Reserved File Address Space

From a0c466cd99e6d62725ac1828755b042c2dcb6c85 Mon Sep 17 00:00:00 2001 From: James Laird Date: Wed, 14 Jul 2004 14:34:24 -0500 Subject: [svn-r8877] Purpose: Bug Fix Description: If an HDF5 file grows larger than its address space, it dies and is unable to write any data. This is more likely to happen since users are able to change the number of bytes used to store addresses in the file. Solution: HDF5 now throws an error instead of dying. In addition, it "reserves" address space for the local heap and for object headers (which do not allocate space immediately). This ensures that after the error occurs, there is enough address space left to flush the entire file to disk, so no data is lost. A more complete explanation is at /doc/html/TechNotes/ReservedFileSpace.html Platforms tested: sleipnir, copper (parallel), verbena, arabica, Windows (Visual Studio 7) Solution: Platforms tested: Misc. update: --- MANIFEST | 2 + doc/html/TechNotes.html | 5 + doc/html/TechNotes/ReservedFileSpace.html | 29 ++++++ src/H5B.c | 5 +- src/H5FD.c | 1 + src/H5FDcore.c | 3 +- src/H5FDpublic.h | 1 + src/H5HG.c | 8 +- src/H5HL.c | 27 +++++- src/H5HLpkg.h | 1 + src/H5MF.c | 147 +++++++++++++++++++++++++++++- src/H5MFprivate.h | 3 + src/H5O.c | 34 +++++-- src/H5Tconv.c | 7 +- test/Makefile.in | 7 +- test/lheap.c | 1 - test/ohdr.c | 1 - 17 files changed, 257 insertions(+), 25 deletions(-) create mode 100644 doc/html/TechNotes/ReservedFileSpace.html diff --git a/MANIFEST b/MANIFEST index d5d43b8..51c0682 100644 --- a/MANIFEST +++ b/MANIFEST @@ -219,6 +219,7 @@ ./doc/html/TechNotes/NamingScheme.html ./doc/html/TechNotes/ObjectHeader.html ./doc/html/TechNotes/RawDStorage.html +./doc/html/TechNotes/ReservedFileSpace.html ./doc/html/TechNotes/SWControls.html ./doc/html/TechNotes/SymbolTables.html ./doc/html/TechNotes/TestReview.html @@ -993,6 +994,7 @@ ./test/noencoder.h5 ./test/ntypes.c ./test/ohdr.c +./test/reserved.c ./test/space_overflow.c _DO_NOT_DISTRIBUTE_ ./test/gen_deflate.c _DO_NOT_DISTRIBUTE_ ./test/gen_old_array.c _DO_NOT_DISTRIBUTE_ diff --git a/doc/html/TechNotes.html b/doc/html/TechNotes.html index 2a7e5e8..a02a7cf 100644 --- a/doc/html/TechNotes.html +++ b/doc/html/TechNotes.html @@ -247,6 +247,11 @@ HDF5 Technical Notes Description of various aspects of using variable-length datatypes in HDF5. +Reserved File Address Space + + Description of HDF5's internal system for ensuring that files stay within their address space. + + diff --git a/doc/html/TechNotes/ReservedFileSpace.html b/doc/html/TechNotes/ReservedFileSpace.html new file mode 100644 index 0000000..819e050 --- /dev/null +++ b/doc/html/TechNotes/ReservedFileSpace.html @@ -0,0 +1,29 @@ + + + Reserved File Address Space + + + + Reserved File Address Space + +

HDF5 files use 8-byte addresses by default, but users can change this to 2, 4, or even 16 bytes. This means that it is possible to have files that only address 64 KB of space, and thus that HDF must handle the case of files that have enough space on disk but not enough internal address space to be written.

+ +

Thus, every time space is allocated in a file, HDF needs to check that this allocation is within the file’s address space. If not, HDF should output an error and ensure that all the data currently in the file (everything that is still addressable) is successfully written to disk.

+ +

Unfortunately, some structures are stored in memory and do not allocate space for themselves until the file is actually flushed to disk (object headers and the local heap). This is good for efficiency, since these structures can grow without creating the fragmentation that would result from frequent allocation and deallocation, but means that if the library runs out of addressable space while allocating memory, these structures will not be present in the file. Without them, HDF5 does not know how to parse the data in the file, rendering it unreadable.

