diff options
| -rw-r--r-- | src/H5Dchunk.c | 186 | ||||
| -rw-r--r-- | src/H5Dmpio.c | 4 | ||||
| -rw-r--r-- | src/H5Dpkg.h | 2 | ||||
| -rw-r--r-- | test/dsets.c | 135 |
4 files changed, 309 insertions, 18 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c index 7627cec..1c27ede 100644 --- a/src/H5Dchunk.c +++ b/src/H5Dchunk.c @@ -172,6 +172,12 @@ static ssize_t H5D_null_readvv(const H5D_io_info_t *io_info, size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]); +/* "Unexisted" layout operation callback */ +static ssize_t +H5D_unexisted_readvv(const H5D_io_info_t *io_info, + size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[], + size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]); + /* Helper routines */ static void *H5D_chunk_alloc(size_t size, const H5O_pline_t *pline); static void *H5D_chunk_xfree(void *chk, const H5O_pline_t *pline); @@ -229,6 +235,22 @@ const H5D_layout_ops_t H5D_LOPS_NULL[1] = {{ NULL }}; +/* "unexisted" storage layout I/O ops */ +const H5D_layout_ops_t H5D_LOPS_UNEXISTED[1] = {{ + NULL, + NULL, + NULL, + NULL, + NULL, +#ifdef H5_HAVE_PARALLEL + NULL, + NULL, +#endif /* H5_HAVE_PARALLEL */ + H5D_unexisted_readvv, + NULL, + NULL +}}; + /* Declare a free list to manage the H5F_rdcc_ent_ptr_t sequence information */ H5FL_SEQ_DEFINE_STATIC(H5D_rdcc_ent_ptr_t); @@ -1335,10 +1357,17 @@ done: * Programmer: Raymond Lu * 17 July 2007 * + * Modification:Raymond Lu + * 4 Feb 2009 + * Took out the parameter chunk address. This function doesn't + * need to check the address. One case that was considered + * cacheable was when the chunk is bigger than the cache size + * but not allocated on disk. I moved it to uncacheable to + * bypass the cache to improve performance. *------------------------------------------------------------------------- */ hbool_t -H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr) +H5D_chunk_cacheable(const H5D_io_info_t *io_info) { const H5D_t *dataset = io_info->dset; hbool_t ret_value; @@ -1367,8 +1396,7 @@ H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr) * cache, just write the data to it directly. */ H5_CHECK_OVERFLOW(dataset->shared->layout.u.chunk.size, uint32_t, size_t); - if((size_t)dataset->shared->layout.u.chunk.size > dataset->shared->cache.chunk.nbytes - && H5F_addr_defined(caddr)) + if((size_t)dataset->shared->layout.u.chunk.size > dataset->shared->cache.chunk.nbytes) ret_value = FALSE; else ret_value = TRUE; @@ -1447,6 +1475,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, { H5SL_node_t *chunk_node; /* Current node in chunk skip list */ H5D_io_info_t nul_io_info; /* "null" I/O info object */ + H5D_io_info_t unexist_io_info; /* "unexisted" I/O info object */ H5D_io_info_t ctg_io_info; /* Contiguous I/O info object */ H5D_storage_t ctg_store; /* Chunk storage information as contiguous dataset */ H5D_io_info_t cpt_io_info; /* Compact I/O info object */ @@ -1469,6 +1498,10 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, HDmemcpy(&nul_io_info, io_info, sizeof(nul_io_info)); nul_io_info.layout_ops = *H5D_LOPS_NULL; + /* Set up "unexisted" I/O info object */ + HDmemcpy(&unexist_io_info, io_info, sizeof(unexist_io_info)); + unexist_io_info.layout_ops = *H5D_LOPS_UNEXISTED; + /* Set up contiguous I/O info object */ HDmemcpy(&ctg_io_info, io_info, sizeof(ctg_io_info)); ctg_io_info.store = &ctg_store; @@ -1527,7 +1560,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, } /* end if */ else { /* Load the chunk into cache and lock