diff options
| -rw-r--r-- | release_docs/RELEASE.txt | 4 | ||||
| -rw-r--r-- | src/H5HG.c | 12 | ||||
| -rw-r--r-- | src/H5HGcache.c | 26 | ||||
| -rw-r--r-- | test/gheap.c | 131 |
4 files changed, 159 insertions, 14 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index b9be3f2..95d02c0 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -194,6 +194,10 @@ Bug Fixes since HDF5-1.8.0 release Library ------- + - Fixed a bug where writing and deleting many global heap objects (i.e. + variable length data) would render the file unreadable. Previously + created files exhibiting this problem should now be readable. + NAF - 2009/10/27 - 1483 - Fixed incorrect return value for H5Pget_preserve. AKC - 2009/10/08 - 1628 - Fixed an assertion failure that occurred when H5Ocopy was called on a dataset using a vlen inside a compound. (NAF - 2009/10/02 - 1597) @@ -310,7 +310,7 @@ H5HG_alloc (H5F_t *f, H5HG_heap_t *heap, size_t size, unsigned * heap_flags_ptr) * Find an ID for the new object. ID zero is reserved for the free space * object. */ - if(heap->nused<H5HG_MAXIDX) + if(heap->nused<=H5HG_MAXIDX) idx=heap->nused++; else { for (idx=1; idx<heap->nused; idx++) @@ -326,17 +326,21 @@ H5HG_alloc (H5F_t *f, H5HG_heap_t *heap, size_t size, unsigned * heap_flags_ptr) H5HG_obj_t *new_obj; /* New array of object descriptions */ /* Determine the new number of objects to index */ - new_alloc=MAX(heap->nalloc*2,(idx+1)); - assert(new_alloc<=(H5HG_MAXIDX+1)); + /* nalloc is *not* guaranteed to be a power of 2! - NAF 10/26/09 */ + new_alloc = MIN(MAX(heap->nalloc * 2, (idx + 1)), (H5HG_MAXIDX + 1)); + HDassert(idx < new_alloc); /* Reallocate array of objects */ if (NULL==(new_obj = H5FL_SEQ_REALLOC (H5HG_obj_t, heap->obj, new_alloc))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation failed") + /* Clear newly allocated space */ + HDmemset(&new_obj[heap->nalloc], 0, (new_alloc - heap->nalloc) * sizeof(heap->obj[0])); + /* Update heap information */ heap->nalloc=new_alloc; heap->obj=new_obj; - assert(heap->nalloc>heap->nused); + HDassert(heap->nalloc>heap->nused); } /* end if */ /* Initialize the new object */ diff --git a/src/H5HGcache.c b/src/H5HGcache.c index f3d0f3a..ee318aa 100644 --- a/src/H5HGcache.c +++ b/src/H5HGcache.c @@ -171,11 +171,12 @@ H5HG_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void UNUSED * udata1, /* Decode each object */ p = heap->chunk + H5HG_SIZEOF_HDR(f); nalloc = H5HG_NOBJS(f, heap->size); - if(NULL == (heap->obj = H5FL_SEQ_MALLOC(H5HG_obj_t, nalloc))) + + /* Calloc the obj array because the file format spec makes no guarantee + * about the order of the objects, and unused slots must be set to zero. + */ + if(NULL == (heap->obj = H5FL_SEQ_CALLOC(H5HG_obj_t, nalloc))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") - heap->obj[0].nrefs = 0; - heap->obj[0].size = 0; - heap->obj[0].begin = NULL; heap->nalloc = nalloc; while(p < (heap->chunk + heap->size)) { @@ -202,14 +203,19 @@ H5HG_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void UNUSED * udata1, /* Determine the new number of objects to index */ new_alloc = MAX(heap->nalloc * 2, (idx + 1)); + HDassert(idx < new_alloc); /* Reallocate array of objects */ if(NULL == (new_obj = H5FL_SEQ_REALLOC(H5HG_obj_t, heap->obj, new_alloc))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed") + /* Clear newly allocated space */ + HDmemset(&new_obj[heap->nalloc], 0, (new_alloc - heap->nalloc) * sizeof(heap->obj[0])); + /* Update heap information */ heap->nalloc = new_alloc; heap->obj = new_obj; + HDassert(heap->nalloc>heap->nused); } /* end if */ UINT16DECODE(p, heap->obj[idx].nrefs); @@ -220,16 +226,16 @@ H5HG_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void UNUSED * udata1, /* * The total storage size includes the size of the object header * and is zero padded so the next object header is properly - * aligned. The last bit of space is the free space object whose - * size is never padded and already includes the object header. + * aligned. The entire obj array was calloc'ed, so no need to zero + * the space here. The last bit of space is the free space object + * whose size is never padded and already includes the object + * header. */ if(idx > 0) { need = H5HG_SIZEOF_OBJHDR(f) + H5HG_ALIGN(heap->obj[idx].size); - /* Check for "gap" in index numbers (caused by deletions) and fill in heap object values */ - if(idx > (max_idx + 