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|
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by The HDF Group. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the COPYING file, which can be found at the root of the source code *
* distribution tree, or in https://www.hdfgroup.org/licenses. *
* If you do not have access to either file, you may request a copy from *
* help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Purpose: Functions to read/write directly between app buffer and file.
*/
/****************/
/* Module Setup */
/****************/
#include "H5Dmodule.h" /* This source code file is part of the H5D module */
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
#include "H5CXprivate.h" /* API Contexts */
#include "H5Dpkg.h" /* Datasets */
#include "H5Eprivate.h" /* Error handling */
#include "H5Fprivate.h" /* File access */
#include "H5FDprivate.h" /* File drivers */
#include "H5FLprivate.h" /* Free Lists */
#include "H5MMprivate.h" /* Memory management */
#include "H5Oprivate.h" /* Object headers */
#include "H5Pprivate.h" /* Property lists */
#include "H5Sprivate.h" /* Dataspaces */
#include "H5VMprivate.h" /* Vector */
#ifdef H5_HAVE_PARALLEL
/****************/
/* Local Macros */
/****************/
/* Macros to represent different IO options */
#define H5D_ONE_LINK_CHUNK_IO 0
#define H5D_MULTI_CHUNK_IO 1
#define H5D_ONE_LINK_CHUNK_IO_MORE_OPT 2
#define H5D_MULTI_CHUNK_IO_MORE_OPT 3
/* Macros to represent different IO modes(NONE, Independent or collective)for multiple chunk IO case */
#define H5D_CHUNK_IO_MODE_COL 1
/* Macros to represent the regularity of the selection for multiple chunk IO case. */
#define H5D_CHUNK_SELECT_REG 1
/*
* Threshold value for redistributing shared filtered chunks
* on all MPI ranks, or just MPI rank 0
*/
#define H5D_CHUNK_REDISTRIBUTE_THRES ((size_t)((25 * H5_MB) / sizeof(H5D_chunk_redistribute_info_t)))
/*
* Initial allocation size for the arrays that hold
* buffers for chunk modification data that is sent
* to other ranks and the MPI_Request objects for
* those send operations
*/
#define H5D_CHUNK_NUM_SEND_MSGS_INIT 64
/*
* Define a tag value for the MPI messages sent/received for
* chunk modification data
*/
#define H5D_CHUNK_MOD_DATA_TAG 64
/*
* Macro to initialize a H5D_chk_idx_info_t
* structure, given a pointer to a H5D_io_info_t
* structure
*/
#define H5D_MPIO_INIT_CHUNK_IDX_INFO(index_info, dset) \
do { \
(index_info).f = (dset)->oloc.file; \
(index_info).pline = &((dset)->shared->dcpl_cache.pline); \
(index_info).layout = &((dset)->shared->layout.u.chunk); \
(index_info).storage = &((dset)->shared->layout.storage.u.chunk); \
} while (0)
/******************/
/* Local Typedefs */
/******************/
/* Combine chunk/piece address and chunk/piece info into a struct for
* better performance. */
typedef struct H5D_chunk_addr_info_t {
/* piece for multi-dset */
haddr_t piece_addr;
H5D_piece_info_t piece_info;
} H5D_chunk_addr_info_t;
/* Rank 0 Bcast values */
typedef enum H5D_mpio_no_rank0_bcast_cause_t {
H5D_MPIO_RANK0_BCAST = 0x00,
H5D_MPIO_RANK0_NOT_H5S_ALL = 0x01,
H5D_MPIO_RANK0_NOT_CONTIGUOUS = 0x02,
H5D_MPIO_RANK0_NOT_FIXED_SIZE = 0x04,
H5D_MPIO_RANK0_GREATER_THAN_2GB = 0x08
} H5D_mpio_no_rank0_bcast_cause_t;
/*
* Information necessary for re-allocating file space for a chunk
* during a parallel write of a chunked dataset with filters
* applied.
*/
typedef struct H5D_chunk_alloc_info_t {
H5F_block_t chunk_current;
H5F_block_t chunk_new;
hsize_t chunk_idx;
haddr_t dset_oloc_addr;
} H5D_chunk_alloc_info_t;
/*
* Information for a chunk pertaining to the dataset's chunk
* index entry for the chunk.
*
* NOTE: To support efficient lookups of H5D_filtered_collective_chunk_info_t
* structures during parallel writes to filtered chunks, the
* chunk_idx and dset_oloc_addr fields of this structure are used
* together as a key for a hash table by following the approach
* outlined at https://troydhanson.github.io/uthash/userguide.html#_compound_keys.
* This means the following:
*
* - Instances of this structure should be memset to 0 when
* used for hashing to ensure that any padding between the
* chunk_idx and dset_oloc_addr fields does not affect the
* generated key.
*
* - The chunk_idx and dset_oloc_addr fields should be arranged
* in that specific order, as the code currently relies on
* this ordering when calculating the key length and it
* performs memory operations on the structure starting from
* the chunk_idx field and using the calculated key length.
*
* - The chunk_idx and dset_oloc_addr fields should ideally
* be arranged next to each other in the structure to minimize
* the calculated key length.
*/
typedef struct H5D_chunk_index_info_t {
/*
* These two fields must come in this order and next to
* each other for proper and efficient hashing
*/
hsize_t chunk_idx;
haddr_t dset_oloc_addr;
unsigned filter_mask;
bool need_insert;
} H5D_chunk_index_info_t;
/*
* Information about a single chunk when performing collective filtered I/O. All
* of the fields of one of these structs are initialized at the start of collective
* filtered I/O in the function H5D__mpio_collective_filtered_chunk_io_setup(). This
* struct's fields are as follows:
*
* index_info - A structure containing the information needed when collectively
* re-inserting the chunk into the dataset's chunk index. The structure
* is distributed to all ranks during the re-insertion operation. Its fields
* are as follows:
*
* chunk_idx - The index of the chunk in the dataset's chunk index.
*
* filter_mask - A bit-mask that indicates which filters are to be applied to the
* chunk. Each filter in a chunk's filter pipeline has a bit position
* that can be masked to disable that particular filter for the chunk.
* This filter mask is saved alongside the chunk in the file.
*
* need_insert - A flag which determines whether or not a chunk needs to be re-inserted into
* the chunk index after the write operation.
*
* chunk_info - A pointer to the chunk's H5D_piece_info_t structure, which contains useful
* information like the dataspaces containing the selection in the chunk.
*
* chunk_current - The address in the file and size of this chunk before the filtering
* operation. When reading a chunk from the file, this field is used to
* read the correct amount of bytes. It is also used when redistributing
* shared chunks among MPI ranks and as a parameter to the chunk file
* space reallocation function.
*
* chunk_new - The address in the file and size of this chunk after the filtering
* operation. This field is relevant when collectively re-allocating space
* in the file for all of the chunks written to in the I/O operation, as
* their sizes may have changed after their data has been filtered.
*
* need_read - A flag which determines whether or not a chunk needs to be read from the
* file. During writes, if a chunk is being fully overwritten (the entire extent
* is selected in its file dataspace), then it is not necessary to read the chunk
* from the file. However, if the chunk is not being fully overwritten, it has to
* be read from the file in order to update the chunk without trashing the parts
* of the chunk that are not selected. During reads, this field should generally
* be true, but may be false if the chunk isn't allocated, for example.
*
* skip_filter_pline - A flag which determines whether to skip calls to the filter pipeline
* for this chunk. This flag is mostly useful for correct handling of
* partial edge chunks when the "don't filter partial edge chunks" flag
* is set on the dataset's DCPL.
*
* io_size - The total size of I/O to this chunk. This field is an accumulation of the size of
* I/O to the chunk from each MPI rank which has the chunk selected and is used to
* determine the value for the previous `full_overwrite` flag.
*
* chunk_buf_size - The size in bytes of the data buffer allocated for the chunk
*
* orig_owner - The MPI rank which originally had this chunk selected at the beginning of
* the collective filtered I/O operation. This field is currently used when
* redistributing shared chunks among MPI ranks.
