diff options
Diffstat (limited to 'src/H5Smpio.c')
| -rw-r--r-- | src/H5Smpio.c | 310 |
1 files changed, 107 insertions, 203 deletions
diff --git a/src/H5Smpio.c b/src/H5Smpio.c index 92974c3..7745374 100644 --- a/src/H5Smpio.c +++ b/src/H5Smpio.c @@ -61,13 +61,6 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, hsize_t *extra_offset, hbool_t *is_derived_type ); static herr_t -H5S_mpio_hyper_contig_type( const H5S_t *space, size_t elmt_size, - /* out: */ - MPI_Datatype *new_type, - size_t *count, - hsize_t *extra_offset, - hbool_t *is_derived_type ); -static herr_t H5S_mpio_space_type( const H5S_t *space, size_t elmt_size, /* out: */ MPI_Datatype *new_type, @@ -208,6 +201,9 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, hsize_t *extra_offset, hbool_t *is_derived_type ) { + H5S_sel_iter_t sel_iter; /* Selection iteration info */ + hbool_t sel_iter_init=0; /* Selection iteration info has been initialized */ + struct dim { /* less hassle than malloc/free & ilk */ hssize_t start; hsize_t strid; @@ -216,8 +212,7 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, hsize_t count; } d[H5S_MAX_RANK]; - int i, new_rank, num_to_collapse; - herr_t ret_value = SUCCEED; + int i; int offset[H5S_MAX_RANK]; int max_xtent[H5S_MAX_RANK]; H5S_hyper_dim_t *diminfo; /* [rank] */ @@ -226,45 +221,92 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, MPI_Datatype inner_type, outer_type, old_type[2]; MPI_Aint extent_len, displacement[2]; int mpi_code; /* MPI return code */ + herr_t ret_value = SUCCEED; FUNC_ENTER_NOINIT(H5S_mpio_hyper_type); - /* Check and abbreviate args */ + /* Check 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<=H5S_MAX_RANK); /* within array bounds */ - for ( i=0; i<rank; ++i) { - d[i].start = diminfo[i].start+space->select.offset[i]; - d[i].strid = diminfo[i].stride; - d[i].block = diminfo[i].block; - d[i].count = diminfo[i].count; - d[i].xtent = space->extent.u.simple.size[i]; + /* Initialize selection iterator */ + if (H5S_select_iter_init(&sel_iter, space, elmt_size)<0) + HGOTO_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, "unable to initialize selection iterator"); + sel_iter_init=1; /* Selection iteration info has been initialized */ + + /* Abbreviate args */ + diminfo=sel_iter.u.hyp.diminfo; + assert (diminfo); + + /* make a local copy of the dimension info so we can operate with them */ + + /* Check if this is a "flattened" regular hyperslab selection */ + if(sel_iter.u.hyp.iter_rank!=0 && sel_iter.u.hyp.iter_rank<space->extent.u.simple.rank) { + /* Flattened selection */ + rank=sel_iter.u.hyp.iter_rank; + assert (rank >= 0 && rank<=H5S_MAX_RANK); /* within array bounds */ + if (0==rank) + goto empty; + #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) - HDfprintf(stdout, " rank=%d\n", rank ); - else - HDfprintf(stdout, "\n" ); + HDfprintf(stderr, "%s: Flattened selection\n",FUNC); #endif - if (0==d[i].block) - goto empty; - if (0==d[i].count) - goto empty; - if (0==d[i].xtent) + for ( i=0; i<rank; ++i) { + d[i].start = diminfo[i].start+sel_iter.u.hyp.sel_off[i]; + d[i].strid = diminfo[i].stride; + d[i].block = diminfo[i].block; + d[i].count = diminfo[i].count; + d[i].xtent = sel_iter.u.hyp.size[i]; +#ifdef H5Smpi_DEBUG + HDfprintf(stderr, "%s: start=%Hd stride=%Hu count=%Hu block=%Hu xtent=%Hu", + FUNC, d[i].start, d[i].strid, d[i].count, d[i].block, d[i].xtent ); + if (i==0) + HDfprintf(stderr, " rank=%d\n", rank ); + else + HDfprintf(stderr, "\n" ); +#endif + if (0==d[i].block) + goto empty; + if (0==d[i].count) + goto empty; + if (0==d[i].xtent) + goto empty; + } + } /* end if */ + else { + /* Non-flattened selection */ + rank = space->extent.u.simple.rank; + assert (rank >= 0 && rank<=H5S_MAX_RANK); /* within array bounds */ + if (0==rank) goto empty; - } + +#ifdef H5Smpi_DEBUG + HDfprintf(stderr, "%s: Non-flattened selection\n",FUNC); +#endif + for ( i=0; i<rank; ++i) { + d[i].start = diminfo[i].start+space->select.offset[i]; + d[i].strid = diminfo[i].stride; + d[i].block = diminfo[i].block; + d[i].count = diminfo[i].count; + d[i].xtent = space->extent.u.simple.size[i]; +#ifdef H5Smpi_DEBUG + HDfprintf(stderr, "%s: start=%Hd stride=%Hu count=%Hu block=%Hu xtent=%Hu", + FUNC, d[i].start, d[i].strid, d[i].count, d[i].block, d[i].xtent ); + if (i==0) + HDfprintf(stderr, " rank=%d\n", rank ); + else + HDfprintf(stderr, "\n" ); +#endif + if (0==d[i].block) + goto empty; + if (0==d[i].count) + goto