diff options
Diffstat (limited to 'src/H5Shyper.c')
| -rw-r--r-- | src/H5Shyper.c | 537 |
1 files changed, 388 insertions, 149 deletions
diff --git a/src/H5Shyper.c b/src/H5Shyper.c index c59d38e..24fca4c 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -12,6 +12,8 @@ #include <H5Sprivate.h> #include <H5Vprivate.h> #include <H5MMprivate.h> +#include <H5TBprivate.h> +#include <H5Dprivate.h> /* Interface initialization */ #define PABLO_MASK H5S_hyper_mask @@ -29,7 +31,7 @@ typedef struct { const H5S_t *space; H5S_sel_iter_t *iter; size_t nelmts; - H5D_transfer_t xfer_mode; + const H5D_xfer_t *xfer_parms; const void *src; void *dst; H5S_hyper_bound_t **lo_bounds; @@ -39,7 +41,7 @@ typedef struct { /* Static function prototypes */ static intn H5S_hyper_bsearch(hssize_t size, H5S_hyper_bound_t *barr, size_t count); -static H5S_hyper_region_t * +static hid_t H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, H5S_hyper_bound_t **lo_bounds, H5S_hyper_bound_t **hi_bounds, hssize_t *pos, @@ -56,14 +58,14 @@ static size_t H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, size_t nelmts, - const H5D_transfer_t xfer_mode, + const void *_xfer_parms, void *buf/*out*/); static herr_t H5S_hyper_fscat (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, H5S_sel_iter_t *file_iter, size_t nelmts, - const H5D_transfer_t xfer_mode, + const void *_xfer_parms, const void *buf); static size_t H5S_hyper_mgath (const void *_buf, size_t elmt_size, const H5S_t *mem_space, @@ -91,6 +93,9 @@ const H5S_mconv_t H5S_HYPER_MCONV[1] = {{ H5S_hyper_mscat, /*scatter */ }}; +/* Array for use with I/O algorithms which frequently need array of zeros */ +static const hssize_t zero[H5O_LAYOUT_NDIMS]={0}; /* Array of zeros */ + /*------------------------------------------------------------------------- * Function: H5S_hyper_init @@ -178,14 +183,12 @@ H5S_hyper_favail (const H5S_t __unused__ *space, int H5S_hyper_compare_regions (const void *r1, const void *r2) { - if (((const H5S_hyper_region_t *)r1)->start < - ((const H5S_hyper_region_t *)r2)->start) + if (((const H5S_hyper_region_t *)r1)->start < ((const H5S_hyper_region_t *)r2)->start) return(-1); - else if (((const H5S_hyper_region_t *)r1)->start > - ((const H5S_hyper_region_t *)r2)->start) - return(1); + else if (((const H5S_hyper_region_t *)r1)->start > ((const H5S_hyper_region_t *)r2)->start) + return(1); else - return(0); + return(0); } /* end H5S_hyper_compare_regions */ /*------------------------------------------------------------------------- @@ -205,12 +208,13 @@ H5S_hyper_compare_regions (const void *r1, const void *r2) * *------------------------------------------------------------------------- */ -static H5S_hyper_region_t * +static hid_t H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, H5S_hyper_bound_t **lo_bounds, H5S_hyper_bound_t **hi_bounds, hssize_t *pos, hssize_t *offset) { - H5S_hyper_region_t *ret_value=NULL; /* Pointer to array to return */ + hid_t ret_value=FAIL; /* Id of temporary buffer to return */ + H5S_hyper_region_t *reg=NULL; /* Pointer to array of regions */ H5S_hyper_node_t *node; /* Region node for a given boundary */ size_t num_reg=0; /* Number of regions in array */ size_t curr_reg=0; /* The current region we are working with */ @@ -219,7 +223,7 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, intn temp_dim; /* Temporary dim. holder */ size_t i; /* Counters */ - FUNC_ENTER (H5S_hyper_get_regions, NULL); + FUNC_ENTER (H5S_hyper_get_regions, FAIL); assert(num_regions); assert(lo_bounds); @@ -242,12 +246,13 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, if(pos[0]==(-1) || ((pos[0]+offset[0])>=lo_bounds[0][i].bound && (pos[0]+offset[0]) <= hi_bounds[0][i].bound)) { /* Check if we've allocated the array yet */ if(num_reg==0) { - /* Allocate array */ - ret_value=H5MM_malloc(sizeof(H5S_hyper_region_t)); + /* Allocate temporary buffer */ + ret_value=H5TB_get_buf(sizeof(H5S_hyper_region_t),0,(void **)®); /* Initialize with first region */ - ret_value[0].start=MAX(lo_bounds[0][i].bound,pos[0])+offset[0]; - ret_value[0].end=hi_bounds[0][i].bound+offset[0]; + reg[0].start=MAX(lo_bounds[0][i].bound,pos[0])+offset[0]; + reg[0].end=hi_bounds[0][i].bound+offset[0]; + reg[0].node=hi_bounds[0][i].node; /* Increment the number of regions */ num_reg++; @@ -256,20 +261,22 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, * Check if we should merge this region into the current * region. */ - if(lo_bounds[0][i].bound<ret_value[curr_reg].end) { - ret_value[curr_reg].end=MAX(hi_bounds[0][i].bound, - ret_value[curr_reg].end)+(offset!