From 5e2f37f579d4280727a052294dc17e92d070e5c0 Mon Sep 17 00:00:00 2001 From: Quincey Koziol Date: Sat, 25 Oct 2003 11:42:00 -0500 Subject: [svn-r7735] Purpose: Bug fix Description: Single hyperslab selections (which were set with only one call to H5Sselect_hyperslab) that had dimensions that could be "flattened" but were interspersed with dimensions that could not be flattened were not correctly handled, causing core dumps. Solution: Re-work "flattening" code to handle this case properly. Platforms tested: FreeBSD 4.9 (sleipnir) h5committest --- release_docs/RELEASE.txt | 4 ++ src/H5Shyper.c | 74 ++++++++++++++---------- test/tselect.c | 145 ++++++++++++++++++++++++++++++++++++++++++++++- 3 files changed, 191 insertions(+), 32 deletions(-) diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index e78b377..e108856 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -60,6 +60,10 @@ Bug Fixes since HDF5-1.6.1 release Library ------- + - Single hyperslab selections (which were set with only one call to + H5Sselect_hyperslab) that had dimensions that could be "flattened" + but were interspersed with dimensions that could not be flattened + were not correctly handled, causing core dumps. QAK - 2003/10/25 - Avoid metadata cache from preempting current dataset object header when looking up information about the named datatype that the dataset uses. QAK - 2003/10/20 diff --git a/src/H5Shyper.c b/src/H5Shyper.c index f3640ac..d8c1500 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -162,7 +162,7 @@ H5S_hyper_iter_init(H5S_sel_iter_t *iter, const H5S_t *space, size_t elmt_size) /* Initialize the information needed for regular hyperslab I/O */ const hsize_t *mem_size; /* Temporary pointer to dataspace extent's dimension sizes */ hsize_t acc; /* Accumulator for "flattened" dimension's sizes */ - unsigned cont_dim; /* Maximum contiguous dimension */ + unsigned cont_dim=0; /* # of contiguous dimensions */ /* Set the temporary pointer to the dataspace extent's dimension sizes */ mem_size=space->extent.u.simple.size; @@ -174,69 +174,83 @@ H5S_hyper_iter_init(H5S_sel_iter_t *iter, const H5S_t *space, size_t elmt_size) * extent in that dimension and all dimensions up to that dimension. */ - /* Initialize the number of contiguous dimensions to be the same as the dataspace's rank */ - cont_dim=rank; - /* Don't flatten adjacent elements into contiguous block if the * element size is 0. This is for the H5S_select_shape_same() code. */ if(elmt_size>0) { - /* Check for a "contiguous" block */ + /* Check for any "contiguous" blocks that can be flattened */ for(u=rank-1; u>0; u--) { if(tdiminfo[u].count==1 && tdiminfo[u].block==mem_size[u]) - cont_dim=u; - else - break; + cont_dim++; } /* end for */ } /* end if */ /* Check if the regular selection can be "flattened" */ - if(cont_dim0) { + unsigned last_dim_flattened=1; /* Flag to indicate that the last dimension was flattened */ + unsigned flat_rank=rank-cont_dim; /* Number of dimensions after flattening */ + unsigned curr_dim; /* Current dimension */ + /* Set the iterator's rank to the contiguous dimensions */ - iter->u.hyp.iter_rank=cont_dim; + iter->u.hyp.iter_rank=flat_rank; /* Allocate the position & initialize to initial location */ - iter->u.hyp.off = H5FL_ARR_MALLOC(hsize_t,cont_dim); + iter->u.hyp.off = H5FL_ARR_MALLOC(hsize_t,flat_rank); assert(iter->u.hyp.off); - iter->u.hyp.diminfo = H5FL_ARR_MALLOC(H5S_hyper_dim_t,cont_dim); + iter->u.hyp.diminfo = H5FL_ARR_MALLOC(H5S_hyper_dim_t,flat_rank); assert(iter->u.hyp.diminfo); - iter->u.hyp.size = H5FL_ARR_MALLOC(hsize_t,cont_dim); + iter->u.hyp.size = H5FL_ARR_MALLOC(hsize_t,flat_rank); assert(iter->u.hyp.size); - iter->u.hyp.sel_off = H5FL_ARR_MALLOC(hssize_t,cont_dim); + iter->u.hyp.sel_off = H5FL_ARR_MALLOC(hssize_t,flat_rank); assert(iter->u.hyp.sel_off); /* "Flatten" dataspace extent and selection information */ + curr_dim=flat_rank-1; for(i=rank-1, acc=1; i>=0; i--) { if(tdiminfo[i].block==mem_size[i] && i>0) { + /* "Flatten" this dimension */ assert(tdiminfo[i].start==0); acc *= mem_size[i]; + + /* Indicate that the dimension was flattened */ + last_dim_flattened=1; } /* end if */ else { - if((unsigned)i==(cont_dim-1)) { - iter->u.hyp.diminfo[i].start = tdiminfo[i].start*acc; + if(last_dim_flattened) { + /* First dimension after flattened dimensions */ + iter->u.hyp.diminfo[curr_dim].start = tdiminfo[i].start*acc; /* Special case for single block regular selections */ - if(tdiminfo[i].count==1) - iter->u.hyp.diminfo[i].stride = 1; + if(tdiminfo[curr_dim].count==1) + iter->u.hyp.diminfo[curr_dim].stride = 1; else - iter->u.hyp.diminfo[i].stride = tdiminfo[i].stride*acc; - iter->u.hyp.diminfo[i].count = tdiminfo[i].count; - iter->u.hyp.diminfo[i].block = tdiminfo[i].block*acc; - iter->u.hyp.size[i] = mem_size[i]*acc; - iter->u.hyp.sel_off[i] = space->select.offset[i]*acc; + iter->u.hyp.diminfo[curr_dim].stride = tdiminfo[i].stride*acc; + iter->u.hyp.diminfo[curr_dim].count = tdiminfo[i].count; + iter->u.hyp.diminfo[curr_dim].block = tdiminfo[i].block*acc; + iter->u.hyp.size[curr_dim] = mem_size[i]*acc; + iter->u.hyp.sel_off[curr_dim] = space->select.offset[i]*acc; + + /* Reset the "last dim flattened" flag to avoid flattened any further dimensions */ + last_dim_flattened=0; + + /* Reset the "accumulator" for possible further dimension flattening */ + acc=1; } /* end if */ else { - iter->u.hyp.diminfo[i].start = tdiminfo[i].start; - iter->u.hyp.diminfo[i].stride = tdiminfo[i].stride; - iter->u.hyp.diminfo[i].count = tdiminfo[i].count; - iter->u.hyp.diminfo[i].block = tdiminfo[i].block; - iter->u.hyp.size[i] = mem_size[i]; - iter->u.hyp.sel_off[i] = space->select.offset[i]; + iter->u.hyp.diminfo[curr_dim].start = tdiminfo[i].start; + iter->u.hyp.diminfo[curr_dim].stride = tdiminfo[i].stride; + iter->u.hyp.diminfo[curr_dim].count = tdiminfo[i].count; + iter->u.hyp.diminfo[curr_dim].block = tdiminfo[i].block; + iter->u.hyp.size[curr_dim] = mem_size[i]; + iter->u.hyp.sel_off[curr_dim] = space->select.offset[i]; } /* end else */ + + /* Decrement "current" flattened dimension */ + curr_dim--; } /* end if */ } /* end for */ /* Initialize "flattened" iterator offset to initial location and dataspace extent and selection information to correct values */ - for(u=0; uu.hyp.off[u]=iter->u.hyp.diminfo[u].start; } /* end if */ else { diff --git a/test/tselect.c b/test/tselect.c index 10265ad..db98f94 100644 --- a/test/tselect.c +++ b/test/tselect.c @@ -1325,13 +1325,13 @@ test_select_hyper_contig2(hid_t dset_type, hid_t xfer_plist) sid2 = H5Screate_simple(SPACE8_RANK, dims2, NULL); CHECK(sid2, FAIL, "H5Screate_simple"); - /* Select 6x5 count with a stride of 2x6 & 2x6 block hyperslab for disk dataset */ + /* Select contiguous hyperslab in memory */ start[0]=0; start[1]=0; start[2]=0; start[3]=0; count[0]=2; count[1]=SPACE8_DIM3; count[2]=SPACE8_DIM2; count[3]=SPACE8_DIM1; ret = H5Sselect_hyperslab(sid1,H5S_SELECT_SET,start,NULL,count,NULL); CHECK(ret, FAIL, "H5Sselect_hyperslab"); - /* Select 3x15 count with a stride of 4x2 & 4x2 block hyperslab for memory dataset */ + /* Select contiguous hyperslab in memory */ start[0]=0; start[1]=0; start[2]=0; start[3]=0; count[0]=2; count[1]=SPACE8_DIM3; count[2]=SPACE8_DIM2; count[3]=SPACE8_DIM1; ret = H5Sselect_hyperslab(sid2,H5S_SELECT_SET,start,NULL,count,NULL); @@ -1375,6 +1375,143 @@ test_select_hyper_contig2(hid_t dset_type, hid_t xfer_plist) /**************************************************************** ** +** test_select_hyper_contig3(): Test