diff options
Diffstat (limited to 'src/H5Shyper.c')
| -rw-r--r-- | src/H5Shyper.c | 353 |
1 files changed, 325 insertions, 28 deletions
diff --git a/src/H5Shyper.c b/src/H5Shyper.c index 2904b51..9733152 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -1906,18 +1906,20 @@ H5S_hyper_mread_opt (const void *_buf, size_t elmt_size, size_t nelmts, void *_tconv_buf/*out*/) { hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Size of the source buffer */ - hsize_t hsize[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset on disk */ + hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary block count */ hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block offset */ const uint8_t *src=(const uint8_t *)_buf; /* Alias for pointer arithmetic */ uint8_t *dst=(uint8_t *)_tconv_buf; /* Alias for pointer arithmetic */ intn fast_dim; /* Rank of the fastest changing dimension for the dataspace */ intn temp_dim; /* Temporary rank holder */ + hsize_t acc; /* Accumulator */ + size_t buf_off; /* Buffer offset for copying memory */ intn i; /* Counters */ intn ndims; /* Number of dimensions of dataset */ uintn actual_read; /* The actual number of elements to read in */ + uintn actual_bytes; /* The actual number of bytes to copy */ size_t num_read=0; /* Number of elements read */ FUNC_ENTER (H5S_hyper_fread_opt, 0); @@ -1936,22 +1938,24 @@ for(i=0; i<mem_space->extent.u.simple.rank; i++) printf("%s: mem_file->hyp.pos[%d]=%d\n",FUNC,(int)i,(int)mem_iter->hyp.pos[i]); #endif /* QAK */ - /* Set the rank of the fastest changing dimension */ + /* Set the aliases for dimension information */ fast_dim=mem_space->extent.u.simple.rank-1; - - /* Set up the hyperslab and 'zero' arrays */ ndims=mem_space->extent.u.simple.rank; - /* initialize hyperslab size and offset in memory buffer */ - for(i=0; i<(ndims+1); i++) { - hsize[i]=1; /* hyperslab size is 1, except for last element */ - zero[i]=0; /* memory offset is 0 */ - } /* end for */ - hsize[ndims] = elmt_size; /* Set up the size of the memory space */ HDmemcpy(mem_size, mem_space->extent.u.simple.size,mem_space->extent.u.simple.rank*sizeof(hsize_t)); mem_size[mem_space->extent.u.simple.rank]=elmt_size; + /* initialize row sizes for each dimension */ + for(i=(ndims-1),acc=1; i>=0; i--) { + slab[i]=acc*elmt_size; + acc*=mem_size[i]; + } /* end for */ +#ifdef QAK +for(i=0; i<ndims; i++) + printf("%s: mem_size[%d]=%d, slab[%d]=%d\n",FUNC,(int)i,(int)mem_size[i],(int)i,(int)slab[i]); +#endif /* QAK */ + /* Check if we stopped in the middle of a sequence of elements */ if((mem_iter->hyp.pos[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start)%mem_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0) { uintn leftover; /* The number of elements left over from the last sequence */ @@ -1964,9 +1968,7 @@ printf("%s: Check 1.0\n",FUNC); /* Make certain that we don't read too many */ actual_read=MIN(leftover,nelmts); - - /* Set the hyperslab size in the fastest changing dimension to read in */ - hsize[fast_dim]=actual_read; + actual_bytes=actual_read*elmt_size; /* Copy the location of the point to get */ HDmemcpy(offset, mem_iter->hyp.pos,ndims*sizeof(hssize_t)); @@ -1976,12 +1978,11 @@ printf("%s: Check 1.0\n",FUNC); for(i=0; i<ndims; i++) offset[i] += mem_space->select.offset[i]; - /* Scatter out the rest of the sequence, if possible */ - if (H5V_hyper_copy (ndims+1, hsize, - hsize, zero, dst, - mem_size, offset, src)<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "unable to gather data from memory"); - } + /* Compute the initial buffer offset */ + for(i=0,buf_off=0; i<ndims; i++) + buf_off+=offset[i]*slab[i]; + + HDmemcpy(dst,src+buf_off,actual_bytes); /* Increment the offset of