=NULL ? offset[0] : 0 ); + if(lo_bounds[0][i].bound<reg[curr_reg].end) { + reg[curr_reg].end=MAX(hi_bounds[0][i].bound, + reg[curr_reg].end)+(offset!=NULL ? offset[0] : 0 ); } else { /* no overlap with previous region, add new region */ /* Check if this is actually a different region */ - if(lo_bounds[0][i].bound!=ret_value[curr_reg].start && - hi_bounds[0][i].bound!=ret_value[curr_reg].end) { + if(lo_bounds[0][i].bound!=reg[curr_reg].start && + hi_bounds[0][i].bound!=reg[curr_reg].end) { /* Enlarge array */ - ret_value=H5MM_realloc(ret_value,(sizeof(H5S_hyper_region_t)*(num_reg+1))); + H5TB_resize_buf(ret_value,(sizeof(H5S_hyper_region_t)*(num_reg+1))); + reg=H5TB_buf_ptr(ret_value); /* Initialize with new region */ - ret_value[num_reg].start=lo_bounds[0][i].bound+offset[0]; - ret_value[num_reg].end=hi_bounds[0][i].bound+offset[0]; + reg[num_reg].start=lo_bounds[0][i].bound+offset[0]; + reg[num_reg].end=hi_bounds[0][i].bound+offset[0]; + reg[num_reg].node=hi_bounds[0][i].node; /* * Increment the number of regions & the current @@ -329,19 +336,20 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, #ifdef QAK printf("%s: check 3.1\n", FUNC); #endif /* QAK */ - /* Allocate array */ - ret_value=H5MM_malloc(sizeof(H5S_hyper_region_t)); + /* Allocate temporary buffer */ + ret_value=H5TB_get_buf(sizeof(H5S_hyper_region_t),0,(void **)®); /* Initialize with first region */ - ret_value[0].start=MAX(node->start[next_dim],pos[next_dim])+offset[next_dim]; - ret_value[0].end=node->end[next_dim]+offset[next_dim]; + reg[0].start=MAX(node->start[next_dim],pos[next_dim])+offset[next_dim]; + reg[0].end=node->end[next_dim]+offset[next_dim]; + reg[0].node=node; #ifdef QAK printf("%s: check 3.2, lo_bounds=%d, start=%d, " "hi_bounds=%d, end=%d\n", FUNC, (int)node->start[next_dim], - (int)ret_value[curr_reg].start, + (int)reg[curr_reg].start, (int)node->end[next_dim], - (int)ret_value[curr_reg].end); + (int)reg[curr_reg].end); #endif /* QAK */ /* Increment the number of regions */ @@ -351,18 +359,18 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, printf("%s: check 4.0, lo_bounds=%d, start=%d, " "hi_bounds=%d, end=%d\n", FUNC, (int)node->start[next_dim], - (int)ret_value[curr_reg].start, + (int)reg[curr_reg].start, (int)node->end[next_dim], - (int)ret_value[curr_reg].end); + (int)reg[curr_reg].end); #endif /* QAK */ /* Enlarge array */ - ret_value=H5MM_realloc(ret_value, - (sizeof(H5S_hyper_region_t)* - (num_reg+1))); + H5TB_resize_buf(ret_value,(sizeof(H5S_hyper_region_t)*(num_reg+1))); + reg=H5TB_buf_ptr(ret_value); /* Initialize with new region */ - ret_value[num_reg].start=node->start[next_dim]+offset[next_dim]; - ret_value[num_reg].end=node->end[next_dim]+offset[next_dim]; + reg[num_reg].start=node->start[next_dim]+offset[next_dim]; + reg[num_reg].end=node->end[next_dim]+offset[next_dim]; + reg[num_reg].node=node; /* Increment the number of regions & the current region */ num_reg++; @@ -373,15 +381,15 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, /* Sort region list and eliminate duplicates if necessary */ if(num_reg>1) { - HDqsort(ret_value,num_reg,sizeof(H5S_hyper_region_t), - H5S_hyper_compare_regions); + HDqsort(reg,num_reg,sizeof(H5S_hyper_region_t),H5S_hyper_compare_regions); for(i=1,curr_reg=0,uniq_reg=1; i<num_reg; i++) { - if(ret_value[curr_reg].start!=ret_value[i].start && - ret_value[curr_reg].end!=ret_value[i].end) { + if(reg[curr_reg].start!=reg[i].start && + reg[curr_reg].end!