diff options
| author | jhendersonHDF <jhenderson@hdfgroup.org> | 2023-12-27 22:28:41 (GMT) |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2023-12-27 22:28:41 (GMT) |
| commit | 6ffc55c6d9c1f3a30e4db1bc71c452c50952ee85 (patch) | |
| tree | c4215cf360c4a3350aa5315939622b982390df53 | |
| parent | 695efa94dfcd62c5ef42d03a7f1425c4105819df (diff) | |
| download | hdf5-6ffc55c6d9c1f3a30e4db1bc71c452c50952ee85.zip hdf5-6ffc55c6d9c1f3a30e4db1bc71c452c50952ee85.tar.gz hdf5-6ffc55c6d9c1f3a30e4db1bc71c452c50952ee85.tar.bz2 | |
Implement optimized support for vector I/O in Subfiling VFD (#3896)
Vector I/O requests are now processed within a single
set of I/O call batches, rather than each I/O vector
entry (tuple constructed from the types, addrs, sizes
and bufs arrays) being processed individually. This allows I/O to be
more efficiently parallelized among the I/O concentrator processes
during large I/O requests.
* Fixed some calculations and add test cases for issues spotted from review
* Removed a variable that was compensating for previous miscalculations
| -rw-r--r-- | release_docs/RELEASE.txt | 10 | ||||
| -rw-r--r-- | src/H5FDsubfiling/H5FDioc.c | 50 | ||||
| -rw-r--r-- | src/H5FDsubfiling/H5FDioc_int.c | 8 | ||||
| -rw-r--r-- | src/H5FDsubfiling/H5FDioc_threads.c | 12 | ||||
| -rw-r--r-- | src/H5FDsubfiling/H5FDsubfiling.c | 2395 | ||||
| -rw-r--r-- | src/H5FDsubfiling/H5subfiling_common.c | 33 | ||||
| -rw-r--r-- | src/H5FDsubfiling/H5subfiling_common.h | 3 | ||||
| -rw-r--r-- | testpar/t_subfiling_vfd.c | 739 |
8 files changed, 2190 insertions, 1060 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index fb2769d..dda3852 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -278,6 +278,16 @@ New Features Library: -------- + - Implemented optimized support for vector I/O in the Subfiling VFD + + Previously, the Subfiling VFD would handle vector I/O requests by + breaking them down into individual I/O requests, one for each entry + in the I/O vectors provided. This could result in poor I/O performance + for features in HDF5 that utilize vector I/O, such as parallel I/O + to filtered datasets. The Subfiling VFD now properly handles vector + I/O requests in their entirety, resulting in fewer I/O calls, improved + vector I/O performance and improved vector I/O memory efficiency. + - Added a simple cache to the read-only S3 (ros3) VFD The read-only S3 VFD now caches the first N bytes of a file stored diff --git a/src/H5FDsubfiling/H5FDioc.c b/src/H5FDsubfiling/H5FDioc.c index 80771c0..b019add 100644 --- a/src/H5FDsubfiling/H5FDioc.c +++ b/src/H5FDsubfiling/H5FDioc.c @@ -1610,12 +1610,14 @@ H5FD__ioc_write_vector_internal(H5FD_t *_file, uint32_t count, H5FD_mem_t H5_ATT H5FD_ioc_t *file_ptr = (H5FD_ioc_t *)_file; io_req_t **sf_io_reqs = NULL; int64_t sf_context_id = -1; + size_t io_size = 0; + bool extend_sizes = false; herr_t ret_value = SUCCEED; assert(_file); - assert(addrs); - assert(sizes); - assert(bufs); + assert((addrs) || (count == 0)); + assert((sizes) || (count == 0)); + assert((bufs) || (count == 0)); if (count == 0) H5_SUBFILING_GOTO_DONE(SUCCEED); @@ -1648,12 +1650,22 @@ H5FD__ioc_write_vector_internal(H5FD_t *_file, uint32_t count, H5FD_mem_t H5_ATT for (size_t i = 0; i < (size_t)count; i++) { herr_t write_status; - if (sizes[i] == 0) + if (!extend_sizes) { + if ((i > 0) && (sizes[i] == 0)) { + extend_sizes = true; + io_size = sizes[i - 1]; + } + else { + io_size = sizes[i]; + } + } + + if (io_size == 0) H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "invalid size argument of 0"); H5_CHECK_OVERFLOW(addrs[i], haddr_t, int64_t); - H5_CHECK_OVERFLOW(sizes[i], size_t, int64_t); - write_status = ioc__write_independent_async(sf_context_id, (int64_t)addrs[i], (int64_t)sizes[i], + H5_CHECK_OVERFLOW(io_size, size_t, int64_t); + write_status = ioc__write_independent_async(sf_context_id, (int64_t)addrs[i], (int64_t)io_size, bufs[i], &sf_io_reqs[i]); if (write_status < 0) @@ -1691,12 +1703,14 @@ H5FD__ioc_read_vector_internal(H5FD_t *_file, uint32_t count, haddr_t addrs[], s H5FD_ioc_t *file_ptr = (H5FD_ioc_t *)_file; io_req_t **sf_io_reqs = NULL; int64_t sf_context_id = -1; + size_t io_size = 0; + bool extend_sizes = false; herr_t ret_value = SUCCEED; assert(_file); - assert(addrs); - assert(sizes); - assert(bufs); + assert((addrs) || (count == 0)); + assert((sizes) || (count == 0)); + assert((bufs) || (count == 0)); if (count == 0) H5_SUBFILING_GOTO_DONE(SUCCEED); @@ -1720,12 +1734,22 @@ H5FD__ioc_read_vector_internal(H5FD_t *_file, uint32_t count, haddr_t addrs[], s H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't allocate MPI request array"); for (size_t i = 0; i < (size_t)count; i++) { - int read_status; + herr_t read_status; + + if (!extend_sizes) { + if ((i > 0) && (sizes[i] == 0)) { + extend_sizes = true; + io_size = sizes[i - 1]; + } + else { + io_size = sizes[i]; + } + } H5_CHECK_OVERFLOW(addrs[i], haddr_t, int64_t); - H5_CHECK_OVERFLOW(sizes[i], size_t, int64_t); - read_status = ioc__read_independent_async(sf_context_id, (int64_t)addrs[i], (int64_t)sizes[i], - bufs[i], &sf_io_reqs[i]); + H5_CHECK_OVERFLOW(io_size, size_t, int64_t); + read_status = ioc__read_independent_async(sf_context_id, (int64_t)addrs[i], (int64_t)io_size, bufs[i], + &sf_io_reqs[i]); if (read_status < 0) H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't queue read operation"); diff --git a/src/H5FDsubfiling/H5FDioc_int.c b/src/H5FDsubfiling/H5FDioc_int.c index 5528fc8..75a36d0 100644 --- a/src/H5FDsubfiling/H5FDioc_int.c +++ b/src/H5FDsubfiling/H5FDioc_int.c @@ -297,9 +297,13 @@ ioc__read_independent_async(int64_t context_id, int64_t offset, int64_t elements * unpredictable order. However, if some IOCs own more than * 1 subfile, we need to associate each read with a unique * message tag to make sure the data is received in the - * correct order. + * correct order. We also need a unique message tag in the + * case where only 1 subfile is used in total. In this case, + * vector I/O calls are passed directly down to this VFD without + * being split up into multiple I/O requests, so we need the + * tag to distinguish each I/O request. */ - need_data_tag = num_subfiles != num_io_concentrators; + need_data_tag = (num_subfiles == 1) || (num_subfiles != num_io_concentrators); if (!need_data_tag) data_tag = READ_INDEP_DATA; diff --git a/src/H5FDsubfiling/H5FDioc_threads.c b/src/H5FDsubfiling/H5FDioc_threads.c index c86157b..85c2561 100644 --- a/src/H5FDsubfiling/H5FDioc_threads.c +++ b/src/H5FDsubfiling/H5FDioc_threads.c @@ -456,8 +456,9 @@ translate_opcode(io_op_t op) case LOGGING_OP: return "LOGGING_OP"; break; + default: + return "unknown"; } - return "unknown"; } #endif @@ -873,9 +874,14 @@ ioc_file_queue_read_indep(sf_work_request_t *msg, int ioc_idx, int source, MPI_C * unpredictable order. However, if some IOCs own more than * 1 subfile, we need to associate each read with a unique * message tag to make sure the data is received in the - * correct order. + * correct order. We also need a unique message tag in the + * case where only 1 subfile is used in total. In this case, + * vector I/O calls are passed directly down to this VFD without + * being split up into multiple I/O requests, so we need the + * tag to distinguish each I/O request. */ - need_data_tag = sf_context->sf_num_subfiles != sf_context->topology->n_io_concentrators; + need_data_tag = (sf_context->sf_num_subfiles == 1) || + (sf_context->sf_num_subfiles != sf_context->topology->n_io_concentrators); if (!need_data_tag) send_tag = READ_INDEP_DATA; diff --git a/src/H5FDsubfiling/H5FDsubfiling.c b/src/H5FDsubfiling/H5FDsubfiling.c index 461fa16..bf175e6 100644 --- a/src/H5FDsubfiling/H5FDsubfiling.c +++ b/src/H5FDsubfiling/H5FDsubfiling.c @@ -121,6 +121,11 @@ typedef struct H5FD_subfiling_t { char filename[H5FD_MAX_FILENAME_LEN]; /* Copy of file name from open operation */ } H5FD_subfiling_t; +typedef enum H5FD_subfiling_io_type_t { + IO_TYPE_WRITE, + IO_TYPE_READ, +} H5FD_subfiling_io_type_t; + /* * These macros check for overflow of various quantities. These macros * assume that HDoff_t is signed and haddr_t and size_t are unsigned. @@ -187,27 +192,52 @@ static int H5FD__copy_plist(hid_t fapl_id, hid_t *id_out_ptr); static herr_t H5FD__subfiling_close_int(H5FD_subfiling_t *file_ptr); -static herr_t init_indep_io(subfiling_context_t *sf_context, int64_t file_offset, size_t io_nelemts, - size_t dtype_extent, size_t max_iovec_len, int64_t *mem_buf_offset, - int64_t *target_file_offset, int64_t *io_block_len, int *first_subfile_index, - int *n_subfiles_used, int64_t *max_io_req_per_subfile); -static herr_t iovec_fill_first(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t target_datasize, - int64_t start_mem_offset, int64_t start_file_offset, int64_t first_io_len, - int64_t *mem_offset_out, int64_t *target_file_offset_out, - int64_t *io_block_len_out); -static herr_t iovec_fill_last(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t target_datasize, - int64_t start_mem_offset, int64_t start_file_offset, int64_t last_io_len, - int64_t *mem_offset_out, int64_t *target_file_offset_out, - int64_t *io_block_len_out); -static herr_t iovec_fill_first_last(subfiling_context_t *sf_context, int64_t iovec_depth, - int64_t target_datasize, int64_t start_mem_offset, - int64_t start_file_offset, int64_t first_io_len, int64_t last_io_len, - int64_t *mem_offset_out, int64_t *target_file_offset_out, - int64_t *io_block_len_out); -static herr_t iovec_fill_uniform(subfiling_context_t *sf_context, int64_t iovec_depth, +static herr_t H5FD__subfiling_io_helper(H5FD_subfiling_t *file_ptr, size_t io_count, H5FD_mem_t types[], + haddr_t addrs[], size_t sizes[], H5_flexible_const_ptr_t bufs[], + H5FD_subfiling_io_type_t io_type); +static herr_t H5FD__subfiling_mirror_writes_to_stub(H5FD_subfiling_t *file_ptr, uint32_t count, + H5FD_mem_t types[], haddr_t addrs[], size_t sizes[], + const void *bufs[]); +static herr_t generate_io_vectors(subfiling_context_t *sf_context, size_t in_count, H5FD_mem_t types[], + haddr_t file_offsets[], size_t nelemts[], H5_flexible_const_ptr_t bufs[], + size_t dtype_extent, H5FD_subfiling_io_type_t io_type, size_t *ioreq_count, + uint32_t *iovec_len, H5FD_mem_t **io_types, haddr_t **io_addrs, + size_t **io_sizes, H5_flexible_const_ptr_t **io_bufs); +static void get_iovec_sizes(subfiling_context_t *sf_context, size_t in_count, haddr_t file_offsets[], + size_t nelemts[], size_t dtype_extent, size_t *max_iovec_depth, + size_t *max_num_subfiles); +static herr_t translate_io_req_to_iovec(subfiling_context_t *sf_context, size_t iovec_idx, size_t iovec_len, + size_t iovec_count, H5FD_mem_t type, haddr_t addr, size_t io_size, + H5_flexible_const_ptr_t io_buf, H5FD_subfiling_io_type_t io_type, + H5FD_mem_t *io_types, haddr_t *io_addrs, size_t *io_sizes, + H5_flexible_const_ptr_t *io_bufs); +static herr_t iovec_fill_first(subfiling_context_t *sf_context, size_t iovec_len, int64_t cur_iovec_depth, + int64_t target_datasize, int64_t start_mem_offset, int64_t start_file_offset, + int64_t first_io_len, H5_flexible_const_ptr_t buf, + H5FD_subfiling_io_type_t io_type, haddr_t *io_addrs_ptr, size_t *io_sizes_ptr, + H5_flexible_const_ptr_t *io_bufs_ptr); +static herr_t iovec_fill_last(subfiling_context_t *sf_context, size_t iovec_len, int64_t cur_iovec_depth, + int64_t target_datasize, int64_t start_mem_offset, int64_t start_file_offset, + int64_t last_io_len, H5_flexible_const_ptr_t buf, + H5FD_subfiling_io_type_t io_type, haddr_t *io_addrs_ptr, size_t *io_sizes_ptr, + H5_flexible_const_ptr_t *io_bufs_ptr); +static herr_t iovec_fill_first_last(subfiling_context_t *sf_context, size_t iovec_len, + int64_t cur_iovec_depth, int64_t target_datasize, + int64_t start_mem_offset, int64_t start_file_offset, int64_t first_io_len, + int64_t last_io_len, H5_flexible_const_ptr_t buf, + H5FD_subfiling_io_type_t io_type, haddr_t *io_addrs_ptr, + size_t *io_sizes_ptr, H5_flexible_const_ptr_t *io_bufs_ptr); +static herr_t iovec_fill_uniform(subfiling_context_t *sf_context, size_t iovec_len, int64_t cur_iovec_depth, int64_t target_datasize, int64_t start_mem_offset, int64_t start_file_offset, - int64_t *mem_offset_out, int64_t *target_file_offset_out, - int64_t *io_block_len_out); + H5_flexible_const_ptr_t buf, H5FD_subfiling_io_type_t io_type, + haddr_t *io_addrs_ptr, size_t *io_sizes_ptr, + H5_flexible_const_ptr_t *io_bufs_ptr); + +#ifdef H5_SUBFILING_DEBUG +void H5_subfiling_dump_iovecs(subfiling_context_t *sf_context, size_t ioreq_count, size_t iovec_len, + H5FD_subfiling_io_type_t io_type, H5FD_mem_t *io_types, haddr_t *io_addrs, + size_t *io_sizes, H5_flexible_const_ptr_t *io_bufs); +#endif void H5FD__subfiling_mpi_finalize(void); @@ -384,7 +414,7 @@ H5FD__subfiling_term(void) if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&H5_subfiling_rpc_msg_type))) H5_SUBFILING_MPI_GOTO_ERROR(FAIL, "MPI_Type_free failed", mpi_code); } -#ifdef H5FD_SUBFILING_DEBUG +#ifdef H5_SUBFILING_DEBUG else printf("** WARNING **: HDF5 is terminating the Subfiling VFD after MPI_Finalize() was " "called - an HDF5 ID was probably left unclosed\n"); @@ -1535,199 +1565,16 @@ static herr_t H5FD__subfiling_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr, size_t size, void *buf /*out*/) { - subfiling_context_t *sf_context = NULL; - H5FD_subfiling_t *file_ptr = (H5FD_subfiling_t *)_file; - H5FD_mem_t *io_types = NULL; - haddr_t *io_addrs = NULL; - size_t *io_sizes = NULL; - void **io_bufs = NULL; - int64_t *source_data_offset = NULL; - int64_t *sf_data_size = NULL; - int64_t *sf_offset = NULL; - bool rank0_bcast = false; - int num_subfiles; - herr_t ret_value = SUCCEED; + H5FD_subfiling_t *file_ptr = (H5FD_subfiling_t *)_file; + herr_t ret_value = SUCCEED; - assert(file_ptr && file_ptr->pub.cls); + assert(file_ptr); + assert(file_ptr->pub.driver_id == H5FD_SUBFILING); assert(buf); - /* Check for overflow conditions */ - if (!H5_addr_defined(addr)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr undefined, addr = %" PRIuHADDR, addr); - if (REGION_OVERFLOW(addr, size)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, - "addr overflow, addr = %" PRIuHADDR ", size = %zu", addr, size); - - /* Temporarily reject collective I/O until support is implemented (unless types are simple MPI_BYTE) */ - { - H5FD_mpio_xfer_t xfer_mode; - - if (H5CX_get_io_xfer_mode(&xfer_mode) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, - "can't determine I/O collectivity setting"); - - if (xfer_mode == H5FD_MPIO_COLLECTIVE) { - MPI_Datatype btype, ftype; - - if (H5CX_get_mpi_coll_datatypes(&btype, &ftype) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "can't get MPI-I/O datatypes"); - if (MPI_BYTE != btype || MPI_BYTE != ftype) - H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, - "collective I/O is currently unsupported"); - } - - /* Determine whether a rank 0 bcast approach has been requested */ - rank0_bcast = H5CX_get_mpio_rank0_bcast(); - - /* - * If we reached here, we're still doing independent I/O regardless - * of collectivity setting, so set that. - */ - H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT); - } - - /* - * Retrieve the subfiling context object and the number - * of subfiles. - * - * Given the current I/O and the I/O concentrator info, - * we can determine some I/O transaction parameters. - * In particular, for large I/O operations, each IOC - * may require multiple I/Os to fulfill the user I/O - * request. The block size and number of IOCs are used - * to size the vectors that will be used to invoke the - * underlying I/O operations. - */ - sf_context = (subfiling_context_t *)H5_get_subfiling_object(file_ptr->context_id); - assert(sf_context); - assert(sf_context->topology); - - num_subfiles = sf_context->sf_num_subfiles; - - if (num_subfiles <= 0) { - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid number of subfiles (%d)", - num_subfiles); - } - else if (num_subfiles == 1) { - /*************************************** - * No striping - just a single subfile * - ***************************************/ - - /* Make vector read call to subfile */ - if (H5FD_read_vector(file_ptr->sf_file, 1, &type, &addr, &size, &buf) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_READERROR, FAIL, "read from subfile failed"); - } - else { - int64_t max_io_req_per_subfile; - int64_t file_offset; - int64_t block_size; - size_t max_depth; - herr_t status; - int num_subfiles_used = 0; - int first_subfile_idx = -1; - - /************************************* - * Striping across multiple subfiles * - *************************************/ - - block_size = sf_context->sf_blocksize_per_stripe; - max_depth = (size / (size_t)block_size) + 2; - - /* - * Given the number of subfiles, allocate vectors (one per subfile) - * to contain the translation of the I/O request into a collection of - * I/O requests. - */ - if (NULL == - (source_data_offset = calloc(1, (size_t)num_subfiles * max_depth * sizeof(*source_data_offset)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate source data offset I/O vector"); - if (NULL == (sf_data_size = calloc(1, (size_t)num_subfiles * max_depth * sizeof(*sf_data_size)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile data size I/O vector"); - if (NULL == (sf_offset = calloc(1, (size_t)num_subfiles * max_depth * sizeof(*sf_offset)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile offset I/O vector"); - - H5_CHECKED_ASSIGN(file_offset, int64_t, addr, haddr_t); - - /* - * Get the potential set of IOC transactions; e.g., data sizes, - * offsets and datatypes. - */ - status = init_indep_io(sf_context, /* IN: Context used to look up config info */ - file_offset, /* IN: Starting file offset */ - size, /* IN: I/O size */ - 1, /* IN: Data extent of the 'type' assumes byte */ - max_depth, /* IN: Maximum stripe depth */ - source_data_offset, /* OUT: Memory offset */ - sf_offset, /* OUT: File offset */ - sf_data_size, /* OUT: Length of this contiguous block */ - &first_subfile_idx, /* OUT: Subfile index corresponding to starting offset */ - &num_subfiles_used, /* OUT: Number of actual subfiles used */ - &max_io_req_per_subfile); /* OUT: Maximum number of requests to any subfile */ - - if (status < 0) - H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't initialize IOC transactions"); - - if (max_io_req_per_subfile > 0) { - uint32_t vector_len; - - H5_CHECKED_ASSIGN(vector_len, uint32_t, num_subfiles_used, int); - - /* Allocate I/O vectors */ - if (NULL == (io_types = malloc(vector_len * sizeof(*io_types)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile I/O types vector"); - if (NULL == (io_addrs = malloc(vector_len * sizeof(*io_addrs)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile I/O addresses vector"); - if (NULL == (io_sizes = malloc(vector_len * sizeof(*io_sizes)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile I/O sizes vector"); - if (NULL == (io_bufs = malloc(vector_len * sizeof(*io_bufs)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile I/O buffers vector"); - - for (int64_t i = 0; i < max_io_req_per_subfile; i++) { - uint32_t final_vec_len = vector_len; - int next_subfile_idx = first_subfile_idx; - - /* Fill in I/O types, offsets, sizes and buffers vectors */ - for (uint32_t k = 0, vec_idx = 0; k < vector_len; k++) { - size_t idx = (size_t)next_subfile_idx * max_depth + (size_t)i; - - io_types[vec_idx] = type; - H5_CHECKED_ASSIGN(io_addrs[vec_idx], haddr_t, sf_offset[idx], int64_t); - H5_CHECKED_ASSIGN(io_sizes[vec_idx], size_t, sf_data_size[idx], int64_t); - io_bufs[vec_idx] = ((char *)buf + source_data_offset[idx]); - - next_subfile_idx = (next_subfile_idx + 1) % num_subfiles; - - /* Skip 0-sized I/Os */ - if (io_sizes[vec_idx] == 0) { - final_vec_len--; - continue; - } - - vec_idx++; - } - - if (!rank0_bcast || (file_ptr->mpi_rank == 0)) { - /* Make vector read call to subfile */ - if (H5FD_read_vector(file_ptr->sf_file, final_vec_len, io_types, io_addrs, io_sizes, - io_bufs) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_READERROR, FAIL, "read from subfile failed"); - } - } - - if (rank0_bcast && (file_ptr->mpi_size > 1)) { - H5_CHECK_OVERFLOW(size, size_t, int); - if (MPI_SUCCESS != MPI_Bcast(buf, (int)size, MPI_BYTE, 0, file_ptr->comm)) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_READERROR, FAIL, "can't broadcast data from rank 0"); - } - } - } + if (H5FD__subfiling_io_helper(file_ptr, 1, &type, &addr, &size, (H5_flexible_const_ptr_t *)&buf, + IO_TYPE_READ) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "read from subfiles failed"); /* Point to the end of the current I/O */ addr += (haddr_t)size; @@ -1737,14 +1584,6 @@ H5FD__subfiling_read(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_i file_ptr->op = OP_READ; done: - free(io_bufs); - free(io_sizes); - free(io_addrs); - free(io_types); - free(sf_offset); - free(sf_data_size); - free(source_data_offset); - if (ret_value < 0) { /* Reset last file I/O information */ file_ptr->pos = HADDR_UNDEF; @@ -1769,214 +1608,16 @@ static herr_t H5FD__subfiling_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id, haddr_t addr, size_t size, const void *buf /*in*/) { - subfiling_context_t *sf_context = NULL; - H5FD_subfiling_t *file_ptr = (H5FD_subfiling_t *)_file; - const void **io_bufs = NULL; - H5FD_mem_t *io_types = NULL; - haddr_t *io_addrs = NULL; - size_t *io_sizes = NULL; - int64_t *source_data_offset = NULL; - int64_t *sf_data_size = NULL; - int64_t *sf_offset = NULL; - int num_subfiles; - herr_t ret_value = SUCCEED; + H5FD_subfiling_t *file_ptr = (H5FD_subfiling_t *)_file; + herr_t ret_value = SUCCEED; - assert(file_ptr && file_ptr->pub.cls); + assert(file_ptr); + assert(file_ptr->pub.driver_id == H5FD_SUBFILING); assert(buf); - /* Check for overflow conditions */ - if (!H5_addr_defined(addr)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr undefined, addr = %" PRIuHADDR, addr); - if (REGION_OVERFLOW(addr, size)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, - "addr overflow, addr = %" PRIuHADDR ", size = %zu", addr, size); - - /* Temporarily reject collective I/O until support is implemented (unless types are simple MPI_BYTE) */ - { - H5FD_mpio_xfer_t xfer_mode; - - if (H5CX_get_io_xfer_mode(&xfer_mode) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, - "can't determine I/O collectivity setting"); - - if (xfer_mode == H5FD_MPIO_COLLECTIVE) { - MPI_Datatype btype, ftype; - - if (H5CX_get_mpi_coll_datatypes(&btype, &ftype) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "can't get MPI-I/O datatypes"); - if (MPI_BYTE != btype || MPI_BYTE != ftype) - H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, - "collective I/O is currently unsupported"); - } - - /* - * If we reached here, we're still doing independent I/O regardless - * of collectivity setting, so set that. - */ - H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT); - } - - /* - * Retrieve the subfiling context object and the number - * of subfiles. - * - * Given the current I/O and the I/O concentrator info, - * we can determine some I/O transaction parameters. - * In particular, for large I/O operations, each IOC - * may require multiple I/Os to fulfill the user I/O - * request. The block size and number of IOCs are used - * to size the vectors that will be used to invoke the - * underlying I/O operations. - */ - sf_context = (subfiling_context_t *)H5_get_subfiling_object(file_ptr->context_id); - assert(sf_context); - assert(sf_context->topology); - - num_subfiles = sf_context->sf_num_subfiles; - - if (num_subfiles <= 0) { - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid number of subfiles (%d)", - num_subfiles); - } - else if (num_subfiles == 1) { - /*************************************** - * No striping - just a single subfile * - ***************************************/ - - /* Make vector write call to subfile */ - if (H5FD_write_vector(file_ptr->sf_file, 1, &type, &addr, &size, &buf) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_WRITEERROR, FAIL, "write to subfile failed"); - - /* - * Mirror superblock writes to the stub file so that - * legacy HDF5 applications can check what type of - * file they are reading - */ - if ((type == H5FD_MEM_SUPER) && (file_ptr->mpi_rank == 0)) { - if (H5FD_write_vector(file_ptr->stub_file, 1, &type, &addr, &size, &buf) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, - "couldn't write superblock information to stub file"); - } - } - else { - int64_t max_io_req_per_subfile; - int64_t file_offset; - int64_t block_size; - size_t max_depth; - herr_t status; - int num_subfiles_used = 0; - int first_subfile_idx = -1; - - /************************************* - * Striping across multiple subfiles * - *************************************/ - - block_size = sf_context->sf_blocksize_per_stripe; - max_depth = (size / (size_t)block_size) + 2; - - /* - * Given the number of subfiles, allocate vectors (one per subfile) - * to contain the translation of the I/O request into a collection of - * I/O requests. - */ - if (NULL == - (source_data_offset = calloc(1, (size_t)num_subfiles * max_depth * sizeof(*source_data_offset)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate source data offset I/O vector"); - if (NULL == (sf_data_size = calloc(1, (size_t)num_subfiles * max_depth * sizeof(*sf_data_size)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile data size I/O vector"); - if (NULL == (sf_offset = calloc(1, (size_t)num_subfiles * max_depth * sizeof(*sf_offset)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile offset I/O vector"); - - H5_CHECKED_ASSIGN(file_offset, int64_t, addr, haddr_t); - - /* - * Get the potential set of IOC transactions; e.g., data sizes, - * offsets and datatypes. - */ - status = init_indep_io(sf_context, /* IN: Context used to look up config info */ - file_offset, /* IN: Starting file offset */ - size, /* IN: I/O size */ - 1, /* IN: Data extent of the 'type' assumes byte */ - max_depth, /* IN: Maximum stripe depth */ - source_data_offset, /* OUT: Memory offset */ - sf_offset, /* OUT: File offset */ - sf_data_size, /* OUT: Length of this contiguous block */ - &first_subfile_idx, /* OUT: Subfile index corresponding to starting offset */ - &num_subfiles_used, /* OUT: Number of actual subfiles used */ - &max_io_req_per_subfile); /* OUT: Maximum number of requests to any subfile */ - - if (status < 0) - H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't initialize IOC transactions"); - - if (max_io_req_per_subfile > 0) { - uint32_t vector_len; - - H5_CHECKED_ASSIGN(vector_len, uint32_t, num_subfiles_used, int); - - /* Allocate I/O vectors */ - if (NULL == (io_types = malloc(vector_len * sizeof(*io_types)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile I/O types vector"); - if (NULL == (io_addrs = malloc(vector_len * sizeof(*io_addrs)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile I/O addresses vector"); - if (NULL == (io_sizes = malloc(vector_len * sizeof(*io_sizes)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile I/O sizes vector"); - if (NULL == (io_bufs = malloc(vector_len * sizeof(*io_bufs)))) - H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, - "can't allocate subfile I/O buffers vector"); - - for (int64_t i = 0; i < max_io_req_per_subfile; i++) { - uint32_t final_vec_len = vector_len; - int next_subfile_idx = first_subfile_idx; - - /* Fill in I/O types, offsets, sizes and buffers vectors */ - for (uint32_t k = 0, vec_idx = 0; k < vector_len; k++) { - size_t idx = (size_t)next_subfile_idx * max_depth + (size_t)i; - - io_types[vec_idx] = type; - H5_CHECKED_ASSIGN(io_addrs[vec_idx], haddr_t, sf_offset[idx], int64_t); - H5_CHECKED_ASSIGN(io_sizes[vec_idx], size_t, sf_data_size[idx], int64_t); - io_bufs[vec_idx] = ((const char *)buf + source_data_offset[idx]); - - next_subfile_idx = (next_subfile_idx + 1) % num_subfiles; - - /* Skip 0-sized I/Os */ - if (io_sizes[vec_idx] == 0) { - final_vec_len--; - continue; - } - - vec_idx++; - } - - /* Make vector write call to subfile */ - if (H5FD_write_vector(file_ptr->sf_file, final_vec_len, io_types, io_addrs, io_sizes, - io_bufs) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_WRITEERROR, FAIL, "write to subfile failed"); - - /* - * Mirror superblock writes to the stub file so that - * legacy HDF5 applications can check what type of - * file they are reading - */ - if (file_ptr->mpi_rank == 0) { - for (size_t count_idx = 0; count_idx < (size_t)final_vec_len; count_idx++) { - if (io_types[count_idx] == H5FD_MEM_SUPER) { - if (H5FD_write(file_ptr->stub_file, H5FD_MEM_SUPER, io_addrs[count_idx], - io_sizes[count_idx], io_bufs[count_idx]) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, - "couldn't write superblock information to stub file"); - } - } - } - } - } - } + if (H5FD__subfiling_io_helper(file_ptr, 1, &type, &addr, &size, (H5_flexible_const_ptr_t *)&buf, + IO_TYPE_WRITE) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write to subfiles failed"); /* Point to the end of the current I/O */ addr += (haddr_t)size; @@ -1992,14 +1633,6 @@ H5FD__subfiling_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_ file_ptr->local_eof = file_ptr->pos; done: - free(io_bufs); - free(io_sizes); - free(io_addrs); - free(io_types); - free(sf_offset); - free(sf_data_size); - free(source_data_offset); - if (ret_value < 0) { /* Reset last file I/O information */ file_ptr->pos = HADDR_UNDEF; @@ -2048,31 +1681,21 @@ H5FD__subfiling_read_vector(H5FD_t *_file, hid_t dxpl_id, uint32_t count, H5FD_m size_t sizes[], void *bufs[] /* out */) { H5FD_subfiling_t *file_ptr = (H5FD_subfiling_t *)_file; - H5FD_mpio_xfer_t xfer_mode = H5FD_MPIO_INDEPENDENT; - herr_t ret_value = SUCCEED; /* Return value */ - - /* Check arguments - * RAW - Do we really need to check arguments once again? - * These have already been checked in H5FD__subfiling_read_vector (see below)! - */ - if (!file_ptr) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file pointer cannot be NULL"); - - if ((!types) && (count > 0)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "types parameter can't be NULL if count is positive"); - - if ((!addrs) && (count > 0)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "addrs parameter can't be NULL if count is positive"); + herr_t ret_value = SUCCEED; - if ((!sizes) && (count > 0)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "sizes parameter can't be NULL if count is positive"); + assert(file_ptr); + assert(file_ptr->pub.driver_id == H5FD_SUBFILING); + assert((types) || (count == 0)); + assert((addrs) || (count == 0)); + assert((sizes) || (count == 0)); + assert((bufs) || (count == 0)); - if ((!bufs) && (count > 0)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "bufs parameter can't be NULL if count is positive"); + /* + * Verify that the first elements of the sizes and + * types arrays are valid. + */ + assert((count == 0) || (sizes[0] != 0)); + assert((count == 0) || (types[0] != H5FD_MEM_NOLIST)); /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == dxpl_id) { @@ -2086,98 +1709,27 @@ H5FD__subfiling_read_vector(H5FD_t *_file, hid_t dxpl_id, uint32_t count, H5FD_m /* Set DXPL for operation */ H5CX_set_dxpl(dxpl_id); - /* TODO: setup real support for vector I/O */ if (file_ptr->fa.require_ioc) { - - bool extend_sizes = false; - bool extend_types = false; - int k; - size_t size; - H5FD_mem_t type; - haddr_t eoa; - - assert((count == 0) || (sizes[0] != 0)); - assert((count == 0) || (types[0] != H5FD_MEM_NOLIST)); - - if (H5CX_get_io_xfer_mode(&xfer_mode) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, - "can't determine I/O collectivity setting"); - - /* Currently, treat collective calls as independent */ - if (xfer_mode != H5FD_MPIO_INDEPENDENT) - if (H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_CONTEXT, H5E_CANTSET, FAIL, "can't set I/O collectivity setting"); - - /* Note that the following code does not let the sub-filing VFD participate - * in collective calls when there is no data to write. This is not an issue - * now, as we don't do anything special with collective operations. However - * this needs to be fixed. - */ - for (k = 0; k < (int)count; k++) { - - if (!extend_sizes) { - - if (sizes[k] == 0) { - - extend_sizes = true; - size = sizes[k - 1]; - } - else { - - size = sizes[k]; - } - } - - if (!extend_types) { - - if (types[k] == H5FD_MEM_NOLIST) { - - extend_types = true; - type = types[k - 1]; - } - else { - - type = types[k]; - } - } - - if (HADDR_UNDEF == (eoa = H5FD__subfiling_get_eoa(_file, type))) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_CANTINIT, FAIL, "driver get_eoa request failed"); - - if ((addrs[k] + size) > eoa) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, - "addr overflow, addrs[%d] = %llu, sizes[%d] = %llu, eoa = %llu", - (int)k, (unsigned long long)(addrs[k]), (int)k, - (unsigned long long)size, (unsigned long long)eoa); - - if (H5FD__subfiling_read(_file, type, dxpl_id, addrs[k], size, bufs[k]) != SUCCEED) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_READERROR, FAIL, "file vector read request failed"); - } + if (H5FD__subfiling_io_helper(file_ptr, (size_t)count, types, addrs, sizes, + (H5_flexible_const_ptr_t *)bufs, IO_TYPE_READ) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't read data"); } else { - /* sec2 driver.. - * Call the subfiling 'direct write' version - * of subfiling. - */ - if (H5FD_read_vector(_file, count, types, addrs, sizes, bufs) != SUCCEED) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_READERROR, FAIL, "file vector read request failed"); + if (H5FD_read_vector(_file, count, types, addrs, sizes, bufs) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't read data"); } done: - if (xfer_mode != H5FD_MPIO_INDEPENDENT) - if (H5CX_set_io_xfer_mode(xfer_mode) < 0) - H5_SUBFILING_DONE_ERROR(H5E_CONTEXT, H5E_CANTSET, FAIL, "can't set I/O collectivity setting"); - H5_SUBFILING_FUNC_LEAVE_API; } /* end H5FD__subfiling_read_vector() */ /*------------------------------------------------------------------------- - * Function: H5FD__subfile_write_vector (internal function) + * Function: H5FD__subfiling_write_vector * * Purpose: Perform count writes to the specified file at the offsets - * provided in the addrs array. Lengths and memory - * types provided in the sizes and types arrays. Data to be - * written is referenced by the bufs array. + * provided in the addrs array. Lengths and memory types + * types are provided in the sizes and types arrays. Data to + * be written is referenced by the bufs array. * * All writes are done according to the data transfer property * list dxpl_id (which may be the constant H5P_DEFAULT). @@ -2190,17 +1742,6 @@ done: * input arguments are not valid, or the actual * subfiling writes have failed for some reason. * - * Notes: Thus function doesn't actually implement vector write. - * Instead, it converts the vector write call into a series - * of scalar read calls. Fix this when time permits. - * - * Also, it didn't support the sizes and types optimization. - * I implemented a version of this which is more generous - * than that currently defined in the RFC. This is good - * enough for now, but the final version should follow - * the RFC. - * JRM -- 10/5/21 - * *------------------------------------------------------------------------- */ static herr_t @@ -2208,33 +1749,21 @@ H5FD__subfiling_write_vector(H5FD_t *_file, hid_t dxpl_id, uint32_t count, H5FD_ haddr_t addrs[], size_t sizes[], const void *bufs[] /* in */) { H5FD_subfiling_t *file_ptr = (H5FD_subfiling_t *)_file; - H5FD_mpio_xfer_t xfer_mode = H5FD_MPIO_INDEPENDENT; - herr_t ret_value = SUCCEED; /* Return value */ + herr_t ret_value = SUCCEED; - assert(file_ptr != NULL); /* sanity check */ + assert(file_ptr); + assert(file_ptr->pub.driver_id == H5FD_SUBFILING); + assert((types) || (count == 0)); + assert((addrs) || (count == 0)); + assert((sizes) || (count == 0)); + assert((bufs) || (count == 0)); - /* Check arguments - * RAW - Do we really need to check arguments once again? - * These have already been checked in H5FD__subfiling_write_vector (see below)! + /* + * Verify that the first elements of the sizes and + * types arrays are valid. */ - if (!file_ptr) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "file pointer cannot be NULL"); - - if ((!types) && (count > 0)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "types parameter can't be NULL if count is positive"); - - if ((!addrs) && (count > 0)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "addrs parameter can't be NULL if count is positive"); - - if ((!sizes) && (count > 0)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "sizes parameter can't be NULL if count is positive"); - - if ((!bufs) && (count > 0)) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, - "bufs parameter can't be NULL if count is positive"); + assert((count == 0) || (sizes[0] != 0)); + assert((count == 0) || (types[0] != H5FD_MEM_NOLIST)); /* Get the default dataset transfer property list if the user didn't provide one */ if (H5P_DEFAULT == dxpl_id) { @@ -2244,88 +1773,21 @@ H5FD__subfiling_write_vector(H5FD_t *_file, hid_t dxpl_id, uint32_t count, H5FD_ if (true != H5P_isa_class(dxpl_id, H5P_DATASET_XFER)) H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data transfer property list"); } - /* Call the subfiling IOC write*/ - if (file_ptr->fa.require_ioc) { - - bool extend_sizes = false; - bool extend_types = false; - int k; - size_t size; - H5FD_mem_t type; - haddr_t eoa; - - assert((count == 0) || (sizes[0] != 0)); - assert((count == 0) || (types[0] != H5FD_MEM_NOLIST)); - - if (H5CX_get_io_xfer_mode(&xfer_mode) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, - "can't determine I/O collectivity setting"); - - /* Currently, treat collective calls as independent */ - if (xfer_mode != H5FD_MPIO_INDEPENDENT) - if (H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT) < 0) - H5_SUBFILING_GOTO_ERROR(H5E_CONTEXT, H5E_CANTSET, FAIL, "can't set I/O collectivity setting"); - - /* Note that the following code does not let the sub-filing VFD participate - * in collective calls when there is no data to write. This is not an issue - * now, as we don't do anything special with collective operations. However - * this needs to be fixed. - */ - for (k = 0; k < (int)count; k++) { - - if (!extend_sizes) { - if (sizes[k] == 0) { - - extend_sizes = true; - size = sizes[k - 1]; - } - else { - - size = sizes[k]; - } - } - - if (!extend_types) { - - if (types[k] == H5FD_MEM_NOLIST) { - - extend_types = true; - type = types[k - 1]; - } - else { - - type = types[k]; - } - } - - if (HADDR_UNDEF == (eoa = H5FD__subfiling_get_eoa(_file, type))) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_CANTINIT, FAIL, "driver get_eoa request failed"); - - if ((addrs[k] + size) > eoa) - H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, - "addr overflow, addrs[%d] = %llu, sizes[%d] = %llu, eoa = %llu", - (int)k, (unsigned long long)(addrs[k]), (int)k, - (unsigned long long)size, (unsigned long long)eoa); + /* Set DXPL for operation */ + H5CX_set_dxpl(dxpl_id); - if (H5FD__subfiling_write(_file, type, dxpl_id, addrs[k], size, bufs[k]) != SUCCEED) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_WRITEERROR, FAIL, "file vector write request failed"); - } + if (file_ptr->fa.require_ioc) { + if (H5FD__subfiling_io_helper(file_ptr, (size_t)count, types, addrs, sizes, + (H5_flexible_const_ptr_t *)bufs, IO_TYPE_WRITE) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "couldn't write data"); } else { - /* sec2 driver.. - * Call the subfiling 'direct write' version - * of subfiling. - */ - if (H5FD_write_vector(_file, count, types, addrs, sizes, bufs) != SUCCEED) - H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_WRITEERROR, FAIL, "file vector write request failed"); + if (H5FD_write_vector(_file, count, types, addrs, sizes, bufs) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "couldn't write data"); } done: - if (xfer_mode != H5FD_MPIO_INDEPENDENT) - if (H5CX_set_io_xfer_mode(xfer_mode) < 0) - H5_SUBFILING_DONE_ERROR(H5E_CONTEXT, H5E_CANTSET, FAIL, "can't set I/O collectivity setting"); - H5_SUBFILING_FUNC_LEAVE_API; } /* end H5FDsubfile__write_vector() */ @@ -2581,138 +2043,918 @@ done: } /* end H5FD__subfiling_ctl() */ /*------------------------------------------------------------------------- - * Function: init_indep_io - * - * Purpose: Utility function to initialize the set of I/O transactions - * used to communicate with I/O concentrators for read and - * write I/O operations. - * - * Fills the I/O vectors contained in the output arrays - * `mem_buf_offset`, `target_file_offset` and `io_block_len`. - * As a consequence of not allowing use of MPI derived - * datatypes in the VFD layer, we need to accommodate the - * possibility that large I/O transactions will be required to - * use multiple I/Os per subfile. - * - * Example: Using 4 subfiles, each with 1M stripe-depth; when - * presented an I/O request for 8MB then at a minimum each - * subfile will require 2 I/Os of 1MB each. Depending on the - * starting file offset, the 2 I/Os can instead be 3... - * - * To fully describe the I/O transactions for reads and writes - * the output arrays are therefore arrays of I/O vectors, - * where each vector has a length of which corresponds to the - * max number of I/O transactions per subfile. In the example - * above, these vector lengths can be 2 or 3. The actual - * length is determined by the 'container_depth' variable. - * - * For I/O operations which involve a subset of subfiles, the - * vector entries for the unused subfiles will have lengths of - * zero and be empty. The 'container_depth' in this case will - * always be 1. + * Function: H5FD__subfiling_io_helper + * + * Purpose: Helper routine to manage the common portions of I/O between + * normal and vector I/O calls. + * + * Return: SUCCEED/FAIL + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD__subfiling_io_helper(H5FD_subfiling_t *file_ptr, size_t io_count, H5FD_mem_t types[], haddr_t addrs[], + size_t sizes[], H5_flexible_const_ptr_t bufs[], H5FD_subfiling_io_type_t io_type) +{ + H5_flexible_const_ptr_t *io_bufs = NULL; + subfiling_context_t *sf_context = NULL; + H5FD_mpio_xfer_t xfer_mode = H5FD_MPIO_INDEPENDENT; + H5FD_mem_t *io_types = NULL; + haddr_t *io_addrs = NULL; + size_t *io_sizes = NULL; + haddr_t file_eoa = HADDR_UNDEF; + size_t io_size = 0; + bool rank0_bcast = false; + bool extend_sizes = false; + int num_subfiles; + herr_t ret_value = SUCCEED; + + assert(file_ptr); + + if (HADDR_UNDEF == (file_eoa = H5FD__subfiling_get_eoa((const H5FD_t *)file_ptr, H5FD_MEM_DEFAULT))) + H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "can't get file EOA"); + + /* Perform some sanity checking on the given (address, size) pairs */ + extend_sizes = false; + for (size_t i = 0; i < io_count; i++) { + if (!extend_sizes) { + if ((i > 0) && (sizes[i] == 0)) { + extend_sizes = true; + io_size = sizes[i - 1]; + } + else { + io_size = sizes[i]; + } + } + + if (!H5_addr_defined(addrs[i])) + H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr[%zu] undefined, addr = %" PRIuHADDR, + i, addrs[i]); + if (REGION_OVERFLOW(addrs[i], io_size)) + H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, + "addr[%zu] overflow, addr = %" PRIuHADDR ", size = %zu", i, addrs[i], + io_size); + if ((addrs[i] + io_size) > file_eoa) + H5_SUBFILING_GOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, + "addr overflow, addrs[%zu] = %" PRIuHADDR + ", sizes[%zu] = %zu, eoa = %" PRIuHADDR, + i, addrs[i], i, io_size, file_eoa); + } + + /* + * Temporarily reject collective I/O until support is + * implemented (unless types are simple MPI_BYTE), which + * can be properly handled here. + */ + if (H5CX_get_io_xfer_mode(&xfer_mode) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "can't determine I/O collectivity setting"); + + if (xfer_mode == H5FD_MPIO_COLLECTIVE) { + MPI_Datatype btype, ftype; + + if (H5CX_get_mpi_coll_datatypes(&btype, &ftype) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "can't get MPI-I/O datatypes"); + if (MPI_BYTE != btype || MPI_BYTE != ftype) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "collective I/O is currently unsupported"); + } + + /* + * If we reached here, we're still doing independent I/O regardless + * of collectivity setting, so set that. + */ + H5CX_set_io_xfer_mode(H5FD_MPIO_INDEPENDENT); + + /* Determine whether a rank 0 bcast approach has been requested */ + if (io_type == IO_TYPE_READ) + rank0_bcast = H5CX_get_mpio_rank0_bcast(); + + /* + * Retrieve the subfiling context object and the number + * of subfiles. + * + * Given the current I/O and the I/O concentrator info, + * we can determine some I/O transaction parameters. + * In particular, for large I/O operations, each IOC + * may require multiple I/Os to fulfill the user I/O + * request. The block size and number of IOCs are used + * to size the vectors that will be used to invoke the + * underlying I/O operations. + */ + if (NULL == (sf_context = (subfiling_context_t *)H5_get_subfiling_object(file_ptr->context_id))) + H5_SUBFILING_GOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, + "invalid or missing subfiling context object"); + assert(sf_context->topology); + + if ((num_subfiles = sf_context->sf_num_subfiles) <= 0) + H5_SUBFILING_GOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "invalid number of subfiles (%d)", + num_subfiles); + + if (num_subfiles == 1) { + uint32_t u32_io_count; + + /*************************************** + * No striping - just a single subfile * + ***************************************/ + + /* + * Convert the I/O count back to a uint32_t for the vector I/O + * call until the interface can possibly be changed to use size_t + * in the future + */ + H5_CHECKED_ASSIGN(u32_io_count, uint32_t, io_count, size_t); + + if (io_type == IO_TYPE_WRITE) { + /* Make vector write call to VFD controlling subfiles */ + if (H5FD_write_vector(file_ptr->sf_file, u32_io_count, types, addrs, sizes, (const void **)bufs) < + 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write to subfile failed"); + + /* + * Mirror superblock writes to the stub file so that + * legacy HDF5 applications can check what type of + * file they are reading + */ + if (H5FD__subfiling_mirror_writes_to_stub(file_ptr, u32_io_count, types, addrs, sizes, + (const void **)bufs) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "mirrored write to stub file failed"); + } + else { + /* Make vector read call to VFD controlling subfiles */ + if (H5FD_read_vector(file_ptr->sf_file, u32_io_count, types, addrs, sizes, (void **)bufs) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "read from subfile failed"); + } + } + else { + uint32_t iovec_len; + size_t ioreq_count = 0; + herr_t status; + + /************************************* + * Striping across multiple subfiles * + *************************************/ + + /* + * Generate the types, addrs, sizes and bufs I/O vectors for + * this I/O request. + */ + status = generate_io_vectors( + sf_context, /* IN: Subfiling context used to look up config info */ + io_count, /* IN: Number of entries in `types`, `addrs`, `sizes` and `bufs` */ + types, /* IN: Array of memory types */ + addrs, /* IN: Array of starting file offsets */ + sizes, /* IN: Array of I/O sizes (in terms of elements) */ + bufs, /* IN: Array of I/O buffers */ + 1, /* IN: Data extent of the 'type'; byte is assumed currently */ + io_type, /* IN: Type of I/O being performed (IO_TYPE_WRITE or IO_TYPE_READ) */ + &ioreq_count, /* OUT: Number of I/O requests to be made */ + &iovec_len, /* OUT: Number of elements in I/O vector for a single I/O request */ + &io_types, /* OUT: I/O vector of memory types for each I/O entry */ + &io_addrs, /* OUT: I/O vector of file addresses for each I/O entry */ + &io_sizes, /* OUT: I/O vector of I/O sizes for each I/O entry */ + &io_bufs); /* OUT: I/O vector of buffers for each I/O entry */ + + if (status < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't initialize I/O vectors"); + + /* Nothing to do + * + * TODO: Note that this does not let the sub-filing VFD participate in + * collective calls when there is no data to write. This is not an issue + * now, as we don't do anything special with collective operations. + * However, this needs to be fixed. + */ + if (ioreq_count == 0) + H5_SUBFILING_GOTO_DONE(SUCCEED); + +#ifdef H5_SUBFILING_DEBUG + H5_subfiling_dump_iovecs(sf_context, ioreq_count, iovec_len, io_type, io_types, io_addrs, io_sizes, + io_bufs); +#endif + + /* clang-format off */ + /* + * Having now populated the I/O vectors for this I/O request and + * having determined how many I/O calls need to be made to satisfy + * the entire I/O request, loop that many times, making an I/O call + * with each set of I/O vectors. Each I/O call uses a set of I/O + * vectors with a length of up to 'number of subfiles' elements and + * each I/O call's I/O vectors are setup to ensure that the I/O is + * spread across as many subfiles as possible for each iteration. In + * the simple case of N evenly-distributed and well-aligned I/O + * requests being performed on 4 subfiles, this can be visualized as + * the following: + * + * I/O REQ. 0 I/O REQ. 1 ... I/O REQ. N-1 + * || || || + * VV VV VV + * {IOVEC[0]} {IOVEC[4]} ... {IOVEC[(N-1 * iovec_len)]} -> SUBFILE 0 + * {IOVEC[1]} {IOVEC[5]} ... {IOVEC[(N-1 * iovec_len) + 1]} -> SUBFILE 1 + * {IOVEC[2]} {IOVEC[6]} ... {IOVEC[(N-1 * iovec_len) + 2]} -> SUBFILE 2 + * {IOVEC[3]} {IOVEC[7]} ... {IOVEC[(N-1 * iovec_len) + 3]} -> SUBFILE 3 + * + * where {IOVEC[X]} represents an I/O vector composed of the entries + * at index X of io_types, io_addrs, io_sizes and io_bufs. Note that + * the entire set of I/O vectors, e.g. [ {IOVEC[0]}, {IOVEC[1]}, {IOVEC[2]}, {IOVEC[3]} ] + * from the above visualization will be sent to the underlying I/O + * concentrator VFD in a single I/O call on each iteration. That VFD is + * ultimately responsible for mapping each I/O vector to its corresponding + * subfile (here, pointed to by '->' to the right of each I/O vector). + */ + /* clang-format on */ + for (size_t ioreq_idx = 0; ioreq_idx < ioreq_count; ioreq_idx++) { + H5_flexible_const_ptr_t *io_bufs_ptr = NULL; + H5FD_mem_t *io_types_ptr = NULL; + uint32_t final_vec_len = iovec_len; + haddr_t *io_addrs_ptr = NULL; + size_t *io_sizes_ptr = NULL; + + /* Setup index into I/O vectors for this I/O operation */ + io_types_ptr = &io_types[ioreq_idx * iovec_len]; + io_addrs_ptr = &io_addrs[ioreq_idx * iovec_len]; + io_sizes_ptr = &io_sizes[ioreq_idx * iovec_len]; + io_bufs_ptr = &io_bufs[ioreq_idx * iovec_len]; + + /* Skip 0-sized I/Os */ + for (size_t vec_idx = 0; vec_idx < iovec_len; vec_idx++) + if (io_sizes_ptr[vec_idx] == 0) + final_vec_len--; + + if (io_type == IO_TYPE_WRITE) { + /* Make vector write call to VFD controlling subfiles */ + if (H5FD_write_vector(file_ptr->sf_file, final_vec_len, io_types_ptr, io_addrs_ptr, + io_sizes_ptr, (const void **)io_bufs_ptr) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write to subfile failed"); + + /* + * Mirror superblock writes to the stub file so that + * legacy HDF5 applications can check what type of + * file they are reading + */ + if (H5FD__subfiling_mirror_writes_to_stub(file_ptr, final_vec_len, io_types_ptr, io_addrs_ptr, + io_sizes_ptr, (const void **)io_bufs_ptr) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "mirrored write to stub file failed"); + } + else { + if (!rank0_bcast || (file_ptr->mpi_rank == 0)) { + /* Make vector read call to VFD controlling subfiles */ + if (H5FD_read_vector(file_ptr->sf_file, final_vec_len, io_types_ptr, io_addrs_ptr, + io_sizes_ptr, (void **)io_bufs_ptr) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "read from subfile failed"); + } + } + } + + if (rank0_bcast && (file_ptr->mpi_size > 1)) { + size_t size; + + assert(io_type == IO_TYPE_READ); + + extend_sizes = false; + for (size_t i = 0; i < io_count; i++) { + if (!extend_sizes) { + if ((i > 0) && (sizes[i] == 0)) { + extend_sizes = true; + size = sizes[i - 1]; + } + else { + size = sizes[i]; + } + } + + H5_CHECK_OVERFLOW(size, size_t, int); + if (MPI_SUCCESS != MPI_Bcast(bufs[i].vp, (int)size, MPI_BYTE, 0, file_ptr->comm)) + H5_SUBFILING_GOTO_ERROR(H5E_VFL, H5E_READERROR, FAIL, "can't broadcast data from rank 0"); + } + } + } + +done: + /* Restore original transfer mode if we changed it */ + if (xfer_mode != H5FD_MPIO_INDEPENDENT) + if (H5CX_set_io_xfer_mode(xfer_mode) < 0) + H5_SUBFILING_DONE_ERROR(H5E_CONTEXT, H5E_CANTSET, FAIL, "can't set I/O collectivity setting"); + + free(io_bufs); + free(io_sizes); + free(io_addrs); + free(io_types); + + H5_SUBFILING_FUNC_LEAVE; +} + +/*------------------------------------------------------------------------- + * Function: H5FD__subfiling_mirror_writes_to_stub + * + * Purpose: Mirrors write calls to the Subfiling stub file so that + * legacy HDF5 applications can check what type of file they + * are reading. Only superblock I/O is mirrored to the stub + * file and only if that I/O comes from MPI rank 0. This + * means that file metadata could be missed if it comes from + * other MPI ranks (such as when using a distributed metadata + * write strategy), but, at least currently, we generally only + * care about the first few bytes of the file being properly + * written to the stub file. + * + * Return: SUCCEED/FAIL + * + *------------------------------------------------------------------------- + */ +static herr_t +H5FD__subfiling_mirror_writes_to_stub(H5FD_subfiling_t *file_ptr, uint32_t count, H5FD_mem_t types[], + haddr_t addrs[], size_t sizes[], const void *bufs[]) +{ + const void **copied_bufs = NULL; + H5FD_mem_t *copied_types = NULL; + haddr_t *copied_addrs = NULL; + size_t *copied_sizes = NULL; + H5FD_mem_t type = H5FD_MEM_DEFAULT; + size_t io_size = 0; + bool all_super_writes = true; + bool some_super_writes = false; + bool extend_types = false; + bool extend_sizes = false; + herr_t ret_value = SUCCEED; + + assert(file_ptr); + + /* Only mirror I/O from MPI rank 0 */ + if (file_ptr->mpi_rank != 0) + H5_SUBFILING_GOTO_DONE(SUCCEED); + + if (count == 0) + H5_SUBFILING_GOTO_DONE(SUCCEED); + + for (size_t i = 0; i < count; i++) { + if (!extend_types) { + if ((i > 0) && (types[i] == H5FD_MEM_NOLIST)) { + extend_types = true; + type = types[i - 1]; + } + else { + type = types[i]; + } + } + + if (type == H5FD_MEM_SUPER) + some_super_writes = true; + else + all_super_writes = false; + + /* + * If we find H5FD_MEM_NOLIST, we don't need to + * keep looking through the array entries + */ + if (extend_types) + break; + } + + if (all_super_writes) { + if (H5FD_write_vector(file_ptr->stub_file, count, types, addrs, sizes, bufs) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "couldn't write superblock information to stub file"); + } + else if (some_super_writes) { + uint32_t vec_len = 0; + + /* Copy I/O vectors and strip out non-superblock I/O */ + + if (NULL == (copied_types = malloc(count * sizeof(*copied_types)))) + H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "can't allocate copy of I/O types array"); + if (NULL == (copied_addrs = malloc(count * sizeof(*copied_addrs)))) + H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "can't allocate copy of I/O addresses array"); + if (NULL == (copied_sizes = malloc(count * sizeof(*copied_sizes)))) + H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "can't allocate copy of I/O sizes array"); + if (NULL == (copied_bufs = malloc(count * sizeof(*copied_bufs)))) + H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "can't allocate copy of I/O buffers array"); + + extend_types = false; + extend_sizes = false; + for (size_t i = 0; i < count; i++) { + if (!extend_types) { + if ((i > 0) && (types[i] == H5FD_MEM_NOLIST)) { + extend_types = true; + type = types[i - 1]; + + /* End early if none of the remaining memory types are H5FD_MEM_SUPER */ + if (type != H5FD_MEM_SUPER) + break; + } + else { + type = types[i]; + } + } + + if (!extend_sizes) { + if ((i > 0) && (sizes[i] == 0)) { + extend_sizes = true; + io_size = sizes[i - 1]; + } + else { + io_size = sizes[i]; + } + } + + if (type != H5FD_MEM_SUPER) + continue; + + copied_types[vec_len] = type; + copied_addrs[vec_len] = addrs[i]; + copied_sizes[vec_len] = io_size; + copied_bufs[vec_len] = bufs[i]; + + vec_len++; + } + + if ((vec_len > 0) && (H5FD_write_vector(file_ptr->stub_file, vec_len, copied_types, copied_addrs, + copied_sizes, copied_bufs) < 0)) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, + "couldn't write superblock information to stub file"); + } + +done: + free(copied_bufs); + free(copied_sizes); + free(copied_addrs); + free(copied_types); + + H5_SUBFILING_FUNC_LEAVE; +} + +/*------------------------------------------------------------------------- + * Function: generate_io_vectors + * + * Purpose: Given an array of memory types, an array of file offsets, + * an array of the number of I/O elements for each file + * offset and an array of I/O buffers, translates each (type, + * offset, number of elements, I/O buffer) tuple into a set of + * I/O vectors according to the subfiling configuration + * specified in `sf_context`. These I/O vectors are generated + * such that a set of `iovec_len` elements from each of + * `io_types`, `io_addrs`, `io_sizes` and `io_bufs` can be + * passed to H5FD_write_vector/H5FD_read_vector and that I/O + * call will span as many subfiles as possible, parallelizing + * the I/O. Then, the next set of `iovec_len` elements can be + * passed and so on, until the whole I/O request has been + * parallelized across the subfiles. Once this function + * returns, `io_types`, `io_addrs`, `io_sizes` and `io_bufs` + * will each contain `ioreq_count` sets of I/O vectors, with + * each set containing `iovec_len` elements. * * sf_context (IN) * - the subfiling context for the file * - * file_offset (IN) - * - the starting file offset for I/O + * in_count (IN) + * - the number of entries in the `types`, `file_offsets`, + * `nelemts` and `bufs` arrays + * + * types (IN) + * - the memory types for each I/O entry + * + * file_offsets (IN) + * - array of starting file offsets for I/O + * + * nelemts (IN) + * - array of the number of data elements for the I/O + * operation * - * io_nelemts (IN) - * - the number of data elements for the I/O operation + * bufs (IN) + * - array of the I/O buffers to use for each I/O entry * * dtype_extent (IN) * - the extent of the datatype of each data element for - * the I/O operation - * - * max_iovec_len (IN) - * - the maximum size for a single I/O vector in each of - * the output arrays `mem_buf_offset`, `io_block_len` - * and `sf_offset`. NOTE that this routine expects each - * of these output arrays to have enough space allocated - * for one I/O vector PER subfile. Therefore, the total - * size of each output array should be at least - * `max_iovec_len * num_subfiles`. - * - * mem_buf_offset (OUT) - * - output array of vectors (one vector for each subfile) - * containing the set of offsets into the memory buffer - * for I/O - * - * target_file_offset (OUT) - * - output array of vectors (one vector for each subfile) - * containing the set of offsets into the target file - * - * io_block_len (OUT) - * - output array of vectors (one vector for each subfile) - * containing the set of block lengths for each source - * buffer/target file offset. - * - * first_subfile_index (OUT) - * - the index of the first subfile that this I/O operation - * begins at - * - * n_subfiles_used (OUT) - * - the number of subfiles actually used for this I/O - * operation, which may be different from the total - * number of subfiles for the file - * - * max_io_req_per_subfile (OUT) - * - the maximum number of I/O requests to any particular - * subfile, or the maximum "depth" of each I/O vector - * in the output arrays. + * the I/O operation (currently assumed to be 1, meaning + * entries in `nelemts` are expressed in terms of + * bytes) + * + * io_type (IN) + * - the type of I/O being performed (IO_TYPE_WRITE or + * IO_TYPE_READ) + * + * ioreq_count (OUT) + * - the number of I/O requests needed to fully satisfy the + * I/O operation + * + * iovec_len (OUT) + * - the size of each I/O vector (in terms of array elements) + * for each I/O request to be made + * + * io_types (OUT) + * - I/O vector of memory types for the I/O operation. + * Allocated by this function and must be freed by the + * caller. + * + * io_addrs (OUT) + * - I/O vector of file addresses for the I/O operation. + * Allocated by this function and must be freed by the + * caller. + * + * io_sizes (OUT) + * - I/O vector of the I/O sizes for the I/O operation. + * Allocated by this function and must be freed by the + * caller. + * + * io_bufs (OUT) + * - I/O vector of the I/O buffers for the I/O operation. + * Allocated by this function and must be freed by the + * caller. * * Return: Non-negative on success/Negative on failure * - *------------------------------------------------------------------------- */ static herr_t -init_indep_io(subfiling_context_t *sf_context, int64_t file_offset, size_t io_nelemts, size_t dtype_extent, - size_t max_iovec_len, int64_t *mem_buf_offset, int64_t *target_file_offset, - int64_t *io_block_len, int *first_subfile_index, int *n_subfiles_used, - int64_t *max_io_req_per_subfile) +generate_io_vectors(subfiling_context_t *sf_context, size_t in_count, H5FD_mem_t types[], + haddr_t file_offsets[], size_t nelemts[], H5_flexible_const_ptr_t bufs[], + size_t dtype_extent, H5FD_subfiling_io_type_t io_type, size_t *ioreq_count, + uint32_t *iovec_len, H5FD_mem_t **io_types, haddr_t **io_addrs, size_t **io_sizes, + H5_flexible_const_ptr_t **io_bufs) +{ + H5_flexible_const_ptr_t *loc_io_bufs = NULL; + H5FD_mem_t *loc_io_types = NULL; + H5FD_mem_t mem_type = H5FD_MEM_DEFAULT; + haddr_t *loc_io_addrs = NULL; + size_t *loc_io_sizes = NULL; + size_t max_iovec_depth = 0; + size_t max_num_subfiles_touched = 0; + size_t tot_iovec_len = 0; + size_t io_size = 0; + bool extend_sizes = false; + bool extend_types = false; + herr_t ret_value = SUCCEED; + + assert(sf_context); + assert(sf_context->sf_stripe_size > 0); + assert(sf_context->sf_blocksize_per_stripe > 0); + assert(sf_context->sf_num_subfiles > 0); + assert(sf_context->topology); + assert((types) || (in_count == 0)); + assert((file_offsets) || (in_count == 0)); + assert((nelemts) || (in_count == 0)); + assert((bufs) || (in_count == 0)); + assert(dtype_extent == 1); /* For now, assume 'byte'-sized elements */ + assert(ioreq_count); + assert(iovec_len); + assert(io_types); + assert(io_addrs); + assert(io_sizes); + assert(io_bufs); + + /* Set some returned values early */ + *ioreq_count = 0; + *iovec_len = 0; + + /* Nothing to do */ + if (in_count == 0) + H5_SUBFILING_GOTO_DONE(SUCCEED); + + /* + * Do some initial pre-processing to determine how large of + * I/O vectors we will need to allocate to satisfy the + * entire I/O request + */ + get_iovec_sizes(sf_context, in_count, file_offsets, nelemts, dtype_extent, &max_iovec_depth, + &max_num_subfiles_touched); + + tot_iovec_len = in_count * max_iovec_depth * max_num_subfiles_touched; + +#ifdef H5_SUBFILING_DEBUG + H5_subfiling_log( + sf_context->sf_context_id, + "%s: I/O count: %zu, max_iovec_depth = %zu, max_num_subfiles_touched = %zu, iovec_len = %zu", + __func__, in_count, max_iovec_depth, max_num_subfiles_touched, tot_iovec_len); +#endif + + /* Allocate I/O vectors that will be returned to the caller */ + if (NULL == (loc_io_types = calloc(1, tot_iovec_len * sizeof(*loc_io_types)))) + H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't allocate subfile I/O types vector"); + if (NULL == (loc_io_addrs = calloc(1, tot_iovec_len * sizeof(*loc_io_addrs)))) + H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "can't allocate subfile I/O addresses vector"); + if (NULL == (loc_io_sizes = calloc(1, tot_iovec_len * sizeof(*loc_io_sizes)))) + H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "can't allocate subfile I/O sizes vector"); + if (NULL == (loc_io_bufs = calloc(1, tot_iovec_len * sizeof(*loc_io_bufs)))) + H5_SUBFILING_GOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, + "can't allocate subfile I/O buffers vector"); + + /* + * Populate the I/O vectors by looping through each + * of the (type, addrs, I/O size, buf) tuples + */ + for (size_t io_idx = 0; io_idx < in_count; io_idx++) { + size_t iovec_idx; + + iovec_idx = (io_idx * max_iovec_depth * max_num_subfiles_touched); + assert(iovec_idx < tot_iovec_len); + + if (!extend_types) { + if ((io_idx > 0) && (types[io_idx] == H5FD_MEM_NOLIST)) { + extend_types = true; + mem_type = types[io_idx - 1]; + } + else { + mem_type = types[io_idx]; + } + } + + if (!extend_sizes) { + if ((io_idx > 0) && (nelemts[io_idx] == 0)) { + extend_sizes = true; + io_size = nelemts[io_idx - 1] * dtype_extent; + } + else { + io_size = nelemts[io_idx] * dtype_extent; + } + } + + if (translate_io_req_to_iovec(sf_context, iovec_idx, max_num_subfiles_touched, max_iovec_depth, + mem_type, file_offsets[io_idx], io_size, bufs[io_idx], io_type, + loc_io_types, loc_io_addrs, loc_io_sizes, loc_io_bufs) < 0) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't translate I/O request to I/O vectors"); + } + + *ioreq_count = in_count * max_iovec_depth; + H5_CHECK_OVERFLOW(max_num_subfiles_touched, size_t, uint32_t); + *iovec_len = (uint32_t)max_num_subfiles_touched; + *io_types = loc_io_types; + *io_addrs = loc_io_addrs; + *io_sizes = loc_io_sizes; + *io_bufs = loc_io_bufs; + +done: + if (ret_value < 0) { + free(loc_io_bufs); + free(loc_io_sizes); + free(loc_io_addrs); + free(loc_io_types); + } + + H5_SUBFILING_FUNC_LEAVE; +} + +/*------------------------------------------------------------------------- + * Function: get_iovec_sizes + * + * Purpose: Helper routine to determine the maximum I/O vector depth + * (in terms of array elements) and maximum number of subfiles + * touched for any particular piece of an I/O request. This + * info is used to calculate the total size of I/O vectors we + * need to allocate to satisfy an entire I/O request. + * + * Return: Maximum I/O vector depth and maximum number of subfiles + * touched (can't fail) + * + *------------------------------------------------------------------------- + */ +static void +get_iovec_sizes(subfiling_context_t *sf_context, size_t in_count, haddr_t file_offsets[], size_t nelemts[], + size_t dtype_extent, size_t *max_iovec_depth, size_t *max_num_subfiles) { int64_t stripe_size = 0; int64_t block_size = 0; - int64_t data_size = 0; + size_t loc_max_iovec_depth = 0; + size_t loc_max_num_subfiles = 0; + int num_subfiles = 0; + + assert(sf_context); + assert(file_offsets); + assert(nelemts); + assert(max_iovec_depth); + assert(max_num_subfiles); + + stripe_size = sf_context->sf_stripe_size; + block_size = sf_context->sf_blocksize_per_stripe; + num_subfiles = sf_context->sf_num_subfiles; + + for (size_t io_idx = 0; io_idx < in_count; io_idx++) { + int64_t stripe_idx; + int64_t final_stripe_idx; + int64_t cur_file_offset; + int64_t final_offset; + int64_t data_size; + int64_t first_subfile; + int64_t last_subfile; + int64_t row_stripe_idx_start; + int64_t row_stripe_idx_final; + int64_t cur_max_num_subfiles; + size_t cur_iovec_depth; + + H5_CHECKED_ASSIGN(cur_file_offset, int64_t, file_offsets[io_idx], haddr_t); + H5_CHECKED_ASSIGN(data_size, int64_t, (nelemts[io_idx] * dtype_extent), size_t); + + /* + * Calculate the following from the starting file offset: + * + * stripe_idx + * - a stripe "index" given by the file offset divided by the + * stripe size. Note that when the file offset equals or exceeds + * the block size, we simply wrap around. So, for example, if 4 + * subfiles are being used with a stripe size of 1KiB, the block + * size would be 4KiB and file offset 4096 would have a stripe + * index of 4 and reside in the same subfile as stripe index 0 + * (offsets 0-1023) + * final_offset + * - the last offset in the virtual file covered by this I/O + * operation. Simply the I/O size added to the starting file + * offset. + */ + stripe_idx = cur_file_offset / stripe_size; + final_offset = cur_file_offset + data_size; + + /* Determine which subfile the I/O request begins in */ + first_subfile = stripe_idx % num_subfiles; + + /* + * Determine the stripe "index" of the last offset in the + * virtual file and, from