it. */ - if(H5D_chunk_cacheable(io_info, udata.addr)) { + if(H5D_chunk_cacheable(io_info)) { /* Pass in chunk's coordinates in a union. */ io_info->store->chunk.offset = chunk_info->coords; io_info->store->chunk.index = chunk_info->index; @@ -1545,10 +1578,7 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, /* Point I/O info at contiguous I/O info for this chunk */ chk_io_info = &cpt_io_info; } /* end if */ - else { - /* Sanity check */ - HDassert(H5F_addr_defined(udata.addr)); - + else if(H5F_addr_defined(udata.addr)) { /* Set up the storage address information for this chunk */ ctg_store.contig.dset_addr = udata.addr; @@ -1557,7 +1587,14 @@ H5D_chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, /* Point I/O info at temporary I/O info for this chunk */ chk_io_info = &ctg_io_info; - } /* end else */ + } /* end else if */ + else { + /* No chunk cached */ + chunk = NULL; + + /* Point I/O info at "unexist" I/O info for this chunk */ + chk_io_info = &unexist_io_info; + } } /* end else */ /* Perform the actual read operation */ @@ -1588,6 +1625,12 @@ done: * Programmer: Raymond Lu * Thursday, April 10, 2003 * + * Modification:Raymond Lu + * 4 Feb 2009 + * One case that was considered cacheable was when the chunk + * was bigger than the cache size but not allocated on disk. + * I moved it to uncacheable branch to bypass the cache to + * improve performance. *------------------------------------------------------------------------- */ static herr_t @@ -1644,7 +1687,7 @@ H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, * simply allocate space instead of load the chunk. */ if(H5D_chunk_get_info(io_info->dset, io_info->dxpl_id, chunk_info->coords, &udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address") - if(H5D_chunk_cacheable(io_info, udata.addr)) { + if(H5D_chunk_cacheable(io_info)) { hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */ /* Pass in chunk's coordinates in a union. */ @@ -1670,9 +1713,26 @@ H5D_chunk_write(H5D_io_info_t *io_info, const H5D_type_info_t *type_info, chk_io_info = &cpt_io_info; } /* end if */ else { - /* Sanity check */ - HDassert(H5F_addr_defined(udata.addr)); - + /* If the chunk hasn't been allocated on disk, do so now. */ + if(!H5F_addr_defined(udata.addr)) { + H5D_chk_idx_info_t idx_info; /* Chunked index info */ + + /* Compose chunked index info struct */ + idx_info.f = io_info->dset->oloc.file; + idx_info.dxpl_id = io_info->dxpl_id; + idx_info.layout = &(io_info->dset->shared->layout); + + /* Set up the size of chunk for user data */ + udata.nbytes = io_info->dset->shared->layout.u.chunk.size; + + /* Create the chunk */ + if((io_info->dset->shared->layout.u.chunk.ops->insert)(&idx_info, &udata) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert/resize chunk") + + /* Make sure the address of the chunk is returned. */ + if(!H5F_addr_defined(udata.addr)) + HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined") + } /* Set up the storage address information for this chunk */ ctg_store.contig.dset_addr = udata.addr; @@ -2032,6 +2092,10 @@ done: * Programmer: Albert Cheng * June 27, 1998 * + * Modification:Raymond Lu + * 11 Feb 2009 + * I added a condition check for H5D_chunk_cinfo_cache_update. + * It's the same as H5D_chunk_cacheable. *------------------------------------------------------------------------- */ herr_t @@ -2069,8 +2133,11 @@ H5D_chunk_get_info(const H5D_t *dset, hid_t dxpl_id, const hsize_t *chunk_offset