1)) - HDmemset(&heap->obj[max_idx + 1], 0, sizeof(H5HG_obj_t) * (idx - (max_idx + 1))); - max_idx = idx; + if(idx > max_idx) + max_idx = idx; } /* end if */ else need = heap->obj[idx].size; diff --git a/test/gheap.c b/test/gheap.c index 6dbd8a3..b2c9090 100644 --- a/test/gheap.c +++ b/test/gheap.c @@ -30,11 +30,27 @@ #include "H5Iprivate.h" #include "H5Pprivate.h" +/* Macros for printing error messages in loops. These print up to + * GHEAP_REPEATED_ERR_LIM errors, and suppress the rest */ +#define GHEAP_REPEATED_ERR_LIM 20 + +#define GHEAP_REPEATED_ERR(MSG) \ +{ \ + nerrors++; \ + if(nerrors <= GHEAP_REPEATED_ERR_LIM) { \ + H5_FAILED(); \ + puts(MSG); \ + if(nerrors == GHEAP_REPEATED_ERR_LIM) \ + puts(" Suppressing further errors..."); \ + } /* end if */ \ +} /* end GHEAP_REPEATED_ERR */ + const char *FILENAME[] = { "gheap1", "gheap2", "gheap3", "gheap4", + "gheapooo", NULL }; @@ -385,6 +401,120 @@ test_4 (hid_t fapl) /*------------------------------------------------------------------------- + * Function: test_ooo_indices + * + * Purpose: Tests that indices can be stored out of order. This can + * happen when the indices "wrap around" due to many + * insertions and deletions (for example, from rewriting a + * VL dataset). + * + * Return: Success: 0 + * + * Failure: number of errors + * + * Programmer: Neil Fortner + * Monday, October 26, 2009 + * + * Modifications: + * + *------------------------------------------------------------------------- + */ +static int +test_ooo_indices(hid_t fapl) +{ + hid_t file = -1; + H5F_t *f = NULL; + unsigned i, j; + H5HG_t *obj = NULL; + herr_t status; + int nerrors=0; + char filename[1024]; + + TESTING("out of order indices"); + + if(NULL == (obj = (H5HG_t *)HDmalloc(2000 * sizeof(*obj)))) + goto error; + + /* Open a clean file */ + h5_fixname(FILENAME[4], fapl, filename, sizeof filename); + if((file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) + goto error; + if(NULL == (f = (H5F_t *)H5I_object(file))) { + H5_FAILED(); + puts(" Unable to create file"); + goto error; + } /* end if */ + + /* Alternately insert 1000 entries and remove the previous group of 1000 + * entries, until the indices wrap around */ + for(i=0; i<66; i++) { + /* Insert 1000 entries. The index into the obj array will alternate up + * and down by 1000 so the previous set of insertions is preserved and + * can be deleted. */ + for(j=1000*((~i&1)); j<1000*((~i&1)+1); j++) { + H5Eclear2(H5E_DEFAULT); + status = H5HG_insert(f, H5P_DATASET_XFER_DEFAULT, sizeof(j), &j, &obj[j]); + if (status<0) + GHEAP_REPEATED_ERR(" Unable to insert object into global heap") + + /* Check that the index is as expected */ + if(obj[j].idx != ((1000 * i) + j - (1000 * ((~i & 1)))) % ((1u << 16) - 1) + 1) + GHEAP_REPEATED_ERR(" Unexpected global heap index"); + } /* end for */ + + /* Remove the previous 1000 entries */ + if(i>0) + for(j=1000*(i&1); j<1000*((i&1)+1); j++) { + H5Eclear2(H5E_DEFAULT); + status = H5HG_remove(f, H5P_DATASET_XFER_DEFAULT, &obj[j]); + if (status<0) + GHEAP_REPEATED_ERR(" Unable to remove object from global heap"); + } /* end for */ + } /* end for */ + + /* The indices should have "wrapped around" on the last iteration */ + HDassert(obj[534].idx == 65535); + HDassert(obj[535].idx == 1); + + /* Reopen the file */ + if (H5Fclose(file)<0) goto error; + if((file = H5Fopen(filename, H5F_ACC_RDWR, fapl)) < 0) + goto error; + if(NULL == (f = (H5F_t *)H5I_object(file))) { + H5_FAILED(); + puts(" Unable to open file"); + goto error; + } /* end if */ + + /* Read the objects to make sure the heap is still readable */ + for(i=0; i<1000; i++) { + if(NULL == H5HG_read(f, H5P_DATASET_XFER_DEFAULT, &obj[i], &j, NULL)) + goto error; + if(i != j) { + H5_FAILED(); + puts(" Incorrect read value"); + goto error; + } /* end if */ + } /* end for */ + + if (H5Fclose(file)<0) goto error; + if (nerrors) goto error; + HDfree(obj); + obj = NULL; + PASSED(); + return 0; + + error: + H5E_BEGIN_TRY { + H5Fclose(file); + } H5E_END_TRY; + if(obj) + HDfree(obj); + return MAX(1, nerrors); +} /* end test_ooo_indices */ + + +/*------------------------------------------------------------------------- * Function: main * * Purpose: Tests global heap. @@ -413,6 +543,7 @@ main (void) nerrors += test_2(fapl); nerrors += test_3(fapl); nerrors += test_4(fapl); + nerrors += test_ooo_indices(fapl); if (nerrors) goto error; puts("All global heap tests passed."); |