=reg[i].end) { uniq_reg++; curr_reg++; - ret_value[curr_reg].start=ret_value[i].start; - ret_value[curr_reg].end=ret_value[i].end; + reg[curr_reg].start=reg[i].start; + reg[curr_reg].end=reg[i].end; + reg[curr_reg].node=reg[i].node; } /* end if */ } /* end for */ num_reg=uniq_reg; @@ -392,17 +400,194 @@ H5S_hyper_get_regions (size_t *num_regions, intn dim, size_t bound_count, *num_regions=num_reg; #ifdef QAK - printf("%s: check 10.0, ret_value=%p, num_reg=%d\n", - FUNC,ret_value,num_reg); + printf("%s: check 10.0, reg=%p, num_reg=%d\n", + FUNC,reg,num_reg); for(i=0; i<num_reg; i++) printf("%s: start[%d]=%d, end[%d]=%d\n", - FUNC,i,(int)ret_value[i].start,i,(int)ret_value[i].end); + FUNC,i,(int)reg[i].start,i,(int)reg[i].end); #endif /* QAK */ FUNC_LEAVE (ret_value); } /* end H5S_hyper_get_regions() */ /*------------------------------------------------------------------------- + * Function: H5S_hyper_block_cache + * + * Purpose: Cache a hyperslab block for reading or writing. + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Quincey Koziol + * Monday, September 21, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5S_hyper_block_cache (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_info, uintn block_read) +{ + hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ + hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ + intn i; /* Counters */ + + FUNC_ENTER (H5S_hyper_block_cache, SUCCEED); + + assert(node); + assert(fhyper_info); + + /* Allocate temporary buffer of proper size */ + if((node->cinfo.block_id=H5TB_get_buf(node->cinfo.size*fhyper_info->elmt_size,1,(void **)&(node->cinfo.block)))==FAIL) + HRETURN_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, + "can't allocate hyperslab cache block"); + + /* Read in block, if we are read caching */ + if(block_read) { + /* Copy the location of the region in the file */ + HDmemcpy(file_offset,node->start,(fhyper_info->space->extent.u.simple.rank * sizeof(hssize_t))); + file_offset[fhyper_info->space->extent.u.simple.rank]=0; + + /* Set the hyperslab size to read */ + for(i=0; i<fhyper_info->space->extent.u.simple.rank; i++) + hsize[i]=(node->end[i]-node->start[i])+1; + hsize[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; + + if (H5F_arr_read (fhyper_info->f, fhyper_info->layout, + fhyper_info->pline, fhyper_info->efl, + hsize, hsize, zero, file_offset, + fhyper_info->xfer_parms->xfer_mode, node->cinfo.block/*out*/)<0) + HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, FAIL, "read error"); + } /* end if */ + else { +/* keep information for writing block later? */ + } /* end else */ + + /* Set up parameters for accessing block */ + node->cinfo.left=node->cinfo.size; + node->cinfo.pos=node->cinfo.block; + + /* Set cached flag */ + node->cinfo.cached=1; + + FUNC_LEAVE (SUCCEED); +} /* H5S_hyper_block_cache() */ + +/*------------------------------------------------------------------------- + * Function: H5S_hyper_block_read + * + * Purpose: Read in data from a cached hyperslab block + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Quincey Koziol + * Monday, September 21, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5S_hyper_block_read (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_info, hsize_t region_size) +{ + FUNC_ENTER (H5S_hyper_block_read, SUCCEED); + + assert(node && node->cinfo.cached); + assert(fhyper_info); + + /* Copy the elements into the user's buffer */ + /* + !! NOTE !! This will need to be changed for different dimension + permutations from the standard 'C' ordering! + */ + HDmemcpy(fhyper_info->dst,node->cinfo.pos,region_size*fhyper_info->elmt_size); + + /* Decrement the number of elements left in block to read & move the offset */ + node->cinfo.pos+=region_size*fhyper_info->elmt_size; + node->cinfo.left-=region_size; + + /* If we've read in all the elements from the block, throw it away */ + if(node->cinfo.left==0) { + /* Release the temporary buffer */ + H5TB_release_buf(node->cinfo.block_id); + + /* Reset the caching flag for next time */ + node->cinfo.cached=0; + } /* end if */ + + FUNC_LEAVE (SUCCEED); +} /* H5S_hyper_block_read() */ + +/*------------------------------------------------------------------------- + * Function: