking message passing
• Non-blocking message passing
• Lab day
• Collective communications

3
Review

• Functions we have covered in detail
• MPI_INIT MPI_FINALIZE
• MPI_COMM_SIZE MPI_COMM_RANK
• MPI_SEND MPI_RECV
• Useful constants
• MPI_COMM_WORLD MPI_ANY_SOURCE
• MPI_ANY_TAG MPI_SUCCESS

4
Motivating Example for Deadlock
SEND RECV RECV SEND RECV SEND
5
Motivating Example for Deadlock
Timestep 1
6
Motivating Example for Deadlock
Timestep 2
7
Motivating Example for Deadlock
Timestep 3
8
Motivating Example for Deadlock
Timestep 4
9
Motivating Example for Deadlock
Timestep 5
10
Motivating Example for Deadlock
Timestep 6
11
Motivating Example for Deadlock
Timestep 7
12
Motivating Example for Deadlock
Timestep 8
13
Motivating Example for Deadlock
Timestep 9
14
Motivating Example for Deadlock
Timestep 10!
15
Solution

• MPI_SENDRECV(sendbuf, sendcount, sendtype, dest,
  sendtag, recvbuf, recvcount, recvtype, source,
  recvtag, comm, status, ierror)
• The semantics of a send-receive operation is what
  would be obtained if the caller forked two
  concurrent threads, one to execute the send, and
  one to execute the receive, followed by a join of
  these two threads.

16
Nonblocking Message Passing

• Allows for the overlap of communication and
  computation.
• Completion of a message is broken into four steps
  instead of two.
• post-send
• complete-send
• post-receive
• complete-receive

17
Posting Operations

• MPI_ISEND (BUF, COUNT, DATATYPE, DEST, TAG, COMM,
  REQUEST, IERROR)
• IN lttypegt BUF()
• IN INTEGER, COUNT, DATATYPE, DEST, TAG, COMM,
• OUT IERROR, REQUEST
• MPI_IRECV (BUF, COUNT, DATATYPE, SOURCE, TAG,
  COMM, REQUEST, IERROR)
• IN lttypegt BUF()
• IN INTEGER, COUNT, DATATYPE, SOURCE, TAG, COMM,
• OUT IERROR, REQUEST

18
Request Objects

• All nonblocking communications use request
  objects to identify communication operations and
  link the posting operation with the completion
  operation.
• Conceptually, they can be thought of as a pointer
  to a specific message instance floating around in
  MPI space.
• Just as in pointers, request handles must be
  treated with care or you can create request
  handle leaks (like a memory leak) and completely
  lose access to the status of a message.

19
Request Objects

• The value MPI_REQUEST_NULL is used to indicate an
  invalid request handle. Operations that
  deallocate request objects set the request handle
  to this value.
• Posting operations allocate memory for request
  objects and completion operations deallocate that
  memory and clean up the space.

20
Completion Operations

• MPI_WAIT(REQUEST, STATUS, IERROR)
• INOUT INTEGER REQUEST
• OUT STATUS, IERROR
• A call to MPI_WAIT returns when the operation
  identified by REQUEST is complete.
• MPI_WAIT is the blocking version of completion
  operations where the program has determined it
  cant do any more useful work without completing
  the current message. In this case, it chooses to
  block until the corresponding send or receive
  completes.
• In iterative parallel code, it is often the case
  that an MPI_WAIT is placed directly before the
  next post operation that intends to use the same
  request object variable.
• Successful completion of the function MPI_WAIT
  will set REQUESTMPI_REQUEST_NULL.

21
Completion Operations

• MPI_TEST(REQUEST, FLAG, STATUS, IERROR)
• INOUT INTEGER REQUEST
• OUT STATUS(MPI_STATUS_SIZE)
• OUT LOGICAL FLAG
• A call to MPI_TEST returns flagtrue if the
  operation identified by REQUEST is complete.
• MPI_TEST is the nonblocking version of completion
  operations.
• If flagtrue then MPI_TEST will clean up the
  space associated with REQUEST, deallocating the
  memory and setting REQUEST MPI_REQUEST_NULL.
• MPI_TEST allows the user to create code that can
  attempt to communicate as much as possible but
  continue doing useful work if messages are not
  ready.

22
Maximizing Overlap

• To achieve maximum overlap between computation
  and communication, communications should be
  started as soon as possible and completed as late
  as possible.
• Sends should be posted as soon as the data to be
  sent is available.
• Receives should be posted as soon as the receive
  buffer can be used.
• Sends should be completed just before the send
  buffer is to be reused.
• Receives should be completed just before the data
  in the buffer is to be reused.
• Overlap can often be increased by reordering the
  computation.

23
Setting up your account for MPI

• http//courses.cs.vt.edu/cs4234/MPI/first_exercis
  e.html
• List of 124 machine names
• http//courses.cs.vt.edu/cs4234/MPI/124hosts.txt

24
More Stuff

• Note to login the 124 linux machines from the
  outside world, you do "ssh rlogin.cslab.vt.edu".
  You will then be logged into one of the machines
  in the lab.
• Set up public/private key pair. You only have to
  do this once. It will allow you to launch mpi
  jobs from any of the McB 124 machines, and have
  them run on any of these machines, without having
  to type passwords.
• First, enter the command ssh-keygen -t dsa -N ""
  The result of this command will be something like
  this Generating public/private dsa key pair.
  Enter file in which to save the key
  (/home/ugrads/NAME/.ssh/id_dsa) Your
  identification has been saved in
  /home/ugrads/NAME/.ssh/id_dsa. Your public key
  has been saved in /home/ugrads/NAME/.ssh/id_dsa.pu
  b. The key fingerprint is 89ff005f06fdd0a2
  9e51b100cd0a766f NAME_at_MachineName.cslab.vt
  .edu
• Then do this cd .ssh cp id_dsa.pub
  authorized_keys2
• To make sure this step worked, try ssh'ing to
  another machine in the lab, e.g., "ssh
  strawberry". You should be able to do this
  without being prompted for a password

25
Even More Stuff

• Put /home/staff/ribbens/mpich-1.2.6/bin in your
  path.
• Make a subdirectory, mkdir MPI, and cd to it.
• Hello world example
• Copy hello.c from /home/staff/ribbens/MPI.
• Compile and link mpicc -o hello hello.c
• Run on 4 processors mpirun -np 4 hello
• Learn more about mpirun mpirun -help