+ +

Thus, HDF keeps track of the space “reserved for allocation” in the file (H5FD_t struct). When a function tries to allocate space in the file, it first checks that the allocation would not overflow the address space, taking the reserved space into account. When object headers or the heap finally allocate the space they have reserved, they free the reserved space before allocating file space.

+ +

A given object header is only flushed to disk once, but the heap can be flushed to disk multiple times over the life of the file and will require contiguous space every time. To handle this, the heap keeps track of how much space it has reserved. This allows it to reserve space only when it grows (when it is dirty and needs to be re-written to disk).

+ +

For instance, if the heap is flushed to disk, it frees its reserved space. If new data is inserted into the heap in memory, the heap may need to flush to disk again in a new, larger section of memory. Thus, not only does it reserve space in the file for this new data, but also for all of the previously-existing data in the heap to be re-written. The next insert, however, will only need to reserve space for its new data, since the rest of the heap already has space reserved for it.

+ +

Potential issues: +

This system does not take into accout deleted space. Deleted space can still be allocated as usual, but "reserved" space is always taken off the end of a file. This means that a file that was filled to capacity but then had a significant number of objects deleted will still throw errors if more data is written. This occurs because the file's free space is in the middle of the file, not at the end. A more complete space-reservation system would test if the reserved data can fit into the file's free list, but this would be significantly more complicated to implement.
HDF5 currently claims to support 16-byte addresses, but since the size of a long long is only 8 bytes, addresses of this size cannot be represented in memory. This solution does not attempt to address this issue.