that, determine the subfile that + * the I/O request ends in. + */ + final_stripe_idx = final_offset / stripe_size; + last_subfile = final_stripe_idx % num_subfiles; + + /* + * Determine how "deep" the resulting I/O vectors are at + * most by calculating the maximum number of "rows" spanned + * for any particular subfile; e.g. the maximum number of + * I/O requests for any particular subfile + */ + row_stripe_idx_start = stripe_idx - first_subfile; + row_stripe_idx_final = final_stripe_idx - last_subfile; + cur_iovec_depth = (size_t)((row_stripe_idx_final - row_stripe_idx_start) / num_subfiles) + 1; + + /* + * If the I/O request "wrapped around" and ends in a subfile + * less than the subfile we started in, subtract one from the + * I/O vector length to account for "empty space". This can be + * visualized as follows: + * + * SUBFILE 0 SUBFILE 1 SUBFILE 2 SUBFILE 3 + * _______________________________________________ + * | | | XXXXX | XXXXX | ROW 0 + * | XXXXX | XXXXX | XXXXX | XXXXX | ROW 1 + * | XXXXX | XXXXX | | | ROW 2 + * | | | | | ROW ... + * | | | | | + * | | | | | + * | | | | | + * |___________|___________|___________|___________| + * + * Here, `stripe_idx` would be calculated as 2 (I/O begins in + * the 3rd stripe, or subfile index 2), `first_subfile` would be + * calculated as 2 and the starting "row" (row_stripe_idx_start) + * would be calculated as "row" index 0. `final_stripe_idx` would + * be calculated as 9, `last_subfile` would be calculated as + * (9 % 4) = 1 and the ending "row" (row_stripe_idx_final) would + * be calculated as (9 - 1) = 8. Thus, the calculated I/O vector + * length would be ((8 - 0) / 4) + 1 = 3. However, since there is + * no I/O to stripe indices 0 and 1 (residing in "row" 0 of subfile + * index 0 and 1, respectively), it can be seen that the real I/O + * vector length is 2. + */ + if (last_subfile < first_subfile) + cur_iovec_depth--; + + loc_max_iovec_depth = MAX(cur_iovec_depth, loc_max_iovec_depth); + + /* + * Determine the maximum number of subfiles this piece of the + * I/O request could touch + */ + if (data_size >= block_size) { + /* + * I/O of a size greater than the block size definitionally + * touches all subfiles at least once. + */ + cur_max_num_subfiles = (size_t)num_subfiles; + } + else if (data_size < stripe_size) { + /* + * I/O of a size smaller than the stripe size could + * touch one or two subfiles at most, depending on + * the file offset. + */ + cur_max_num_subfiles = 2; + } + else { + /* + * I/O of a size smaller than the block size, but larger + * than or equal to the stripe size must touch at least + * (data_size / stripe_size) subfiles, but could touch + * an additional subfile, depending on the file offset. + */ + cur_max_num_subfiles = (((cur_file_offset % stripe_size) + data_size - 1) / stripe_size) + 1; + } + + loc_max_num_subfiles = MAX((size_t)cur_max_num_subfiles, loc_max_num_subfiles); + } + + *max_iovec_depth = loc_max_iovec_depth; + *max_num_subfiles = loc_max_num_subfiles; +} + +/*------------------------------------------------------------------------- + * Function: translate_io_req_to_iovec + * + * Purpose: Helper routine to perform the translation between an I/O + * request (type, addr, size, buf tuple) and a set of I/O + * vectors that spans all the subfiles touched by that I/O + * request. Once finished, this function will have generated + * at most `iovec_count` sets of I/O vectors, each containing + * `iovec_len` elements, but a smaller number of I/O vector + * sets could be generated, depending on the I/O request. + * + * sf_context (IN) + * - the subfiling context for the file + * + * iovec_idx (IN) + * - the index into `io_types`, `io_addrs`, `io_sizes` and + * `io_bufs` where this function should begin filling in + * the I/O vectors + * + * iovec_len (IN) + * - the number of elements in each I/O vector generated + * + * iovec_count (IN) + * - the maximum number of I/O vectors to be generated, as + * calculated in generate_io_vectors() + * + * type (IN) + * - the memory type to use for each component of the I/O + * vectors generated + * + * addr (IN) + * - the starting file offset used to generate the I/O + * vectors + * + * io_size (IN) + * - the size of the I/O to the given file offset, which is + * used when generating the I/O vectors + * + * io_buf (IN) + * - the I/O buffer to be partitioned up while generating + * the I/O vectors + * + * io_type (IN) + * - the type of I/O being performed (IO_TYPE_WRITE or + * IO_TYPE_READ) + * + * io_types (OUT) + * - pointer to the memory types I/O vector to populate + * + * io_addrs (OUT) + * - pointer to the file offsets I/O vector to populate + * + * io_sizes (OUT) + * - pointer to the I/O sizes I/O vector to populate + * + * io_bufs (OUT) + * - pointer to the I/O buffers I/O vector to populate + * + * Return: Non-negative on success/Negative on failure + * + *------------------------------------------------------------------------- + */ +static herr_t +translate_io_req_to_iovec(subfiling_context_t *sf_context, size_t iovec_idx, size_t iovec_len, + size_t iovec_count, H5FD_mem_t type, haddr_t addr, size_t io_size, + H5_flexible_const_ptr_t io_buf, H5FD_subfiling_io_type_t io_type, + H5FD_mem_t *io_types, haddr_t *io_addrs, size_t *io_sizes, + H5_flexible_const_ptr_t *io_bufs) +{ int64_t stripe_idx = 0; int64_t final_stripe_idx = 0; - int64_t curr_stripe_idx = 0; + int64_t stripe_size = 0; + int64_t block_size = 0; + int64_t file_offset = 0; int64_t offset_in_stripe = 0; int64_t offset_in_block = 0; int64_t final_offset = 0; int64_t start_length = 0; int64_t final_length = 0; - int64_t first_subfile = 0; - int64_t last_subfile = 0; + int64_t first_subfile_idx = 0; + int64_t last_subfile_idx = 0; int64_t start_row = 0; int64_t row_offset = 0; int64_t row_stripe_idx_start = 0; int64_t row_stripe_idx_final = 0; + int64_t cur_stripe_idx = 0; int64_t max_iovec_depth = 0; - int64_t curr_max_iovec_depth = 0; - int64_t total_bytes = 0; int64_t mem_offset = 0; + size_t total_bytes = 0; int num_subfiles = 0; herr_t ret_value = SUCCEED; assert(sf_context); - assert(sf_context->sf_stripe_size > 0); - assert(sf_context->sf_blocksize_per_stripe > 0); - assert(sf_context->sf_num_subfiles > 0); - assert(sf_context->topology); - assert(mem_buf_offset); - assert(target_file_offset); - assert(io_block_len); - assert(first_subfile_index); - assert(n_subfiles_used); - assert(max_io_req_per_subfile); - - *first_subfile_index = 0; - *n_subfiles_used = 0; - *max_io_req_per_subfile = 0; + assert(io_types); + assert(io_addrs); + assert(io_sizes); + assert(io_bufs); /* - * Retrieve the needed fields from the subfiling context. + * Retrieve some needed fields from the subfiling context. * * stripe_size * - the size of the data striping across the file's subfiles @@ -2723,15 +2965,13 @@ init_indep_io(subfiling_context_t *sf_context, int64_t file_offset, size_t io_ne * num_subfiles * - the total number of subfiles for the logical * HDF5 file - * num_io_concentrators - * - the number of I/O concentrators currently being - * used */ stripe_size = sf_context->sf_stripe_size; block_size = sf_context->sf_blocksize_per_stripe; num_subfiles = sf_context->sf_num_subfiles; - H5_CHECKED_ASSIGN(data_size, int64_t, (io_nelemts * dtype_extent), size_t); + H5_CHECKED_ASSIGN(file_offset, int64_t, addr, haddr_t); + H5_CHECK_OVERFLOW(io_size, size_t, int64_t); /* * Calculate the following from the starting file offset: @@ -2740,8 +2980,8 @@ init_indep_io(subfiling_context_t *sf_context, int64_t file_offset, size_t io_ne * - a stripe "index" given by the file offset divided by the * stripe size. Note that when the file offset equals or exceeds * the block size, we simply wrap around. So, for example, if 4 - * subfiles are being used with a stripe size of 1MiB, the block - * size would be 4MiB and file offset 4096 would have a stripe + * subfiles are being used with a stripe size of 1KiB, the block + * size would be 4KiB and file offset 4096 would have a stripe * index of 4 and reside in the same subfile as stripe index 0 * (offsets 0-1023) * offset_in_stripe @@ -2752,17 +2992,22 @@ init_indep_io(subfiling_context_t *sf_context, int64_t file_offset, size_t io_ne * subfiles * final_offset * - the last offset in the virtual file covered by this I/O - * operation. Simply the I/O size added to the starting file - * offset. + * request. Simply the I/O size minus one byte added to the + * starting file offset. */ stripe_idx = file_offset / stripe_size; offset_in_stripe = file_offset % stripe_size; offset_in_block = file_offset % block_size; - final_offset = file_offset + data_size; + final_offset = file_offset + (int64_t)(io_size > 0 ? io_size - 1 : 0); /* Determine the size of data written to the first and last stripes */ - start_length = MIN(data_size, (stripe_size - offset_in_stripe)); - final_length = (start_length == data_size ? 0 : final_offset % stripe_size); + start_length = MIN((int64_t)io_size, (stripe_size - offset_in_stripe)); + if (start_length == (int64_t)io_size) + final_length = 0; + else if (((final_offset + 1) % stripe_size) == 0) + final_length = stripe_size; + else + final_length = (final_offset + 1) % stripe_size; assert(start_length <= stripe_size); assert(final_length <= stripe_size); @@ -2776,9 +3021,9 @@ init_indep_io(subfiling_context_t *sf_context, int64_t file_offset, size_t io_ne * file offsets that are multiples of the block size begin a new * "row". */ - start_row = stripe_idx / num_subfiles; - first_subfile = stripe_idx % num_subfiles; - H5_CHECK_OVERFLOW(first_subfile, int64_t, int); + start_row = stripe_idx / num_subfiles; + first_subfile_idx = stripe_idx % num_subfiles; + H5_CHECK_OVERFLOW(first_subfile_idx, int64_t, int); /* * Set initial file offset for starting "row" @@ -2792,34 +3037,62 @@ init_indep_io(subfiling_context_t *sf_context, int64_t file_offset, size_t io_ne * the I/O request ends in. */ final_stripe_idx = final_offset / stripe_size; - last_subfile = final_stripe_idx % num_subfiles; + last_subfile_idx = final_stripe_idx % num_subfiles; /* - * Determine how "deep" the resulting I/O vectors are at - * most by calculating the maximum number of "rows" spanned - * for any particular subfile; e.g. the maximum number of - * I/O requests for any particular subfile + * Determine how "deep" the current I/O vector is at most + * by calculating the maximum number of "rows" spanned for + * any particular subfile; e.g. the maximum number of I/O + * requests for any particular subfile */ - row_stripe_idx_start = stripe_idx - first_subfile; - row_stripe_idx_final = final_stripe_idx - last_subfile; + row_stripe_idx_start = stripe_idx - first_subfile_idx; + row_stripe_idx_final = final_stripe_idx - last_subfile_idx; max_iovec_depth = ((row_stripe_idx_final - row_stripe_idx_start) / num_subfiles) + 1; - if (last_subfile < first_subfile) + /* + * If the I/O request "wrapped around" and ends in a subfile + * less than the subfile we started in, subtract one from the + * I/O vector length to account for "empty space". This can be + * visualized as follows: + * + * SUBFILE 0 SUBFILE 1 SUBFILE 2 SUBFILE 3 + * _______________________________________________ + * | | | XXXXX | XXXXX | ROW 0 + * | XXXXX | XXXXX | XXXXX | XXXXX | ROW 1 + * | XXXXX | XXXXX | | | ROW 2 + * | | | | | ROW ... + * | | | | | + * | | | | | + * | | | | | + * |___________|___________|___________|___________| + * + * Here, `stripe_idx` would be calculated as 2 (I/O begins in + * the 3rd stripe, or subfile index 2), `first_subfile` would be + * calculated as 2 and the starting "row" (row_stripe_idx_start) + * would be calculated as "row" index 0. `final_stripe_idx` would + * be calculated as 9, `last_subfile` would be calculated as + * (9 % 4) = 1 and the ending "row" (row_stripe_idx_final) would + * be calculated as (9 - 1) = 8. Thus, the calculated I/O vector + * length would be ((8 - 0) / 4) + 1 = 3. However, since there is + * no I/O to stripe indices 0 and 1 (residing in "row" 0 of subfile + * index 0 and 1, respectively), it can be seen that the real I/O + * vector length is 2. + */ + if (last_subfile_idx < first_subfile_idx) max_iovec_depth--; - /* Set returned parameters early */ - *first_subfile_index = (int)first_subfile; - *n_subfiles_used = num_subfiles; - *max_io_req_per_subfile = max_iovec_depth; - #ifdef H5_SUBFILING_DEBUG - H5_subfiling_log(sf_context->sf_context_id, - "%s: FILE OFFSET = %" PRId64 ", DATA SIZE = %zu, STRIPE SIZE = %" PRId64, __func__, - file_offset, io_nelemts, stripe_size); - H5_subfiling_log(sf_context->sf_context_id, - "%s: FIRST SUBFILE = %" PRId64 ", LAST SUBFILE = %" PRId64 ", " - "MAX IOVEC DEPTH = %" PRId64 ", START LENGTH = %" PRId64 ", FINAL LENGTH = %" PRId64, - __func__, first_subfile, last_subfile, max_iovec_depth, start_length, final_length); + H5_subfiling_log( + sf_context->sf_context_id, + "%s: TRANSLATING I/O REQUEST (MEMORY TYPE: %d, ADDR: %" PRIuHADDR ", I/O SIZE: %zu, BUF: %p)\n" + "STRIPE SIZE: %" PRId64 ", BLOCK SIZE: %" PRId64 ", NUM SUBFILES: %d\n" + "STRIPE IDX: %" PRId64 ", LAST STRIPE IDX: %" PRId64 ", FIRST SUBFILE IDX: %" PRId64 + ", LAST SUBFILE IDX: %" PRId64 "\n" + "START SEGMENT LENGTH: %" PRId64 ", LAST SEGMENT LENGTH: %" PRId64 ", MAX IOVEC DEPTH: %" PRId64, + __func__, type, addr, io_size, + (io_type == IO_TYPE_WRITE) ? (const void *)io_buf.cvp : (void *)io_buf.vp, stripe_size, block_size, + num_subfiles, stripe_idx, final_stripe_idx, first_subfile_idx, last_subfile_idx, start_length, + final_length, max_iovec_depth); #endif /* @@ -2827,131 +3100,162 @@ init_indep_io(subfiling_context_t *sf_context, int64_t file_offset, size_t io_ne * vector components for each. Subfiles whose data size is * zero will not have I/O requests passed to them. */ - curr_stripe_idx = stripe_idx; - curr_max_iovec_depth = max_iovec_depth; - for (int i = 0, k = (int)first_subfile; i < num_subfiles; i++) { - int64_t *_mem_buf_offset; - int64_t *_target_file_offset; - int64_t *_io_block_len; - int64_t subfile_bytes = 0; - int64_t iovec_depth; - bool is_first = false; - bool is_last = false; - size_t output_offset; - - iovec_depth = curr_max_iovec_depth; + cur_stripe_idx = stripe_idx; + for (int i = 0, subfile_idx = (int)first_subfile_idx; i < num_subfiles; i++) { + H5_flexible_const_ptr_t *_io_bufs_ptr; + H5FD_mem_t *_io_types_ptr; + haddr_t *_io_addrs_ptr; + size_t *_io_sizes_ptr; + int64_t iovec_depth; + int64_t num_full_stripes; + int64_t subfile_bytes = 0; + bool is_first = false; + bool is_last = false; + + if (total_bytes >= io_size) + break; - /* - * Setup the pointers to the next set of I/O vectors in - * the output arrays and clear those vectors - */ - output_offset = (size_t)(k)*max_iovec_len; - _mem_buf_offset = mem_buf_offset + output_offset; - _target_file_offset = target_file_offset + output_offset; - _io_block_len = io_block_len + output_offset; - - memset(_mem_buf_offset, 0, (max_iovec_len * sizeof(*_mem_buf_offset))); - memset(_target_file_offset, 0, (max_iovec_len * sizeof(*_target_file_offset))); - memset(_io_block_len, 0, (max_iovec_len * sizeof(*_io_block_len))); - - if (total_bytes == data_size) { - *n_subfiles_used = i; - goto done; - } + iovec_depth = max_iovec_depth; + num_full_stripes = iovec_depth; + + if (subfile_idx == first_subfile_idx) { + is_first = true; - if (total_bytes < data_size) { - int64_t num_full_stripes = iovec_depth; + /* + * Add partial segment length if not + * starting on a stripe boundary + */ + if (start_length < stripe_size) { + subfile_bytes += start_length; + num_full_stripes--; + } + } - if (k == first_subfile) { - is_first = true; + if (subfile_idx == last_subfile_idx) { + is_last = true; - /* - * Add partial segment length if not - * starting on a stripe boundary - */ - if (start_length < stripe_size) { - subfile_bytes += start_length; + /* + * Add partial segment length if not + * ending on a stripe boundary + */ + if (final_length < stripe_size) { + subfile_bytes += final_length; + if (num_full_stripes) num_full_stripes--; - } } + } - if (k == last_subfile) { - is_last = true; + /* Account for subfiles with uniform segments */ + if (!is_first && !is_last) { + bool thin_uniform_section = false; + if (last_subfile_idx >= first_subfile_idx) { /* - * Add partial segment length if not - * ending on a stripe boundary + * In the case where the subfile with the final data + * segment has an index value greater than or equal + * to the subfile with the first data segment, I/O + * vectors directed to a subfile with an index value + * that is greater than the last subfile or less than + * the first subfile will be "thin", or rather will + * have a vector depth of 1 less than normal, which + * will be accounted for below. This can be visualized + * with the following I/O pattern: + * + * SUBFILE 0 SUBFILE 1 SUBFILE 2 SUBFILE 3 + * _______________________________________________ + * | | XXXXX | XXXXX | XXXXX | ROW 0 + * | XXXXX | XXXXX | XXXXX | | ROW 1 + * | | | | | ROW 2 + * | | | | | ROW ... + * | | | | | + * | | | | | + * | | | | | + * |___________|___________|___________|___________| + * (thin) (thin) */ - if (final_length < stripe_size) { - subfile_bytes += final_length; - if (num_full_stripes) - num_full_stripes--; - } + thin_uniform_section = (subfile_idx > last_subfile_idx) || (subfile_idx < first_subfile_idx); + } + else { /* last_subfile_idx < first_subfile_idx */ + /* + * This can also happen when the subfile with the final + * data segment has a smaller subfile index than the + * subfile with the first data segment and the current + * subfile index falls between the two. + */ + thin_uniform_section = + ((last_subfile_idx < subfile_idx) && (subfile_idx < first_subfile_idx)); } - /* Account for subfiles with uniform segments */ - if (!is_first && !is_last) { - bool thin_uniform_section = false; - - if (last_subfile >= first_subfile) { - /* - * When a subfile has an index value that is greater - * than both the starting subfile and ending subfile - * indices, it is a "thinner" section with a smaller - * I/O vector depth. - */ - thin_uniform_section = (k > first_subfile) && (k > last_subfile); - } + if (thin_uniform_section) { + assert(iovec_depth > 1); + assert(num_full_stripes > 1); - if (last_subfile < first_subfile) { - /* - * This can also happen when the subfile with the final - * data segment has a smaller subfile index than the - * subfile with the first data segment and the current - * subfile index falls between the two. - */ - thin_uniform_section = - thin_uniform_section || ((last_subfile < k) && (k < first_subfile)); - } + iovec_depth--; + num_full_stripes--; + } + } - if (thin_uniform_section) { - assert(iovec_depth > 1); - assert(num_full_stripes > 1); + /* + * After accounting for the length of the initial + * and/or final data segments, add the combined + * size of the fully selected I/O stripes to the + * running bytes total + */ + subfile_bytes += num_full_stripes * stripe_size; + total_bytes += (size_t)subfile_bytes; - iovec_depth--; - num_full_stripes--; - } - } + /* + * Setup the pointers to the next set of I/O vectors + * in the output arrays + */ + _io_types_ptr = &io_types[iovec_idx + (size_t)i]; + _io_addrs_ptr = &io_addrs[iovec_idx + (size_t)i]; + _io_sizes_ptr = &io_sizes[iovec_idx + (size_t)i]; + _io_bufs_ptr = &io_bufs[iovec_idx + (size_t)i]; - /* - * After accounting for the length of the initial - * and/or final data segments, add the combined - * size of the fully selected I/O stripes to the - * running bytes total - */ - subfile_bytes += num_full_stripes * stripe_size; - total_bytes += subfile_bytes; - } + /* + * Fill in I/O vector with initial values. If more than 1 + * subfile is involved, these values will be adjusted below. + */ + for (size_t vec_idx = 0; vec_idx < iovec_count; vec_idx++) + *(_io_types_ptr + (vec_idx * iovec_len)) = type; + *_io_addrs_ptr = (haddr_t)(row_offset + offset_in_block); + *_io_sizes_ptr = (size_t)subfile_bytes; - _mem_buf_offset[0] = mem_offset; - _target_file_offset[0] = row_offset + offset_in_block; - _io_block_len[0] = subfile_bytes; + if (io_type == IO_TYPE_WRITE) + _io_bufs_ptr->cvp = (const char *)(io_buf.cvp) + mem_offset; + else + _io_bufs_ptr->vp = (char *)(io_buf.vp) + mem_offset; if (num_subfiles > 1) { - int64_t curr_file_offset = row_offset + offset_in_block; + int64_t cur_file_offset = row_offset + offset_in_block; - /* Fill the I/O vectors */ + assert(iovec_depth <= max_iovec_depth); + + /* Fill the I/O vectors for the current subfile */ if (is_first) { - if (is_last) { /* First + Last */ - if (iovec_fill_first_last(sf_context, iovec_depth, subfile_bytes, mem_offset, - curr_file_offset, start_length, final_length, _mem_buf_offset, - _target_file_offset, _io_block_len) < 0) + if (is_last) { + /* + * The current subfile being processed is both the first + * subfile touched by I/O and the last subfile touched by + * I/O. In this case, we may have to deal with partial + * stripe I/O in the first and last I/O segments. + */ + if (iovec_fill_first_last(sf_context, iovec_len, iovec_depth, subfile_bytes, mem_offset, + cur_file_offset, start_length, final_length, io_buf, io_type, + _io_addrs_ptr, _io_sizes_ptr, _io_bufs_ptr) < 0) H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't fill I/O vectors"); } - else { /* First ONLY */ - if (iovec_fill_first(sf_context, iovec_depth, subfile_bytes, mem_offset, curr_file_offset, - start_length, _mem_buf_offset, _target_file_offset, - _io_block_len) < 0) + else { + /* + * The current subfile being processed is the first + * subfile touched by I/O. In this case, we may have + * to deal with partial stripe I/O in the first I/O + * segment. + */ + if (iovec_fill_first(sf_context, iovec_len, iovec_depth, subfile_bytes, mem_offset, + cur_file_offset, start_length, io_buf, io_type, _io_addrs_ptr, + _io_sizes_ptr, _io_bufs_ptr) < 0) H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't fill I/O vectors"); } /* Move the memory pointer to the starting location @@ -2959,31 +3263,43 @@ init_indep_io(subfiling_context_t *sf_context, int64_t file_offset, size_t io_ne */ mem_offset += start_length; } - else if (is_last) { /* Last ONLY */ - if (iovec_fill_last(sf_context, iovec_depth, subfile_bytes, mem_offset, curr_file_offset, - final_length, _mem_buf_offset, _target_file_offset, _io_block_len) < 0) + else if (is_last) { + /* + * The current subfile being processed is the last subfile + * touched by I/O. In this case, we may have to deal with + * partial stripe I/O in the last I/O segment. + */ + if (iovec_fill_last(sf_context, iovec_len, iovec_depth, subfile_bytes, mem_offset, + cur_file_offset, final_length, io_buf, io_type, _io_addrs_ptr, + _io_sizes_ptr, _io_bufs_ptr) < 0) H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't fill I/O vectors"); mem_offset += stripe_size; } - else { /* Everything else (uniform) */ - if (iovec_fill_uniform(sf_context, iovec_depth, subfile_bytes, mem_offset, curr_file_offset, - _mem_buf_offset, _target_file_offset, _io_block_len) < 0) + else { + /* + * The current subfile being processed is neither the first + * nor the last subfile touched by I/O. In this case, no + * partial stripe I/O will need to be dealt with; all I/O + * segments will cover a full I/O stripe. + */ + if (iovec_fill_uniform(sf_context, iovec_len, iovec_depth, subfile_bytes, mem_offset, + cur_file_offset, io_buf, io_type, _io_addrs_ptr, _io_sizes_ptr, + _io_bufs_ptr) < 0) H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "can't fill I/O vectors"); mem_offset += stripe_size; } } - offset_in_block += _io_block_len[0]; + offset_in_block += (int64_t)*_io_sizes_ptr; - k++; - curr_stripe_idx++; + subfile_idx++; + cur_stripe_idx++; - if (k == num_subfiles) { - k = 0; - offset_in_block = 0; - curr_max_iovec_depth = ((final_stripe_idx - curr_stripe_idx) / num_subfiles) + 1; + if (subfile_idx == num_subfiles) { + subfile_idx = 0; + offset_in_block = 0; row_offset += block_size; } @@ -2991,13 +3307,12 @@ init_indep_io(subfiling_context_t *sf_context, int64_t file_offset, size_t io_ne assert(offset_in_block <= block_size); } - if (total_bytes != data_size) - H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, - "total bytes (%" PRId64 ") didn't match data size (%" PRId64 ")!", - total_bytes, data_size); + if (total_bytes != io_size) + H5_SUBFILING_GOTO_ERROR(H5E_IO, H5E_CANTINIT, FAIL, "total bytes (%zu) didn't match data size (%zu)!", + total_bytes, io_size); done: - return ret_value; + H5_SUBFILING_FUNC_LEAVE; } /*------------------------------------------------------------------------- @@ -3020,9 +3335,10 @@ done: *------------------------------------------------------------------------- */ static herr_t -iovec_fill_first(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t target_datasize, - int64_t start_mem_offset, int64_t start_file_offset, int64_t first_io_len, - int64_t *mem_offset_out, int64_t *target_file_offset_out, int64_t *io_block_len_out) +iovec_fill_first(subfiling_context_t *sf_context, size_t iovec_len, int64_t cur_iovec_depth, + int64_t target_datasize, int64_t start_mem_offset, int64_t start_file_offset, + int64_t first_io_len, H5_flexible_const_ptr_t buf, H5FD_subfiling_io_type_t io_type, + haddr_t *io_addrs_ptr, size_t *io_sizes_ptr, H5_flexible_const_ptr_t *io_bufs_ptr) { int64_t stripe_size; int64_t block_size; @@ -3030,10 +3346,10 @@ iovec_fill_first(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t t herr_t ret_value = SUCCEED; assert(sf_context); - assert(mem_offset_out); - assert(target_file_offset_out); - assert(io_block_len_out); - assert(iovec_depth > 0); + assert(cur_iovec_depth > 0); + assert(io_addrs_ptr); + assert(io_sizes_ptr); + assert(io_bufs_ptr); stripe_size = sf_context->sf_stripe_size; block_size = sf_context->sf_blocksize_per_stripe; @@ -3045,16 +3361,13 @@ iovec_fill_first(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t t __func__, start_mem_offset, start_file_offset, first_io_len); #endif - mem_offset_out[0] = start_mem_offset; - target_file_offset_out[0] = start_file_offset; - io_block_len_out[0] = first_io_len; + *io_addrs_ptr = (haddr_t)start_file_offset; + *io_sizes_ptr = (size_t)first_io_len; -#ifdef H5_SUBFILING_DEBUG - H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[0] = %" PRId64 ", file_offset[0] = %" PRId64 - ", io_block_len[0] = %" PRId64, - __func__, mem_offset_out[0], target_file_offset_out[0], io_block_len_out[0]); -#endif + if (io_type == IO_TYPE_WRITE) + io_bufs_ptr->cvp = (const char *)(buf.cvp) + start_mem_offset; + else + io_bufs_ptr->vp = (char *)(buf.vp) + start_mem_offset; if (first_io_len == target_datasize) H5_SUBFILING_GOTO_DONE(SUCCEED); @@ -3066,17 +3379,20 @@ iovec_fill_first(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t t total_bytes = first_io_len; - for (int64_t i = 1; i < iovec_depth; i++) { - mem_offset_out[i] = next_mem_offset; - target_file_offset_out[i] = next_file_offset; - io_block_len_out[i] = stripe_size; + for (size_t i = 1; i < (size_t)cur_iovec_depth; i++) { + *(io_addrs_ptr + (i * iovec_len)) = (haddr_t)next_file_offset; + *(io_sizes_ptr + (i * iovec_len)) = (size_t)stripe_size; + + if (io_type == IO_TYPE_WRITE) + (io_bufs_ptr + (i * iovec_len))->cvp = (const char *)(buf.cvp) + next_mem_offset; + else + (io_bufs_ptr + (i * iovec_len))->vp = (char *)(buf.vp) + next_mem_offset; #ifdef H5_SUBFILING_DEBUG H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[%" PRId64 "] = %" PRId64 ", file_offset[%" PRId64 "] = %" PRId64 - ", io_block_len[%" PRId64 "] = %" PRId64, - __func__, i, mem_offset_out[i], i, target_file_offset_out[i], i, - io_block_len_out[i]); + "%s: mem_offset[%zu] = %" PRId64 ", file_offset[%zu] = %" PRId64 + ", io_block_len[%zu] = %" PRId64, + __func__, i, next_mem_offset, i, next_file_offset, i, stripe_size); #endif next_mem_offset += block_size; @@ -3116,9 +3432,10 @@ done: *------------------------------------------------------------------------- */ static herr_t -iovec_fill_last(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t target_datasize, - int64_t start_mem_offset, int64_t start_file_offset, int64_t last_io_len, - int64_t *mem_offset_out, int64_t *target_file_offset_out, int64_t *io_block_len_out) +iovec_fill_last(subfiling_context_t *sf_context, size_t iovec_len, int64_t cur_iovec_depth, + int64_t target_datasize, int64_t start_mem_offset, int64_t start_file_offset, + int64_t last_io_len, H5_flexible_const_ptr_t buf, H5FD_subfiling_io_type_t io_type, + haddr_t *io_addrs_ptr, size_t *io_sizes_ptr, H5_flexible_const_ptr_t *io_bufs_ptr) { int64_t stripe_size; int64_t block_size; @@ -3126,10 +3443,10 @@ iovec_fill_last(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t ta herr_t ret_value = SUCCEED; assert(sf_context); - assert(mem_offset_out); - assert(target_file_offset_out); - assert(io_block_len_out); - assert(iovec_depth > 0); + assert(cur_iovec_depth > 0); + assert(io_addrs_ptr); + assert(io_sizes_ptr); + assert(io_bufs_ptr); stripe_size = sf_context->sf_stripe_size; block_size = sf_context->sf_blocksize_per_stripe; @@ -3141,52 +3458,45 @@ iovec_fill_last(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t ta __func__, start_mem_offset, start_file_offset, last_io_len); #endif - mem_offset_out[0] = start_mem_offset; - target_file_offset_out[0] = start_file_offset; - io_block_len_out[0] = last_io_len; + *io_addrs_ptr = (haddr_t)start_file_offset; + *io_sizes_ptr = (size_t)last_io_len; - if (last_io_len == target_datasize) { -#ifdef H5_SUBFILING_DEBUG - H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[0] = %" PRId64 ", file_offset[0] = %" PRId64 - ", io_block_len[0] = %" PRId64, - __func__, mem_offset_out[0], target_file_offset_out[0], io_block_len_out[0]); -#endif + if (io_type == IO_TYPE_WRITE) + io_bufs_ptr->cvp = (const char *)(buf.cvp) + start_mem_offset; + else + io_bufs_ptr->vp = (char *)(buf.vp) + start_mem_offset; + if (last_io_len == target_datasize) H5_SUBFILING_GOTO_DONE(SUCCEED); - } - else { + + { int64_t next_mem_offset = start_mem_offset + block_size; int64_t next_file_offset = start_file_offset + block_size; - int64_t i; + size_t i; /* * If the last I/O size doesn't cover the target data * size, there is at least one full stripe preceding * the last I/O block */ - io_block_len_out[0] = stripe_size; - -#ifdef H5_SUBFILING_DEBUG - H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[0] = %" PRId64 ", file_offset[0] = %" PRId64 - ", io_block_len[0] = %" PRId64, - __func__, mem_offset_out[0], target_file_offset_out[0], io_block_len_out[0]); -#endif + *io_sizes_ptr = (size_t)stripe_size; total_bytes = stripe_size; - for (i = 1; i < iovec_depth - 1;) { - mem_offset_out[i] = next_mem_offset; - target_file_offset_out[i] = next_file_offset; - io_block_len_out[i] = stripe_size; + for (i = 1; i < (size_t)cur_iovec_depth - 1;) { + *(io_addrs_ptr + (i * iovec_len)) = (haddr_t)next_file_offset; + *(io_sizes_ptr + (i * iovec_len)) = (size_t)stripe_size; + + if (io_type == IO_TYPE_WRITE) + (io_bufs_ptr + (i * iovec_len))->cvp = (const char *)(buf.cvp) + next_mem_offset; + else + (io_bufs_ptr + (i * iovec_len))->vp = (char *)(buf.vp) + next_mem_offset; #ifdef H5_SUBFILING_DEBUG H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[%" PRId64 "] = %" PRId64 ", file_offset[%" PRId64 "] = %" PRId64 - ", io_block_len[%" PRId64 "] = %" PRId64, - __func__, i, mem_offset_out[i], i, target_file_offset_out[i], i, - io_block_len_out[i]); + "%s: mem_offset[%zu] = %" PRId64 ", file_offset[%zu] = %" PRId64 + ", io_block_len[%zu] = %" PRId64, + __func__, i, next_mem_offset, i, next_file_offset, i, stripe_size); #endif next_mem_offset += block_size; @@ -3196,16 +3506,19 @@ iovec_fill_last(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t ta i++; } - mem_offset_out[i] = next_mem_offset; - target_file_offset_out[i] = next_file_offset; - io_block_len_out[i] = last_io_len; + *(io_addrs_ptr + (i * iovec_len)) = (haddr_t)next_file_offset; + *(io_sizes_ptr + (i * iovec_len)) = (size_t)last_io_len; + + if (io_type == IO_TYPE_WRITE) + (io_bufs_ptr + (i * iovec_len))->cvp = (const char *)(buf.cvp) + next_mem_offset; + else + (io_bufs_ptr + (i * iovec_len))->vp = (char *)(buf.vp) + next_mem_offset; #ifdef H5_SUBFILING_DEBUG H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[%" PRId64 "] = %" PRId64 ", file_offset[%" PRId64 "] = %" PRId64 - ", io_block_len[%" PRId64 "] = %" PRId64, - __func__, i, mem_offset_out[i], i, target_file_offset_out[i], i, - io_block_len_out[i]); + "%s: mem_offset[%zu] = %" PRId64 ", file_offset[%zu] = %" PRId64 + ", io_block_len[%zu] = %" PRId64, + __func__, i, next_mem_offset, i, next_file_offset, i, last_io_len); #endif total_bytes += last_io_len; @@ -3244,10 +3557,11 @@ done: *------------------------------------------------------------------------- */ static herr_t -iovec_fill_first_last(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t target_datasize, - int64_t start_mem_offset, int64_t start_file_offset, int64_t first_io_len, - int64_t last_io_len, int64_t *mem_offset_out, int64_t *target_file_offset_out, - int64_t *io_block_len_out) +iovec_fill_first_last(subfiling_context_t *sf_context, size_t iovec_len, int64_t cur_iovec_depth, + int64_t target_datasize, int64_t start_mem_offset, int64_t start_file_offset, + int64_t first_io_len, int64_t last_io_len, H5_flexible_const_ptr_t buf, + H5FD_subfiling_io_type_t io_type, haddr_t *io_addrs_ptr, size_t *io_sizes_ptr, + H5_flexible_const_ptr_t *io_bufs_ptr) { int64_t stripe_size; int64_t block_size; @@ -3255,10 +3569,10 @@ iovec_fill_first_last(subfiling_context_t *sf_context, int64_t iovec_depth, int6 herr_t ret_value = SUCCEED; assert(sf_context); - assert(mem_offset_out); - assert(target_file_offset_out); - assert(io_block_len_out); - assert(iovec_depth > 0); + assert(cur_iovec_depth > 0); + assert(io_addrs_ptr); + assert(io_sizes_ptr); + assert(io_bufs_ptr); stripe_size = sf_context->sf_stripe_size; block_size = sf_context->sf_blocksize_per_stripe; @@ -3270,16 +3584,13 @@ iovec_fill_first_last(subfiling_context_t *sf_context, int64_t iovec_depth, int6 __func__, start_mem_offset, start_file_offset, first_io_len, last_io_len); #endif - mem_offset_out[0] = start_mem_offset; - target_file_offset_out[0] = start_file_offset; - io_block_len_out[0] = first_io_len; + *io_addrs_ptr = (haddr_t)start_file_offset; + *io_sizes_ptr = (size_t)first_io_len; -#ifdef H5_SUBFILING_DEBUG - H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[0] = %" PRId64 ", file_offset[0] = %" PRId64 - ", io_block_len[0] = %" PRId64, - __func__, mem_offset_out[0], target_file_offset_out[0], io_block_len_out[0]); -#endif + if (io_type == IO_TYPE_WRITE) + io_bufs_ptr->cvp = (const char *)(buf.cvp) + start_mem_offset; + else + io_bufs_ptr->vp = (char *)(buf.vp) + start_mem_offset; if (first_io_len == target_datasize) H5_SUBFILING_GOTO_DONE(SUCCEED); @@ -3288,21 +3599,24 @@ iovec_fill_first_last(subfiling_context_t *sf_context, int64_t iovec_depth, int6 int64_t offset_in_stripe = start_file_offset % stripe_size; int64_t next_mem_offset = block_size - offset_in_stripe; int64_t next_file_offset = start_file_offset + (block_size - offset_in_stripe); - int64_t i; + size_t i; total_bytes = first_io_len; - for (i = 1; i < iovec_depth - 1;) { - mem_offset_out[i] = next_mem_offset; - target_file_offset_out[i] = next_file_offset; - io_block_len_out[i] = stripe_size; + for (i = 1; i < (size_t)cur_iovec_depth - 1;) { + *(io_addrs_ptr + (i * iovec_len)) = (haddr_t)next_file_offset; + *(io_sizes_ptr + (i * iovec_len)) = (size_t)stripe_size; + + if (io_type == IO_TYPE_WRITE) + (io_bufs_ptr + (i * iovec_len))->cvp = (const char *)(buf.cvp) + next_mem_offset; + else + (io_bufs_ptr + (i * iovec_len))->vp = (char *)(buf.vp) + next_mem_offset; #ifdef H5_SUBFILING_DEBUG H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[%" PRId64 "] = %" PRId64 ", file_offset[%" PRId64 "] = %" PRId64 - ", io_block_len[%" PRId64 "] = %" PRId64, - __func__, i, mem_offset_out[i], i, target_file_offset_out[i], i, - io_block_len_out[i]); + "%s: mem_offset[%zu] = %" PRId64 ", file_offset[%zu] = %" PRId64 + ", io_block_len[%zu] = %" PRId64, + __func__, i, next_mem_offset, i, next_file_offset, i, stripe_size); #endif next_mem_offset += block_size; @@ -3312,16 +3626,19 @@ iovec_fill_first_last(subfiling_context_t *sf_context, int64_t iovec_depth, int6 i++; } - mem_offset_out[i] = next_mem_offset; - target_file_offset_out[i] = next_file_offset; - io_block_len_out[i] = last_io_len; + *(io_addrs_ptr + (i * iovec_len)) = (haddr_t)next_file_offset; + *(io_sizes_ptr + (i * iovec_len)) = (size_t)last_io_len; + + if (io_type == IO_TYPE_WRITE) + (io_bufs_ptr + (i * iovec_len))->cvp = (const char *)(buf.cvp) + next_mem_offset; + else + (io_bufs_ptr + (i * iovec_len))->vp = (char *)(buf.vp) + next_mem_offset; #ifdef H5_SUBFILING_DEBUG H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[%" PRId64 "] = %" PRId64 ", file_offset[%" PRId64 "] = %" PRId64 - ", io_block_len[%" PRId64 "] = %" PRId64, - __func__, i, mem_offset_out[i], i, target_file_offset_out[i], i, - io_block_len_out[i]); + "%s: mem_offset[%zu] = %" PRId64 ", file_offset[%zu] = %" PRId64 + ", io_block_len[%zu] = %" PRId64, + __func__, i, next_mem_offset, i, next_file_offset, i, last_io_len); #endif total_bytes += last_io_len; @@ -3352,9 +3669,10 @@ done: *------------------------------------------------------------------------- */ static herr_t -iovec_fill_uniform(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t target_datasize, - int64_t start_mem_offset, int64_t start_file_offset, int64_t *mem_offset_out, - int64_t *target_file_offset_out, int64_t *io_block_len_out) +iovec_fill_uniform(subfiling_context_t *sf_context, size_t iovec_len, int64_t cur_iovec_depth, + int64_t target_datasize, int64_t start_mem_offset, int64_t start_file_offset, + H5_flexible_const_ptr_t buf, H5FD_subfiling_io_type_t io_type, haddr_t *io_addrs_ptr, + size_t *io_sizes_ptr, H5_flexible_const_ptr_t *io_bufs_ptr) { int64_t stripe_size; int64_t block_size; @@ -3362,10 +3680,10 @@ iovec_fill_uniform(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t herr_t ret_value = SUCCEED; assert(sf_context); - assert(mem_offset_out); - assert(target_file_offset_out); - assert(io_block_len_out); - assert((iovec_depth > 0) || (target_datasize == 0)); + assert((cur_iovec_depth > 0) || (target_datasize == 0)); + assert(io_addrs_ptr); + assert(io_sizes_ptr); + assert(io_bufs_ptr); stripe_size = sf_context->sf_stripe_size; block_size = sf_context->sf_blocksize_per_stripe; @@ -3377,23 +3695,20 @@ iovec_fill_uniform(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t __func__, start_mem_offset, start_file_offset, stripe_size); #endif - mem_offset_out[0] = start_mem_offset; - target_file_offset_out[0] = start_file_offset; - io_block_len_out[0] = stripe_size; + *io_addrs_ptr = (haddr_t)start_file_offset; + *io_sizes_ptr = (size_t)stripe_size; -#ifdef H5_SUBFILING_DEBUG - H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[0] = %" PRId64 ", file_offset[0] = %" PRId64 - ", io_block_len[0] = %" PRId64, - __func__, mem_offset_out[0], target_file_offset_out[0], io_block_len_out[0]); -#endif + if (io_type == IO_TYPE_WRITE) + io_bufs_ptr->cvp = (const char *)(buf.cvp) + start_mem_offset; + else + io_bufs_ptr->vp = (char *)(buf.vp) + start_mem_offset; if (target_datasize == 0) { #ifdef H5_SUBFILING_DEBUG H5_subfiling_log(sf_context->sf_context_id, "%s: target_datasize = 0", __func__); #endif - io_block_len_out[0] = 0; + *io_sizes_ptr = (size_t)0; H5_SUBFILING_GOTO_DONE(SUCCEED); } @@ -3403,17 +3718,20 @@ iovec_fill_uniform(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t total_bytes = stripe_size; - for (int64_t i = 1; i < iovec_depth; i++) { - mem_offset_out[i] = next_mem_offset; - target_file_offset_out[i] = next_file_offset; - io_block_len_out[i] = stripe_size; + for (size_t i = 1; i < (size_t)cur_iovec_depth; i++) { + *(io_addrs_ptr + (i * iovec_len)) = (haddr_t)next_file_offset; + *(io_sizes_ptr + (i * iovec_len)) = (size_t)stripe_size; + + if (io_type == IO_TYPE_WRITE) + (io_bufs_ptr + (i * iovec_len))->cvp = (const char *)(buf.cvp) + next_mem_offset; + else + (io_bufs_ptr + (i * iovec_len))->vp = (char *)(buf.vp) + next_mem_offset; #ifdef H5_SUBFILING_DEBUG H5_subfiling_log(sf_context->sf_context_id, - "%s: mem_offset[%" PRId64 "] = %" PRId64 ", file_offset[%" PRId64 "] = %" PRId64 - ", io_block_len[%" PRId64 "] = %" PRId64, - __func__, i, mem_offset_out[i], i, target_file_offset_out[i], i, - io_block_len_out[i]); + "%s: mem_offset[%zu] = %" PRId64 ", file_offset[%zu] = %" PRId64 + ", io_block_len[%zu] = %" PRId64, + __func__, i, next_mem_offset, i, next_file_offset, i, stripe_size); #endif next_mem_offset += block_size; @@ -3430,3 +3748,38 @@ iovec_fill_uniform(subfiling_context_t *sf_context, int64_t iovec_depth, int64_t done: return ret_value; } + +#ifdef H5_SUBFILING_DEBUG +void +H5_subfiling_dump_iovecs(subfiling_context_t *sf_context, size_t ioreq_count, size_t iovec_len, + H5FD_subfiling_io_type_t io_type, H5FD_mem_t *io_types, haddr_t *io_addrs, + size_t *io_sizes, H5_flexible_const_ptr_t *io_bufs) +{ + assert(sf_context); + assert(io_types); + assert(io_addrs); + assert(io_sizes); + assert(io_bufs); + + H5_subfiling_log(sf_context->sf_context_id, + "%s: I/O REQUEST VECTORS (mem type, addr, size, buf):", __func__); + + for (size_t ioreq_idx = 0; ioreq_idx < ioreq_count; ioreq_idx++) { + H5_subfiling_log_nonewline(sf_context->sf_context_id, " -> I/O REQUEST %zu: ", ioreq_idx); + + H5_subfiling_log_nonewline(sf_context->sf_context_id, "["); + for (size_t i = 0; i < iovec_len; i++) { + if (i > 0) + H5_subfiling_log_nonewline(sf_context->sf_context_id, ", "); + + H5_subfiling_log_nonewline( + sf_context->sf_context_id, "(%d, %" PRIuHADDR ", %zu, %p)", + *(io_types + (ioreq_idx * iovec_len) + i), *(io_addrs + (ioreq_idx * iovec_len) + i), + *(io_sizes + (ioreq_idx * iovec_len) + i), + (io_type == IO_TYPE_WRITE) ? (const void *)(io_bufs + (ioreq_idx * iovec_len) + i)->cvp + : (void *)(io_bufs + (ioreq_idx * iovec_len) + i)->vp); + } + H5_subfiling_log_nonewline(sf_context->sf_context_id, "]\n"); + } +} +#endif diff --git a/src/H5FDsubfiling/H5subfiling_common.c b/src/H5FDsubfiling/H5subfiling_common.c index f9cc0dc..1127ae0 100644 --- a/src/H5FDsubfiling/H5subfiling_common.c +++ b/src/H5FDsubfiling/H5subfiling_common.c @@ -3156,4 +3156,37 @@ done: return; } + +void +H5_subfiling_log_nonewline(int64_t sf_context_id, const char *fmt, ...) +{ + subfiling_context_t *sf_context = NULL; + va_list log_args; + + va_start(log_args, fmt); + + /* Retrieve the subfiling object for the newly-created context ID */ + if (NULL == (sf_context = H5_get_subfiling_object(sf_context_id))) { + printf("%s: couldn't get subfiling object from context ID\n", __func__); + goto done; + } + + H5FD_ioc_begin_thread_exclusive(); + + if (sf_context->sf_logfile) { + vfprintf(sf_context->sf_logfile, fmt, log_args); + fflush(sf_context->sf_logfile); + } + else { + vprintf(fmt, log_args); + fflush(stdout); + } + + H5FD_ioc_end_thread_exclusive(); + +done: + va_end(log_args); + + return; +} #endif diff --git a/src/H5FDsubfiling/H5subfiling_common.h b/src/H5FDsubfiling/H5subfiling_common.h index 395183a..156902a 100644 --- a/src/H5FDsubfiling/H5subfiling_common.h +++ b/src/H5FDsubfiling/H5subfiling_common.h @@ -284,7 +284,10 @@ H5_DLL herr_t H5_subfiling_validate_config(const H5FD_subfiling_params_t *subf_c H5_DLL herr_t H5_subfiling_terminate(void); +#ifdef H5_SUBFILING_DEBUG H5_DLL void H5_subfiling_log(int64_t sf_context_id, const char *fmt, ...); +H5_DLL void H5_subfiling_log_nonewline(int64_t sf_context_id, const char *fmt, ...); +#endif #ifdef __cplusplus } diff --git a/testpar/t_subfiling_vfd.c b/testpar/t_subfiling_vfd.c index 45cb363..4f109cb 100644 --- a/testpar/t_subfiling_vfd.c +++ b/testpar/t_subfiling_vfd.c @@ -40,7 +40,7 @@ #define PATH_MAX 4096 #endif -#define DEFAULT_DEFLATE_LEVEL 9 +#define DEFAULT_DEFLATE_LEVEL 4 #define ARRAY_SIZE(a) sizeof(a) / sizeof(a[0]) @@ -99,6 +99,7 @@ static void test_create_and_close(void); static void test_ioc_only_fail(void); static void test_config_file(void); static void test_stripe_sizes(void); +static void test_iovec_translation(void); static void test_selection_strategies(void); static void test_read_different_stripe_size(void); static void test_subfiling_precreate_rank_0(void); @@ -111,6 +112,7 @@ static test_func tests[] = { test_ioc_only_fail, test_config_file, test_stripe_sizes, + test_iovec_translation, test_selection_strategies, test_read_different_stripe_size, test_subfiling_precreate_rank_0, @@ -888,6 +890,697 @@ test_stripe_sizes(void) #undef SUBF_NITER /* + * Test the I/O vector translation code by writing with some + * different specific I/O patterns + */ +#define SUBF_FILENAME "test_subfiling_iovec_translation.h5" +static void +test_iovec_translation(void) +{ + H5FD_subfiling_params_t cfg; + const void *c_write_buf; + h5_stat_t file_info; + int64_t stripe_size; + haddr_t write_addr; + size_t nbytes; + size_t buf_size; + herr_t status; + hid_t file_id; + H5FD_t *file_ptr = NULL; + FILE *subfile_ptr = NULL; + void *write_buf = NULL; + void *read_buf = NULL; + char *tmp_filename = NULL; + hid_t dxpl_id = H5I_INVALID_HID; + hid_t fapl_id = H5I_INVALID_HID; + bool skip = false; + int num_subfiles; + int num_digits; + + curr_nerrors = nerrors; + + if (MAINPROCESS) + TESTING_2("I/O vector translation"); + + /* + * Don't run this test if subfiling configuration + * environment variables have been set since we + * want to use fixed configurations for testing. + */ + if (getenv(H5FD_SUBFILING_STRIPE_SIZE) || getenv(H5FD_SUBFILING_IOC_PER_NODE)) + skip = true; + + /* I/O only needs to be done from a single rank */ + if (MAINPROCESS && !skip) { + + /* Use a fixed configuration for these tests */ + stripe_size = 1048576; + num_subfiles = 4; + num_digits = (int)(log10(num_subfiles) + 1); + + /* Allocate enough buffer space for up to 2 "subfile blocks" of I/O */ + buf_size = (size_t)(2 * stripe_size * num_subfiles); + write_buf = malloc(buf_size); + VRFY(write_buf, "malloc succeeded"); + read_buf = malloc(buf_size); + VRFY(read_buf, "malloc succeeded"); + + c_write_buf = write_buf; + + tmp_filename = malloc(PATH_MAX); + VRFY(tmp_filename, "malloc succeeded"); + + dxpl_id = H5Pcreate(H5P_DATASET_XFER); + VRFY((dxpl_id >= 0), "DXPL creation succeeded"); + + /* Set selection I/O mode on DXPL */ + VRFY((H5Pset_selection_io(dxpl_id, H5D_SELECTION_IO_MODE_ON) >= 0), "H5Pset_selection_io succeeded"); + + cfg.ioc_selection = SELECT_IOC_ONE_PER_NODE; + cfg.stripe_size = stripe_size; + cfg.stripe_count = 4; + + fapl_id = create_subfiling_ioc_fapl(MPI_COMM_SELF, MPI_INFO_NULL, true, &cfg, + H5FD_IOC_DEFAULT_THREAD_POOL_SIZE); + VRFY((fapl_id >= 0), "FAPL creation succeeded"); + + /* Set independent I/O on DXPL */ + VRFY((H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_INDEPENDENT) >= 0), "H5Pset_dxpl_mpio succeeded"); + + /* + * Test the case where the index value of the last subfile + * touched by I/O is greater than or equal to the index + * value of the first subfile touched by I/O, and this results + * in "thin" I/O segments directed to the subfiles with index + * values greater than the index values of the first and + * last subfiles. This might appear as the following I/O + * pattern: + * + * SUBFILE 0 SUBFILE 1 SUBFILE 2 SUBFILE 3 + * _______________________________________________ + * | XXXXX | XXXXX | XXXXX | XXXXX | ROW 0 + * | XXXXX | XXXXX | | | ROW 1 + * | | | | | ROW 2 + * | | | | | ROW ... + * | | | | | + * | | | | | + * | | | | | + * |___________|___________|___________|___________| + */ + + /* Create/truncate the file */ + file_id = H5Fcreate(SUBF_FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); + VRFY((file_id >= 0), "H5Fcreate succeeded"); + VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded"); + + /* Retrieve file info to get the file inode for later use */ + VRFY((HDstat(SUBF_FILENAME, &file_info) >= 0), "HDstat succeeded"); + + /* Re-open file through H5FDopen for direct writes */ + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + nbytes = (size_t)(6 * stripe_size); + memset(write_buf, 255, nbytes); + memset(read_buf, 0, buf_size); + + write_addr = 0; + + /* Set EOA for following write call */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Write according to the above pattern */ + status = H5FDwrite(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, c_write_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + /* Close and re-open the file */ + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + /* + * Set EOA for following read call (since we wrote over any + * superblock information in the file) + */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Read the written bytes and verify */ + status = H5FDread(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, read_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + VRFY((0 == memcmp(write_buf, read_buf, nbytes)), "memcmp succeeded"); + + /* Verify the size of each subfile */ + for (int i = 0; i < num_subfiles; i++) { + h5_stat_size_t subfile_size; + h5_stat_t subfile_info; + + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, i + 1, num_subfiles); + + /* Ensure file exists */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr, "fopen on subfile succeeded"); + VRFY((fclose(subfile_ptr) >= 0), "fclose on subfile succeeded"); + + /* Check file size */ + VRFY((HDstat(tmp_filename, &subfile_info) >= 0), "HDstat succeeded"); + subfile_size = (h5_stat_size_t)subfile_info.st_size; + + if (i <= 1) { + /* + * Subfiles with index values <= 1 should have full + * I/O segments (2 * stripe size) written to them. + */ + VRFY((subfile_size == 2 * cfg.stripe_size), "File size verification succeeded"); + } + else { + /* + * Subfiles with index values > 1 should have "thin" + * I/O segments (1 * stripe size) written to them. + */ + VRFY((subfile_size == cfg.stripe_size), "File size verification succeeded"); + } + } + + /* Verify that there aren't too many subfiles */ + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, num_subfiles + 1, num_subfiles); + + /* Ensure file doesn't exist */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr == NULL, "fopen on subfile correctly failed"); + + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + + /* + * Test the case where the index value of the last subfile + * touched by I/O is greater than or equal to the index + * value of the first subfile touched by I/O, and this results + * in "thin" I/O segments directed to the subfiles with index + * values less than the index values of the first and + * last subfiles. This might appear as the following I/O + * pattern: + * + * SUBFILE 0 SUBFILE 1 SUBFILE 2 SUBFILE 3 + * _______________________________________________ + * | | XXXXX | XXXXX | XXXXX | ROW 0 + * | XXXXX | XXXXX | XXXXX | XXXXX | ROW 1 + * | | | | | ROW 2 + * | | | | | ROW ... + * | | | | | + * | | | | | + * | | | | | + * |___________|___________|___________|___________| + */ + + /* Create/truncate the file */ + file_id = H5Fcreate(SUBF_FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); + VRFY((file_id >= 0), "H5Fcreate succeeded"); + VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded"); + + /* Retrieve file info to get the file inode for later use */ + VRFY((HDstat(SUBF_FILENAME, &file_info) >= 0), "HDstat succeeded"); + + /* Re-open file through H5FDopen for direct writes */ + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + nbytes = (size_t)(7 * stripe_size); + memset(write_buf, 255, nbytes); + memset(read_buf, 0, buf_size); + + write_addr = (haddr_t)stripe_size; + + /* Set EOA for following write call */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Write according to the above pattern */ + status = H5FDwrite(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, c_write_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + /* Close and re-open the file */ + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + /* + * Set EOA for following read call (since we wrote over any + * superblock information in the file) + */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Read the written bytes and verify */ + status = H5FDread(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, read_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + VRFY((0 == memcmp(write_buf, read_buf, nbytes)), "memcmp succeeded"); + + /* Verify the size of each subfile */ + for (int i = 0; i < num_subfiles; i++) { + h5_stat_size_t subfile_size; + h5_stat_t subfile_info; + + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, i + 1, num_subfiles); + + /* Ensure file exists */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr, "fopen on subfile succeeded"); + VRFY((fclose(subfile_ptr) >= 0), "fclose on subfile succeeded"); + + /* Check file size */ + VRFY((HDstat(tmp_filename, &subfile_info) >= 0), "HDstat succeeded"); + subfile_size = (h5_stat_size_t)subfile_info.st_size; + + /* + * Every subfile should be (2 * stripe size) bytes due to + * space allocated in the file for subfile index 0 + */ + VRFY((subfile_size == 2 * cfg.stripe_size), "File size verification succeeded"); + } + + /* Verify that there aren't too many subfiles */ + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, num_subfiles + 1, num_subfiles); + + /* Ensure file doesn't exist */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr == NULL, "fopen on subfile correctly failed"); + + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + + /* + * Test the case where the index value of the last subfile + * touched by I/O is less than the index value of the first + * subfile touched by I/O, and this results in "thin" I/O + * segments directed to the subfiles with index values that + * fall between the values of the first and last subfiles. + * This might appear as the following I/O pattern: + * + * SUBFILE 0 SUBFILE 1 SUBFILE 2 SUBFILE 3 + * _______________________________________________ + * | | | XXXXX | XXXXX | ROW 0 + * | XXXXX | XXXXX | XXXXX | XXXXX | ROW 1 + * | XXXXX | | | | ROW 2 + * | | | | | ROW ... + * | | | | | + * | | | | | + * | | | | | + * |___________|___________|___________|___________| + */ + + /* Create/truncate the file */ + file_id = H5Fcreate(SUBF_FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); + VRFY((file_id >= 0), "H5Fcreate succeeded"); + VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded"); + + /* Retrieve file info to get the file inode for later use */ + VRFY((HDstat(SUBF_FILENAME, &file_info) >= 0), "HDstat succeeded"); + + /* Re-open file through H5FDopen for direct writes */ + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + nbytes = (size_t)(7 * stripe_size); + memset(write_buf, 255, nbytes); + memset(read_buf, 0, buf_size); + + write_addr = (haddr_t)(2 * stripe_size); + + /* Set EOA for following write call */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Write according to the above pattern */ + status = H5FDwrite(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, c_write_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + /* Close and re-open the file */ + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + /* + * Set EOA for following read call (since we wrote over any + * superblock information in the file) + */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Read the written bytes and verify */ + status = H5FDread(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, read_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + VRFY((0 == memcmp(write_buf, read_buf, nbytes)), "memcmp succeeded"); + + /* Verify the size of each subfile */ + for (int i = 0; i < num_subfiles; i++) { + h5_stat_size_t subfile_size; + h5_stat_t subfile_info; + + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, i + 1, num_subfiles); + + /* Ensure file exists */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr, "fopen on subfile succeeded"); + VRFY((fclose(subfile_ptr) >= 0), "fclose on subfile succeeded"); + + /* Check file size */ + VRFY((HDstat(tmp_filename, &subfile_info) >= 0), "HDstat succeeded"); + subfile_size = (h5_stat_size_t)subfile_info.st_size; + + /* + * Subfile index 0 should be (3 * stripe size) bytes due to + * space allocated in the file, while others should be + * (2 * stripe size) bytes. + */ + if (i == 0) { + VRFY((subfile_size == 3 * cfg.stripe_size), "File size verification succeeded"); + } + else { + VRFY((subfile_size == 2 * cfg.stripe_size), "File size verification succeeded"); + } + } + + /* Verify that there aren't too many subfiles */ + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, num_subfiles + 1, num_subfiles); + + /* Ensure file doesn't exist */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr == NULL, "fopen on subfile correctly failed"); + + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + + /* + * Test the case where I/O is 2 stripe sizes in total, but + * is offset from a stripe boundary by a single byte, causing + * the I/O to cross 3 subfiles. + */ + + /* Create/truncate the file */ + file_id = H5Fcreate(SUBF_FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); + VRFY((file_id >= 0), "H5Fcreate succeeded"); + VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded"); + + /* Retrieve file info to get the file inode for later use */ + VRFY((HDstat(SUBF_FILENAME, &file_info) >= 0), "HDstat succeeded"); + + /* Re-open file through H5FDopen for direct writes */ + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + nbytes = (size_t)(2 * stripe_size); + memset(write_buf, 255, nbytes); + memset(read_buf, 0, buf_size); + + write_addr = (haddr_t)1; + + /* Set EOA for following write call */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Write according to the above pattern */ + status = H5FDwrite(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, c_write_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + /* Close and re-open the file */ + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + /* + * Set EOA for following read call (since we wrote over any + * superblock information in the file) + */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Read the written bytes and verify */ + status = H5FDread(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, read_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + VRFY((0 == memcmp(write_buf, read_buf, nbytes)), "memcmp succeeded"); + + /* Verify the size of each subfile */ + for (int i = 0; i < num_subfiles; i++) { + h5_stat_size_t subfile_size; + h5_stat_t subfile_info; + + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, i + 1, num_subfiles); + + /* Ensure file exists */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr, "fopen on subfile succeeded"); + VRFY((fclose(subfile_ptr) >= 0), "fclose on subfile succeeded"); + + /* Check file size */ + VRFY((HDstat(tmp_filename, &subfile_info) >= 0), "HDstat succeeded"); + subfile_size = (h5_stat_size_t)subfile_info.st_size; + + /* + * Subfiles indexed 0 and 1 should both be (1 * stripe size) + * bytes (Subfile index 0 was written to with an offset of 1 + * byte, but that space will still be allocated in the file). + * Subfile index 2 should have a single byte written to it and + * Subfile index 3 should have nothing written to it. + */ + if (i == 2) { + VRFY((subfile_size == 1), "File size verification succeeded"); + } + else if (i == 3) { + VRFY((subfile_size == 0), "File size verification succeeded"); + } + else { + VRFY((subfile_size == cfg.stripe_size), "File size verification succeeded"); + } + } + + /* Verify that there aren't too many subfiles */ + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, num_subfiles + 1, num_subfiles); + + /* Ensure file doesn't exist */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr == NULL, "fopen on subfile correctly failed"); + + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + + /* + * Test the case where I/O is 2 stripe sizes in total, but + * is offset from a stripe boundary by (stripe size - 1) bytes, + * causing the I/O to start at the last byte of a subfile and + * cross 3 subfiles. + */ + + /* Create/truncate the file */ + file_id = H5Fcreate(SUBF_FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); + VRFY((file_id >= 0), "H5Fcreate succeeded"); + VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded"); + + /* Retrieve file info to get the file inode for later use */ + VRFY((HDstat(SUBF_FILENAME, &file_info) >= 0), "HDstat succeeded"); + + /* Re-open file through H5FDopen for direct writes */ + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + nbytes = (size_t)(2 * stripe_size); + memset(write_buf, 255, nbytes); + memset(read_buf, 0, buf_size); + + write_addr = (haddr_t)(stripe_size - 1); + + /* Set EOA for following write call */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Write according to the above pattern */ + status = H5FDwrite(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, c_write_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + /* Close and re-open the file */ + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + /* + * Set EOA for following read call (since we wrote over any + * superblock information in the file) + */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Read the written bytes and verify */ + status = H5FDread(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, read_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + VRFY((0 == memcmp(write_buf, read_buf, nbytes)), "memcmp succeeded"); + + /* Verify the size of each subfile */ + for (int i = 0; i < num_subfiles; i++) { + h5_stat_size_t subfile_size; + h5_stat_t subfile_info; + + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, i + 1, num_subfiles); + + /* Ensure file exists */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr, "fopen on subfile succeeded"); + VRFY((fclose(subfile_ptr) >= 0), "fclose on subfile succeeded"); + + /* Check file size */ + VRFY((HDstat(tmp_filename, &subfile_info) >= 0), "HDstat succeeded"); + subfile_size = (h5_stat_size_t)subfile_info.st_size; + + /* + * Subfiles indexed 0 and 1 should both be (1 * stripe size) + * bytes (Subfile index 0 was written to with an offset of + * stripe size - 1 bytes, but that space will still be allocated + * in the file). Subfile index 2 should be (1 * stripe size) - 1 + * bytes. Subfile index 3 should have nothing written to it. + */ + if (i == 2) { + VRFY((subfile_size == cfg.stripe_size - 1), "File size verification succeeded"); + } + else if (i == 3) { + VRFY((subfile_size == 0), "File size verification succeeded"); + } + else { + VRFY((subfile_size == cfg.stripe_size), "File size verification succeeded"); + } + } + + /* Verify that there aren't too many subfiles */ + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, num_subfiles + 1, num_subfiles); + + /* Ensure file doesn't exist */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr == NULL, "fopen on subfile correctly failed"); + + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + + /* + * Test the case where I/O is 2 stripe sizes + 1 byte in total + * and starts aligned to a stripe boundary, causing the I/O + * to cross 3 subfiles. + */ + + /* Create/truncate the file */ + file_id = H5Fcreate(SUBF_FILENAME, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); + VRFY((file_id >= 0), "H5Fcreate succeeded"); + VRFY((H5Fclose(file_id) >= 0), "H5Fclose succeeded"); + + /* Retrieve file info to get the file inode for later use */ + VRFY((HDstat(SUBF_FILENAME, &file_info) >= 0), "HDstat succeeded"); + + /* Re-open file through H5FDopen for direct writes */ + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + nbytes = (size_t)((2 * stripe_size) + 1); + memset(write_buf, 255, nbytes); + memset(read_buf, 0, buf_size); + + write_addr = (haddr_t)0; + + /* Set EOA for following write call */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Write according to the above pattern */ + status = H5FDwrite(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, c_write_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + /* Close and re-open the file */ + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + file_ptr = H5FDopen(SUBF_FILENAME, H5F_ACC_RDWR, fapl_id, HADDR_UNDEF); + VRFY(file_ptr, "H5FDopen succeeded"); + + /* + * Set EOA for following read call (since we wrote over any + * superblock information in the file) + */ + VRFY((H5FDset_eoa(file_ptr, H5FD_MEM_DEFAULT, write_addr + nbytes) >= 0), "H5FDset_eoa succeeded"); + + /* Read the written bytes and verify */ + status = H5FDread(file_ptr, H5FD_MEM_DRAW, dxpl_id, write_addr, nbytes, read_buf); + VRFY((status >= 0), "H5FDwrite succeeded"); + + VRFY((0 == memcmp(write_buf, read_buf, nbytes)), "memcmp succeeded"); + + /* Verify the size of each subfile */ + for (int i = 0; i < num_subfiles; i++) { + h5_stat_size_t subfile_size; + h5_stat_t subfile_info; + + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, i + 1, num_subfiles); + + /* Ensure file exists */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr, "fopen on subfile succeeded"); + VRFY((fclose(subfile_ptr) >= 0), "fclose on subfile succeeded"); + + /* Check file size */ + VRFY((HDstat(tmp_filename, &subfile_info) >= 0), "HDstat succeeded"); + subfile_size = (h5_stat_size_t)subfile_info.st_size; + + /* + * Subfiles indexed 0 and 1 should both be (1 * stripe size) + * bytes. Subfile index 2 should have a single byte written to + * it and Subfile index 3 should have nothing written to it. + */ + if (i == 2) { + VRFY((subfile_size == 1), "File size verification succeeded"); + } + else if (i == 3) { + VRFY((subfile_size == 0), "File size verification succeeded"); + } + else { + VRFY((subfile_size == cfg.stripe_size), "File size verification succeeded"); + } + } + + /* Verify that there aren't too many subfiles */ + snprintf(tmp_filename, PATH_MAX, H5FD_SUBFILING_FILENAME_TEMPLATE, SUBF_FILENAME, + (uint64_t)file_info.st_ino, num_digits, num_subfiles + 1, num_subfiles); + + /* Ensure file doesn't exist */ + subfile_ptr = fopen(tmp_filename, "r"); + VRFY(subfile_ptr == NULL, "fopen on subfile correctly failed"); + + VRFY((H5FDclose(file_ptr) >= 0), "H5FDclose succeeded"); + + free(write_buf); + write_buf = NULL; + free(read_buf); + write_buf = NULL; + + free(tmp_filename); + + VRFY((H5Pclose(dxpl_id) >= 0), "DXPL close succeeded"); + + H5E_BEGIN_TRY + { + H5Fdelete(SUBF_FILENAME, fapl_id); + } + H5E_END_TRY + + VRFY((H5Pclose(fapl_id) >= 0), "FAPL close succeeded"); + } + + mpi_code_g = MPI_Barrier(comm_g); + VRFY((mpi_code_g == MPI_SUCCESS), "MPI_Barrier succeeded"); + + if (skip) { + if (MAINPROCESS) + SKIPPED(); + } + else + CHECK_PASSED(); +} +#undef SUBF_FILENAME + +/* * Test the different I/O Concentator selection strategies * for the Subfiling VFD */ @@ -2360,11 +3053,33 @@ main(int argc, char **argv) if (MAINPROCESS) puts(""); + if (MAINPROCESS) + printf(" Re-running tests with compression enabled\n"); + +#ifdef H5_HAVE_FILTER_DEFLATE + enable_compression = true; + for (size_t i = 0; i < ARRAY_SIZE(tests); i++) { + if (MPI_SUCCESS == (mpi_code_g = MPI_Barrier(comm_g))) { + (*tests[i])(); + } + else { + if (MAINPROCESS) + MESG("MPI_Barrier failed"); + nerrors++; + } + } + enable_compression = false; +#else + if (MAINPROCESS) + SKIPPED(); +#endif + /* * Set any unset Subfiling environment variables and re-run * the tests as a quick smoke check of whether those are * working correctly */ + if (stripe_size_g < 0) { int64_t stripe_size; char tmp[64]; @@ -2488,26 +3203,6 @@ main(int argc, char **argv) num_iocs_g = mpi_size; if (MAINPROCESS) - printf(" Re-running tests with compression enabled\n"); - -#ifdef H5_HAVE_FILTER_DEFLATE - enable_compression = true; - for (size_t i = 0; i < ARRAY_SIZE(tests); i++) { - if (MPI_SUCCESS == (mpi_code_g = MPI_Barrier(comm_g))) { - (*tests[i])(); - } - else { - if (MAINPROCESS) - MESG("MPI_Barrier failed"); - nerrors++; - } - } - enable_compression = false; -#else - if (MAINPROCESS) - SKIPPED(); -#endif - if (MAINPROCESS) printf("\nRe-running tests with environment variables set\n"); for (size_t i = 0; i < ARRAY_SIZE(tests); i++) { @@ -2523,6 +3218,7 @@ main(int argc, char **argv) if (MAINPROCESS) printf("\n Re-running tests with compression enabled\n"); + #ifdef H5_HAVE_FILTER_DEFLATE enable_compression = true; for (size_t i = 0; i < ARRAY_SIZE(tests); i++) { @@ -2540,6 +3236,7 @@ main(int argc, char **argv) if (MAINPROCESS) SKIPPED(); #endif + if (nerrors) goto exit; |