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Message Passing Programming Based on MPI

Message Passing Programming Based on MPI. Bora AKAYDIN. Derived Data Types. 15.06.2012. Outline. Derived Data types Packing/Unpacking Datatypes. Derived Data Types. 15.06.2012. V(0). V(1). V(2). V(3). V(4). V(5). V(6). V(7). V(8). V(9). T(0). T(1). T(2). Derived Datatypes.

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Message Passing Programming Based on MPI

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  1. Message Passing Programming Based on MPI Bora AKAYDIN Derived Data Types 15.06.2012

  2. Outline • Derived Datatypes • Packing/Unpacking Datatypes Derived Data Types 15.06.2012

  3. V(0) V(1) V(2) V(3) V(4) V(5) V(6) V(7) V(8) V(9) T(0) T(1) T(2) Derived Datatypes • How to send only the red elements of V in a single communication? This method requires inefficient copy of non- contiguous data MPI_Send One possibility, copy these elements to a temporary array before sending. Derived Data Types 15.06.2012

  4. Non-struct Derived Data Types • There are routines available in MPI library that are more suitable for an array or vector like data structures: • MPI_Type_contiguous • MPI_Type_vector • MPI_Type_indexed • All above functions work with a single data type! Derived Data Types 15.06.2012

  5. x count (4) = old type new type MPI_Type_contiguous (C) • Constructs a type consisting of the replication of a data type into continuous locations. int MPI_Type_contiguous( int count, MPI_Datatype old_type, MPI_Datatype *newtype) Data constructor withMPI_Type_contiguous Derived Data Types 15.06.2012

  6. x count (4) = old type new type mpi_type_contiguous (Fortran) • Constructs a type consisting of the replication of a data type into continuous locations. MPI_TYPE_CONTIGUOUS( count, MPI_Datatype old_type, MPI_Datatype newtype,ierr) Data constructor withmpi_type_contiguous Derived Data Types 15.06.2012

  7. A (0,0) A (0,1) A (0,2) A (1,0) A (1,1) A (1,2) A (2,0) A (2,1) A (2,2) in the memory (C) A (0,0) A (0,1) A (0,2) A (1,0) A (1,1) A (1,2) A (2,0) A (2,1) A (2,2) in the memory (fortran) A (0,0) A (1,0) A (2,0) A (0,1) A (1,1) A (2,1) A (0,2) A (1,2) A (2,2) MPI_Type_contiguous • In C, if we create a matrix with static memory allocation, we can say that data of the matrix will be in contiguous memory. double A[3][3]; Derived Data Types 15.06.2012

  8. double A[3][3]; A (0,0) A (0,1) A (0,2) A (1,0) A (1,1) A (1,2) A (2,0) A (2,1) A (2,2) in the memory A (0,0) A (0,1) A (0,2) A (1,0) A (1,1) A (1,2) A (2,0) A (2,1) A (2,2) MPI_Type_contiguous (C) count =3 old_type =MPI_DOUBLE new_type =rowtype MPI_Type_contiguous(int count, MPI_Datatype old_type, MPI_Datatype *newtype); Derived Data Types 15.06.2012

  9. in the memory (fortran) A (0,0) A (0,1) A (0,2) A (1,0) A (1,1) A (1,2) A (2,0) A (2,1) A (2,2) mpi_type_contiguous (Fortran) count =3 old_type =MPI_REAL new_type =columntype A (2,0) A (0,0) A (1,0) A (0,1) A (1,1) A (2,1) A (0,2) A (1,2) A (2,2) call mpi_type_contiguous(count, MPI_Datatype old_type, MPI_Datatype newtype,ierr); Derived Data Types 15.06.2012

  10. V(0) V(1) V(2) V(3) V(4) V(5) V(6) V(7) V(8) V(9) vType Handling Non-Contiguous Data • How to send only the red elements of V, while avoiding copying non-contiguous data to a temporary array? • Define a new data type, in this case a vector with stride of two from original. Derived Data Types 15.06.2012