H5S_hyper_block_write + * + * Purpose: Write out data to a cached hyperslab block + * + * Return: Success: SUCCEED + * + * Failure: FAIL + * + * Programmer: Quincey Koziol + * Monday, September 21, 1998 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5S_hyper_block_write (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_info, hsize_t region_size) +{ + hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ + hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ + intn i; /* Counters */ + + FUNC_ENTER (H5S_hyper_block_write, SUCCEED); + + assert(node && node->cinfo.cached); + assert(fhyper_info); + + /* Copy the elements into the user's buffer */ + /* + !! NOTE !! This will need to be changed for different dimension + permutations from the standard 'C' ordering! + */ + HDmemcpy(node->cinfo.pos,fhyper_info->src,region_size*fhyper_info->elmt_size); + + /* Decrement the number of elements left in block to read & move the offset */ + node->cinfo.pos+=region_size*fhyper_info->elmt_size; + node->cinfo.left-=region_size; + + /* If we've read in all the elements from the block, throw it away */ + if(node->cinfo.left==0) { + /* Copy the location of the region in the file */ + HDmemcpy(file_offset,node->start,(fhyper_info->space->extent.u.simple.rank * sizeof(hssize_t))); + file_offset[fhyper_info->space->extent.u.simple.rank]=0; + + /* Set the hyperslab size to write */ + for(i=0; i<fhyper_info->space->extent.u.simple.rank; i++) + hsize[i]=(node->end[i]-node->start[i])+1; + hsize[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; + + if (H5F_arr_write (fhyper_info->f, fhyper_info->layout, + fhyper_info->pline, fhyper_info->efl, + hsize, hsize, zero, file_offset, + fhyper_info->xfer_parms->xfer_mode, node->cinfo.block/*out*/)<0) + HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); + + /* Release the temporary buffer */ + H5TB_release_buf(node->cinfo.block_id); + + /* Reset the caching flag for next time */ + node->cinfo.cached=0; + } /* end if */ + + FUNC_LEAVE (SUCCEED); +} /* H5S_hyper_block_write() */ + +/*------------------------------------------------------------------------- * Function: H5S_hyper_fread * * Purpose: Recursively gathers data points from a file using the @@ -425,7 +610,8 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ hsize_t region_size; /* Size of lowest region */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ + uintn parm_init=0; /* Whether one-shot parameters set up */ + hid_t reg_id; /* ID of temporary region buffer */ H5S_hyper_region_t *regions; /* Pointer to array of hyperslab nodes overlapped */ size_t num_regions; /* number of regions overlapped */ size_t i; /* Counters */ @@ -442,10 +628,13 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) /* Get a sorted list (in the next dimension down) of the regions which */ /* overlap the current index in this dim */ - if((regions=H5S_hyper_get_regions(&num_regions,dim, + if((reg_id=H5S_hyper_get_regions(&num_regions,dim, fhyper_info->space->select.sel_info.hyper.hyper_lst->count, fhyper_info->lo_bounds, fhyper_info->hi_bounds, - fhyper_info->iter->hyp.pos,fhyper_info->space->select.offset))!=NULL) { + fhyper_info->iter->hyp.pos,fhyper_info->space->select.offset))!=FAIL) { + + /* Get the pointer to the actual regions array */ + regions=H5TB_buf_ptr(reg_id); /* * Check if this is the second to last dimension in dataset (Which @@ -461,50 +650,63 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) #endif /* QAK */ if((dim+2)==fhyper_info->space->extent.u.simple.rank) { - /* Set up hyperslab I/O parameters which apply to all regions */ - - /* Copy the location of the region in the file */ - HDmemcpy(file_offset, fhyper_info->iter->hyp.pos, - (fhyper_info->space->extent.u.simple.rank * - sizeof(hssize_t))); - file_offset[fhyper_info->space->extent.u.simple.rank]=0; + /* perform I/O on data from regions */ + for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { + /* Compute the size of the region to read */ + region_size=MIN(fhyper_info->nelmts, (regions[i].end-regions[i].start)+1); - /* Set