/* * Copyright (C) 1998 NCSA * All rights reserved. * * Programmer: rky 980813 * * Purpose: Functions to read/write directly between app buffer and file. * * Beware of the ifdef'ed print statements. * I didn't make them portable. */ #define H5F_PACKAGE /*suppress error about including H5Fpkg */ #define H5S_PACKAGE /*suppress error about including H5Spkg */ #include #include #include /* Ugly, but necessary for the MPIO I/O accesses */ #include #include /*the MPIO file driver */ #ifndef H5_HAVE_PARALLEL /* * The H5S_mpio_xxxx functions are for parallel I/O only and are * valid only when H5_HAVE_PARALLEL is #defined. This empty #ifndef * body is used to allow this source file be included in the serial * distribution. * Some compilers/linkers may complain about "empty" object file. * If that happens, uncomment the following statement to pacify * them. */ /* const hbool_t H5S_mpio_avail = FALSE; */ #else /* H5_HAVE_PARALLEL */ /* Interface initialization */ #define PABLO_MASK H5Sall_mask #define INTERFACE_INIT NULL static intn interface_initialize_g = 0; static herr_t H5S_mpio_all_type( const H5S_t *space, const size_t elmt_size, /* out: */ MPI_Datatype *new_type, hsize_t *count, hbool_t *is_derived_type ); static herr_t H5S_mpio_hyper_type( const H5S_t *space, const size_t elmt_size, /* out: */ MPI_Datatype *new_type, hsize_t *count, hbool_t *is_derived_type ); static herr_t H5S_mpio_space_type( const H5S_t *space, const size_t elmt_size, /* out: */ MPI_Datatype *new_type, hsize_t *count, hbool_t *is_derived_type ); static herr_t H5S_mpio_spaces_xfer(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t UNUSED *pline, const struct H5O_efl_t UNUSED *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, void *buf/*out*/, hbool_t *must_convert/*out*/, const hbool_t do_write); /*------------------------------------------------------------------------- * Function: H5S_mpio_all_type * * Purpose: Translate an HDF5 "all" selection into an MPI type. * * Return: non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection * (useful if this is the buffer type for xfer) * *is_derived_type 0 if MPI primitive type, 1 if derived * * Programmer: rky 980813 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5S_mpio_all_type( const H5S_t *space, const size_t elmt_size, /* out: */ MPI_Datatype *new_type, hsize_t *count, hbool_t *is_derived_type ) { hsize_t total_bytes; int i; FUNC_ENTER (H5S_mpio_all_type, FAIL); /* Check args */ assert (space); /* Just treat the entire extent as a block of bytes */ total_bytes = (hsize_t)elmt_size; for (i=0; iextent.u.simple.rank; ++i) { total_bytes *= space->extent.u.simple.size[i]; } /* fill in the return values */ *new_type = MPI_BYTE; *count = total_bytes; *is_derived_type = 0; #ifdef H5Smpi_DEBUG fprintf(stdout, "Leave %s total_bytes=%Hu\n", FUNC, total_bytes ); #endif FUNC_LEAVE (SUCCEED); } /*------------------------------------------------------------------------- * Function: H5S_mpio_hyper_type * * Purpose: Translate an HDF5 hyperslab selection into an MPI type. * * Return: non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection * (useful if this is the buffer type for xfer) * *is_derived_type 0 if MPI primitive type, 1 if derived * * Programmer: rky 980813 * * Modifications: ppw 990401 * rky, ppw 2000-09-26 Freed old type after creating struct type. * rky 2000-10-05 Changed displacements to be MPI_Aint. * rky 2000-10-06 Added code for cases of empty hyperslab. * *------------------------------------------------------------------------- */ herr_t H5S_mpio_hyper_type( const H5S_t *space, const size_t elmt_size, /* out: */ MPI_Datatype *new_type, hsize_t *count, hbool_t *is_derived_type ) { struct dim { /* less hassle than malloc/free & ilk */ hssize_t start; hsize_t strid; hsize_t block; hsize_t xtent; hsize_t count; } d[32]; int i, err, new_rank, num_to_collapse; int offset[32], max_xtent[32], block_length[2]; H5S_hyper_dim_t *diminfo; /* [rank] */ intn rank; MPI_Datatype inner_type, outer_type, old_type[32]; MPI_Aint extent_len, displacement[2]; FUNC_ENTER (H5S_mpio_hyper_type, FAIL); /* Check and abbreviate args */ assert (space); assert(sizeof(MPI_Aint) >= sizeof(elmt_size)); diminfo = space->select.sel_info.hslab.diminfo; assert (diminfo); rank = space->extent.u.simple.rank; assert (rank >= 0); if (0==rank) goto empty; if (0==elmt_size) goto empty; /* make a local copy of the dimension info so we can