  11. MPI_Type_vector • Similar to contiguous, but allows for regular gaps (stride) in the displacements. (MPI_INT) old type new type blocklength=3 stride=5 count=2 Data constructor withMPI_Type_vector. Derived Data Types 15.06.2012

  12. A (0,0) A (0,1) A (0,2) A (1,0) A (1,1) A (1,2) A (2,0) A (2,1) A (2,2) MPI_Type_vector • In C, if we create a matrix with static memory allocation, we can say that data of the matrix will be in contiguous memory. • Suppose that, we want to send columns to the each task, instead of rows. double A[3][3]; in the memory A (0,0) A (0,1) A (0,2) A (1,0) A (1,1) A (1,2) A (2,0) A (2,1) A (2,2) • We can use, MPI_Type_vector to create vector (strided) data type. Derived Data Types 15.06.2012

  13. A (0,0) A (0,1) A (0,2) A (1,0) A (1,1) A (1,2) A (2,0) A (2,1) A (2,2) MPI_Type_vector double A[3][3]; in the memory A (0,0) A (0,1) A (0,2) A (1,0) A (1,1) A (1,2) A (2,0) A (2,1) A (2,2) blocklength=1 stride=3 count=3 Derived Data Types 15.06.2012

  14. MPI_Type_vector (C) blocklength=1 stride=3 count=3 MPI_Type_vector(int count, int blocklength, int stride, MPI_Datatypeold_type, MPI_Datatype *new_type); Derived Data Types 15.06.2012

  15. mpi_type_vector (Fortran) blocklength=1 stride=3 count=3 mpi_type_vector(count, blocklength, stride, MPI_Datatypeold_type, MPI_Datatypenew_type,ierr); Derived Data Types 15.06.2012

  16. V(0) V(1) V(2) V(3) V(4) V(5) V(6) V(7) V(8) V(9) vType MPI_Type_vector (C) • Sending reds blocklength = 1 stride = 2 count = 3 old_type =MPI_DOUBLE new_type =vtype blocklength= ? 1 stride= ? 2 3 count= ? MPI_Type_vector( count, blocklength, stride, old_type, &vType); MPI_Send(&V[2], 1, vType, dest, tag, MPI_COMM_WORLD); Derived Data Types 15.06.2012

  17. V(0) V(1) V(2) V(3) V(4) V(5) V(6) V(7) V(8) V(9) type mpi_type_vector (Fortran) • Sending reds blocklength = 1 stride = 2 count = 3 old_type =MPI_INTEGER new_type =type blocklength= ? 1 stride= ? 2 3 count= ? call mpi_type_vector(count,blocklength,stride,old_type,type,ierr); call mpi_send(V(2), 1, type, dest, tag, MPI_COMM_WORLD,ierr); Derived Data Types 15.06.2012

  18. A (0,0) A (0,1) A (0,2) A (0,3) A (1,0) A (1,1) A (1,2) A (1,3) A (2,0) A (2,1) A (2,2) A (2,3) A (3,0) A (3,1) A (3,2) A (3,3) MPI_Type_indexed • Indexed constructor allows one to specify a non-contiguous data layout where displacements between successive blocks need not be equal. double A[4][4]; Derived Data Types 15.06.2012

  19. MPI_Type_indexed • This allows: • Gathering of arbitrary entries from an array and sending them in one message, or • Receiving one message and scattering the received message entries into arbitrary locations in an array. Derived Data Types 15.06.2012

  20. MPI_Type_indexed (C) • count:number of blocks • blocklength:number of elements in each block • indices:displacement for each block, measured as number ofelements int MPI_Type_indexed(int count, int blocklength[], int indices[], MPI_Datatype old_type, MPI_Datatype *newtype ) Derived Data Types 15.06.2012