H5S (dataspace) selection code. +** Tests contiguous hyperslabs of various sizes and dimensionalities. +** This test uses a hyperslab that is contiguous in the lowest dimension, +** not contiguous in a dimension, then has a selection across the entire next +** dimension (which should be "flattened" out also). +** +****************************************************************/ +static void +test_select_hyper_contig3(hid_t dset_type, hid_t xfer_plist) +{ + hid_t fid1; /* HDF5 File IDs */ + hid_t dataset; /* Dataset ID */ + hid_t sid1,sid2; /* Dataspace ID */ + hsize_t dims2[] = {SPACE8_DIM4, SPACE8_DIM3, SPACE8_DIM2, SPACE8_DIM1}; + hssize_t start[SPACE8_RANK]; /* Starting location of hyperslab */ + hsize_t count[SPACE8_RANK]; /* Element count of hyperslab */ + uint16_t *wbuf, /* Buffer to write to disk */ + *rbuf, /* Buffer read from disk */ + *tbuf, *tbuf2; /* Temporary buffer pointers */ + int i,j,k,l; /* Counters */ + herr_t ret; /* Generic return value */ + + /* Output message about test being performed */ + MESSAGE(5, ("Testing Yet More Contiguous Hyperslabs Functionality\n")); + + /* Allocate write & read buffers */ + wbuf=malloc(sizeof(uint16_t)*SPACE8_DIM1*SPACE8_DIM2*SPACE8_DIM3*SPACE8_DIM4); + rbuf=calloc(sizeof(uint16_t),SPACE8_DIM1*SPACE8_DIM2*SPACE8_DIM3*SPACE8_DIM4); + + /* Initialize write buffer */ + for(i=0, tbuf=wbuf; i=start[0] && i<(int)(start[0]+count[0])) && + (j>=start[1] && j<(int)(start[1]+count[1])) && + (k>=start[2] && k<(int)(start[2]+count[2])) && + (l>=start[3] && l<(int)(start[3]+count[3])) ) { + if(*tbuf!=*tbuf2) { + num_errs++; + printf("Error: hyperslab values don't match!\n"); + printf("Line: %d, i=%d, j=%d, k=%d, l=%d, *tbuf=%u,*tbuf2=%u\n",__LINE__,i,j,k,l,(unsigned)*tbuf,(unsigned)*tbuf2); + } /* end if */ + } /* end if */ + else { + if(*tbuf2!=0) { + num_errs++; + printf("Error: invalid data in read buffer!\n"); + printf("Line: %d, i=%d, j=%d, k=%d, l=%d, *tbuf=%u,*tbuf2=%u\n",__LINE__,i,j,k,l,(unsigned)*tbuf,(unsigned)*tbuf2); + } /* end if */ + } /* end else */ + + /* Close memory dataspace */ + ret = H5Sclose(sid2); + CHECK(ret, FAIL, "H5Sclose"); + + /* Close disk dataspace */ + ret = H5Sclose(sid1); + CHECK(ret, FAIL, "H5Sclose"); + + /* Close Dataset */ + ret = H5Dclose(dataset); + CHECK(ret, FAIL, "H5Dclose"); + + /* Close file */ + ret = H5Fclose(fid1); + CHECK(ret, FAIL, "H5Fclose"); + + /* Free memory buffers */ + free(wbuf); + free(rbuf); +} /* test_select_hyper_contig3() */ + +/**************************************************************** +** ** test_select_hyper_copy(): Test H5S (dataspace) selection code. ** Tests copying hyperslab selections ** @@ -6466,6 +6603,10 @@ test_select(void) test_select_hyper_contig2(H5T_STD_U16LE,plist_id); /* Test more contiguous hyperslab selection cases */ test_select_hyper_contig2(H5T_STD_U16BE,H5P_DEFAULT); /* Test more contiguous hyperslab selection cases */ test_select_hyper_contig2(H5T_STD_U16BE,plist_id); /* Test more contiguous hyperslab selection cases */ + test_select_hyper_contig3(H5T_STD_U16LE,H5P_DEFAULT); /* Test yet more contiguous hyperslab selection cases */ + test_select_hyper_contig3(H5T_STD_U16LE,plist_id); /* Test yet more contiguous hyperslab selection cases */ + test_select_hyper_contig3(H5T_STD_U16BE,H5P_DEFAULT); /* Test yet more contiguous hyperslab selection cases */ + test_select_hyper_contig3(H5T_STD_U16BE,plist_id); /* Test yet more contiguous hyperslab selection cases */ test_select_hyper_copy(); /* Test hyperslab selection copying code */ test_select_point_copy(); /* Test point selection copying code */ test_select_hyper_offset(); /* Test selection offset code with hyperslabs */ -- cgit v0.12