if((dset->shared->layout.u.chunk.ops->get_addr)(&idx_info, udata) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't query chunk address") - /* Cache the information retrieved */ - H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata); + /* The same condition check as H5D_chunk_cacheable. */ + if(dset->shared->dcpl_cache.pline.nused || + ((size_t)dset->shared->layout.u.chunk.size <= dset->shared->cache.chunk.nbytes)) + /* Cache the information retrieved */ + H5D_chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata); } /* end if */ done: @@ -4546,3 +4613,92 @@ H5D_null_readvv(const H5D_io_info_t UNUSED *io_info, FUNC_LEAVE_NOAPI(bytes_processed) } /* H5D_null_readvv() */ + +/*------------------------------------------------------------------------- + * Function: H5D_unexisted_readvv + * + * Purpose: When the chunk doesn't exist on disk and the chunk is bigger + * than the cache size, performs fill value I/O operation on + * memory buffer, advancing through two I/O vectors, until one + * runs out. + * + * Return: Non-negative on success/Negative on failure + * + * Programmer: Raymond Lu + * 6 Feb 2009 + * + *------------------------------------------------------------------------- + */ +static ssize_t +H5D_unexisted_readvv(const H5D_io_info_t *io_info, + size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[], + size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[]) +{ + H5D_t *dset = io_info->dset; /* Local pointer to the dataset info */ + unsigned char *buf; + const H5O_fill_t *fill = &(io_info->dset->shared->dcpl_cache.fill); /*Fill value info*/ + H5D_fill_buf_info_t fb_info; /* Dataset's fill buffer info */ + hbool_t fb_info_init = FALSE; /* Whether the fill value buffer has been initialized */ + ssize_t ret_value; /* Return value */ + + size_t u, v; /* Local index variables */ + size_t size; /* Size of sequence in bytes */ + ssize_t bytes_processed = 0; /* Eventual return value */ + + FUNC_ENTER_NOAPI_NOINIT(H5D_unexisted_readvv) + + /* Check args */ + HDassert(chunk_len_arr); + HDassert(chunk_offset_arr); + HDassert(mem_len_arr); + HDassert(mem_offset_arr); + + /* Work through all the sequences */ + for(u = *mem_curr_seq, v = *chunk_curr_seq; u < mem_max_nseq && v < chunk_max_nseq; ) { + /* Choose smallest buffer to write */ + if(chunk_len_arr[v] < mem_len_arr[u]) + size = chunk_len_arr[v]; + else + size = mem_len_arr[u]; + + /* Compute offset in memory */ + buf = (unsigned char *)io_info->u.rbuf + mem_offset_arr[v]; + + /* Initialize the fill value buffer */ + /* (use the compact dataset storage buffer as the fill value buffer) */ + if(H5D_fill_init(&fb_info, buf, FALSE, + NULL, NULL, NULL, NULL, + &dset->shared->dcpl_cache.fill, dset->shared->type, + dset->shared->type_id, (size_t)0, mem_len_arr[u], io_info->dxpl_id) < 0) + HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill buffer info") + + /* Check for VL datatype & non-default fill value. + * Fill the buffer with VL datatype fill values */ + if(fb_info.has_vlen_fill_type && (H5D_fill_refill_vl(&fb_info, fb_info.elmts_per_buf, + io_info->dxpl_id) < 0)) + HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "can't refill fill value buffer") + + /* Update source information */ + chunk_len_arr[v] -= size; + chunk_offset_arr[v] += size; + if(chunk_len_arr[v] == 0) + v++; + + /* Update destination information */ + mem_len_arr[u] -= size; + mem_offset_arr[u] += size; + if(mem_len_arr[u] == 0) + u++; + + /* Increment number of bytes copied */ + bytes_processed += (ssize_t)size; + } /* end