  21. mpi_type_indexed (Fortran) mpi_type_indexed(count, blocklength(), indices(), MPI_Datatype old_type, MPI_Datatype newtype,ierr ) • count:number of blocks • blocklength:number of elements in each block • indices:displacement for each block, measured as number ofelements Derived Data Types 15.06.2012

  22. MPI_Type_indexed old type blen[0]= 2 blen[1]= 3 blen[2]= 1 new type indices[0]=0 indices[1]=3 indices[2]=8 count= 3 Derived Data Types 15.06.2012

  23. A (0,0) A (0,1) A (0,2) A (0,3) A (1,0) A (1,1) A (1,2) A (1,3) A (2,0) A (2,1) A (2,2) A (2,3) A (3,0) A (3,1) A (3,2) A (3,3) MPI_Type_indexed • Suppose that, we have a matrix A(4x4) • We want to send upper triangular matrix double A[4][4]; old type = MPI_DOUBLE new type = upper count= 4 blocklen[]= (4, 3, 2, 1) indices[]=(0, 5, 10, 15) MPI_Type_indexed(count, blocklen, indices, MPI_DOUBLE, upper ) Derived Data Types 15.06.2012

  24. MPI_Type_commit • Commits new datatype to the system. • Required for all user constructed (derived) data types. int MPI_Type_commit( MPI_Datatype *datatype) MPI_TYPE_COMMIT( MPI_Datatype datatype,ierr ) Derived Data Types 15.06.2012

  25. MPI_Type_free • Deallocates the specified data type object. • Use of this routine is especially important to prevent memory exhaustion if many data type objects are created, as in a loop. int MPI_Type_free( MPI_Datatype *datatype ) MPI_TYPE_FREE( MPI_Datatype datatype,ierr ) Derived Data Types 15.06.2012

  26. Packing Different Data • Sometimes, users need to send non-contiguous data in a single package. • MPI allows them to • explicitly pack data into a contiguous buffer before sending it, and • unpack it from a contiguous buffer after receiving. • Several messages can be successively packed into one packing unit. Derived Data Types 15.06.2012

  27. MPI_Pack (C) data to be buffered int MPI_Pack ( void *packdata, int count, MPI_Datatype datatype, void *buffer, int size, int *position, MPI_Comm comm ) number of input data items datatype of each input data item output buffer start size of buffer, in bytes current position in buffer, in bytes communicator for packed message Derived Data Types 15.06.2012

  28. mpi_pack (Fortran) data to be buffered MPI_PACK ( packdata, count, MPI_Datatype datatype, buffer, size, position, MPI_Comm comm,ierr ) number of input data items datatype of each input data item output buffer start size of buffer, in bytes current position in buffer, in bytes communicator for packed message Derived Data Types 15.06.2012

  29. char: (1 Byte) integer: (4 Byte) T o d a y i s a w o n d e r f u l d a y ! 18 7 2007 Packing Data char array with 25 element char c[25]: integer array with 3 elements int date[3]: buffer Derived Data Types 15.06.2012

  30. T o d a y i s a w o n d e r f u l d a y ! 18 7 2007 Packing Data buffer • At the beginningposition=0 MPI_Pack(c, 25, MPI_CHAR, buffer, 37, &position, MPI_Comm comm ) • positionvalue is updated by MPI_Pack asposition=25 MPI_Pack(date, 3, MPI_INT, buffer, 37, &position, MPI_Comm comm ) • position value is updated by MPI_Pack asposition=37 Derived Data Types 15.06.2012

  31. T o d a y i s a w o n d e r f u l d a y ! 18 7 2007 Packing Data buffer • At the beginningposition=0 call MPI_PACK(c, 25, MPI_CHARACTER, buffer, 37, &position, MPI_Comm comm,ierr ) • positionvalue is updated by MPI_Pack asposition=25 MPI_Pack(date, 3, MPI_INTEGER, buffer, 37, &position, MPI_Comm comm,ierr ) • position value is updated by MPI_Pack asposition=37 Derived Data Types 15.06.2012