*
* new_owner - The MPI rank which has been selected to perform the modifications to this chunk.
*
* num_writers - The total number of MPI ranks writing to this chunk. This field is used when
* the new owner of a chunk is receiving messages from other MPI ranks that
* contain their selections in the chunk and the data to update the chunk with.
* The new owner must know how many MPI ranks it should expect messages from so
* that it can post an equal number of receive calls.
*
* buf - A pointer which serves the dual purpose of holding either the chunk data which is to be
* written to the file or the chunk data which has been read from the file.
*
* hh - A handle for hash tables provided by the uthash.h header
*
*/
typedef struct H5D_filtered_collective_chunk_info_t {
H5D_chunk_index_info_t index_info;
H5D_piece_info_t *chunk_info;
H5F_block_t chunk_current;
H5F_block_t chunk_new;
bool need_read;
bool skip_filter_pline;
size_t io_size;
size_t chunk_buf_size;
int orig_owner;
int new_owner;
int num_writers;
void *buf;
UT_hash_handle hh;
} H5D_filtered_collective_chunk_info_t;
/*
* Information cached about each dataset involved when performing
* collective I/O on filtered chunks.
*/
typedef struct H5D_mpio_filtered_dset_info_t {
const H5D_dset_io_info_t *dset_io_info;
H5D_fill_buf_info_t fb_info;
H5D_chk_idx_info_t chunk_idx_info;
hsize_t file_chunk_size;
haddr_t dset_oloc_addr;
H5S_t *fill_space;
bool should_fill;
bool fb_info_init;
bool index_empty;
UT_hash_handle hh;
} H5D_mpio_filtered_dset_info_t;
/*
* Top-level structure that contains an array of H5D_filtered_collective_chunk_info_t
* chunk info structures for collective filtered I/O, as well as other useful information.
* The struct's fields are as follows:
*
* chunk_infos - An array of H5D_filtered_collective_chunk_info_t structures that each
* contain information about a single chunk when performing collective filtered
* I/O.
*
* chunk_hash_table - A hash table storing H5D_filtered_collective_chunk_info_t structures
* that is populated when chunk modification data has to be shared between
* MPI processes during collective filtered I/O. This hash table facilitates
* quicker and easier lookup of a particular chunk by its "chunk index"
* value when applying chunk data modification messages from another MPI
* process. Each modification message received from another MPI process
* will contain the chunk's "chunk index" value that can be used for chunk
* lookup operations.
*
* chunk_hash_table_keylen - The calculated length of the key used for the chunk info hash
* table, depending on whether collective I/O is being performed
* on a single or multiple filtered datasets.
*
* num_chunks_infos - The number of entries in the `chunk_infos` array.
*
* num_chunks_to_read - The number of entries (or chunks) in the `chunk_infos` array that
* will need to be read in the case of a read operation (which can
* occur during dataset reads or during dataset writes when a chunk
* has to go through a read - modify - write cycle). The value for
* this field is based on a chunk's `need_read` field in its particular
* H5D_filtered_collective_chunk_info_t structure, but may be adjusted
* later depending on file space allocation timing and other factors.
*
* This field can be helpful to avoid needing to scan through the list
* of chunk info structures to determine how big of I/O vectors to
* allocate during read operations, as an example.
*
* all_dset_indices_empty - A boolean determining whether all the datasets involved in the
* I/O operation have empty chunk indices. If this is the case,
* collective read operations can be skipped during processing
* of chunks.
*
* no_dset_index_insert_methods - A boolean determining whether all the datasets involved
* in the I/O operation have no chunk index insertion
* methods. If this is the case, collective chunk reinsertion
* operations can be skipped during processing of chunks.
*
* single_dset_info - A pointer to a H5D_mpio_filtered_dset_info_t structure containing
* information that is used when performing collective I/O on a single
* filtered dataset.
*
* dset_info_hash_table - A hash table storing H5D_mpio_filtered_dset_info_t structures
* that is populated when performing collective I/O on multiple
* filtered datasets at a time using the multi-dataset I/O API
* routines.
*
*/
typedef struct H5D_filtered_collective_io_info_t {
H5D_filtered_collective_chunk_info_t *chunk_infos;
H5D_filtered_collective_chunk_info_t *chunk_hash_table;
size_t chunk_hash_table_keylen;
size_t num_chunk_infos;
size_t num_chunks_to_read;
bool all_dset_indices_empty;
bool no_dset_index_insert_methods;
union {
H5D_mpio_filtered_dset_info_t *single_dset_info;
H5D_mpio_filtered_dset_info_t *dset_info_hash_table;
} dset_info;
} H5D_filtered_collective_io_info_t;
/*
* Information necessary for redistributing shared chunks during
* a parallel write of a chunked dataset with filters applied.
*/
typedef struct H5D_chunk_redistribute_info_t {
H5F_block_t chunk_block;
hsize_t chunk_idx;
haddr_t dset_oloc_addr;
int orig_owner;
int new_owner;
int num_writers;
} H5D_chunk_redistribute_info_t;
/*
* Information used when re-inserting a chunk into a dataset's
* chunk index during a parallel write of a chunked dataset with
* filters applied.
*/
typedef struct H5D_chunk_insert_info_t {
H5F_block_t chunk_block;
H5D_chunk_index_info_t index_info;
} H5D_chunk_insert_info_t;
/********************/
/* Local Prototypes */
/********************/
static herr_t H5D__piece_io(H5D_io_info_t *io_info);
static herr_t H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info,
int mpi_rank, int mpi_size);
static herr_t H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_infos,
size_t num_dset_infos, int mpi_rank, int mpi_size);
static herr_t H5D__link_piece_collective_io(H5D_io_info_t *io_info, int mpi_rank);
static herr_t H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_infos,
size_t num_dset_infos, int mpi_rank, int mpi_size);
static herr_t H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_dset_io_info_t *di,
H5S_t *file_space, H5S_t *mem_space);
static herr_t H5D__final_collective_io(H5D_io_info_t *io_info, hsize_t mpi_buf_count,
MPI_Datatype mpi_file_type, MPI_Datatype mpi_buf_type);
static herr_t H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_dset_io_info_t *di, uint8_t assign_io_mode[],
haddr_t chunk_addr[], int mpi_rank, int mpi_size);
static herr_t H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info, int *sum_chunkf);
static herr_t H5D__mpio_get_sum_chunk_dset(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info,
int *sum_chunkf);
static herr_t H5D__mpio_collective_filtered_chunk_io_setup(const H5D_io_info_t *io_info,
const H5D_dset_io_info_t *di,
size_t num_dset_infos, int mpi_rank,
H5D_filtered_collective_io_info_t *chunk_list);
static herr_t H5D__mpio_redistribute_shared_chunks(H5D_filtered_collective_io_info_t *chunk_list,
const H5D_io_info_t *io_info, int mpi_rank, int mpi_size,
size_t **rank_chunks_assigned_map);
static herr_t H5D__mpio_redistribute_shared_chunks_int(H5D_filtered_collective_io_info_t *chunk_list,
size_t *num_chunks_assigned_map,
bool all_ranks_involved, const H5D_io_info_t *io_info,
int mpi_rank, int mpi_size);
static herr_t H5D__mpio_share_chunk_modification_data(H5D_filtered_collective_io_info_t *chunk_list,
H5D_io_info_t *io_info, int mpi_rank,
int H5_ATTR_NDEBUG_UNUSED mpi_size,
unsigned char ***chunk_msg_bufs,
int *chunk_msg_bufs_len);
static herr_t H5D__mpio_collective_filtered_chunk_read(H5D_filtered_collective_io_info_t *chunk_list,
const H5D_io_info_t *io_info, size_t num_dset_infos,
int mpi_rank);
static herr_t H5D__mpio_collective_filtered_chunk_update(H5D_filtered_collective_io_info_t *chunk_list,
unsigned char **chunk_msg_bufs,
int chunk_msg_bufs_len, const H5D_io_info_t *io_info,
size_t num_dset_infos, int mpi_rank);
static herr_t H5D__mpio_collective_filtered_chunk_reallocate(H5D_filtered_collective_io_info_t *chunk_list,
size_t *num_chunks_assigned_map,
H5D_io_info_t *io_info, size_t num_dset_infos,
int mpi_rank, int mpi_size);
static herr_t H5D__mpio_collective_filtered_chunk_reinsert(H5D_filtered_collective_io_info_t *chunk_list,
size_t *num_chunks_assigned_map,
H5D_io_info_t *io_info, size_t num_dset_infos,
int mpi_rank, int mpi_size);
static herr_t H5D__mpio_get_chunk_redistribute_info_types(MPI_Datatype *contig_type,
bool *contig_type_derived,
MPI_Datatype *resized_type,
bool *resized_type_derived);
static herr_t H5D__mpio_get_chunk_alloc_info_types(MPI_Datatype *contig_type, bool *contig_type_derived,
MPI_Datatype *resized_type, bool *resized_type_derived);
static herr_t H5D__mpio_get_chunk_insert_info_types(MPI_Datatype *contig_type, bool *contig_type_derived,
MPI_Datatype *resized_type, bool *resized_type_derived);
static herr_t H5D__mpio_collective_filtered_vec_io(const H5D_filtered_collective_io_info_t *chunk_list,
H5F_shared_t *f_sh, H5D_io_op_type_t op_type);
static int H5D__cmp_piece_addr(const void *chunk_addr_info1, const void *chunk_addr_info2);
static int H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_info_entry1,
const void *filtered_collective_io_info_entry2);
static int H5D__cmp_chunk_redistribute_info(const void *entry1, const void *entry2);
static int H5D__cmp_chunk_redistribute_info_orig_owner(const void *entry1, const void *entry2);
#ifdef H5Dmpio_DEBUG
static herr_t H5D__mpio_debug_init(void);
static herr_t H5D__mpio_dump_collective_filtered_chunk_list(H5D_filtered_collective_io_info_t *chunk_list,
int mpi_rank);
#endif
/*********************/
/* Package Variables */
/*********************/
/*******************/
/* Local Variables */
/*******************/
/* Declare extern free list to manage the H5S_sel_iter_t struct */
H5FL_EXTERN(H5S_sel_iter_t);
#ifdef H5Dmpio_DEBUG
/* Flags to control debug actions in this file.