the buffer */ dst+=elmt_size*actual_read; @@ -2031,9 +2032,19 @@ printf("%s: Check 2.0\n",FUNC); tmp_block[i] = (mem_iter->hyp.pos[i]-mem_space->select.sel_info.hslab.diminfo[i].start)/mem_space->select.sel_info.hslab.diminfo[i].stride; } /* end for */ + /* Compute the initial buffer offset */ + for(i=0,buf_off=0; i<ndims; i++) + buf_off+=offset[i]*slab[i]; + /* Set the number of elements to read each time */ actual_read=mem_space->select.sel_info.hslab.diminfo[fast_dim].block; - hsize[fast_dim]=actual_read; + + /* Set the number of actual bytes */ + actual_bytes=actual_read*elmt_size; +#ifdef QAK +printf("%s: buf_off=%u, actual_bytes=%u\n",FUNC,(unsigned)buf_off,(int)actual_bytes); +#endif /* QAK */ + #ifdef QAK printf("%s: actual_read=%d\n",FUNC,(int)actual_read); for(i=0; i<file_space->extent.u.simple.rank; i++) @@ -2049,7 +2060,7 @@ for(i=0; i<file_space->extent.u.simple.rank; i++) /* Check if we are running out of room in the buffer */ if((actual_read+num_read)>nelmts) { actual_read=nelmts-num_read; - hsize[fast_dim]=actual_read; + actual_bytes=actual_read*elmt_size; } /* end if */ #ifdef QAK @@ -2058,12 +2069,8 @@ for(i=0; i<mem_space->extent.u.simple.rank; i++) printf("%s: tmp_count[%d]=%d, offset[%d]=%d\n",FUNC,(int)i,(int)tmp_count[i],(int)i,(int)offset[i]); #endif /* QAK */ - /* Scatter out the rest of the sequence, if possible */ - if (H5V_hyper_copy (ndims+1, hsize, - hsize, zero, dst, - mem_size, offset, src)<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_READERROR, 0, "unable to gather data from memory"); - } + /* Scatter out the rest of the sequence */ + HDmemcpy(dst,src+buf_off,actual_bytes); /* Increment the offset of the buffer */ dst+=elmt_size*actual_read; @@ -2082,10 +2089,12 @@ for(i=0; i<mem_space->extent.u.simple.rank; i++) /* Check for partial block read! */ if(actual_read<mem_space->select.sel_info.hslab.diminfo[fast_dim].block) { offset[temp_dim]+=actual_read; + buf_off+=actual_bytes; break; } /* end if */ else { offset[temp_dim]+=mem_space->select.sel_info.hslab.diminfo[temp_dim].stride; /* reset the offset in the fastest dimension */ + buf_off+=slab[temp_dim]*mem_space->select.sel_info.hslab.diminfo[temp_dim].stride; tmp_count[temp_dim]++; } /* end else */ @@ -2095,11 +2104,16 @@ for(i=0; i<mem_space->extent.u.simple.rank; i++) else { tmp_count[temp_dim]=0; /* reset back to the beginning of the line */ offset[temp_dim]=mem_space->select.sel_info.hslab.diminfo[temp_dim].start+mem_space->select.offset[temp_dim]; + + /* Re-compute the initial buffer offset */ + for(i=0,buf_off=0; i<ndims; i++) + buf_off+=offset[i]*slab[i]; } /* end else */ } /* end if */ else { /* Move to the next row in the curent dimension */ offset[temp_dim]++; + buf_off+=slab[temp_dim]; tmp_block[temp_dim]++; /* If this block is still in the range of blocks to output for the dimension, break out of loop */ @@ -2108,6 +2122,7 @@ for(i=0; i<mem_space->extent.u.simple.rank; i++) else { /* Move to the next block in the current dimension */ offset[temp_dim]+=(mem_space->select.sel_info.hslab.diminfo[temp_dim].stride-mem_space->select.sel_info.hslab.diminfo[temp_dim].block); + buf_off+=(mem_space->select.sel_info.hslab.diminfo[temp_dim].stride-mem_space->select.sel_info.hslab.diminfo[temp_dim].block)*slab[temp_dim]; tmp_block[temp_dim]=0; tmp_count[temp_dim]++; @@ -2118,6 +2133,10 @@ for(i=0; i<mem_space->extent.u.simple.rank; i++) tmp_count[temp_dim]=0; /* reset back to the beginning of the line */ tmp_block[temp_dim]=0; offset[temp_dim]=mem_space->select.sel_info.hslab.diminfo[temp_dim].start+mem_space->select.offset[temp_dim]; + + /* Re-compute the initial buffer offset */ + for(i=0,buf_off=0; i<ndims; i++) + buf_off+=offset[i]*slab[i]; } } /* end