  32. Sending Packed Data • MPI_Send function used to send packed data, • MPI_PACKED type is used as datatype. • Size of the data must be specified in Bytes. • Now, buffer size is 37 Bytes Derived Data Types 15.06.2012

  33. char: (1 Byte) integer: (4 Byte) T o d a y i s a w o n d e r f u l d a y ! 18 7 2007 Sending Packed Data buffer MPI_Send(buffer, position, MPI_PACKED, dest, tag, MPI_Comm comm); Derived Data Types 15.06.2012

  34. char: (1 Byte) integer: (4 Byte) T o d a y i s a w o n d e r f u l d a y ! 18 7 2007 Sending Packed Data buffer call MPI_SEND(buffer, position, MPI_PACKED, dest, tag, MPI_Comm comm,ierr) Derived Data Types 15.06.2012

  35. Receiving Packed Data • MPI_Recv function used to receive packed data, • MPI_PACKED type is used as datatype. • Size of the data must be specified in Bytes. Derived Data Types 15.06.2012

  36. T o d a y i s a w o n d e r f u l d a y ! 18 7 2007 Receiving Packed Data MPI_Recv(Rbuffer, 37, MPI_PACKED, source, tag, comm, &status); Rbuffer Derived Data Types 15.06.2012

  37. T o d a y i s a w o n d e r f u l d a y ! 18 7 2007 Receiving Packed Data MPI_RECV(Rbuffer, 37, MPI_PACKED, source, tag, comm, status,ierr); Rbuffer Derived Data Types 15.06.2012

  38. MPI_Unpack (C) input buffer start int MPI_Unpack(void *buffer, int size, int *position, void *packdata, int count, MPI_Datatype datatype, MPI_Comm comm ) size of buffer, in bytes current position in buffer, in bytes output buffer start number of items to be unpacked datatype of each output data item communicator for packed message Derived Data Types 15.06.2012

  39. mpi_unpack (Fortran) input buffer start int MPI_UNPACK(buffer, size, position, packdata, count, MPI_Datatype datatype, MPI_Comm comm,ierr ) size of buffer, in bytes current position in buffer, in bytes output buffer start number of items to be unpacked datatype of each output data item communicator for packed message Derived Data Types 15.06.2012

  40. MPI_Unpack • The output buffer can be any communication buffer allowed in MPI_Recv. • The buffer is a contiguous storage area containing size bytes, starting at address buffer. • The value of position is the first location in the buffer occupied by the packed message. • position is incremented by the size of the packed message, so that the output value of position is the first location in the buffer after the locations occupied by the message that was unpacked. Derived Data Types 15.06.2012

  41. T o d a y i s a w o n d e r f u l d a y ! Unpacking Packed Data (C) MPI_Unpack(buffer, 37, &position, &Rc, 25, MPI_CHAR, MPI_Comm comm); First value position=0 Updated to position=25 char Rc[25]: Derived Data Types 15.06.2012

  42. T o d a y i s a w o n d e r f u l d a y ! Unpacking Packed Data (Fortran) MPI_UNPACK(buffer, 37, position, Rc, 25, MPI_CHARACTER, MPI_Comm comm,ierr); First value position=0 Updated to position=25 char Rc[25]: Derived Data Types 15.06.2012

  43. 18 7 2007 Unpacking Packed Data (C) MPI_Unpack(buffer, 37, &position, &Rdate, 3, MPI_INT, MPI_Comm comm); First value position=25 Updated to position=37 int Rdate[3]: Derived Data Types 15.06.2012

  44. 18 7 2007 Unpacking Packed Data (Fortran) MPI_UNPACK(buffer, 37, position, Rdate, 3, MPI_INTEGER, MPI_Comm comm,ierr); First value position=25 Updated to position=37 int Rdate[3]: Derived Data Types 15.06.2012

  45. Programming Activities Writing parallel MPI codes using following routines • Contiguous • Indexed • Vector • Pack-unpack Derived Data Types 15.06.2012

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