empty; + if (0==d[i].xtent) + goto empty; + } + } /* end else */ /********************************************************************** Compute array "offset[rank]" which gives the offsets for a multi- @@ -274,14 +316,14 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, max_xtent[rank-1] = d[rank-1].xtent; #ifdef H5Smpi_DEBUG i=rank-1; - HDfprintf(stdout, " offset[%2d]=%d; max_xtent[%2d]=%d\n", + HDfprintf(stderr, " 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 - HDfprintf(stdout, " offset[%2d]=%d; max_xtent[%2d]=%d\n", + HDfprintf(stderr, " offset[%2d]=%d; max_xtent[%2d]=%d\n", i, offset[i], i, max_xtent[i]); #endif } @@ -291,71 +333,13 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, * 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<=d<rank) is contiguous if: - * dim d+1 is contiguous - * and stride[d] = block[d] - * and count[d] * block[d] = extent.u.simple.size[d] - * - * There is also a weak sense in which the first noncollapsible dim - * is contiguous if it consists of a single unbroken range, - * and we also take advantage of that. - */ - - /* figure out how many dimensions we can eliminate */ - /* This loop examines contiguity from the inside out. */ - for ( i=0; i<rank; ++i) { - if ((d[rank-i-1].strid != d[rank-i-1].block) - || (d[rank-i-1].count*d[rank-i-1].block) != space->extent.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<rank); - new_rank = rank - num_to_collapse; -#ifdef H5Smpi_DEBUG - HDfprintf(stdout, "num_to_collapse=%d\n", num_to_collapse); - HDfprintf(stdout, "hyper_type: new_rank=%d\n", new_rank ); -#endif - - /* To collapse dims, just transform dimension info (from inner to outer) */ - /* must multiply r.h.s. by "count" --- ppw 03/11/99 */ - for (i=rank-1; i>=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<new_rank; ++i) { - if (d[i].strid == d[i].block) { - /* transform smaller blocks to 1 larger block of combined size */ - d[i].strid = d[i].block *= d[i].count; - d[i].count = 1; - } - } - /******************************************************* * Construct contig type for inner contig dims: *******************************************************/ #ifdef H5Smpi_DEBUG - HDfprintf(stdout, "hyper_type: Making contig type %d MPI_BYTEs\n", elmt_size ); - for (i=new_rank-1; i>=0; --i) - HDfprintf(stdout, "d[%d].xtent=%Hu \n", i, d[i].xtent); + HDfprintf(stderr, "%s: Making contig type %d MPI_BYTEs\n", FUNC,elmt_size ); + for (i=rank-1; i>=0; --i) + HDfprintf(stderr, "d[%d].xtent=%Hu \n", i, d[i].xtent); #endif if (MPI_SUCCESS != (mpi_code= MPI_Type_contiguous( (int)elmt_size, MPI_BYTE, &inner_type ))) HMPI_GOTO_ERROR(FAIL, "MPI_Type_contiguous failed", mpi_code); @@ -364,21 +348,21 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, * Construct the type by walking the hyperslab dims * from the inside out: *******************************************************/ - for ( i=new_rank-1; i>=0; --i) { + for ( i=rank-1; i>=0; --i) { #ifdef H5Smpi_DEBUG - HDfprintf(stdout, "hyper_type: Dimension i=%d \n" + HDfprintf(stderr, "%s: Dimension i=%d \n" "count=%Hu block=%Hu stride=%Hu\n", - i, d[i].count, d[i].block, d[i].strid ); + FUNC, 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); + HDfprintf(stderr, "%s: i=%d Making vector-type \n", FUNC,i); #endif /**************************************** * Build vector in current dimension: ****************************************/ - mpi_code = MPI_Type_vector ( (int)(d[i].count), /* count */ - (int)(d[i].block), /* blocklength */ + mpi_code =MPI_Type_vector((int)(d[i].count), /* count */ + (int)(d[i].block), /* blocklength */ (int)(d[i].strid), /* stride */ inner_type, /* old type */ &outer_type ); /* new type */ @@ -399,11 +383,11 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, 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]); + HDfprintf(stderr, "%s: i=%d Extending struct type\n" + "***displacements: 0, %d\n", FUNC, i, displacement[1]); #endif -#ifdef H5_HAVE_MPI2 /* have MPI-2 */ +#ifdef H5_HAVE_MPI2 /* have MPI-2 (this function is not included in MPICH) */ mpi_code = MPI_Type_create_resized ( outer_type, /* old type */ 0, /* blocklengths */ @@ -417,10 +401,6 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, 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 mpi_code = MPI_Type_struct ( 2, /* count */ block_length, /* blocklengths */ displacement, /* displacements */ @@ -450,7 +430,7 