* (Meant to be indexed by characters)
*
* These flags can be set with either (or both) the environment variable
* "H5D_mpio_Debug" set to a string containing one or more characters
* (flags) or by setting them as a string value for the
* "H5D_mpio_debug_key" MPI Info key.
*
* Supported characters in 'H5D_mpio_Debug' string:
* 't' trace function entry and exit
* 'f' log to file rather than debugging stream
* 'm' show (rough) memory usage statistics
* 'c' show critical timing information
*
* To only show output from a particular MPI rank, specify its rank
* number as a character, e.g.:
*
* '0' only show output from rank 0
*
* To only show output from a particular range (up to 8 ranks supported
* between 0-9) of MPI ranks, specify the start and end ranks separated
* by a hyphen, e.g.:
*
* '0-7' only show output from ranks 0 through 7
*
*/
static int H5D_mpio_debug_flags_s[256];
static int H5D_mpio_debug_rank_s[8] = {-1, -1, -1, -1, -1, -1, -1, -1};
static bool H5D_mpio_debug_inited = false;
static const char *const trace_in_pre = "-> ";
static const char *const trace_out_pre = "<- ";
static int debug_indent = 0;
static FILE *debug_stream = NULL;
/* Determine if this rank should output debugging info */
#define H5D_MPIO_DEBUG_THIS_RANK(rank) \
(H5D_mpio_debug_rank_s[0] < 0 || rank == H5D_mpio_debug_rank_s[0] || rank == H5D_mpio_debug_rank_s[1] || \
rank == H5D_mpio_debug_rank_s[2] || rank == H5D_mpio_debug_rank_s[3] || \
rank == H5D_mpio_debug_rank_s[4] || rank == H5D_mpio_debug_rank_s[5] || \
rank == H5D_mpio_debug_rank_s[6] || rank == H5D_mpio_debug_rank_s[7])
/* Print some debugging string */
#define H5D_MPIO_DEBUG(rank, string) \
do { \
if (debug_stream && H5D_MPIO_DEBUG_THIS_RANK(rank)) { \
fprintf(debug_stream, "%*s(Rank %d) " string "\n", debug_indent, "", rank); \
fflush(debug_stream); \
} \
} while (0)
/* Print some debugging string with printf-style arguments */
#define H5D_MPIO_DEBUG_VA(rank, string, ...) \
do { \
if (debug_stream && H5D_MPIO_DEBUG_THIS_RANK(rank)) { \
fprintf(debug_stream, "%*s(Rank %d) " string "\n", debug_indent, "", rank, __VA_ARGS__); \
fflush(debug_stream); \
} \
} while (0)
#define H5D_MPIO_TRACE_ENTER(rank) \
do { \
bool trace_flag = H5D_mpio_debug_flags_s[(int)'t']; \
\
if (trace_flag) { \
H5D_MPIO_DEBUG_VA(rank, "%s%s", trace_in_pre, __func__); \
debug_indent += (int)strlen(trace_in_pre); \
} \
} while (0)
#define H5D_MPIO_TRACE_EXIT(rank) \
do { \
bool trace_flag = H5D_mpio_debug_flags_s[(int)'t']; \
\
if (trace_flag) { \
debug_indent -= (int)strlen(trace_out_pre); \
H5D_MPIO_DEBUG_VA(rank, "%s%s", trace_out_pre, __func__); \
} \
} while (0)
#define H5D_MPIO_TIME_START(rank, op_name) \
{ \
bool time_flag = H5D_mpio_debug_flags_s[(int)'c']; \
double start_time = 0.0, end_time = 0.0; \
const char *const op = op_name; \
\
if (time_flag) { \
start_time = MPI_Wtime(); \
}
#define H5D_MPIO_TIME_STOP(rank) \
if (time_flag) { \
end_time = MPI_Wtime(); \
H5D_MPIO_DEBUG_VA(rank, "'%s' took %f seconds", op, (end_time - start_time)); \
} \
}
/*---------------------------------------------------------------------------
* Function: H5D__mpio_parse_debug_str
*
* Purpose: Parse a string for H5Dmpio-related debugging flags
*
* Returns: N/A
*
*---------------------------------------------------------------------------
*/
static void
H5D__mpio_parse_debug_str(const char *s)
{
FUNC_ENTER_PACKAGE_NOERR
assert(s);
while (*s) {
int c = (int)(*s);
if (c >= (int)'0' && c <= (int)'9') {
bool range = false;
if (*(s + 1) && *(s + 2))
range = (int)*(s + 1) == '-' && (int)*(s + 2) >= (int)'0' && (int)*(s + 2) <= (int)'9';
if (range) {
int start_rank = c - (int)'0';
int end_rank = (int)*(s + 2) - '0';
int num_ranks = end_rank - start_rank + 1;
int i;
if (num_ranks > 8) {
end_rank = start_rank + 7;
num_ranks = 8;
}
for (i = 0; i < num_ranks; i++)
H5D_mpio_debug_rank_s[i] = start_rank++;
s += 3;
}
else
H5D_mpio_debug_rank_s[0] = c - (int)'0';
}
else
H5D_mpio_debug_flags_s[c]++;
s++;
}
FUNC_LEAVE_NOAPI_VOID
}
static herr_t
H5D__mpio_debug_init(void)
{
const char *debug_str;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE_NOERR
assert(!H5D_mpio_debug_inited);
/* Clear the debug flag buffer */
memset(H5D_mpio_debug_flags_s, 0, sizeof(H5D_mpio_debug_flags_s));
/* Retrieve and parse the H5Dmpio debug string */
debug_str = getenv("H5D_mpio_Debug");
if (debug_str)
H5D__mpio_parse_debug_str(debug_str);
debug_stream = stdout;
H5D_mpio_debug_inited = true;
FUNC_LEAVE_NOAPI(ret_value)
}
#endif
/*-------------------------------------------------------------------------
* Function: H5D__mpio_opt_possible
*
* Purpose: Checks if an direct I/O transfer is possible between memory and
* the file.
