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An Introduction to Parallel Programming with MPI

An Introduction to Parallel Programming with MPI. March 22, 24, 29, 31 2005 David Adams daadams3@vt.edu http://research.cs.vt.edu/lasca/schedule. Outline. Disclaimers Overview of basic parallel programming on a cluster with the goals of MPI Batch system interaction Startup procedures

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An Introduction to Parallel Programming with MPI

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  1. An Introduction to Parallel Programming with MPI March 22, 24, 29, 31 2005 David Adams daadams3@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 <type> BUF(*) • IN INTEGER, COUNT, DATATYPE, DEST, TAG, COMM, • OUT IERROR, REQUEST • MPI_IRECV (BUF, COUNT, DATATYPE, SOURCE, TAG, COMM, REQUEST, IERROR) • IN <type> 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 can’t 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 REQUEST=MPI_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 flag=true if the operation identified by REQUEST is complete. • MPI_TEST is the nonblocking version of completion operations. • If flag=true 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_exercise.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.pub. The key fingerprint is: 89:ff:00:5f:06:fd:d0:a2:9e:51:b1:00:cd:0a:76:6f NAME@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

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