transform them */ assert(rank<=32); /* within array bounds */ for ( i=0; iextent.u.simple.size[i]; #ifdef H5Smpi_DEBUG HDfprintf(stdout, "hyper_type: start=%Hd stride=%Hu count=%Hu " "block=%Hu xtent=%Hu", d[i].start, d[i].strid, d[i].count, d[i].block, d[i].xtent ); if (i==0) fprintf(stdout, " rank=%d\n", rank ); else fprintf(stdout, "\n" ); #endif if (0==d[i].block) goto empty; if (0==d[i].count) goto empty; if (0==d[i].xtent) goto empty; } /********************************************************************** Compute array "offset[rank]" which gives the offsets for a multi- dimensional array with dimensions "d[i].xtent" (i=0,1,...,rank-1). **********************************************************************/ offset[rank-1] = 1; max_xtent[rank-1] = d[rank-1].xtent; #ifdef H5Smpi_DEBUG i=rank-1; fprintf(stdout, " offset[%2d]=%d; max_xtent[%2d]=%d\n", i, offset[i], i, max_xtent[i]); #endif for (i=rank-2; i>=0; --i) { offset[i] = offset[i+1]*d[i+1].xtent; max_xtent[i] = max_xtent[i+1]*d[i].xtent; #ifdef H5Smpi_DEBUG fprintf(stdout, " offset[%2d]=%d; max_xtent[%2d]=%d\n", i, offset[i], i, max_xtent[i]); #endif } /* Create a type covering the selected hyperslab. * Multidimensional dataspaces are stored in row-major order. * The type is built from the inside out, going from the * fastest-changing (i.e., inner) dimension * to the slowest (outer). */ /* Optimization: check for contiguous inner dimensions. * Supposing the dimensions were numbered from 1 to rank, we find that * * dim d=rank is contiguous if: * stride[d] = block[d] * and count[d] * block[d] = extent.u.simple.size[d] * * (i.e., there's no overlap or gaps and the entire extent is filled.) * * dim d (1<=dextent.u.simple.size[rank-i-1]) { break; } } /* end for */ num_to_collapse = i; if (num_to_collapse == rank) num_to_collapse--; assert(0<=num_to_collapse && num_to_collapse=new_rank; --i) { d[i-1].block *= d[i].count * d[i].block; d[i-1].strid *= d[i].count * d[i].block; d[i-1].xtent *= d[i].count * d[i].block; assert( d[i].start == 0 ); /* d[i-1].start stays unchanged */ /* d[i-1].count stays unchanged */ } /* check for possibility to coalesce blocks of the uncoalesced dimensions */ for (i=0; i=0; --i) { HDfprintf(stdout, "d[%d].xtent=%Hu \n", i, d[i].xtent); } #endif err = MPI_Type_contiguous( (int)elmt_size, MPI_BYTE, &inner_type ); if (err) { HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't create MPI contiguous type"); } /******************************************************* * Construct the type by walking the hyperslab dims * from the inside out: *******************************************************/ for ( i=new_rank-1; i>=0; --i) { #ifdef H5Smpi_DEBUG HDfprintf(stdout, "hyper_type: Dimension i=%d \n" "count=%Hu block=%Hu stride=%Hu\n", i, d[i].count, d[i].block, d[i].strid ); #endif #ifdef H5Smpi_DEBUG HDfprintf(stdout, "hyper_type: i=%d Making vector-type \n", i); #endif /**************************************** * Build vector in current dimension: ****************************************/ err = MPI_Type_vector ( (int)(d[i].count), /* count */ (int)(d[i].block), /* blocklength */ (MPI_Aint)(d[i].strid), /* stride */ inner_type, /* old type */ &outer_type ); /* new type */ MPI_Type_free( &inner_type ); if (err) { HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't create MPI vector type"); } displacement[1] = elmt_size * max_xtent[i]; err = MPI_Type_extent(outer_type, &extent_len); /************************************************* * Restructure this datatype ("outer_type") * so that it still starts at 0, but its extent * is the full extent in this dimension. *************************************************/ if ((int)extent_len < displacement[1]) { #ifdef H5Smpi_DEBUG HDfprintf(stdout, "hyper_type: i=%d Extending struct type\n" "***displacements: 0, %d\n", i, displacement[1]); #endif #ifdef H5_HAVE_MPI2 /* have MPI-2 */ err = MPI_Type_create_resized ( outer_type, /* old type */ 0, /* blocklengths */ displacement[1], /* displacements */ &inner_type); /* new type */ #else /* do not have MPI-2 */ block_length[0] = 1; block_length[1] = 1; displacement[0] = 0; old_type[0] = outer_type; old_type[1] = MPI_UB; #ifdef H5Smpi_DEBUG HDfprintf(stdout, "hyper_type: i=%d Extending struct type\n" "***displacements: 0, %d\n", i, displacement[1]); #endif err = MPI_Type_struct ( 2, /* count */ block_length, /* blocklengths */ displacement, /* displacements */ old_type, /* old