*
* This was derived from H5D__mpio_opt_possible for
* multi-dset work.
*
* Return: Success: Non-negative: true or false
* Failure: Negative
*
*-------------------------------------------------------------------------
*/
htri_t
H5D__mpio_opt_possible(H5D_io_info_t *io_info)
{
H5FD_mpio_xfer_t io_xfer_mode; /* MPI I/O transfer mode */
size_t i;
H5D_t *dset;
const H5S_t *file_space;
const H5S_t *mem_space;
H5D_type_info_t *type_info;
unsigned local_cause[2] = {0, 0}; /* [0] Local reason(s) for breaking collective mode */
/* [1] Flag if dataset is both: H5S_ALL and small */
unsigned global_cause[2] = {0, 0}; /* Global reason(s) for breaking collective mode */
htri_t is_vl_storage; /* Whether the dataset's datatype is stored in a variable-length form */
htri_t ret_value = true; /* Return value */
FUNC_ENTER_PACKAGE
/* Check args */
assert(io_info);
for (i = 0; i < io_info->count; i++) {
assert(io_info->dsets_info[i].file_space);
assert(io_info->dsets_info[i].mem_space);
}
/* For independent I/O, get out quickly and don't try to form consensus */
if (H5CX_get_io_xfer_mode(&io_xfer_mode) < 0)
/* Set error flag, but keep going */
local_cause[0] |= H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE;
if (io_xfer_mode == H5FD_MPIO_INDEPENDENT)
local_cause[0] |= H5D_MPIO_SET_INDEPENDENT;
for (i = 0; i < io_info->count; i++) {
/* Check for skipped I/O */
if (io_info->dsets_info[i].skip_io)
continue;
/* Set convenience pointers */
dset = io_info->dsets_info[i].dset;
file_space = io_info->dsets_info[i].file_space;
mem_space = io_info->dsets_info[i].mem_space;
type_info = &io_info->dsets_info[i].type_info;
/* Optimized MPI types flag must be set */
/* (based on 'HDF5_MPI_OPT_TYPES' environment variable) */
if (!H5FD_mpi_opt_types_g)
local_cause[0] |= H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED;
/* Decision on whether to use selection I/O should have been made by now */
assert(io_info->use_select_io != H5D_SELECTION_IO_MODE_DEFAULT);
/* Datatype conversions and transformations are allowed with selection I/O. If the selection I/O mode
* is auto (default), disable collective for now and re-enable later if we can */
if (io_info->use_select_io != H5D_SELECTION_IO_MODE_ON) {
/* Don't allow collective operations if datatype conversions need to happen */
if (!type_info->is_conv_noop)
local_cause[0] |= H5D_MPIO_DATATYPE_CONVERSION;
/* Don't allow collective operations if data transform operations should occur */
if (!type_info->is_xform_noop)
local_cause[0] |= H5D_MPIO_DATA_TRANSFORMS;
}
/* Check whether these are both simple or scalar dataspaces */
if (!((H5S_SIMPLE == H5S_GET_EXTENT_TYPE(mem_space) || H5S_SCALAR == H5S_GET_EXTENT_TYPE(mem_space) ||
H5S_NULL == H5S_GET_EXTENT_TYPE(mem_space)) &&
(H5S_SIMPLE == H5S_GET_EXTENT_TYPE(file_space) ||
H5S_SCALAR == H5S_GET_EXTENT_TYPE(file_space))))
local_cause[0] |= H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES;
/* Dataset storage must be contiguous or chunked */
if (!(dset->shared->layout.type == H5D_CONTIGUOUS || dset->shared->layout.type == H5D_CHUNKED))
local_cause[0] |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET;
/* check if external-file storage is used */
if (dset->shared->dcpl_cache.efl.nused > 0)
local_cause[0] |= H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET;
/* The handling of memory space is different for chunking and contiguous
* storage. For contiguous storage, mem_space and file_space won't change
* when it it is doing disk IO. For chunking storage, mem_space will
* change for different chunks. So for chunking storage, whether we can
* use collective IO will defer until each chunk IO is reached.
*/
#ifndef H5_HAVE_PARALLEL_FILTERED_WRITES
/* Don't allow writes to filtered datasets if the functionality is disabled */
if (io_info->op_type == H5D_IO_OP_WRITE && dset->shared->dcpl_cache.pline.nused > 0)
local_cause[0] |= H5D_MPIO_PARALLEL_FILTERED_WRITES_DISABLED;
#endif
/* Check if we would be able to perform collective if we could use selection I/O. If so add reasons
* for not using selection I/O to local_cause[0] */
if ((io_info->use_select_io == H5D_SELECTION_IO_MODE_OFF) && local_cause[0] &&
!(local_cause[0] &
~((unsigned)H5D_MPIO_DATATYPE_CONVERSION | (unsigned)H5D_MPIO_DATA_TRANSFORMS))) {
assert(io_info->no_selection_io_cause & H5D_MPIO_NO_SELECTION_IO_CAUSES);
local_cause[0] |= H5D_MPIO_NO_SELECTION_IO;
}
/* Check if we are able to do a MPI_Bcast of the data from one rank
* instead of having all the processes involved in the collective I/O call.
*/
/* Check to see if the process is reading the entire dataset */
if (H5S_GET_SELECT_TYPE(file_space) != H5S_SEL_ALL)
local_cause[1] |= H5D_MPIO_RANK0_NOT_H5S_ALL;
/* Only perform this optimization for contiguous datasets, currently */
else if (H5D_CONTIGUOUS != dset->shared->layout.type)
/* Flag to do a MPI_Bcast of the data from one proc instead of
* having all the processes involved in the collective I/O.
*/
local_cause[1] |= H5D_MPIO_RANK0_NOT_CONTIGUOUS;
else if ((is_vl_storage = H5T_is_vl_storage(type_info->dset_type)) < 0)
local_cause[0] |= H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE;
else if (is_vl_storage)
local_cause[1] |= H5D_MPIO_RANK0_NOT_FIXED_SIZE;
else {
size_t type_size; /* Size of dataset's datatype */
/* Retrieve the size of the dataset's datatype */
if (0 == (type_size = H5T_GET_SIZE(type_info->dset_type)))
local_cause[0] |= H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE;
else {
hssize_t snelmts; /* [Signed] # of elements in dataset's dataspace */
/* Retrieve the size of the dataset's datatype */
if ((snelmts = H5S_GET_EXTENT_NPOINTS(file_space)) < 0)
local_cause[0] |= H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE;
else {
hsize_t dset_size;
/* Determine dataset size */
dset_size = ((hsize_t)snelmts) * type_size;
/* If the size of the dataset is less than 2GB then do an MPI_Bcast
* of the data from one process instead of having all the processes
* involved in the collective I/O.
