diff options
Diffstat (limited to 'src/H5Sall.c')
| -rw-r--r-- | src/H5Sall.c | 261 |
1 files changed, 47 insertions, 214 deletions
diff --git a/src/H5Sall.c b/src/H5Sall.c index 36e4e46..80abaea 100644 --- a/src/H5Sall.c +++ b/src/H5Sall.c @@ -23,7 +23,7 @@ static intn interface_initialize_g = 0; static herr_t H5S_all_init (const struct H5O_layout_t *layout, - const H5S_t *space, H5S_sel_iter_t *iter, size_t *min_elem_out); + const H5S_t *space, H5S_sel_iter_t *iter); static hsize_t H5S_all_favail (const H5S_t *space, const H5S_sel_iter_t *iter, hsize_t max); static hsize_t H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, @@ -65,6 +65,7 @@ const H5S_mconv_t H5S_ALL_MCONV[1] = {{ H5S_all_mscat, /*scatter */ }}; + /*------------------------------------------------------------------------- * Function: H5S_all_init * @@ -81,13 +82,8 @@ const H5S_mconv_t H5S_ALL_MCONV[1] = {{ */ static herr_t H5S_all_init (const struct H5O_layout_t UNUSED *layout, - const H5S_t *space, H5S_sel_iter_t *sel_iter, size_t *min_elem_out) + const H5S_t *space, H5S_sel_iter_t *sel_iter) { - hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ - intn space_ndims; /*dimensionality of space*/ - hsize_t acc; /*accumulator */ - intn i; /*counters */ - FUNC_ENTER (H5S_all_init, FAIL); /* Check args */ @@ -101,21 +97,9 @@ H5S_all_init (const struct H5O_layout_t UNUSED *layout, /* Start at the upper left location */ sel_iter->all.offset=0; - /* Get the dimensions of the space, to set the min. # of elements */ - if ((space_ndims=H5S_get_simple_extent_dims (space, hsize, NULL))<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, - "unable to retrieve hyperslab parameters"); - } - - /* Adjust the slowest varying dimension to account for strip mining */ - for (i=1, acc=1; i<space_ndims; i++) - acc *= hsize[i]; - - /* Set the minimum # of elements to output */ - *min_elem_out=acc; - FUNC_LEAVE (SUCCEED); } + /*------------------------------------------------------------------------- * Function: H5S_all_favail @@ -134,36 +118,20 @@ H5S_all_init (const struct H5O_layout_t UNUSED *layout, *------------------------------------------------------------------------- */ static hsize_t -H5S_all_favail (const H5S_t *space, const H5S_sel_iter_t *sel_iter, hsize_t max) +H5S_all_favail (const H5S_t UNUSED *space, const H5S_sel_iter_t *sel_iter, hsize_t max) { - hsize_t nelmts; - int m_ndims; /* file dimensionality */ - hsize_t size[H5O_LAYOUT_NDIMS]; /*size of selected hyperslab */ - hsize_t acc; - int i; - FUNC_ENTER (H5S_all_favail, 0); /* Check args */ assert (space && H5S_SEL_ALL==space->select.type); assert (sel_iter); - /* - * The stripmine size is such that only the slowest varying dimension can - * be split up. We choose the largest possible strip mine size which is - * not larger than the desired size. - */ - m_ndims = H5S_get_simple_extent_dims (space, size, NULL); - for (i=m_ndims-1, acc=1; i>0; --i) - acc *= size[i]; - nelmts = (max/acc) * acc; - if (nelmts<=0) { - HRETURN_ERROR (H5E_IO, H5E_UNSUPPORTED, 0, - "strip mine buffer is too small"); - } - - FUNC_LEAVE (MIN(sel_iter->all.elmt_left,nelmts)); +#ifdef QAK + printf("%s: sel_iter->all.elmt_left=%u, max=%u\n",FUNC,(unsigned)sel_iter->all.elmt_left,(unsigned)max); +#endif /* QAK */ + FUNC_LEAVE (MIN(sel_iter->all.elmt_left,max)); } /* H5S_all_favail() */ + /*------------------------------------------------------------------------- * Function: H5S_all_fgath @@ -197,15 +165,10 @@ H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, hsize_t