for */ + + /* Update current sequence vectors */ + *mem_curr_seq = u; + *chunk_curr_seq = v; + + ret_value = bytes_processed; +done: + FUNC_LEAVE_NOAPI(ret_value) +} /* H5D_unexisted_readvv() */ diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index 99ad001..19be413 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -1224,7 +1224,7 @@ if(H5DEBUG(D)) HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "couldn't get chunk info from skipped list") /* Load the chunk into cache and lock it. */ - if(H5D_chunk_cacheable(io_info, udata.addr)) { + if(H5D_chunk_cacheable(io_info)) { hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */ /* Compute # of bytes accessed in chunk */ @@ -1449,7 +1449,7 @@ if(H5DEBUG(D)) { HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't switch to independent I/O") /* Load the chunk into cache and lock it. */ - if(H5D_chunk_cacheable(io_info, udata.addr)) { + if(H5D_chunk_cacheable(io_info)) { hbool_t entire_chunk = TRUE; /* Whether whole chunk is selected */ /* Compute # of bytes accessed in chunk */ diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index 4bf4e75..e2600a3 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -571,7 +571,7 @@ H5_DLL herr_t H5D_contig_copy(H5F_t *f_src, const H5O_layout_t *layout_src, H5F_ H5O_layout_t *layout_dst, H5T_t *src_dtype, H5O_copy_t *cpy_info, hid_t dxpl_id); /* Functions that operate on chunked dataset storage */ -H5_DLL hbool_t H5D_chunk_cacheable(const H5D_io_info_t *io_info, haddr_t caddr); +H5_DLL hbool_t H5D_chunk_cacheable(const H5D_io_info_t *io_info); H5_DLL herr_t H5D_chunk_cinfo_cache_reset(H5D_chunk_cached_t *last); H5_DLL herr_t H5D_chunk_create(H5D_t *dset /*in,out*/, hid_t dxpl_id); H5_DLL herr_t H5D_chunk_init(H5F_t *f, hid_t dapl_id, hid_t dxpl_id, const H5D_t *dset); diff --git a/test/dsets.c b/test/dsets.c index e3bac54..575449a 100644 --- a/test/dsets.c +++ b/test/dsets.c @@ -44,6 +44,7 @@ const char *FILENAME[] = { "random_chunks", "huge_chunks", "chunk_cache", + "big_chunk", NULL }; #define FILENAME_BUF_SIZE 1024 @@ -163,6 +164,12 @@ const char *FILENAME[] = { #define TOO_HUGE_CHUNK_DIM2_1 ((hsize_t)1024) #define TOO_HUGE_CHUNK_DIM2_2 ((hsize_t)1024) +/* Parameters for testing bypassing chunk cache */ +#define BYPASS_DATASET "Dset" +#define BYPASS_DIM 1000 +#define BYPASS_CHUNK_DIM 500 +#define BYPASS_FILL_VALUE 7 + /* Shared global arrays */ #define DSET_DIM1 100 #define DSET_DIM2 200 @@ -6683,6 +6690,133 @@ error: /*------------------------------------------------------------------------- + * Function: test_big_chunks_bypass_cache + * + * Purpose: When the chunk size is bigger than the cache size and the + * chunk isn't on disk, this test verifies that the library + * bypasses the cache. + * + * Return: Success: 0 + * Failure: -1 + * + * Programmer: Raymond Lu + * 11 Feb 2009 + * + *------------------------------------------------------------------------- + */ +static herr_t +test_big_chunks_bypass_cache(hid_t fapl) +{ + char filename[FILENAME_BUF_SIZE]; + hid_t fid = -1; /* File ID */ + hid_t dcpl = -1; /* Dataset creation property list ID */ + hid_t sid = -1; /* Dataspace ID */ + hid_t dsid = -1; /* Dataset ID */ + hsize_t dim, chunk_dim; /* Dataset and chunk dimensions */ + size_t rdcc_nelmts, rdcc_nbytes; + int fvalue = BYPASS_FILL_VALUE; + hsize_t count, stride, offset, block; + static int wdata[BYPASS_CHUNK_DIM], rdata[BYPASS_DIM]; + int i, j; + herr_t ret; /* Generic return value */ + + TESTING("big