+ + diff --git a/src/H5B.c b/src/H5B.c index bdcca7c..d17e5df 100644 --- a/src/H5B.c +++ b/src/H5B.c @@ -229,7 +229,7 @@ H5B_create(H5F_t *f, hid_t dxpl_id, const H5B_class_t *type, void *udata, bt->right = HADDR_UNDEF; bt->nchildren = 0; if((bt->rc_shared=(type->get_shared)(f, udata))==NULL) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "can't retrieve B-tree node buffer") + HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "can't retrieve B-tree node buffer") shared=H5RC_GET_OBJ(bt->rc_shared); HDassert(shared); if (NULL==(bt->native=H5FL_BLK_MALLOC(native_block,shared->sizeof_keys)) || @@ -536,9 +536,6 @@ H5B_dest(H5F_t UNUSED *f, H5B_t *bt) */ assert(bt); - /* Verify that node is clean */ - assert(bt->cache_info.is_dirty==0); - H5FL_SEQ_FREE(haddr_t,bt->child); H5FL_BLK_FREE(native_block,bt->native); H5RC_DEC(bt->rc_shared); diff --git a/src/H5FD.c b/src/H5FD.c index 4d619d6..a5bbd9d 100644 --- a/src/H5FD.c +++ b/src/H5FD.c @@ -1061,6 +1061,7 @@ H5FD_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr) HGOTO_ERROR(H5E_VFL, H5E_CANTINC, NULL, "unable to increment ref count on VFL driver") file->cls = driver; file->maxaddr = maxaddr; + file->reserved_alloc = 0; HDmemset(file->fl, 0, sizeof(file->fl)); if(H5P_get(plist, H5F_ACS_META_BLOCK_SIZE_NAME, &(meta_block_size)) < 0) HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't get meta data block size") diff --git a/src/H5FDcore.c b/src/H5FDcore.c index 95783aa..eecd336 100644 --- a/src/H5FDcore.c +++ b/src/H5FDcore.c @@ -382,7 +382,8 @@ done: */ static H5FD_t * H5FD_core_open(const char *name, unsigned UNUSED flags, hid_t fapl_id, - haddr_t maxaddr) + haddr_t + maxaddr) { H5FD_core_t *file=NULL; H5FD_core_fapl_t *fa=NULL; diff --git a/src/H5FDpublic.h b/src/H5FDpublic.h index 3454f28..596e0f1 100644 --- a/src/H5FDpublic.h +++ b/src/H5FDpublic.h @@ -187,6 +187,7 @@ struct H5FD_t { unsigned long feature_flags; /* VFL Driver feature Flags */ hsize_t threshold; /* Threshold for alignment */ hsize_t alignment; /* Allocation alignment */ + hsize_t reserved_alloc; /* Space reserved for later alloc calls */ /* Metadata aggregation fields */ hsize_t def_meta_block_size; /* Metadata allocation diff --git a/src/H5HG.c b/src/H5HG.c index 181728e..2741fe7 100644 --- a/src/H5HG.c +++ b/src/H5HG.c @@ -955,8 +955,14 @@ H5HG_insert (H5F_t *f, hid_t dxpl_id, size_t size, void *obj, H5HG_t *hobj/*out* * we can extend any of the collections to make enough room. */ if (!found) { + size_t new_need; + for (cwfsno=0; cwfsnoshared->ncwfs; cwfsno++) { - if((f->shared->cwfs[cwfsno]->size+need)<=H5HG_MAXSIZE && H5MF_can_extend(f,H5FD_MEM_GHEAP,f->shared->cwfs[cwfsno]->addr,(hsize_t)f->shared->cwfs[cwfsno]->size,(hsize_t)need)) { + new_need = need; + new_need -= f->shared->cwfs[cwfsno]->obj[0].size; + new_need = MAX(f->shared->cwfs[cwfsno]->size, new_need); + + if((f->shared->cwfs[cwfsno]->size+need)<=H5HG_MAXSIZE && H5MF_can_extend(f,H5FD_MEM_GHEAP,f->shared->cwfs[cwfsno]->addr,(hsize_t)f->shared->cwfs[cwfsno]->size,(hsize_t)new_need)) { if(H5HG_extend(f,f->shared->cwfs[cwfsno],size)<0) HGOTO_ERROR (H5E_HEAP, H5E_CANTINIT, FAIL, "unable to extend global heap collection"); addr = f->shared->cwfs[cwfsno]->addr; diff --git a/src/H5HL.c b/src/H5HL.c index bf402b0..bfbb2ac 100644 --- a/src/H5HL.c +++ b/src/H5HL.c @@ -155,6 +155,7 @@ H5HL_create(H5F_t *f, hid_t dxpl_id, size_t size_hint, haddr_t *addr_p/*out*/) heap->addr = *addr_p + (hsize_t)sizeof_hdr; heap->disk_alloc = size_hint; heap->mem_alloc = size_hint; + heap->disk_resrv = 0; if (NULL==(heap->chunk = H5FL_BLK_CALLOC(heap_chunk,(sizeof_hdr + size_hint)))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); @@ -253,7 +254,7 @@ H5HL_load(H5F_t *f, hid_t dxpl_id, haddr_t addr, const void UNUSED * udata1, /* Allocate space in memory for the heap */ if (NULL==(heap = H5FL_CALLOC(H5HL_t))) HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed"); - + /* heap data size */ H5F_DECODE_LENGTH(f, p, heap->disk_alloc); heap->mem_alloc = heap->disk_alloc; @@ -337,6 +338,13 @@ H5HL_minimize_heap_space(H5F_t *f, hid_t dxpl_id, H5HL_t *heap) sizeof_hdr = H5HL_SIZEOF_HDR(f); /* cache H5HL header size for