nelmts, hid_t dxpl_id, - void *_buf/*out*/) + void *buf/*out*/) { - hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of slab in file*/ - hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ - uint8_t *buf=(uint8_t*)_buf; /*for pointer arithmetic*/ - hsize_t acc; /*accumulator */ - intn space_ndims; /*dimensionality of space*/ - intn i; /*counters */ + hsize_t actual_bytes; /* The actual number of bytes to read */ + hsize_t buf_off; /* Dataset offset for copying memory */ FUNC_ENTER (H5S_all_fgath, 0); @@ -218,40 +181,15 @@ H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, assert (nelmts>0); assert (buf); - /* - * Get hyperslab information to determine what elements are being - * selected (there might eventually be other selection methods too). - * We only support hyperslabs with unit sample because there's no way to - * currently pass sample information into H5F_arr_read() much less - * H5F_istore_read(). - */ - if ((space_ndims=H5S_get_simple_extent_dims (file_space, hsize, NULL))<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, 0, - "unable to retrieve hyperslab parameters"); - } - - if(space_ndims>0) { - HDmemset(file_offset,0,sizeof(hssize_t)*space_ndims); - - /* Adjust the slowest varying dimension to take care of strip mining */ - for (i=1, acc=1; i<space_ndims; i++) - acc *= hsize[i]; - assert (0==file_iter->all.offset % acc); - assert (0==nelmts % acc); - file_offset[0] += file_iter->all.offset / acc; - hsize[0] = nelmts / acc; - } /* end if */ - - /* The fastest varying dimension is for the data point itself */ - file_offset[space_ndims] = 0; - hsize[space_ndims] = elmt_size; - HDmemset (zero, 0, (space_ndims+1)*sizeof(*zero)); + /* Set the offset in the dataset and the number of bytes to read */ + buf_off=file_iter->all.offset*elmt_size; + actual_bytes=elmt_size*nelmts; /* - * Gather from file. + * Read piece from file. */ - if (H5F_arr_read(f, dxpl_id, layout, pline, fill, efl, hsize, hsize, - zero, file_offset, buf/*out*/)<0) { + if (H5F_seq_read(f, dxpl_id, layout, pline, fill, efl, file_space, + elmt_size, actual_bytes, buf_off, buf/*out*/)<0) { HRETURN_ERROR(H5E_DATASPACE, H5E_READERROR, 0, "read error"); } @@ -261,6 +199,7 @@ H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout, FUNC_LEAVE (nelmts); } /* H5S_all_fgath() */ + /*------------------------------------------------------------------------- * Function: H5S_all_fscat @@ -287,15 +226,10 @@ H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, const struct H5O_pline_t *pline, const struct H5O_fill_t *fill, const struct H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space, H5S_sel_iter_t *file_iter, - hsize_t nelmts, hid_t dxpl_id, const void *_buf) + hsize_t nelmts, hid_t dxpl_id, const void *buf) { - hssize_t file_offset[H5O_LAYOUT_NDIMS]; /*offset of hyperslab */ - hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero vector */ - const uint8_t *buf=(const uint8_t*)_buf; /*for pointer arithmetic*/ - hsize_t acc; /*accumulator */ - intn space_ndims; /*space dimensionality */ - intn i; /*counters */ + hsize_t actual_bytes; /* The actual number of bytes to write */ + hsize_t buf_off; /* Dataset offset for copying memory */ FUNC_ENTER (H5S_all_fscat, FAIL); @@ -308,37 +242,16 @@ H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, assert (nelmts>0); assert (buf); - /* - * Get information to determine what elements are being selected. - */ - if ((space_ndims=H5S_get_simple_extent_dims (file_space, hsize, NULL))<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, - "unable