else */ } /* end else */ @@ -2356,6 +2375,7 @@ H5S_hyper_mwrite (intn dim, H5S_hyper_io_info_t *io_info) FUNC_LEAVE (num_read); } /* H5S_hyper_mwrite() */ +#ifdef WORKS_QAK /*------------------------------------------------------------------------- * Function: H5S_hyper_mwrite_opt @@ -2607,6 +2627,283 @@ for(i=0; i<mem_space->extent.u.simple.rank; i++) FUNC_LEAVE (num_write); } /* end H5S_hyper_mwrite_opt() */ +#else /* WORKS_QAK */ + +/*------------------------------------------------------------------------- + * Function: H5S_hyper_mwrite_opt + * + * Purpose: Performs an optimized scatter to a memory buffer, based on a + * regular hyperslab (i.e. one which was generated from just one call to + * H5Sselect_hyperslab). + * + * Return: Success: Number of elements copied. + * Failure: 0 + * + * Programmer: Quincey Koziol + * Tuesday, September 12, 2000 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static herr_t +H5S_hyper_mwrite_opt (const void *_tconv_buf, size_t elmt_size, + const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, + size_t nelmts, void *_buf/*out*/) +{ + hsize_t mem_size[H5O_LAYOUT_NDIMS]; /* Size of the source buffer */ + hsize_t slab[H5O_LAYOUT_NDIMS]; /* Hyperslab size */ + hssize_t offset[H5O_LAYOUT_NDIMS]; /* Offset on disk */ + hsize_t tmp_count[H5O_LAYOUT_NDIMS]; /* Temporary block count */ + hsize_t tmp_block[H5O_LAYOUT_NDIMS]; /* Temporary block offset */ + const uint8_t *src=(const uint8_t *)_tconv_buf; /* Alias for pointer arithmetic */ + uint8_t *dst=(uint8_t *)_buf; /* Alias for pointer arithmetic */ + intn fast_dim; /* Rank of the fastest changing dimension for the dataspace */ + intn temp_dim; /* Temporary rank holder */ + hsize_t acc; /* Accumulator */ + size_t buf_off; /* Buffer offset for copying memory */ + intn i; /* Counters */ + intn ndims; /* Number of dimensions of dataset */ + uintn actual_write; /* The actual number of elements to read in */ + uintn actual_bytes; /* The actual number of bytes to copy */ + size_t num_write=0; /* Number of elements read */ + + FUNC_ENTER (H5S_hyper_fwrite_opt, 0); + +#ifdef QAK +printf("%s: Called!, elmt_size=%d\n",FUNC,(int)elmt_size); +#endif /* QAK */ + /* Check if this is the first element read in from the hyperslab */ + if(mem_iter->hyp.pos[0]==(-1)) { + for(i=0; i<mem_space->extent.u.simple.rank; i++) + mem_iter->hyp.pos[i]=mem_space->select.sel_info.hslab.diminfo[i].start; + } /* end if */ + +#ifdef QAK +for(i=0; i<mem_space->extent.u.simple.rank; i++) + printf("%s: mem_file->hyp.pos[%d]=%d\n",FUNC,(int)i,(int)mem_iter->hyp.pos[i]); +#endif /* QAK */ + + /* Set the aliases for a few important dimension ranks */ + fast_dim=mem_space->extent.u.simple.rank-1; + ndims=mem_space->extent.u.simple.rank; + + /* Set up the size of the memory space */ + HDmemcpy(mem_size, mem_space->extent.u.simple.size,mem_space->extent.u.simple.rank*sizeof(hsize_t)); + mem_size[mem_space->extent.u.simple.rank]=elmt_size; + + /* initialize row sizes for each dimension */ + for(i=(ndims-1),acc=1; i>=0; i--) { + slab[i]=acc*elmt_size; + acc*=mem_size[i]; + } /* end for */ +#ifdef QAK +for(i=0; i<ndims; i++) + printf("%s: mem_size[%d]=%d, slab[%d]=%d\n",FUNC,(int)i,(int)mem_size[i],(int)i,(int)slab[i]); +#endif /* QAK */ + + /* Check if we stopped in the middle of a sequence of elements */ + if((mem_iter->hyp.pos[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start)%mem_space->select.sel_info.hslab.diminfo[fast_dim].stride!