tools forcomputational physics mpi tutorial

1 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS 2005    Stefano Cozzini cozzini@democritos.it Democritos/INFM + SISSA MPI tutorial 2 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS 2005  !" • Shared memory (load, store, lock, unlock) • Message Passing (send, receive, broadcast, ) • Transparent (compiler works magic) • Directive-based (compiler needs help) • Others (BSP, OpenMP, ) 3 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS 2005   ""!" • Parallel programs consist of separate processes, each with its own address space – Programmer manages memory by placing data in a particular process • Data sent explicitly between processes – Programmer manages memory motion • Collective operations – On arbitrary set of processes • Data distribution – Also managed by programmer 4 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS 2005  "" • Data Parallel - the same instructions are carried out simultaneously on multiple data items (SIMD) • Task Parallel - different instructions on different data (MIMD) • SPMD (single program, multiple data) not synchronized at individual operation level • SPMD is equivalent to MIMD since each MIMD program can be made SPMD (similarly for SIMD, but not in practical sense.) • Message passing is for MIMD/SPMD parallelism. HPF is an example of an SIMD 5 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS 2005  #!$!" % 6 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS 2005  & ' • A message-passing library specification – extended message-passing model – not a language or compiler specification – not a specific implementation or product • For parallel computers, clusters, and heterogeneous networks • Full-featured • Designed to provide access to advanced parallel hardware for end users, library writers, and tool developers 7 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS 2005  & ' A STANDARD The actual implementation of the standard is demanded to the software developers of the different systems In all systems MPI has been implemented as a library of subroutines over the network drivers and primitives many different implementations LAM/MPI (today's TOY) www.lam-mpi.org MPICH 8 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS 2005  ( !! MPI’s prime goals are: • To provide source-code portability • To allow efficient implementations MPI also offers: • A great deal of functionality • Support for heterogeneous parallel architectures 9 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS 2005   • The Standard itself: – at http://www.mpi-forum.org – All MPI official releases, in both postscript and HTML • Other information on Web: – at http://www.mcs.anl.gov/mpi – pointers to lots of stuff, including talks and tutorials, a FAQ, other MPI pages 10 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS 2005  )*"*  • MPI is a library – All operations are performed with routine calls – Basic definitions are in • mpi.h for C • mpif.h for Fortran 77 and 90 • MPI module for Fortran 90 (optional) [...]... ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS C - MPI Basic Datatypes MPI Data type C Data type MPI_ CHAR signed char MPI_ SHORT signed short int MPI_ INT signed int MPI_ LONG Signed log int MPI_ UNSIGNED_CHAR unsigned char MPI_ UNSIGNED_SHORT unsigned short int MPI_ UNSIGNED unsigned int MPI_ UNSIGNED_LONG unsigned long int MPI_ FLOAT float MPI_ DOUBLE double MPI_ LONG_DOUBLE long double MPI_ BYTE MPI_ PACKED 28... MPI functions to construct custom datatypes, in particular ones for subarrays 26 February 2005 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS Fortran - MPI Basic Datatypes MPI Data type Fortran Data type MPI_ INTEGER INTEGER MPI_ REAL REAL MPI_ DOUBLE_PRECISION DOUBLE PRECISION MPI_ COMPLEX COMPLEX MPI_ DOUBLE_COMPLEX DOUBLE COMPLEX MPI_ LOGICAL LOGICAL MPI_ CHARACTER CHARACTER(1) MPI_ PACKED MPI_ BYTE... TOOLS FOR COMPUTATIONAL PHYSICS MPI basic functions (subroutines) MPI_ INIT: initialize MPI MPI_COMM_SIZE: how many PE ? MPI_ COMM_RANK: identify the PE MPI_ SEND : MPI_ RECV: MPI_ FINALIZE: close MPI • All you need is to know this 6 calls 12 February 2005 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS A First Program: Hello World! C Fortran include #include PROGRAM hello void... char * argv[]) { INCLUDE ‘mpif.h‘ int rank, size; INTEGER err MPI_ Init( &argc, &argv ); CALL MPI_ INIT(err) call MPI_ COMM_RANK( MPI_ COMM_WORLD, rank, ierr ) MPI_ Comm_rank( MPI_ COMM_WORLD,&rank ); MPI_ Comm_size( MPI_ COMM_WORLD,&size ); printf( "I am %d of %d\n", rank, size ); call MPI_ COMM_SIZE( MPI_ COMM_WORLD, size, ierr ) MPI_ Finalize(); print *, 'I am ', rank, ' of ', size CALL MPI_ FINALIZE(err) return... the appropriate include directory (i.e -I/mpidir/include) • You should specify the mpi library (i.e -L/mpidir/lib -lmpi) • Usually MPI compiler wrappers do this job for you (i.e Mpif77)  Check on your machine 15 February 2005 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS Running MPI programs • The MPI- 1 Standard does not specify how to run an MPI program, just as the Fortran standard... ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS Basic Structures of MPI Programs  Header files  MPI Communicator  MPI Function format  Communicator Size and Process Rank  Initializing and Exiting MPI 17 February 2005 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS Header files All Subprogram that contains calls to MPI subroutine must include the MPI header file C: #include Fortran:... Call MPI_ send( buffer, 1, MPI_ integer, 1, 10, & MPI_ comm_world, error ) End If ! If( rank == 1 ) Then Call MPI_ recv( buffer, 1, MPI_ integer, 0, 10, & MPI_ comm_world, status, error ) Print*, 'Rank ', rank, ' buffer=', buffer If( buffer /= 33 ) Print*, 'fail' End If Call MPI_ finalize( error ) End Program MPI 33 February 2005 33 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS Summary: MPI send/receive... CALL MPI_ FINALIZE(IERR) This two subprograms should be called by all processes, and no other MPI calls are allowed before mpi_ init and after mpi_ finalize 20 February 2005 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS C and Fortran: a note • C and Fortran bindings correspond closely • In C: – mpi. h must be #included – MPI functions return error codes or – MPI_ SUCCESS • In Fortran: – mpif.h... in case of error • MPI_ recv is blocking Return when all the data are in BUFFER 32 4/13/99 February 2005 32 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS MPI: a fortran example Program MPI Implicit None ! Include 'mpif.h' ! Integer :: Integer :: Integer, Dimension( 1 :MPI_ status_size ) :: Integer :: rank buffer status error ! Call MPI_ init( error ) Call MPI_ comm_rank( MPI_ comm_world, rank,... 2005 DEMOCRITOS/ ICTP course in TOOLS FOR COMPUTATIONAL PHYSICS Notes on hello • All MPI programs begin with MPI_ Init and end with MPI_ Finalize • MPI_ COMM_WORLD is defined by mpi. h (in C) or mpif.h (in Fortran) and designates all processes in the MPI “job” • Each statement executes independently in each process – including the printf/print statements • I/O not part of MPI- 1 – print and write to standard .  0 • All MPI programs begin with MPI_ Init and end with MPI_ Finalize • MPI_ COMM_WORLD is defined by mpi. h (in C) or mpif.h (in Fortran) and designates all processes in the MPI “job” • Each. include directory (i.e. -I/mpidir/include) • You should specify the mpi library (i.e. -L/mpidir/lib -lmpi) • Usually MPI compiler wrappers do this job for you. (i.e. Mpif77)  Check on your machine.  -,".)&!/ Fortran PROGRAM hello INCLUDE ‘mpif.h‘ INTEGER err CALL MPI_ INIT(err) call MPI_ COMM_RANK( MPI_ COMM_WORLD, rank, ierr ) call MPI_ COMM_SIZE( MPI_ COMM_WORLD, size, ierr ) print *,