the hyperslab size to copy */ - hsize[0]=1; - H5V_array_fill(hsize, hsize, sizeof(hsize[0]), - fhyper_info->space->extent.u.simple.rank); - hsize[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; + /* Check if this hyperslab block is cached or could be cached */ + if(!regions[i].node->cinfo.cached && (fhyper_info->xfer_parms->cache_hyper && (fhyper_info->xfer_parms->block_limit==0 || fhyper_info->xfer_parms->block_limit>=(regions[i].node->cinfo.size*fhyper_info->elmt_size)))) { + /* if we aren't cached, attempt to cache the block */ + H5S_hyper_block_cache(regions[i].node,fhyper_info,1); + } /* end if */ - /* Set the memory offset to the origin */ - HDmemset (zero, 0, fhyper_info->layout->ndims*sizeof(*zero)); + /* Read information from the cached block */ + if(regions[i].node->cinfo.cached) { + if(H5S_hyper_block_read(regions[i].node,fhyper_info,region_size)==FAIL) + HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "read error"); + } + else { + /* Set up hyperslab I/O parameters which apply to all regions */ + if(!parm_init) { + /* Copy the location of the region in the file */ + HDmemcpy(file_offset,fhyper_info->iter->hyp.pos,(fhyper_info->space->extent.u.simple.rank * sizeof(hssize_t))); + file_offset[fhyper_info->space->extent.u.simple.rank]=0; + + /* Set the hyperslab size to copy */ + hsize[0]=1; + H5V_array_fill(hsize,hsize,sizeof(hsize[0]),fhyper_info->space->extent.u.simple.rank); + hsize[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; + + /* Set flag */ + parm_init=1; + } /* end if */ - /* perform I/O on data from regions */ - for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { #ifdef QAK - printf("%s: check 2.2, i=%d\n",FUNC,(int)i); + printf("%s: check 2.2, i=%d\n",FUNC,(int)i); #endif /* QAK */ - region_size=MIN(fhyper_info->nelmts, - (regions[i].end-regions[i].start)+1); - hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size; - file_offset[fhyper_info->space->extent.u.simple.rank-1]=regions[i].start; + /* Fill in the region specific parts of the I/O request */ + hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size; + file_offset[fhyper_info->space->extent.u.simple.rank-1]=regions[i].start; - /* - * Gather from file. - */ - if (H5F_arr_read (fhyper_info->f, fhyper_info->layout, - fhyper_info->pline, fhyper_info->efl, - hsize, hsize, zero, file_offset, - fhyper_info->xfer_mode, - fhyper_info->dst/*out*/)<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, - "read error"); - } + /* + * Gather from file. + */ + if (H5F_arr_read (fhyper_info->f, fhyper_info->layout, + fhyper_info->pline, fhyper_info->efl, + hsize, hsize, zero, file_offset, + fhyper_info->xfer_parms->xfer_mode, + fhyper_info->dst/*out*/)<0) { + HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, + "read error"); + } #ifdef QAK - printf("%s: check 2.3, region #%d\n",FUNC,(int)i); - for(j=0; j<fhyper_info->space->extent.u.simple.rank; j++) - printf("%s: %d - pos=%d\n", - FUNC,j,(int)fhyper_info->iter->hyp.pos[j]); + printf("%s: check 2.3, region #%d\n",FUNC,(int)i); + for(j=0; j<fhyper_info->space->extent.u.simple.rank; j++) + printf("%s: %d - pos=%d\n", + FUNC,j,(int)fhyper_info->iter->hyp.pos[j]); #endif /* QAK */ + } /* end else */ /* Advance the pointer in the buffer */ fhyper_info->dst = ((uint8 *)fhyper_info->dst) + @@ -520,8 +722,7 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) if(region_size==(hsize_t)((regions[i].end-regions[i].start)+1)) fhyper_info->iter->hyp.pos[dim+1]=(-1); else - fhyper_info->iter->hyp.pos[dim+1] = regions[i].start + - region_size; + fhyper_info->iter->hyp.pos[dim+1] = regions[i].start + region_size; /* Decrement the iterator count */ fhyper_info->iter->hyp.elmt_left-=region_size; @@ -537,9 +738,7 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) /* Step through each region in this dimension */ for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { /* Step through each location in each region */ - for(j=regions[i].start; - j<=regions[i].end && fhyper_info->nelmts>0; - j++) { + for(j=regions[i].start; j<=regions[i].end && fhyper_info->nelmts>0; j++) { #ifdef QAK printf("%s: check 4.0, dim=%d, location=%d\n",FUNC,dim,j); #endif /* QAK */ @@ -560,8 +759,8 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) } /* end for */ } /* end else */ - /* Free the region space */ - H5MM_xfree(regions); + /* Release the temporary buffer */ + H5TB_release_buf(reg_id); } /* end if */ FUNC_LEAVE (num_read); @@ -595,9 +794,10 @@ H5S_hyper_fgath (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, H5S_sel_iter_t *file_iter, - size_t nelmts, const H5D_transfer_t xfer_mode, + size_t nelmts, const void *_xfer_parms, void *_buf/*out*/) { + const H5D_xfer_t *xfer_parms=(const H5D_xfer_t *)_xfer_parms; /* Coerce the type */ H5S_hyper_bound_t **lo_bounds; /* Lower (closest to the origin) bound array for each dimension */ H5S_hyper_bound_t **hi_bounds; /* Upper (farthest from the origin) bound array for each dimension */ H5S_hyper_fhyper_info_t fhyper_info; /* Block of parameters to pass into recursive calls */ @@ -642,7 +842,7 @@ H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout, fhyper_info.space=file_space; fhyper_info.iter=file_iter; fhyper_info.nelmts=nelmts; - fhyper_info.xfer_mode=xfer_mode; + fhyper_info.xfer_parms=xfer_parms; fhyper_info.src=NULL; fhyper_info.dst=_buf; fhyper_info.lo_bounds=lo_bounds; @@ -688,7 +888,8 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ hsize_t region_size; /* Size of lowest region */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ + uintn parm_init=0; /* Whether one-shot parameters set up */ + hid_t reg_id; /* ID of temporary region buffer */ H5S_hyper_region_t *regions; /* Pointer to array of hyperslab nodes overlapped */ size_t num_regions; /* number of regions overlapped */ size_t i; /* Counters */ @@ -699,52 +900,77 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) assert(fhyper_info); +#ifdef QAK + printf("%s: check 1.0\n", FUNC); +#endif /* QAK */ /* Get a sorted list (in the next dimension down) of the regions which */ /* overlap the current index in this dim */ - if((regions=H5S_hyper_get_regions(&num_regions,dim, + if((reg_id=H5S_hyper_get_regions(&num_regions,dim, fhyper_info->space->select.sel_info.hyper.hyper_lst->count, fhyper_info->lo_bounds, fhyper_info->hi_bounds, - fhyper_info->iter->hyp.pos,fhyper_info->space->select.offset))!=NULL) { + fhyper_info->iter->hyp.pos,fhyper_info->space->select.offset))!=FAIL) { + + /* Get the pointer to the actual regions array */ + regions=H5TB_buf_ptr(reg_id); +#ifdef QAK + printf("%s: check 1.1, regions=%p\n", FUNC,regions); +#endif /* QAK */ /* Check if this is the second to last dimension in dataset */ /* (Which means that we've got a list of the regions in the fastest */ /* changing dimension and should input those regions) */ if((dim+2)==fhyper_info->space->extent.u.simple.rank) { - /* Set up hyperslab I/O parameters which apply to all regions */ + /* perform I/O on data from regions */ + for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { + /* Compute the size of the region to read */ + region_size=MIN(fhyper_info->nelmts, (regions[i].end-regions[i].start)+1); - /* Copy the location of the region in the file */ - HDmemcpy(file_offset, fhyper_info->iter->hyp.pos, - (fhyper_info->space->extent.u.simple.rank * - sizeof(hssize_t))); - file_offset[fhyper_info->space->extent.u.simple.rank]=0; + /* Check if this hyperslab block is cached or could be cached */ + if(!regions[i].node->cinfo.cached && (fhyper_info->xfer_parms->cache_hyper && (fhyper_info->xfer_parms->block_limit==0 || fhyper_info->xfer_parms->block_limit>=(regions[i].node->cinfo.size*fhyper_info->elmt_size)))) { + /* if we aren't cached, attempt to cache the block */ + H5S_hyper_block_cache(regions[i].node,fhyper_info,0); + } /* end if */ - /* Set the hyperslab size to copy */ - hsize[0]=1; - H5V_array_fill(hsize, hsize, sizeof(hsize[0]), - fhyper_info->space->extent.u.simple.rank); - hsize[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; + /* Read information from the cached block */ + if(regions[i].node->cinfo.cached) { + if(H5S_hyper_block_write(regions[i].node,fhyper_info,region_size)==FAIL) + HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); + } + else { + /* Set up hyperslab I/O parameters which apply to all regions */ + if(!parm_init) { - /* Set the memory offset to the origin */ - HDmemset (zero, 0, fhyper_info->layout->ndims*sizeof(*zero)); + /* Copy the location of the region in the file */ + HDmemcpy(file_offset, fhyper_info->iter->hyp.pos, + (fhyper_info->space->extent.u.simple.rank * + sizeof(hssize_t))); + file_offset[fhyper_info->space->extent.u.simple.rank]=0; - /* perform I/O on data from regions */ - for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { - region_size=MIN(fhyper_info->nelmts, - (regions[i].end-regions[i].start)+1); - hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size; - file_offset[fhyper_info->space->extent.u.simple.rank-1]=regions[i].start; + /* Set the hyperslab size to copy */ + hsize[0]=1; + H5V_array_fill(hsize, hsize, sizeof(hsize[0]), + fhyper_info->space->extent.u.simple.rank); + hsize[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; - /* - * Scatter from file. - */ - if (H5F_arr_write (fhyper_info->f, fhyper_info->layout, - fhyper_info->pline, fhyper_info->efl, - hsize, hsize, zero, file_offset, - fhyper_info->xfer_mode, - fhyper_info->src)<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); - } + /* Set flag */ + parm_init=1; + } /* end if */ + + hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size; + file_offset[fhyper_info->space->extent.u.simple.rank-1]=regions[i].start; + + /* + * Scatter to file. + */ + if (H5F_arr_write (fhyper_info->f, fhyper_info->layout, + fhyper_info->pline, fhyper_info->efl, + hsize, hsize, zero, file_offset, + fhyper_info->xfer_parms->xfer_mode, + fhyper_info->src)<0) { + HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); + } + } /* end else */ /* Advance the pointer in the buffer */ fhyper_info->src = ((const uint8 *)fhyper_info->src) + @@ -794,10 +1020,13 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) } /* end for */ } /* end else */ - /* Free the region space */ - H5MM_xfree(regions); + /* Release the temporary buffer */ + H5TB_release_buf(reg_id); } /* end if */ +#ifdef QAK + printf("%s: check 2.0\n", FUNC); +#endif /* QAK */ FUNC_LEAVE (num_written); } /* H5S_hyper_fwrite() */ @@ -826,9 +1055,10 @@ H5S_hyper_fscat (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, H5S_sel_iter_t *file_iter, - size_t nelmts, const H5D_transfer_t xfer_mode, + size_t nelmts, const void *_xfer_parms, const void *_buf) { + const H5D_xfer_t *xfer_parms=(const H5D_xfer_t *)_xfer_parms; /* Coerce the type */ H5S_hyper_bound_t **lo_bounds; /* Lower (closest to the origin) bound array for each dimension */ H5S_hyper_bound_t **hi_bounds; /* Upper (farthest from the origin) bound array for each dimension */ H5S_hyper_fhyper_info_t fhyper_info; /* Block of parameters to pass into recursive calls */ @@ -874,7 +1104,7 @@ H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout, fhyper_info.space=file_space; fhyper_info.iter=file_iter; fhyper_info.nelmts=nelmts; - fhyper_info.xfer_mode=xfer_mode; + fhyper_info.xfer_parms=xfer_parms; fhyper_info.src=_buf; fhyper_info.dst=NULL; fhyper_info.lo_bounds=lo_bounds; @@ -888,6 +1118,9 @@ H5S_hyper_fscat (H5F_t *f, const struct H5O_layout_t *layout, H5MM_xfree(lo_bounds); H5MM_xfree(hi_bounds); +#ifdef QAK + printf("%s: check 2.0\n", FUNC); +#endif /* QAK */ FUNC_LEAVE (num_written); } /* H5S_hyper_fscat() */ @@ -915,7 +1148,7 @@ H5S_hyper_mread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in memory*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ hsize_t region_size; /* Size of lowest region */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ + hid_t reg_id; /* ID of temporary region buffer */ H5S_hyper_region_t *regions; /* Pointer to array of hyperslab nodes overlapped */ size_t num_regions; /* number of regions overlapped */ size_t i; /* Counters */ @@ -932,10 +1165,13 @@ H5S_hyper_mread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) /* Get a sorted list (in the next dimension down) of the regions which */ /* overlap the current index in this dim */ - if((regions=H5S_hyper_get_regions(&num_regions,dim, + if((reg_id=H5S_hyper_get_regions(&num_regions,dim, fhyper_info->space->select.sel_info.hyper.hyper_lst->count, fhyper_info->lo_bounds, fhyper_info->hi_bounds, - fhyper_info->iter->hyp.pos,fhyper_info->space->select.offset))!