=0) { + uintn leftover; /* The number of elements left over from the last sequence */ + +#ifdef QAK +printf("%s: Check 1.0\n",FUNC); +#endif /* QAK */ + /* Calculate the number of elements left in the sequence */ + leftover=mem_space->select.sel_info.hslab.diminfo[fast_dim].block-((mem_iter->hyp.pos[fast_dim]-mem_space->select.sel_info.hslab.diminfo[fast_dim].start)%mem_space->select.sel_info.hslab.diminfo[fast_dim].stride); + + /* Make certain that we don't write too many */ + actual_write=MIN(leftover,nelmts); + actual_bytes=actual_write*elmt_size; + + /* Copy the location of the point to get */ + HDmemcpy(offset, mem_iter->hyp.pos,ndims*sizeof(hssize_t)); + offset[ndims] = 0; + + /* Add in the selection offset */ + for(i=0; i<ndims; i++) + offset[i] += mem_space->select.offset[i]; + + /* Compute the initial buffer offset */ + for(i=0,buf_off=0; i<ndims; i++) + buf_off+=offset[i]*slab[i]; + + /* Scatter out the rest of the sequence */ + HDmemcpy(dst+buf_off,src,actual_bytes); + + /* Increment the offset of the buffer */ + src+=elmt_size*actual_write; + + /* Increment the count write */ + num_write+=actual_write; + + /* Decrement the number of elements left in selection */ + mem_iter->hyp.elmt_left-=actual_write; + + /* Advance the point iterator */ + /* If we had enough buffer space to write out the rest of the sequence + * in the fastest changing dimension, move the iterator offset to + * the beginning of the next block to write. Otherwise, just advance + * the iterator in the fastest changing dimension. + */ + if(actual_write==leftover) { + /* Move iterator offset to beginning of next sequence in the fastest changing dimension */ + H5S_hyper_iter_next(mem_space,mem_iter); + } /* end if */ + else { + mem_iter->hyp.pos[fast_dim]+=actual_write; /* whole sequence not written out, just advance fastest dimension offset */ + } /* end if */ + } /* end if */ + + /* Now that we've cleared the "remainder" of the previous fastest dimension + * sequence, we must be at the beginning of a sequence, so use the fancy + * algorithm to compute the offsets and run through as many as possible, + * until the buffer fills up. + */ + if(num_write<nelmts) { /* Just in case the "remainder" above filled the buffer */ +#ifdef QAK +printf("%s: Check 2.0\n",FUNC); +#endif /* QAK */ + /* Compute the arrays to perform I/O on */ + /* Copy the location of the point to get */ + HDmemcpy(offset, mem_iter->hyp.pos,ndims*sizeof(hssize_t)); + offset[ndims] = 0; + + /* Add in the selection offset */ + for(i=0; i<ndims; i++) + offset[i] += mem_space->select.offset[i]; + + /* Compute the current "counts" for this location */ + for(i=0; i<ndims; i++) { + tmp_count[i] = (mem_iter->hyp.pos[i]-mem_space->select.sel_info.hslab.diminfo[i].start)%mem_space->select.sel_info.hslab.diminfo[i].stride; + tmp_block[i] = (mem_iter->hyp.pos[i]-mem_space->select.sel_info.hslab.diminfo[i].start)/mem_space->select.sel_info.hslab.diminfo[i].stride; + } /* end for */ + + /* Compute the initial buffer offset */ + for(i=0,buf_off=0; i<ndims; i++) + buf_off+=offset[i]*slab[i]; + + /* Set the number of elements to write each time */ + actual_write=mem_space->select.sel_info.hslab.diminfo[fast_dim].block; + + /* Set the number of actual bytes */ + actual_bytes=actual_write*elmt_size; +#ifdef QAK +printf("%s: buf_off=%u, actual_bytes=%u\n",FUNC,(unsigned)buf_off,(int)actual_bytes); +#endif /* QAK */ + +#ifdef QAK +printf("%s: actual_write=%d\n",FUNC,(int)actual_write); +for(i=0; i<file_space->extent.u.simple.rank; i++) + printf("%s: diminfo: start[%d]=%d, stride[%d]=%d, block[%d]=%d, count[%d]=%d\n",FUNC, + (int)i,(int)mem_space->select.sel_info.hslab.diminfo[i].start, + (int)i,(int)mem_space->select.sel_info.hslab.diminfo[i].stride, + (int)i,(int)mem_space->select.sel_info.hslab.diminfo[i].block, + (int)i,(int)mem_space->select.sel_info.hslab.diminfo[i].count); +#endif /* QAK */ + + /* Read in data