chunks bypassing the cache"); + + h5_fixname(FILENAME[9], fapl, filename, sizeof filename); + + /* Define cache size to be smaller than chunk size */ + rdcc_nelmts = BYPASS_CHUNK_DIM/5; + rdcc_nbytes = sizeof(int)*BYPASS_CHUNK_DIM/5; + if(H5Pset_cache(fapl, 0, rdcc_nelmts, rdcc_nbytes, 0) < 0) FAIL_STACK_ERROR + + /* Create file */ + if((fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl)) < 0) FAIL_STACK_ERROR + + /* Create 1-D dataspace */ + dim = BYPASS_DIM; + if((sid = H5Screate_simple(1, &dim, NULL)) < 0) FAIL_STACK_ERROR + + /* Create dataset creation property list */ + if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0) FAIL_STACK_ERROR + + /* Define chunk size. There will be only 2 chunks in the dataset. */ + chunk_dim = BYPASS_CHUNK_DIM; + if(H5Pset_chunk(dcpl, 1, &chunk_dim) < 0) FAIL_STACK_ERROR + + /* Define fill value, fill time, and chunk allocation time */ + if(H5Pset_fill_value(dcpl, H5T_NATIVE_INT, &fvalue) < 0) FAIL_STACK_ERROR + + if(H5Pset_fill_time(dcpl, H5D_FILL_TIME_IFSET) < 0) FAIL_STACK_ERROR + + if(H5Pset_alloc_time(dcpl, H5D_ALLOC_TIME_INCR) < 0) FAIL_STACK_ERROR + + /* Try to create dataset */ + dsid = H5Dcreate2(fid, BYPASS_DATASET, H5T_NATIVE_INT, sid, H5P_DEFAULT, dcpl, H5P_DEFAULT); + + /* Select first chunk to write the data */ + offset = 0; + count = 1; + stride = 1; + block = BYPASS_CHUNK_DIM; + if(H5Sselect_hyperslab(sid, H5S_SELECT_SET, &offset, &stride, &count, &block) < 0) + FAIL_STACK_ERROR + + for(i = 0; i < BYPASS_CHUNK_DIM; i++) + wdata[i] = i; + + /* This write should bypass the cache because the chunk is bigger than the cache size + * and it's not allocated on disk. */ + if(H5Dwrite(dsid, H5T_NATIVE_INT, H5S_ALL, sid, H5P_DEFAULT, wdata) < 0) + FAIL_STACK_ERROR + + if(H5Dclose(dsid) < 0) FAIL_STACK_ERROR + + /* Reopen the dataset */ + if((dsid = H5Dopen(fid, BYPASS_DATASET, H5P_DEFAULT)) < 0) FAIL_STACK_ERROR + + /* Reads both 2 chunks. Reading the second chunk should bypass the cache because the + * chunk is bigger than the cache size and it isn't allocated on disk. */ + if(H5Dread(dsid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, rdata) < 0) + FAIL_STACK_ERROR + + for(i = 0; i < BYPASS_CHUNK_DIM; i++) + if(rdata[i] != i) { + printf(" Read different values than written in the 1st chunk.\n"); + printf(" At line %d and index %d, rdata = %d. It should be %d.\n", __LINE__, + i, rdata[i], i); + FAIL_STACK_ERROR + } + + for(j = BYPASS_CHUNK_DIM; j < BYPASS_DIM; j++) + if(rdata[j] != fvalue) { + printf(" Read different values than written in the 2nd chunk.\n"); + printf(" At line %d and index %d, rdata = %d. It should be %d.\n", __LINE__, + i, rdata[i], fvalue); + FAIL_STACK_ERROR + } + + /* Close IDs */ + if(H5Sclose(sid) < 0) FAIL_STACK_ERROR + if(H5Dclose(dsid) < 0) FAIL_STACK_ERROR + if(H5Pclose(dcpl) < 0) FAIL_STACK_ERROR + if(H5Fclose(fid) < 0) FAIL_STACK_ERROR + + PASSED(); + return 0; + +error: + H5E_BEGIN_TRY { + H5Pclose(dcpl); + H5Dclose(dsid); + H5Sclose(sid); + H5Fclose(fid); + } H5E_END_TRY; + return -1; +} /* end test_huge_chunks() */ + + + +/*------------------------------------------------------------------------- * Function: main * * Purpose: Tests the dataset interface (H5D) @@ -6803,6 +6937,7 @@ main(void) #endif /* H5_NO_DEPRECATED_SYMBOLS */ nerrors += (test_huge_chunks(my_fapl) < 0 ? 1 : 0); nerrors += (test_chunk_cache(my_fapl) < 0 ? 1 : 0); + nerrors += (test_big_chunks_bypass_cache(my_fapl) < 0 ? 1 : 0); if(H5Fclose(file) < 0) goto error; |