to retrieve hyperslab parameters"); - } - - if(space_ndims>0) { - HDmemset(file_offset,0,sizeof(hssize_t)*space_ndims); - - /* Adjust the slowest varying dimension to account for strip mining */ - for (i=1, acc=1; i<space_ndims; i++) - acc *= hsize[i]; - assert (0==file_iter->all.offset % acc); - assert (0==nelmts % acc); - file_offset[0] += file_iter->all.offset / acc; - hsize[0] = nelmts / acc; - } /* end if */ - - /* The fastest varying dimension is for the data point itself */ - file_offset[space_ndims] = 0; - hsize[space_ndims] = elmt_size; - HDmemset (zero, 0, (space_ndims+1)*sizeof(*zero)); + /* Set the offset in the dataset and the number of bytes to write */ + buf_off=file_iter->all.offset*elmt_size; + actual_bytes=elmt_size*nelmts; /* - * Scatter to file. + * Write piece from file. */ - if (H5F_arr_write (f, dxpl_id, layout, pline, fill, efl, hsize, hsize, - zero, file_offset, buf)<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error"); + if (H5F_seq_write(f, dxpl_id, layout, pline, fill, efl, file_space, + elmt_size, actual_bytes, buf_off, buf/*out*/)<0) { + HRETURN_ERROR(H5E_DATASPACE, H5E_WRITEERROR, 0, "write error"); } /* Advance iterator */ @@ -347,6 +260,7 @@ H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, FUNC_LEAVE (SUCCEED); } /* H5S_all_fscat() */ + /*------------------------------------------------------------------------- * Function: H5S_all_mgath @@ -371,17 +285,10 @@ H5S_all_fscat (H5F_t *f, const struct H5O_layout_t *layout, static hsize_t H5S_all_mgath (const void *_buf, size_t elmt_size, const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, - hsize_t nelmts, void *_tconv_buf/*out*/) + hsize_t nelmts, void *tconv_buf/*out*/) { - hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /*slab offset in app buf*/ - hsize_t mem_size[H5O_LAYOUT_NDIMS]; /*total size of app buf */ - hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ const uint8_t *buf=(const uint8_t*)_buf; /* Get local copies for address arithmetic */ - uint8_t *tconv_buf=(uint8_t*)_tconv_buf; - hsize_t acc; /*accumulator */ - intn space_ndims; /*dimensionality of space*/ - intn i; /*counters */ + size_t actual_bytes; /* The actual number of bytes to read */ FUNC_ENTER (H5S_all_mgath, 0); @@ -393,45 +300,12 @@ H5S_all_mgath (const void *_buf, size_t elmt_size, assert (nelmts>0); assert (tconv_buf); - /* - * Retrieve information to determine what elements are being selected. - */ - if ((space_ndims=H5S_get_simple_extent_dims (mem_space, hsize, NULL))<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, 0, - "unable to retrieve hyperslab parameters"); - } - if(space_ndims>0) { - HDmemset(mem_offset,0,sizeof(hssize_t)*space_ndims); - - if (H5S_get_simple_extent_dims (mem_space, mem_size, NULL)<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, 0, - "unable to retrieve data space dimensions"); - } - - /* Adjust the slowest varying dimension to account for strip mining */ - for (i=1, acc=1; i<space_ndims; i++) - acc *= hsize[i]; - assert (0==mem_iter->all.offset % acc); - assert (0==nelmts % acc); - mem_offset[0] += mem_iter->all.offset / acc; - hsize[0] = nelmts / acc; - } /* end if */ - - /* The fastest varying dimension is for the data point itself */ - mem_offset[space_ndims] = 0; - mem_size[space_ndims] = elmt_size; - hsize[space_ndims] = elmt_size; - HDmemset (zero, 0, (space_ndims+1)*sizeof(*zero)); + /* Set the offset in the dataset and the number of bytes to read */ + buf += mem_iter->all.offset*elmt_size; + actual_bytes=elmt_size*nelmts; - /* - * Scatter