until an entire sequence can't be written out any longer */ + while(num_write<nelmts) { + /* Check if we are running out of room in the buffer */ + if((actual_write+num_write)>nelmts) { + actual_write=nelmts-num_write; + actual_bytes=actual_write*elmt_size; + } /* end if */ + +#ifdef QAK +printf("%s: num_write=%d\n",FUNC,(int)num_write); +for(i=0; i<mem_space->extent.u.simple.rank; i++) + printf("%s: tmp_count[%d]=%d, offset[%d]=%d\n",FUNC,(int)i,(int)tmp_count[i],(int)i,(int)offset[i]); +#endif /* QAK */ + + /* Scatter out the rest of the sequence */ + HDmemcpy(dst+buf_off,src,actual_bytes); + +#ifdef QAK +printf("%s: buf_off=%u, actual_bytes=%u\n",FUNC,(unsigned)buf_off,(int)actual_bytes); +#endif /* QAK */ + + /* Increment the offset of the buffer */ + src+=elmt_size*actual_write; + + /* Increment the count write */ + num_write+=actual_write; + + /* Decrement the number of elements left in selection */ + mem_iter->hyp.elmt_left-=actual_write; + + /* Increment the offset and count */ + temp_dim=fast_dim; + while(temp_dim>=0) { + if(temp_dim==fast_dim) { + /* Move to the next block in the current dimension */ + /* Check for partial block write! */ + if(actual_write<mem_space->select.sel_info.hslab.diminfo[fast_dim].block) { + offset[temp_dim]+=actual_write; + buf_off+=actual_bytes; + break; + } /* end if */ + else { + offset[temp_dim]+=mem_space->select.sel_info.hslab.diminfo[temp_dim].stride; /* reset the offset in the fastest dimension */ + buf_off+=slab[temp_dim]*mem_space->select.sel_info.hslab.diminfo[temp_dim].stride; + tmp_count[temp_dim]++; + } /* end else */ + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_count[temp_dim]<mem_space->select.sel_info.hslab.diminfo[temp_dim].count) + break; + else { + tmp_count[temp_dim]=0; /* reset back to the beginning of the line */ + offset[temp_dim]=mem_space->select.sel_info.hslab.diminfo[temp_dim].start+mem_space->select.offset[temp_dim]; + + /* Re-compute the initial buffer offset */ + for(i=0,buf_off=0; i<ndims; i++) + buf_off+=offset[i]*slab[i]; + } /* end else */ + } /* end if */ + else { + /* Move to the next row in the curent dimension */ + offset[temp_dim]++; + buf_off+=slab[temp_dim]; + tmp_block[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_block[temp_dim]<mem_space->select.sel_info.hslab.diminfo[temp_dim].block) + break; + else { + /* Move to the next block in the current dimension */ + offset[temp_dim]+=(mem_space->select.sel_info.hslab.diminfo[temp_dim].stride-mem_space->select.sel_info.hslab.diminfo[temp_dim].block); + buf_off+=(mem_space->select.sel_info.hslab.diminfo[temp_dim].stride-mem_space->select.sel_info.hslab.diminfo[temp_dim].block)*slab[temp_dim]; + tmp_block[temp_dim]=0; + tmp_count[temp_dim]++; + + /* If this block is still in the range of blocks to output for the dimension, break out of loop */ + if(tmp_count[temp_dim]<mem_space->select.sel_info.hslab.diminfo[temp_dim].count) + break; + else { + tmp_count[temp_dim]=0; /* reset back to the beginning of the line */ + tmp_block[temp_dim]=0; + offset[temp_dim]=mem_space->select.sel_info.hslab.diminfo[temp_dim].start+mem_space->select.offset[temp_dim]; + + /* Re-compute the initial buffer offset */ + for(i=0,buf_off=0; i<ndims; i++) + buf_off+=offset[i]*slab[i]; + } + } /* end else */ + } /* end else */ + + /* Decrement dimension count */ + temp_dim--; + } /* end while */ + } /* end while */ + + /* Update the iterator with the location we stopped */ + HDmemcpy(mem_iter->hyp.pos, offset, ndims*sizeof(hssize_t)); + } /* end if */ + + FUNC_LEAVE (num_write); +} /* end H5S_hyper_mwrite_opt() */ +#endif /* WORKS_QAK */ /*------------------------------------------------------------------------- |