*/
if (dset_size > ((hsize_t)(2.0F * H5_GB) - 1))
local_cause[1] |= H5D_MPIO_RANK0_GREATER_THAN_2GB;
} /* end else */
} /* end else */
} /* end else */
} /* end for loop */
/* Check for independent I/O */
if (local_cause[0] & H5D_MPIO_SET_INDEPENDENT)
global_cause[0] = local_cause[0];
else {
int mpi_code; /* MPI error code */
/* Form consensus opinion among all processes about whether to perform
* collective I/O
*/
if (MPI_SUCCESS !=
(mpi_code = MPI_Allreduce(local_cause, global_cause, 2, MPI_UNSIGNED, MPI_BOR, io_info->comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code)
} /* end else */
/* Set the local & global values of no-collective-cause in the API context */
H5CX_set_mpio_local_no_coll_cause(local_cause[0]);
H5CX_set_mpio_global_no_coll_cause(global_cause[0]);
/* Set read-with-rank0-and-bcast flag if possible */
if (global_cause[0] == 0 && global_cause[1] == 0) {
H5CX_set_mpio_rank0_bcast(true);
#ifdef H5_HAVE_INSTRUMENTED_LIBRARY
H5CX_test_set_mpio_coll_rank0_bcast(true);
#endif /* H5_HAVE_INSTRUMENTED_LIBRARY */
} /* end if */
/* Set the return value, based on the global cause */
ret_value = global_cause[0] > 0 ? false : true;
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D__mpio_opt_possible() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_get_no_coll_cause_strings
*
* Purpose: When collective I/O is broken internally, it can be useful
* for users to see a representative string for the reason(s)
* why it was broken. This routine inspects the current
* "cause" flags from the API context and prints strings into
* the caller's buffers for the local and global reasons that
* collective I/O was broken.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__mpio_get_no_coll_cause_strings(char *local_cause, size_t local_cause_len, char *global_cause,
size_t global_cause_len)
{
uint32_t local_no_coll_cause;
uint32_t global_no_coll_cause;
size_t local_cause_bytes_written = 0;
size_t global_cause_bytes_written = 0;
int nbits;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert((local_cause && local_cause_len > 0) || (global_cause && global_cause_len > 0));
/*
* Use compile-time assertion so this routine is updated
* when any new "no collective cause" values are added
*/
HDcompile_assert(H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE == (H5D_mpio_no_collective_cause_t)0x200);
/* Initialize output buffers */
if (local_cause)
*local_cause = '\0';
if (global_cause)
*global_cause = '\0';
/* Retrieve the local and global cause flags from the API context */
if (H5CX_get_mpio_local_no_coll_cause(&local_no_coll_cause) < 0)
HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "unable to get local no collective cause value");
if (H5CX_get_mpio_global_no_coll_cause(&global_no_coll_cause) < 0)
HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "unable to get global no collective cause value");
/*
* Append each of the "reason for breaking collective I/O"
* error messages to the local and global cause string buffers
*/
nbits = 8 * sizeof(local_no_coll_cause);
for (int bit_pos = 0; bit_pos < nbits; bit_pos++) {
H5D_mpio_no_collective_cause_t cur_cause;
const char *cause_str;
size_t buf_space_left;
cur_cause = (H5D_mpio_no_collective_cause_t)(1 << bit_pos);
if (cur_cause == H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE)
break;
switch (cur_cause) {
case H5D_MPIO_SET_INDEPENDENT:
cause_str = "independent I/O was requested";
break;
case H5D_MPIO_DATATYPE_CONVERSION:
cause_str = "datatype conversions were required";
break;
case H5D_MPIO_DATA_TRANSFORMS:
cause_str = "data transforms needed to be applied";
break;
case H5D_MPIO_MPI_OPT_TYPES_ENV_VAR_DISABLED:
cause_str = "optimized MPI types flag wasn't set";
break;
case H5D_MPIO_NOT_SIMPLE_OR_SCALAR_DATASPACES:
cause_str = "one of the dataspaces was neither simple nor scalar";
break;
case H5D_MPIO_NOT_CONTIGUOUS_OR_CHUNKED_DATASET:
cause_str = "dataset was not contiguous or chunked";
break;
case H5D_MPIO_PARALLEL_FILTERED_WRITES_DISABLED:
cause_str = "parallel writes to filtered datasets are disabled";
break;
case H5D_MPIO_ERROR_WHILE_CHECKING_COLLECTIVE_POSSIBLE:
cause_str = "an error occurred while checking if collective I/O was possible";
break;
case H5D_MPIO_NO_SELECTION_IO:
cause_str = "collective I/O may be supported by selection or vector I/O but that feature was "
"not possible (see causes via H5Pget_no_selection_io_cause())";
break;
case H5D_MPIO_COLLECTIVE:
case H5D_MPIO_NO_COLLECTIVE_MAX_CAUSE:
default:
cause_str = "invalid or unknown no collective cause reason";
assert(0 && "invalid or unknown no collective cause reason");
break;
}
/*
* Determine if the local reasons for breaking collective I/O
* included the current cause
*/
if (local_cause && (cur_cause & local_no_coll_cause)) {
buf_space_left = local_cause_len - local_cause_bytes_written;
/*
* Check if there were any previous error messages included. If
* so, prepend a semicolon to separate the messages.
*/
if (buf_space_left && local_cause_bytes_written) {
strncat(local_cause, "; ", buf_space_left);
local_cause_bytes_written += MIN(buf_space_left, 2);
buf_space_left -= MIN(buf_space_left, 2);
}
if (buf_space_left) {
strncat(local_cause, cause_str, buf_space_left);
local_cause_bytes_written += MIN(buf_space_left, strlen(cause_str));
}
}
/*
* Determine if the global reasons for breaking collective I/O
* included the current cause
*/
if (global_cause && (cur_cause & global_no_coll_cause)) {
buf_space_left = global_cause_len - global_cause_bytes_written;
/*
* Check if there were any previous error messages included. If
* so, prepend a semicolon to separate the messages.
*/
if (buf_space_left && global_cause_bytes_written) {
strncat(global_cause, "; ", buf_space_left);
global_cause_bytes_written += MIN(buf_space_left, 2);
buf_space_left -= MIN(buf_space_left, 2);
}
if (buf_space_left) {
strncat(global_cause, cause_str, buf_space_left);
global_cause_bytes_written += MIN(buf_space_left, strlen(cause_str));
}
}
}
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_get_no_coll_cause_strings() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_select_read
*
* Purpose: MPI-IO function to read directly from app buffer to file.
*
* This was referred from H5D__mpio_select_read for
* multi-dset work.
*
* Return: non-negative on success, negative on failure.
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__mpio_select_read(const H5D_io_info_t *io_info, hsize_t mpi_buf_count, H5S_t H5_ATTR_UNUSED *file_space,
H5S_t H5_ATTR_UNUSED *mem_space)
{
void *rbuf = NULL;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
/* memory addr from a piece with lowest file addr */
rbuf = io_info->base_maddr.vp;
/*OKAY: CAST DISCARDS CONST QUALIFIER*/
H5_CHECK_OVERFLOW(mpi_buf_count, hsize_t, size_t);
if (H5F_shared_block_read(io_info->f_sh, H5FD_MEM_DRAW, io_info->store_faddr, (size_t)mpi_buf_count,
rbuf) < 0)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "can't finish collective parallel read");
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_select_read() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_select_write
*
* Purpose: MPI-IO function to write directly from app buffer to file.
*
* This was referred from H5D__mpio_select_write for
* multi-dset work.
*
* Return: non-negative on success, negative on failure.