file */ /* + * When the heap is being flushed to disk, release the file space reserved + * for it. + */ + H5MF_free_reserved(f, heap->disk_resrv); + heap->disk_resrv = 0; + + /* * Check to see if we can reduce the size of the heap in memory by * eliminating free blocks at the tail of the buffer before flushing the * buffer out. @@ -406,8 +414,9 @@ H5HL_minimize_heap_space(H5F_t *f, hid_t dxpl_id, H5HL_t *heap) assert(last_fl->size == H5HL_ALIGN(last_fl->size)); } - /* Resize the memory buffer */ + /* Resize the memory buffer and reserved space in file */ if (new_mem_size != heap->mem_alloc) { + heap->mem_alloc = new_mem_size; heap->chunk = H5FL_BLK_REALLOC(heap_chunk, heap->chunk, (sizeof_hdr + new_mem_size)); @@ -939,6 +948,7 @@ H5HL_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, size_t buf_size, const void * size_t offset = 0; size_t need_size, old_size, need_more; hbool_t found; + size_t disk_resrv; /* Amount of additional space to reserve in file */ size_t sizeof_hdr; /* Cache H5HL header size for file */ size_t ret_value; /* Return value */ @@ -1004,6 +1014,19 @@ H5HL_insert(H5F_t *f, hid_t dxpl_id, haddr_t addr, size_t buf_size, const void * if (found==FALSE) { need_more = MAX3(need_size, heap->mem_alloc, H5HL_SIZEOF_FREE(f)); + /* Reserve space in the file to hold the increased heap size + */ + if( heap->disk_resrv == heap->mem_alloc) + disk_resrv = need_more; + else + disk_resrv = heap->mem_alloc + need_more - heap->disk_resrv; + + if( H5MF_reserve(f, disk_resrv) < 0 ) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, (size_t)(-1), "unable to reserve space in file"); + + /* Update heap's record of how much space it has reserved */ + heap->disk_resrv += disk_resrv; + if (max_fl && max_fl->offset + max_fl->size == heap->mem_alloc) { /* * Increase the size of the maximum free block. diff --git a/src/H5HLpkg.h b/src/H5HLpkg.h index 8b099cc..1a61866 100644 --- a/src/H5HLpkg.h +++ b/src/H5HLpkg.h @@ -67,6 +67,7 @@ struct H5HL_t { haddr_t addr; /*address of data */ size_t disk_alloc; /*data bytes allocated on disk */ size_t mem_alloc; /*data bytes allocated in mem */ + size_t disk_resrv; /*data bytes "reserved" on disk */ uint8_t *chunk; /*the chunk, including header */ H5HL_free_t *freelist; /*the free list */ }; diff --git a/src/H5MF.c b/src/H5MF.c index 9ea2d79..bc241e8 100644 --- a/src/H5MF.c +++ b/src/H5MF.c @@ -78,10 +78,13 @@ H5MF_alloc(H5F_t *f, H5FD_mem_t type, hid_t dxpl_id, hsize_t size) /* Fail if we don't have write access */ if (0==(f->intent & H5F_ACC_RDWR)) HGOTO_ERROR(H5E_RESOURCE, H5E_CANTINIT, HADDR_UNDEF, "file is read-only"); + /* Check that the file can address the new space */ + if( H5MF_alloc_overflow(f, size) != 0 ) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "not enough address space in file"); /* Allocate space from the virtual file layer */ if (HADDR_UNDEF==(ret_value=H5FD_alloc(f->shared->lf, type, dxpl_id, size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "file allocation failed"); + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "file allocation failed"); /* Convert absolute file address to relative file address */ assert(ret_value>=f->shared->base_addr); @@ -192,6 +195,11 @@ H5MF_realloc(H5F_t *f, H5FD_mem_t type, hid_t dxpl_id, haddr_t old_addr, hsize_t /* Convert old relative address to absolute address */ old_addr += f->shared->base_addr; + /* Check that the file can address the new space. */ + /* In the worst case, this means adding new_size bytes to the end of the file. */ + if( H5MF_alloc_overflow(f, new_size) != 0 ) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "not enough address space in file"); + /* Reallocate memory from the virtual file layer */ ret_value = H5FD_realloc(f->shared->lf, type, dxpl_id, old_addr, old_size, new_size); @@ -208,6 +216,133 @@ done: FUNC_LEAVE_NOAPI(ret_value); } + +/*------------------------------------------------------------------------- + * Function: H5MF_reserve + * + * Purpose: Sets aside file space that has not yet been allocated, but will + * be (or might be in the worst case). This number is used to + * ensure that there is room in the file when it is flushed to disk. + * + * Nothing