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, * values given in the hyperslab description: ***************************************************************/ displacement[0] = 0; - for (i=new_rank-1; i>=0; i--) + for (i=rank-1; i>=0; i--) displacement[0] += d[i].start * offset[i]; if (displacement[0] > 0) { @@ -459,8 +439,8 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, 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", + HDfprintf(stderr, "%s: Making final struct\n***count=1:\n", FUNC); + HDfprintf(stderr, "\tblocklength[0]=%d; displacement[0]=%d\n", block_length[0], displacement[0]); #endif @@ -497,8 +477,14 @@ empty: *is_derived_type = 0; done: + /* Release selection iterator */ + if(sel_iter_init) { + if (H5S_select_iter_release(&sel_iter)<0) + HDONE_ERROR (H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection iterator"); + } /* end if */ + #ifdef H5Smpi_DEBUG - HDfprintf(stdout, "Leave %s, count=%Hu is_derived_type=%d\n", + HDfprintf(stderr, "Leave %s, count=%Hu is_derived_type=%d\n", FUNC, *count, *is_derived_type ); #endif FUNC_LEAVE_NOAPI(ret_value); @@ -506,81 +492,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5S_mpio_hyper_contig_type - * - * Purpose: Translate a contiguous 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) - * *extra_offset Number of bytes of offset within dataset - * *is_derived_type 0 if MPI primitive type, 1 if derived - * - * Programmer: Quincey Koziol, 2002/06/17 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -static herr_t -H5S_mpio_hyper_contig_type( const H5S_t *space, size_t elmt_size, - /* out: */ - MPI_Datatype *new_type, - size_t *count, - hsize_t *extra_offset, - hbool_t *is_derived_type ) -{ - hsize_t total_bytes; /* Number of bytes in selection */ - hssize_t nelem; /* Number of elements in selection */ - hsize_t byte_offset; /* Byte offset of contiguous region within selection */ - hsize_t acc; /* Accumulator */ - hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ - hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset in selection */ - int ndims; /* Number of dimensions of dataset */ - int i; /* Local index */ - - FUNC_ENTER_NOINIT(H5S_mpio_hyper_contig_type); - - /* Check args */ - assert (space); - - /* Get the number of elements in the selection */ - nelem=(*space->select.get_npoints)(space); - - /* Compute the number of bytes in selection */ - total_bytes = (hsize_t)elmt_size*nelem; - - /* Set up convenient alias */ - ndims=space->extent.u.simple.rank; - - /* Initialize row sizes for each dimension */ - for(i=(ndims-1),acc=1; i>=0; i--) { - slab[i]=acc*elmt_size; - acc*=space->extent.u.simple.size[i]; - } /* end for */ - - /* Get in the selection offset */ - assert(space->select.sel_info.hslab.diminfo); - for(i=0; i<ndims; i++) - offset[i] = space->select.sel_info.hslab.diminfo[i].start+space->select.offset[i]; - - /* Compute the initial buffer offset */ - for(i=0,byte_offset=0; i<ndims; i++) - byte_offset+=offset[i]*slab[i]; - - /* fill in the return values */ - *new_type = MPI_BYTE; - H5_ASSIGN_OVERFLOW(*count, total_bytes, hsize_t, size_t); - *extra_offset = byte_offset; - *is_derived_type = 0; - - FUNC_LEAVE_NOAPI(SUCCEED); -} /* end H5S_mpio_hyper_contig_type() */ - - -/*------------------------------------------------------------------------- * Function: H5S_mpio_space_type * * Purpose: Translate an HDF5 dataspace selection into an MPI type. @@ -641,16 +552,9 @@ H5S_mpio_space_type( const H5S_t *space, size_t elmt_size, break; case H5S_SEL_HYPERSLABS: - if((*space->select.is_contiguous)(space)) { - if(H5S_mpio_hyper_contig_type( space, elmt_size, - /* out: */ new_type, count, extra_offset, is_derived_type )<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type"); - } /* end if */ - else { - if(H5S_mpio_hyper_type( space, elmt_size, - /* out: */ new_type, count, extra_offset, is_derived_type )<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type"); - } /* end else */ + if(H5S_mpio_hyper_type( space, elmt_size, + /* out: */ new_type, count, extra_offset, is_derived_type )<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type"); break; default: @@ -770,7 +674,7 @@ H5S_mpio_spaces_xfer(H5F_t *f, const H5O_layout_t *layout, size_t elmt_size, */ addr = f->shared->base_addr + layout->addr + mpi_file_offset; #ifdef H5Smpi_DEBUG - HDfprintf(stdout, "spaces_xfer: addr=%a\n", addr ); + HDfprintf(stderr, "spaces_xfer: addr=%a\n", addr ); #endif /* |