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__mpio_select_write(const H5D_io_info_t *io_info, hsize_t mpi_buf_count, H5S_t H5_ATTR_UNUSED *file_space,
H5S_t H5_ATTR_UNUSED *mem_space)
{
const void *wbuf = NULL;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
/* memory addr from a piece with lowest file addr */
wbuf = io_info->base_maddr.cvp;
/*OKAY: CAST DISCARDS CONST QUALIFIER*/
H5_CHECK_OVERFLOW(mpi_buf_count, hsize_t, size_t);
if (H5F_shared_block_write(io_info->f_sh, H5FD_MEM_DRAW, io_info->store_faddr, (size_t)mpi_buf_count,
wbuf) < 0)
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "can't finish collective parallel write");
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_select_write() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_get_sum_chunk
*
* Purpose: Routine for obtaining total number of chunks to cover
* hyperslab selection selected by all processors. Operates
* on all datasets in the operation.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_get_sum_chunk(const H5D_io_info_t *io_info, int *sum_chunkf)
{
int num_chunkf; /* Number of chunks to iterate over */
size_t ori_num_chunkf;
int mpi_code; /* MPI return code */
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
/* Get the number of chunks to perform I/O on */
num_chunkf = 0;
ori_num_chunkf = io_info->pieces_added;
H5_CHECKED_ASSIGN(num_chunkf, int, ori_num_chunkf, size_t);
/* Determine the summation of number of chunks for all processes */
if (MPI_SUCCESS !=
(mpi_code = MPI_Allreduce(&num_chunkf, sum_chunkf, 1, MPI_INT, MPI_SUM, io_info->comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code)
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_get_sum_chunk() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_get_sum_chunk_dset
*
* Purpose: Routine for obtaining total number of chunks to cover
* hyperslab selection selected by all processors. Operates
* on a single dataset.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_get_sum_chunk_dset(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *dset_info,
int *sum_chunkf)
{
int num_chunkf; /* Number of chunks to iterate over */
size_t ori_num_chunkf;
int mpi_code; /* MPI return code */
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
/* Check for non-chunked dataset, in this case we know the number of "chunks"
* is simply the mpi size */
assert(dset_info->layout->type == H5D_CHUNKED);
/* Get the number of chunks to perform I/O on */
num_chunkf = 0;
ori_num_chunkf = H5SL_count(dset_info->layout_io_info.chunk_map->dset_sel_pieces);
H5_CHECKED_ASSIGN(num_chunkf, int, ori_num_chunkf, size_t);
/* Determine the summation of number of chunks for all processes */
if (MPI_SUCCESS !=
(mpi_code = MPI_Allreduce(&num_chunkf, sum_chunkf, 1, MPI_INT, MPI_SUM, io_info->comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code)
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_get_sum_chunk_dset() */
/*-------------------------------------------------------------------------
* Function: H5D__piece_io
*
* Purpose: Routine for
* 1) choose an IO option:
* a) One collective IO defined by one MPI derived datatype to link through all chunks
* or b) multiple chunk IOs,to do MPI-IO for each chunk, the IO mode may be adjusted
* due to the selection pattern for each chunk.
* For option a)
* 1. Sort the chunk address, obtain chunk info according to the sorted chunk address
* 2. Build up MPI derived datatype for each chunk
* 3. Build up the final MPI derived datatype
* 4. Set up collective IO property list
* 5. Do IO
* For option b)
* 1. Use MPI_gather and MPI_Bcast to obtain information of *collective/independent/none*
* IO mode for each chunk of the selection
* 2. Depending on whether the IO mode is collective or independent or none,
* Create either MPI derived datatype for each chunk to do collective IO or
* just do independent IO or independent IO with file set view
* 3. Set up collective IO property list for collective mode
* 4. DO IO
*
* Return: Non-negative on success/Negative on failure
*-------------------------------------------------------------------------
*/
static herr_t
H5D__piece_io(H5D_io_info_t *io_info)
{
H5FD_mpio_chunk_opt_t chunk_opt_mode;
#ifdef H5Dmpio_DEBUG
bool log_file_flag = false;
FILE *debug_log_file = NULL;
#endif
int io_option = H5D_MULTI_CHUNK_IO_MORE_OPT;
bool recalc_io_option = false;
bool use_multi_dset = false;
unsigned one_link_chunk_io_threshold; /* Threshold to use single collective I/O for all chunks */
int sum_chunk = -1;
int mpi_rank;
int mpi_size;
size_t i;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
/* Sanity checks */
assert(io_info);
assert(io_info->using_mpi_vfd);
assert(io_info->count > 0);
/* Obtain the current rank of the process and the number of ranks */
if ((mpi_rank = H5F_mpi_get_rank(io_info->dsets_info[0].dset->oloc.file)) < 0)
HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain MPI rank");
if ((mpi_size = H5F_mpi_get_size(io_info->dsets_info[0].dset->oloc.file)) < 0)
HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain MPI size");
#ifdef H5Dmpio_DEBUG
/* Initialize file-level debugging if not initialized */
if (!H5D_mpio_debug_inited && H5D__mpio_debug_init() < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize H5Dmpio debugging");
/* Open file for debugging if necessary */
log_file_flag = H5D_mpio_debug_flags_s[(int)'f'];
if (log_file_flag) {
char debug_log_filename[1024];
time_t time_now;
snprintf(debug_log_filename, 1024, "H5Dmpio_debug.rank%d", mpi_rank);
if (NULL == (debug_log_file = fopen(debug_log_filename, "a")))
HGOTO_ERROR(H5E_IO, H5E_OPENERROR, FAIL, "couldn't open debugging log file");
/* Print a short header for this I/O operation */
time_now = HDtime(NULL);
fprintf(debug_log_file, "##### %s", HDasctime(HDlocaltime(&time_now)));
debug_stream = debug_log_file;
}
#endif
/* Check the optional property list for the collective chunk IO optimization option.
* Only set here if it's a static option, if it needs to be calculated using the
* number of chunks per process delay that calculation until later. */
if (H5CX_get_mpio_chunk_opt_mode(&chunk_opt_mode) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't get chunk optimization option");
if (H5FD_MPIO_CHUNK_ONE_IO == chunk_opt_mode)
io_option = H5D_ONE_LINK_CHUNK_IO; /*no opt*/
/* direct request to multi-chunk-io */
else if (H5FD_MPIO_CHUNK_MULTI_IO == chunk_opt_mode)
io_option = H5D_MULTI_CHUNK_IO;
else
recalc_io_option = true;
/* Check if we can and should use multi dataset path */
if (io_info->count > 1 && (io_option == H5D_ONE_LINK_CHUNK_IO || recalc_io_option)) {
/* Use multi dataset path for now */
use_multi_dset = true;
/* Check if this I/O exceeds one linked chunk threshold */
if (recalc_io_option && use_multi_dset) {
/* Get the chunk optimization option threshold */
if (H5CX_get_mpio_chunk_opt_num(&one_link_chunk_io_threshold) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,
"couldn't get chunk optimization option threshold value");
/* If the threshold is 0, no need to check number of chunks */
if (one_link_chunk_io_threshold > 0) {
/* Get number of chunks for all processes */
if (H5D__mpio_get_sum_chunk(io_info, &sum_chunk) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSWAP, FAIL,
"unable to obtain the total chunk number of all processes");
/* If the average number of chunk per process is less than the threshold, we will do multi
* chunk IO. If this threshold is not exceeded for all datasets, no need to check it again
* for each individual dataset. */
if ((unsigned)sum_chunk / (unsigned)mpi_size < one_link_chunk_io_threshold) {
recalc_io_option = false;
use_multi_dset = false;
}
}
}
}
/* Perform multi dataset I/O if appropriate */
if (use_multi_dset) {
#ifdef H5_HAVE_INSTRUMENTED_LIBRARY
/*** Set collective chunk user-input optimization API. ***/
if (H5D_ONE_LINK_CHUNK_IO == io_option) {
if (H5CX_test_set_mpio_coll_chunk_link_hard(0) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value");
} /* end if */
#endif /* H5_HAVE_INSTRUMENTED_LIBRARY */
/* Process all the filtered datasets first */
if (io_info->filtered_count > 0) {
if (H5D__link_chunk_filtered_collective_io(io_info, io_info->dsets_info, io_info->count, mpi_rank,
mpi_size) < 0)
HGOTO_ERROR(H5E_IO, (H5D_IO_OP_READ == io_info->op_type ? H5E_READERROR : H5E_WRITEERROR),
FAIL, "couldn't finish filtered linked chunk MPI-IO");
}
/* Process all the unfiltered datasets */
if ((io_info->filtered_count == 0) || (io_info->filtered_count < io_info->count)) {
/* Perform unfiltered link chunk collective IO */
if (H5D__link_piece_collective_io(io_info, mpi_rank) < 0)
HGOTO_ERROR(H5E_IO, (H5D_IO_OP_READ == io_info->op_type ? H5E_READERROR : H5E_WRITEERROR),
FAIL, "couldn't finish linked chunk MPI-IO");
}
}
else {
/* Loop over datasets */
for (i = 0; i < io_info->count; i++) {
if (io_info->dsets_info[i].skip_io)
continue;
if (io_info->dsets_info[i].layout->type == H5D_CONTIGUOUS) {
/* Contiguous: call H5D__inter_collective_io() directly */
H5D_mpio_actual_io_mode_t actual_io_mode = H5D_MPIO_CONTIGUOUS_COLLECTIVE;
io_info->store_faddr = io_info->dsets_info[i].store->contig.dset_addr;
io_info->base_maddr = io_info->dsets_info[i].buf;
if (H5D__inter_collective_io(io_info, &io_info->dsets_info[i],
io_info->dsets_info[i].file_space,
io_info->dsets_info[i].mem_space) < 0)
HGOTO_ERROR(H5E_IO, (H5D_IO_OP_READ == io_info->op_type ? H5E_READERROR : H5E_WRITEERROR),
FAIL, "couldn't finish shared collective MPI-IO");
/* Set the actual I/O mode property. internal_collective_io will not break to
* independent I/O, so we set it here.