=NULL) { + fhyper_info->iter->hyp.pos,fhyper_info->space->select.offset))!=FAIL) { + + /* Get the pointer to the actual regions array */ + regions=H5TB_buf_ptr(reg_id); /* Check if this is the second to last dimension in dataset */ /* (Which means that we've got a list of the regions in the fastest */ @@ -970,10 +1206,6 @@ H5S_hyper_mread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) fhyper_info->space->extent.u.simple.rank); hsize[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; - /* Set the memory offset to the origin */ - HDmemset (zero, 0, ((fhyper_info->space->extent.u.simple.rank+1)* - sizeof(*zero))); - /* perform I/O on data from regions */ for(i=0; i<num_regions && fhyper_info->nelmts>0; i++) { region_size=MIN(fhyper_info->nelmts, @@ -1049,8 +1281,8 @@ H5S_hyper_mread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) } /* end for */ } /* end else */ - /* Free the region space */ - H5MM_xfree(regions); + /* Release the temporary buffer */ + H5TB_release_buf(reg_id); } /* end if */ FUNC_LEAVE (num_read); @@ -1190,7 +1422,7 @@ H5S_hyper_mwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ hsize_t region_size; /* Size of lowest region */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ + hid_t reg_id; /* ID of temporary region buffer */ H5S_hyper_region_t *regions; /* Pointer to array of hyperslab nodes overlapped */ size_t num_regions; /* number of regions overlapped */ size_t i; /* Counters */ @@ -1206,10 +1438,13 @@ H5S_hyper_mwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) /* Get a sorted list (in the next dimension down) of the regions which */ /* overlap the current index in this dim */ - if((regions=H5S_hyper_get_regions(&num_regions,dim, + if((reg_id=H5S_hyper_get_regions(&num_regions,dim, fhyper_info->space->select.sel_info.hyper.hyper_lst->count, fhyper_info->lo_bounds, fhyper_info->hi_bounds, - fhyper_info->iter->hyp.pos,fhyper_info->space->select.offset))!=NULL) { + fhyper_info->iter->hyp.pos,fhyper_info->space->select.offset))!=FAIL) { + + /* Get the pointer to the actual regions array */ + regions=H5TB_buf_ptr(reg_id); #ifdef QAK printf("%s: check 2.0, rank=%d\n", @@ -1242,10 +1477,6 @@ H5S_hyper_mwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) fhyper_info->space->extent.u.simple.rank); hsize[fhyper_info->space->extent.u.simple.rank]=fhyper_info->elmt_size; - /* Set the memory offset to the origin */ - HDmemset (zero, 0, ((fhyper_info->space->extent.u.simple.rank+1)* - sizeof(*zero))); - #ifdef QAK printf("%s: check 3.0\n",FUNC); #endif /* QAK */ @@ -1323,8 +1554,8 @@ H5S_hyper_mwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info) } /* end for */ } /* end else */ - /* Free the region space */ - H5MM_xfree(regions); + /* Release the temporary buffer */ + H5TB_release_buf(reg_id); } /* end if */ FUNC_LEAVE (num_read); @@ -1545,6 +1776,13 @@ H5S_hyper_add (H5S_t *space, const hssize_t *start, const hsize_t *size) elem_count*=size[i]; } /* end for */ + /* Initialize caching parameters */ + slab->cinfo.cached=0; + slab->cinfo.size=elem_count; + slab->cinfo.left=0; + slab->cinfo.block_id=(-1); + slab->cinfo.block=slab->cinfo.pos=NULL; + #ifdef QAK printf("%s: check 3.0, lo_bounds=%p, hi_bounds=%p\n", FUNC, space->select.sel_info.hyper.hyper_lst->lo_bounds, @@ -1942,6 +2180,7 @@ H5S_hyper_copy (H5S_t *dst, const H5S_t *src) if((new = H5MM_malloc(sizeof(H5S_hyper_node_t)))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate point node"); + HDmemcpy(new,curr,sizeof(H5S_hyper_node_t)); /* copy caching information */ if((new->start = H5MM_malloc(src->extent.u.simple.rank*sizeof(hssize_t)))==NULL) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't allocate coordinate information"); |