changes (and no error is generated) if the file is opened + * as read-only. + * + * Return: Success: 0 + * + * Failure: negative + * + * Programmer: James Laird + * Nat Furrer + * Thursday, May 27, 2004 + * + * Modifications: + *------------------------------------------------------------------------- + */ +herr_t H5MF_reserve(H5F_t *f, hsize_t size) +{ + herr_t ret_value = SUCCEED; + FUNC_ENTER_NOAPI(H5MF_reserve, FAIL); + + /* Check arguments */ + assert(f); + + /* Check that there is room in the file to reserve this space */ + if( H5MF_alloc_overflow( f, size ) != 0) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "not enough address space in file"); + + f->shared->lf->reserved_alloc += size; + +done: + FUNC_LEAVE_NOAPI(ret_value); +} + +/*------------------------------------------------------------------------- + * Function: H5MF_free_reserved + * + * Purpose: Releases the file space set aside by H5MF_reserve. This should + * be called immediately before allocating the file space for which + * the space was reserved. + * + * Return: None + * + * Programmer: James Laird + * Nat Furrer + * Thursday, May 27, 2004 + * + * Modifications: + *------------------------------------------------------------------------- + */ +void H5MF_free_reserved(H5F_t *f, hsize_t size) +{ + /* Check arguments */ + assert(f); + + /* If this assert breaks, it means that HDF5 is trying to free file space + * that was never reserved. + */ + assert(size <= f->shared->lf->reserved_alloc); + + f->shared->lf->reserved_alloc -= size; +} + +/*------------------------------------------------------------------------- + * Function: H5MF_alloc_overflow + * + * Purpose: Checks if an allocation of file space would cause an overflow. + * F is the file whose space is being allocated, SIZE is the amount + * of space needed. + * + * Return: 0 if no overflow would result + * 1 if overflow would result (the allocation should not be allowed) + * + * Programmer: James Laird + * Nat Furrer + * Tuesday, June 1, 2004 + * + * Modifications: + *------------------------------------------------------------------------- + */ +int H5MF_alloc_overflow(H5F_t *f, hsize_t size) +{ + unsigned long long space_needed; /* Accumulator variable */ + hsize_t c; + + /* Start with the current end of the file's address. */ + space_needed = f->shared->lf->cls->get_eoa(f->shared->lf); + + /* Subtract the file's base address to get the actual amount of + * space being used: + * (end of allocated space - beginning of allocated space) + */ + assert(f->shared->base_addr < space_needed); + space_needed -= f->shared->base_addr; + + /* Add the amount of space requested for this allocation */ + space_needed += size; + + /* Also add space that is "reserved" for data to be flushed + * to disk (e.g., for object headers and the heap). + * This is the total amount of file space that will be + * allocated. + */ + space_needed += f->shared->lf->reserved_alloc; + + /* Ensure that this final number is less than the file's + * address space. We do this by shifting in multiples + * of 16 bits because some systems will do nothing if + * we shift by the size of a long long (64 bits) all at + * once ( Linux ). Thus, we break one shift + * into several smaller shifts. + */ + for(c=0; c < H5F_SIZEOF_ADDR(f); c += 2) + space_needed = space_needed >> 16; + + if(space_needed != 0) + return 1; + else + return 0; +} + /*------------------------------------------------------------------------- * Function: H5MF_can_extend @@ -234,7 +369,6 @@ htri_t H5MF_can_extend(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size, hsize_t extra_requested) { htri_t ret_value; /* Return value */ - FUNC_ENTER_NOAPI(H5MF_can_extend, FAIL); /* Convert old relative address to absolute address */ @@ -244,6 +378,10 @@ H5MF_can_extend(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size, hsize_t e if((ret_value=H5FD_can_extend(f->shared->lf, type, addr, size, extra_requested))<0) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate new file memory"); + /* Make sure there is enough addressable space to satisfy the request */ + if (ret_value == TRUE) + ret_value = !H5MF_alloc_overflow(f, extra_requested); + done: FUNC_LEAVE_NOAPI(ret_value); } /* end H5MF_can_extend() */ @@ -269,12 +407,15 @@ htri_t H5MF_extend(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size, hsize_t extra_requested) { htri_t ret_value; /* Return value */ - FUNC_ENTER_NOAPI(H5MF_extend, FAIL); /* Convert old relative address to absolute address */ addr += f->shared->base_addr; + /* Make sure there is enough addressable space to satisfy the request */ + if ( H5MF_alloc_overflow(f, extra_requested) ) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate new file memory: out of address space"); + /* Pass the request down to the virtual file layer */ if((ret_value=H5FD_extend(f->shared->lf, type, addr, size, extra_requested))<0) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate new file memory"); diff --git a/src/H5MFprivate.h b/src/H5MFprivate.h index 14b2761..2a129ea 100644 --- a/src/H5MFprivate.h +++ b/src/H5MFprivate.h @@ -48,6 +48,9 @@ H5_DLL herr_t H5MF_xfree(H5F_t *f, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size); H5_DLL haddr_t H5MF_realloc(H5F_t *f, H5FD_mem_t type, hid_t dxpl_id, haddr_t old_addr, hsize_t old_size, hsize_t new_size); +H5_DLL herr_t H5MF_reserve(H5F_t *f, hsize_t size); +H5_DLL void H5MF_free_reserved(H5F_t *f, hsize_t size); +H5_DLL int H5MF_alloc_overflow(H5F_t *f, hsize_t size); H5_DLL htri_t H5MF_can_extend(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size, hsize_t extra_requested); H5_DLL htri_t H5MF_extend(H5F_t *f, H5FD_mem_t type, haddr_t addr, hsize_t size, diff --git a/src/H5O.c b/src/H5O.c index f1b4a23..0ee7706 100644 --- a/src/H5O.c +++ b/src/H5O.c @@ -75,7 +75,7 @@ static herr_t H5O_remove_real(H5G_entry_t *ent, const H5O_class_t *type, int sequence, hid_t dxpl_id); static unsigned H5O_alloc(H5F_t *f, H5O_t *oh, const H5O_class_t *type, size_t size); -static unsigned H5O_alloc_extend_chunk(H5O_t *oh, unsigned chunkno, size_t size); +static unsigned H5O_alloc_extend_chunk(H5F_t *f, H5O_t *oh, unsigned chunkno, size_t size); static unsigned H5O_alloc_new_chunk(H5F_t *f, H5O_t *oh, size_t size); static herr_t H5O_delete_oh(H5F_t *f, hid_t dxpl_id, H5O_t *oh); static herr_t H5O_delete_mesg(H5F_t *f, hid_t dxpl_id, H5O_mesg_t *mesg); @@ -715,7 +715,11 @@ H5O_flush(H5F_t *f, hid_t dxpl_id, hbool_t destroy, haddr_t addr, H5O_t *oh) assert(cont->chunkno < oh->nchunks); assert(!H5F_addr_defined(oh->chunk[cont->chunkno].addr)); cont->size = oh->chunk[cont->chunkno].size; - if (HADDR_UNDEF==(cont->addr=H5MF_alloc(f, + + /* Free the space we'd reserved in the file to hold this chunk */ + H5MF_free_reserved(f, cont->size); + + if (HADDR_UNDEF==(cont->addr=H5MF_alloc(f, H5FD_MEM_OHDR, dxpl_id, (hsize_t)cont->size))) HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate space for object header data"); oh->chunk[cont->chunkno].addr = cont->addr; @@ -2592,6 +2596,10 @@ done: * that message will be extended with the chunk. Otherwise a * new null message is created. * + * F is the file in which the chunk will be written. It is + * included to ensure that there is enough space to extend + * this chunk. + * * Return: Success: Message index for null message which * is large enough to hold SIZE bytes. * @@ -2610,7 +2618,7 @@ done: *------------------------------------------------------------------------- */ static unsigned -H5O_alloc_extend_chunk(H5O_t *oh, unsigned chunkno, size_t size) +H5O_alloc_extend_chunk(H5F_t *f, H5O_t *oh, unsigned chunkno, size_t size) { unsigned u; unsigned idx; @@ -2638,6 +2646,11 @@ H5O_alloc_extend_chunk(H5O_t *oh, unsigned chunkno, size_t size) delta = MAX (H5O_MIN_SIZE, aligned_size - oh->mesg[idx].raw_size); assert (delta=H5O_ALIGN (delta)); + + /* Reserve space in the file to hold the increased chunk size */ + if( H5MF_reserve(f, delta) < 0 ) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, UFAIL, "unable to reserve space in file"); + oh->mesg[idx].dirty = TRUE; oh->mesg[idx].raw_size += delta; @@ -2665,6 +2678,13 @@ H5O_alloc_extend_chunk(H5O_t *oh, unsigned chunkno, size_t size) } /* end if */ } + /* Reserve space in the file */ + delta = MAX(H5O_MIN_SIZE, aligned_size+H5O_SIZEOF_MSGHDR(f)); + delta = H5O_ALIGN(delta); + + if( H5MF_reserve(f, delta) < 0 ) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, UFAIL, "unable to reserve space in file"); + /* create a new null message */ if (oh->nmesgs >= oh->alloc_nmesgs) { unsigned na = oh->alloc_nmesgs + H5O_NMESGS; @@ -2675,8 +2695,6 @@ H5O_alloc_extend_chunk(H5O_t *oh, unsigned chunkno, size_t size) oh->alloc_nmesgs = na; oh->mesg = x; } - delta = MAX(H5O_MIN_SIZE, aligned_size+H5O_SIZEOF_MSGHDR(f)); - delta = H5O_ALIGN(delta); idx = oh->nmesgs++; oh->mesg[idx].type = H5O_NULL; oh->mesg[idx].dirty = TRUE; @@ -2805,6 +2823,10 @@ H5O_alloc_new_chunk(H5F_t *f, H5O_t *oh, size_t size) size = MAX(H5O_MIN_SIZE, size + H5O_SIZEOF_MSGHDR(f)); assert (size == H5O_ALIGN (size)); + /* Reserve space in the file to hold the new chunk */ + if( H5MF_reserve(f, size) < 0 ) + HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, UFAIL, "unable to reserve space in file for new chunk"); + /* * Create the new chunk without giving it a file address. */ @@ -2969,7 +2991,7 @@ H5O_alloc(H5F_t *f, H5O_t *oh, const H5O_class_t *type, size_t size) * since we can just increase the size of that chunk. */ for (chunkno = 0; chunkno < oh->nchunks; chunkno++) { - if ((idx = H5O_alloc_extend_chunk(oh, chunkno, size)) != UFAIL) { + if ((idx = H5O_alloc_extend_chunk(f, oh, chunkno, size)) != UFAIL) { break; } H5E_clear(NULL); diff --git a/src/H5Tconv.c b/src/H5Tconv.c index 82c7084..698c99f 100644 --- a/src/H5Tconv.c +++ b/src/H5Tconv.c @@ -2685,10 +2685,6 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, nelmts-=safe; } /* end while */ - /* Reset the conversion buffer pointer, so it doesn't get freed */ - if(write_to_file && noop_conv) - conv_buf=NULL; - /* Release the temporary datatype IDs used */ if (tsrc_id >= 0) H5I_dec_ref(tsrc_id); @@ -2701,6 +2697,9 @@ H5T_conv_vlen(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts, } /* end switch */ done: + /* If the conversion buffer doesn't need to be freed, reset its pointer */ + if(write_to_file && noop_conv) + conv_buf=NULL; /* Release the conversion buffer (always allocated, except on errors) */ if(conv_buf!=NULL) H5FL_BLK_FREE(vlen_seq,conv_buf); diff --git a/test/Makefile.in b/test/Makefile.in index 1fe85e5..e19a60a 100644 --- a/test/Makefile.in +++ b/test/Makefile.in @@ -31,7 +31,7 @@ TEST_PROGS=testhdf5 lheap ohdr stab gheap cache hyperslab istore bittests \ dtypes dsets cmpd_dset extend external links unlink big mtime \ fillval mount flush1 flush2 enum gass_write gass_read gass_append \ set_extent srb_write srb_append srb_read ttsafe stream_test \ - getname file_handle ntypes dangle dtransform filename + getname file_handle ntypes dangle dtransform filename reserved ## Test programs for Error API. Only compile them but let testerror.sh run ## them to compare the output error messages with standard ones. 'make check' @@ -88,7 +88,7 @@ TEST_SRC=big.c bittests.c cache.c cmpd_dset.c dsets.c dtypes.c extend.c \ ttsafe_cancel.c ttsafe_acreate.c gass_write.c gass_read.c \ gass_append.c srb_read.c srb_write.c srb_append.c stream_test.c \ set_extent.c getname.c file_handle.c ntypes.c dangle.c error_test.c \ - err_compat.c dtransform.c filename.c + err_compat.c dtransform.c filename.c reserved.c TEST_OBJ=$(TEST_SRC:.c=.lo) @@ -245,4 +245,7 @@ dtransform: dtransform.lo filename: filename.lo @$(LT_LINK_EXE) $(CFLAGS) -o $@ filename.lo $(LIB) $(LIBHDF5) $(LDFLAGS) $(LIBS) +reserved: reserved.lo + @$(LT_LINK_EXE) $(CFLAGS) -o $@ reserved.lo $(LIB) $(LIBHDF5) $(LDFLAGS) $(LIBS) + @CONCLUDE@ diff --git a/test/lheap.c b/test/lheap.c index e1694ba..5fe6c1f 100644 --- a/test/lheap.c +++ b/test/lheap.c @@ -29,7 +29,6 @@ const char *FILENAME[] = { #define NOBJS 40 - /*------------------------------------------------------------------------- * Function: main * diff --git a/test/ohdr.c b/test/ohdr.c index a893d08..aa9259c 100644 --- a/test/ohdr.c +++ b/test/ohdr.c @@ -39,7 +39,6 @@ const char *FILENAME[] = { * the library and simply compile gen_bogus.c with that HDF5 library and run it. */ #define FILE_BOGUS "tbogus.h5" - /*------------------------------------------------------------------------- * Function: main * -- cgit v0.12