*/
H5CX_set_mpio_actual_io_mode(actual_io_mode);
}
else {
/* Chunked I/O path */
assert(io_info->dsets_info[i].layout->type == H5D_CHUNKED);
/* Recalculate io_option if necessary */
if (recalc_io_option) {
/* Get the chunk optimization option threshold */
if (H5CX_get_mpio_chunk_opt_num(&one_link_chunk_io_threshold) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,
"couldn't get chunk optimization option threshold value");
/* If the threshold is 0, no need to check number of chunks */
if (one_link_chunk_io_threshold == 0) {
io_option = H5D_ONE_LINK_CHUNK_IO_MORE_OPT;
recalc_io_option = false;
}
else {
/* Get number of chunks for all processes */
if (H5D__mpio_get_sum_chunk_dset(io_info, &io_info->dsets_info[i], &sum_chunk) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTSWAP, FAIL,
"unable to obtain the total chunk number of all processes");
/* step 1: choose an IO option */
/* If the average number of chunk per process is greater than a threshold, we will do
* one link chunked IO. */
if ((unsigned)sum_chunk / (unsigned)mpi_size >= one_link_chunk_io_threshold)
io_option = H5D_ONE_LINK_CHUNK_IO_MORE_OPT;
else
io_option = H5D_MULTI_CHUNK_IO_MORE_OPT;
}
}
/* step 2: Go ahead to do IO.*/
switch (io_option) {
case H5D_ONE_LINK_CHUNK_IO:
case H5D_ONE_LINK_CHUNK_IO_MORE_OPT:
/* Check if there are any filters in the pipeline */
if (io_info->dsets_info[i].dset->shared->dcpl_cache.pline.nused > 0) {
if (H5D__link_chunk_filtered_collective_io(io_info, &io_info->dsets_info[i], 1,
mpi_rank, mpi_size) < 0)
HGOTO_ERROR(
H5E_IO,
(H5D_IO_OP_READ == io_info->op_type ? H5E_READERROR : H5E_WRITEERROR),
FAIL, "couldn't finish filtered linked chunk MPI-IO");
} /* end if */
else {
/* If there is more than one dataset we cannot make the multi dataset call here,
* fall back to multi chunk */
if (io_info->count > 1) {
io_option = H5D_MULTI_CHUNK_IO_MORE_OPT;
recalc_io_option = true;
if (H5D__multi_chunk_collective_io(io_info, &io_info->dsets_info[i], mpi_rank,
mpi_size) < 0)
HGOTO_ERROR(
H5E_IO,
(H5D_IO_OP_READ == io_info->op_type ? H5E_READERROR : H5E_WRITEERROR),
FAIL, "couldn't finish optimized multiple chunk MPI-IO");
}
else {
/* Perform unfiltered link chunk collective IO */
if (H5D__link_piece_collective_io(io_info, mpi_rank) < 0)
HGOTO_ERROR(
H5E_IO,
(H5D_IO_OP_READ == io_info->op_type ? H5E_READERROR : H5E_WRITEERROR),
FAIL, "couldn't finish linked chunk MPI-IO");
}
}
break;
case H5D_MULTI_CHUNK_IO: /* direct request to do multi-chunk IO */
default: /* multiple chunk IO via threshold */
/* Check if there are any filters in the pipeline */
if (io_info->dsets_info[i].dset->shared->dcpl_cache.pline.nused > 0) {
if (H5D__multi_chunk_filtered_collective_io(io_info, &io_info->dsets_info[i], 1,
mpi_rank, mpi_size) < 0)
HGOTO_ERROR(
H5E_IO,
(H5D_IO_OP_READ == io_info->op_type ? H5E_READERROR : H5E_WRITEERROR),
FAIL, "couldn't finish optimized multiple filtered chunk MPI-IO");
} /* end if */
else {
/* Perform unfiltered multi chunk collective IO */
if (H5D__multi_chunk_collective_io(io_info, &io_info->dsets_info[i], mpi_rank,
mpi_size) < 0)
HGOTO_ERROR(
H5E_IO,
(H5D_IO_OP_READ == io_info->op_type ? H5E_READERROR : H5E_WRITEERROR),
FAIL, "couldn't finish optimized multiple chunk MPI-IO");
}
break;
} /* end switch */
#ifdef H5_HAVE_INSTRUMENTED_LIBRARY
{
/*** Set collective chunk user-input optimization APIs. ***/
if (H5D_ONE_LINK_CHUNK_IO == io_option) {
if (H5CX_test_set_mpio_coll_chunk_link_hard(0) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value");
} /* end if */
else if (H5D_MULTI_CHUNK_IO == io_option) {
if (H5CX_test_set_mpio_coll_chunk_multi_hard(0) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value");
} /* end else-if */
else if (H5D_ONE_LINK_CHUNK_IO_MORE_OPT == io_option) {
if (H5CX_test_set_mpio_coll_chunk_link_num_true(0) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value");
} /* end if */
else if (H5D_MULTI_CHUNK_IO_MORE_OPT == io_option) {
if (H5CX_test_set_mpio_coll_chunk_link_num_false(0) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value");
} /* end if */
}
#endif /* H5_HAVE_INSTRUMENTED_LIBRARY */
}
}
}
done:
#ifdef H5Dmpio_DEBUG
/* Close debugging log file */
if (debug_log_file) {
fprintf(debug_log_file, "##############\n\n");
if (EOF == fclose(debug_log_file))
HDONE_ERROR(H5E_IO, H5E_CLOSEERROR, FAIL, "couldn't close debugging log file");
debug_stream = stdout;
}
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__piece_io */
/*-------------------------------------------------------------------------
* Function: H5D__collective_read
*
* Purpose: Read directly from pieces (chunks/contig) in file into
* application memory using collective I/O.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__collective_read(H5D_io_info_t *io_info)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Call generic selection operation */
if (H5D__piece_io(io_info) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_READERROR, FAIL, "read error");
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__collective_read() */
/*-------------------------------------------------------------------------
* Function: H5D__collective_write
*
* Purpose: Write directly to pieces (chunks/contig) in file into
* application memory using collective I/O.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
herr_t
H5D__collective_write(H5D_io_info_t *io_info)
{
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE
/* Call generic selection operation */
if (H5D__piece_io(io_info) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_WRITEERROR, FAIL, "write error");
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__collective_write() */
/*-------------------------------------------------------------------------
* Function: H5D__link_piece_collective_io
*
* Purpose: Routine for single collective IO with one MPI derived datatype
* to link with all pieces (chunks + contig)
*
* 1. Use the piece addresses and piece info sorted in skiplist
* 2. Build up MPI derived datatype for each chunk
* 3. Build up the final MPI derived datatype
* 4. Use common collective IO routine to do MPI-IO
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
#ifdef H5Dmpio_DEBUG
H5D__link_piece_collective_io(H5D_io_info_t *io_info, int mpi_rank)
#else
H5D__link_piece_collective_io(H5D_io_info_t *io_info, int H5_ATTR_UNUSED mpi_rank)
#endif
{
MPI_Datatype chunk_final_mtype; /* Final memory MPI datatype for all chunks with selection */
bool chunk_final_mtype_is_derived = false;
MPI_Datatype chunk_final_ftype; /* Final file MPI datatype for all chunks with selection */
bool chunk_final_ftype_is_derived = false;
H5D_storage_t ctg_store; /* Storage info for "fake" contiguous dataset */
MPI_Datatype *chunk_mtype = NULL;
MPI_Datatype *chunk_ftype = NULL;
MPI_Aint *chunk_file_disp_array = NULL;
MPI_Aint *chunk_mem_disp_array = NULL;
bool *chunk_mft_is_derived_array = NULL; /* Flags to indicate each chunk's MPI file datatype is derived */
bool *chunk_mbt_is_derived_array =
NULL; /* Flags to indicate each chunk's MPI memory datatype is derived */
int *chunk_mpi_file_counts = NULL; /* Count of MPI file datatype for each chunk */
int *chunk_mpi_mem_counts = NULL; /* Count of MPI memory datatype for each chunk */
int mpi_code; /* MPI return code */
H5D_mpio_actual_chunk_opt_mode_t actual_chunk_opt_mode = H5D_MPIO_LINK_CHUNK;
H5D_mpio_actual_io_mode_t actual_io_mode = 0;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
/* set actual_io_mode */
for (size_t i = 0; i < io_info->count; i++) {
/* Skip this dataset if no I/O is being performed */
if (io_info->dsets_info[i].skip_io)
continue;
/* Filtered datasets are processed elsewhere. A contiguous dataset
* could possibly have filters in the DCPL pipeline, but the library
* will currently ignore optional filters in that case.