from conversion buffer to application memory. - */ - H5_CHECK_OVERFLOW(space_ndims+1,intn,uintn); - if (H5V_hyper_copy ((uintn)(space_ndims+1), hsize, hsize, zero, tconv_buf, - mem_size, mem_offset, buf)<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, 0, - "unable to scatter data to memory"); - } + /* "read" in the bytes from the source (buf) to the destination (tconv_buf) */ + HDmemcpy(tconv_buf,buf,actual_bytes); /* Advance iterator */ mem_iter->all.elmt_left-=nelmts; @@ -440,6 +314,7 @@ H5S_all_mgath (const void *_buf, size_t elmt_size, FUNC_LEAVE (nelmts); } /* H5S_all_mgath() */ + /*------------------------------------------------------------------------- * Function: H5S_all_mscat * @@ -458,19 +333,12 @@ H5S_all_mgath (const void *_buf, size_t elmt_size, *------------------------------------------------------------------------- */ static herr_t -H5S_all_mscat (const void *_tconv_buf, size_t elmt_size, +H5S_all_mscat (const void *tconv_buf, size_t elmt_size, const H5S_t *mem_space, H5S_sel_iter_t *mem_iter, hsize_t nelmts, void *_buf/*out*/) { - hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /*slab offset in app buf*/ - hsize_t mem_size[H5O_LAYOUT_NDIMS]; /*total size of app buf */ - hsize_t hsize[H5O_LAYOUT_NDIMS]; /*size of hyperslab */ - hssize_t zero[H5O_LAYOUT_NDIMS]; /*zero */ - uint8_t *buf=(uint8_t*)_buf; /* Get local copies for address arithmetic */ - const uint8_t *tconv_buf=(const uint8_t *)_tconv_buf; - hsize_t acc; /*accumulator */ - intn space_ndims; /*dimensionality of space*/ - intn i; /*counters */ + uint8_t *buf=(uint8_t *)_buf; + size_t actual_bytes; /* The actual number of bytes to write */ FUNC_ENTER (H5S_all_mscat, FAIL); @@ -482,47 +350,12 @@ H5S_all_mscat (const void *_tconv_buf, size_t elmt_size, assert (nelmts>0); assert (buf); - /* - * Retrieve information to determine what elements are being selected. - */ - if ((space_ndims=H5S_get_simple_extent_dims (mem_space, hsize, NULL))<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, - "unable to retrieve hyperslab parameters"); - } - - if(space_ndims>0) { - HDmemset(mem_offset,0,sizeof(hssize_t)*space_ndims); - - if (H5S_get_simple_extent_dims (mem_space, mem_size, NULL)<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, - "unable to retrieve data space dimensions"); - } - - /* Adjust the slowest varying dimension to take care of strip mining */ - for (i=1, acc=1; i<space_ndims; i++) { - acc *= hsize[i]; - } - assert (0==mem_iter->all.offset % acc); - assert (0==nelmts % acc); - mem_offset[0] += mem_iter->all.offset / acc; - hsize[0] = nelmts / acc; - } /* end if */ - - /* The fastest varying dimension is for the data point itself */ - mem_offset[space_ndims] = 0; - mem_size[space_ndims] = elmt_size; - hsize[space_ndims] = elmt_size; - HDmemset (zero, 0, (space_ndims+1)*sizeof(*zero)); + /* Set the offset in the dataset and the number of bytes to write */ + buf += mem_iter->all.offset*elmt_size; + actual_bytes=elmt_size*nelmts; - /* - * Scatter from conversion buffer to application memory. - */ - H5_CHECK_OVERFLOW(space_ndims+1,intn,uintn); - if (H5V_hyper_copy ((uintn)(space_ndims+1), hsize, mem_size, mem_offset, buf, - hsize, zero, tconv_buf)<0) { - HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL, - "unable to scatter data to memory"); - } + /* "write" the bytes from the source (tconv_buf) to the destination (buf) */ + HDmemcpy(buf,tconv_buf,actual_bytes); /* Advance iterator */ mem_iter->all.elmt_left-=nelmts; |