types */ &inner_type); /* new type */ #endif MPI_Type_free (&outer_type); if (err) { HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't resize MPI vector type"); } } else { inner_type = outer_type; } } /* end for */ /*************************** * End of loop, walking * thru dimensions. ***************************/ /* At this point inner_type is actually the outermost type, even for 0-trip loop */ /*************************************************************** * Final task: create a struct which is a "clone" of the * current struct, but displaced according to the d[i].start * values given in the hyperslab description: ***************************************************************/ displacement[0] = 0; for (i=new_rank-1; i>=0; i--) displacement[0] += d[i].start * offset[i]; if (displacement[0] > 0) { displacement[0] *= elmt_size; block_length[0] = 1; old_type[0] = inner_type; #ifdef H5Smpi_DEBUG HDfprintf(stdout, "hyper_type: Making final struct\n" "***count=1:\n"); HDfprintf(stdout, "\tblocklength[0]=%d; displacement[0]=%d\n", block_length[0], displacement[0]); #endif err = MPI_Type_struct( 1, /* count */ block_length, /* blocklengths */ displacement, /* displacements */ old_type, /* old type */ new_type ); /* new type */ if (err) { HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't create MPI struct type"); } MPI_Type_free (&old_type[0]); if (err) { HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't resize MPI vector type"); } } else { *new_type = inner_type; } err = MPI_Type_commit( new_type ); if (err) { HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't commit MPI vector type"); } /* fill in the remaining return values */ *count = 1; /* only have to move one of these suckers! */ *is_derived_type = 1; goto done; empty: /* special case: empty hyperslab */ *new_type = MPI_BYTE; *count = 0; *is_derived_type = 0; done: #ifdef H5Smpi_DEBUG HDfprintf(stdout, "Leave %s, count=%Hu is_derived_type=%d\n", FUNC, *count, *is_derived_type ); #endif FUNC_LEAVE (SUCCEED); } /*------------------------------------------------------------------------- * Function: H5S_mpio_space_type * * Purpose: Translate an HDF5 dataspace selection into an MPI type. * Currently handle only hyperslab and "all" selections. * * Return: non-negative on success, negative on failure. * * Outputs: *new_type the MPI type corresponding to the selection * *count how many objects of the new_type in selection * (useful if this is the buffer type for xfer) * *is_derived_type 0 if MPI primitive type, 1 if derived * * Programmer: rky 980813 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5S_mpio_space_type( const H5S_t *space, const size_t elmt_size, /* out: */ MPI_Datatype *new_type, hsize_t *count, hbool_t *is_derived_type ) { int err; herr_t ret_value = SUCCEED; FUNC_ENTER (H5S_mpio_space_type, FAIL); /* Check args */ assert (space); /* Creat MPI type based on the kind of selection */ switch (space->extent.type) { case H5S_SCALAR: /* not yet implemented */ ret_value = FAIL; break; case H5S_SIMPLE: switch(space->select.type) { case H5S_SEL_NONE: case H5S_SEL_ALL: err = H5S_mpio_all_type( space, elmt_size, /* out: */ new_type, count, is_derived_type ); if (err<0) { HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type"); } break; case H5S_SEL_POINTS: /* not yet implemented */ ret_value = FAIL; break; case H5S_SEL_HYPERSLABS: err = H5S_mpio_hyper_type( space, elmt_size, /* out: */ new_type, count, is_derived_type ); if (err) { HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type"); } break; default: assert("unknown selection type" && 0); break; } /* end switch */ break; case H5S_COMPLEX: /* not yet implemented */ ret_value = FAIL; break; default: assert("unknown data space type" && 0); break; } FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5S_mpio_spaces_xfer * * Purpose: Use MPI-IO to transfer data efficiently * directly between app buffer and file. * * Return: non-negative on success, negative on failure. * * Programmer: rky 980813 * * Modifications: * * rky 980918 * Added must_convert parameter to let caller know we can't optimize the xfer. * *------------------------------------------------------------------------- */ herr_t H5S_mpio_spaces_xfer(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t UNUSED *pline, const struct H5O_efl_t UNUSED *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, void *buf /*out*/, hbool_t *must_convert /*out*/, const hbool_t do_write ) { herr_t ret_value = SUCCEED; int err; haddr_t disp, addr; size_t mpi_count; hsize_t mpi_buf_count, mpi_unused_count; MPI_Datatype mpi_buf_type, mpi_file_type; hbool_t mbt_is_derived, mft_is_derived; FUNC_ENTER (H5S_mpio_spaces_xfer, FAIL); *must_convert = 0; /* means we at least tried to do optimized xfer */ /* Check args */ assert (f); assert (layout); assert (file_space); assert (mem_space); assert (buf); assert (IS_H5FD_MPIO(f)); /* INCOMPLETE!!! rky 980816 */ /* Currently can only handle H5D_CONTIGUOUS layout */ if (layout->type != H5D_CONTIGUOUS) { #ifdef H5S_DEBUG if (H5DEBUG(S)) { fprintf (H5DEBUG(S), "H5S: can only create MPI datatype for hyperslab when layout is contiguous.\n" ); } #endif *must_convert = 1; /* can't do optimized xfer; do the old way */ goto done; } /* create the MPI buffer type */ err = H5S_mpio_space_type( mem_space, elmt_size, /* out: */ &mpi_buf_type, &mpi_buf_count, &mbt_is_derived ); if (MPI_SUCCESS != err) HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI buf type"); /* create the MPI file type */ err = H5S_mpio_space_type( file_space, elmt_size, /* out: */ &mpi_file_type, &mpi_unused_count, &mft_is_derived ); if (MPI_SUCCESS != err) HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI file type"); /* calculate the absolute base addr (i.e., the file view disp) */ disp = f->shared->base_addr + layout->addr; #ifdef H5Smpi_DEBUG HDfprintf(stdout, "spaces_xfer: disp=%Hu\n", disp ); #endif /* Effective address determined by base addr and the MPI file type */ addr = 0; /* * Pass buf type, file type, and absolute base address (i.e., the file * view disp) to the file driver. Request a dataspace transfer (instead * of an elementary byteblock transfer). */ H5FD_mpio_setup(f->shared->lf, mpi_buf_type, mpi_file_type, disp, 1); /* transfer the data */ mpi_count = (size_t)mpi_buf_count; if (mpi_count != mpi_buf_count) { HRETURN_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "transfer size overflows size_t"); } if (do_write) { err = H5FD_write(f->shared->lf, H5FD_MEM_DRAW, dxpl_id, addr, mpi_count, buf); if (err) { HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,"MPI write failed"); } } else { err = H5FD_read (f->shared->lf, H5FD_MEM_DRAW, dxpl_id, addr, mpi_count, buf); if (err) { HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,"MPI read failed"); } } /* free the MPI buf and file types */ if (mbt_is_derived) { err = MPI_Type_free( &mpi_buf_type ); if (MPI_SUCCESS != err) { HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL, "unable to free MPI file type"); } } if (mft_is_derived) { err = MPI_Type_free( &mpi_file_type ); if (MPI_SUCCESS != err) { HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL, "unable to free MPI file type"); } } done: FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5S_mpio_spaces_read * * Purpose: MPI-IO function to read directly from app buffer to file. * * Return: non-negative on success, negative on failure. * * Programmer: rky 980813 * * Modifications: * * rky 980918 * Added must_convert parameter to let caller know we can't optimize the xfer. * *------------------------------------------------------------------------- */ herr_t H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, void *buf/*out*/, hbool_t *must_convert/*out*/) { herr_t ret_value = FAIL; FUNC_ENTER (H5S_mpio_spaces_read, FAIL); ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size, file_space, mem_space, dxpl_id, buf, must_convert/*out*/, 0/*read*/); FUNC_LEAVE (ret_value); } /*------------------------------------------------------------------------- * Function: H5S_mpio_spaces_write * * Purpose: MPI-IO function to write directly from app buffer to file. * * Return: non-negative on success, negative on failure. * * Programmer: rky 980813 * * Modifications: * * rky 980918 * Added must_convert parameter to let caller know we can't optimize the xfer. * *------------------------------------------------------------------------- */ herr_t H5S_mpio_spaces_write(H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, hid_t dxpl_id, const void *buf, hbool_t *must_convert/*out*/) { herr_t ret_value = FAIL; FUNC_ENTER (H5S_mpio_spaces_write, FAIL); ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size, file_space, mem_space, dxpl_id, (void*)buf, must_convert/*out*/, 1/*write*/); FUNC_LEAVE (ret_value); } #endif /* H5_HAVE_PARALLEL */