*/
if ((io_info->dsets_info[i].dset->shared->dcpl_cache.pline.nused > 0) &&
(io_info->dsets_info[i].layout->type != H5D_CONTIGUOUS))
continue;
if (io_info->dsets_info[i].layout->type == H5D_CHUNKED)
actual_io_mode |= H5D_MPIO_CHUNK_COLLECTIVE;
else if (io_info->dsets_info[i].layout->type == H5D_CONTIGUOUS)
actual_io_mode |= H5D_MPIO_CONTIGUOUS_COLLECTIVE;
else
HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
}
/* Set the actual-chunk-opt-mode property. */
H5CX_set_mpio_actual_chunk_opt(actual_chunk_opt_mode);
/* Set the actual-io-mode property.
* Link chunk I/O does not break to independent, so can set right away */
H5CX_set_mpio_actual_io_mode(actual_io_mode);
/* Code block for actual actions (Build a MPI Type, IO) */
{
hsize_t mpi_buf_count; /* Number of MPI types */
size_t num_chunk; /* Number of chunks for this process */
H5D_piece_info_t *piece_info;
/* local variable for base address for buffer */
H5_flexible_const_ptr_t base_buf_addr;
base_buf_addr.cvp = NULL;
/* Get the number of unfiltered chunks with a selection */
assert(io_info->filtered_pieces_added <= io_info->pieces_added);
num_chunk = io_info->pieces_added - io_info->filtered_pieces_added;
H5_CHECK_OVERFLOW(num_chunk, size_t, int);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_DEBUG_VA(mpi_rank, "num_chunk = %zu\n", num_chunk);
#endif
/* Set up MPI datatype for chunks selected */
if (num_chunk) {
bool need_sort = false;
/* Check if sel_pieces array is sorted */
assert(io_info->sel_pieces[0]->faddr != HADDR_UNDEF);
for (size_t i = 1; i < io_info->pieces_added; i++) {
assert(io_info->sel_pieces[i]->faddr != HADDR_UNDEF);
if (io_info->sel_pieces[i]->faddr < io_info->sel_pieces[i - 1]->faddr) {
need_sort = true;
break;
}
}
/* Sort sel_pieces if necessary */
if (need_sort)
qsort(io_info->sel_pieces, io_info->pieces_added, sizeof(io_info->sel_pieces[0]),
H5D__cmp_piece_addr);
/* Allocate chunking information */
if (NULL == (chunk_mtype = (MPI_Datatype *)H5MM_malloc(num_chunk * sizeof(MPI_Datatype))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"couldn't allocate chunk memory datatype buffer");
if (NULL == (chunk_ftype = (MPI_Datatype *)H5MM_malloc(num_chunk * sizeof(MPI_Datatype))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk file datatype buffer");
if (NULL == (chunk_file_disp_array = (MPI_Aint *)H5MM_malloc(num_chunk * sizeof(MPI_Aint))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"couldn't allocate chunk file displacement buffer");
if (NULL == (chunk_mem_disp_array = (MPI_Aint *)H5MM_calloc(num_chunk * sizeof(MPI_Aint))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"couldn't allocate chunk memory displacement buffer");
if (NULL == (chunk_mpi_mem_counts = (int *)H5MM_calloc(num_chunk * sizeof(int))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk memory counts buffer");
if (NULL == (chunk_mpi_file_counts = (int *)H5MM_calloc(num_chunk * sizeof(int))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk file counts buffer");
if (NULL == (chunk_mbt_is_derived_array = (bool *)H5MM_calloc(num_chunk * sizeof(bool))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"couldn't allocate chunk memory is derived datatype flags buffer");
if (NULL == (chunk_mft_is_derived_array = (bool *)H5MM_calloc(num_chunk * sizeof(bool))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"couldn't allocate chunk file is derived datatype flags buffer");
/*
* After sorting sel_pieces according to file address, locate
* the first unfiltered chunk and save its file address and
* base memory address for read/write
*/
ctg_store.contig.dset_addr = HADDR_UNDEF;
for (size_t i = 0; i < io_info->pieces_added; i++) {
if (!io_info->sel_pieces[i]->filtered_dset) {
ctg_store.contig.dset_addr = io_info->sel_pieces[i]->faddr;
base_buf_addr = io_info->sel_pieces[i]->dset_info->buf;
break;
}
}
assert(ctg_store.contig.dset_addr != HADDR_UNDEF);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_DEBUG(mpi_rank, "before iterate over selected pieces\n");
#endif
/* Obtain MPI derived datatype from all individual pieces */
/* Iterate over selected pieces for this process */
for (size_t i = 0, curr_idx = 0; i < io_info->pieces_added; i++) {
hsize_t *permute_map = NULL; /* array that holds the mapping from the old,
out-of-order displacements to the in-order
displacements of the MPI datatypes of the
point selection of the file space */
bool is_permuted = false;
/* Assign convenience pointer to piece info */
piece_info = io_info->sel_pieces[i];
/* Skip over filtered pieces as they are processed elsewhere */
if (piece_info->filtered_dset)
continue;
/* Obtain disk and memory MPI derived datatype */
/* NOTE: The permute_map array can be allocated within H5S_mpio_space_type
* and will be fed into the next call to H5S_mpio_space_type
* where it will be freed.
*/
if (H5S_mpio_space_type(piece_info->fspace, piece_info->dset_info->type_info.src_type_size,
&chunk_ftype[curr_idx], /* OUT: datatype created */
&chunk_mpi_file_counts[curr_idx], /* OUT */
&(chunk_mft_is_derived_array[curr_idx]), /* OUT */
true, /* this is a file space,
so permute the
datatype if the point
selections are out of
order */
&permute_map, /* OUT: a map to indicate the
permutation of points
selected in case they
are out of order */
&is_permuted /* OUT */) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI file type");
/* Sanity check */
if (is_permuted)
assert(permute_map);
if (H5S_mpio_space_type(piece_info->mspace, piece_info->dset_info->type_info.dst_type_size,
&chunk_mtype[curr_idx], &chunk_mpi_mem_counts[curr_idx],
&(chunk_mbt_is_derived_array[curr_idx]), false, /* this is a memory
space, so if the
file space is not
permuted, there is
no need to permute
the datatype if the
point selections
are out of order */
&permute_map, /* IN: the permutation map
generated by the
file_space selection
and applied to the
memory selection */
&is_permuted /* IN */) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI buf type");
/* Sanity check */
if (is_permuted)
assert(!permute_map);
/* Piece address relative to the first piece addr
* Assign piece address to MPI displacement
* (assume MPI_Aint big enough to hold it) */
chunk_file_disp_array[curr_idx] =
(MPI_Aint)piece_info->faddr - (MPI_Aint)ctg_store.contig.dset_addr;
if (io_info->op_type == H5D_IO_OP_WRITE) {
chunk_mem_disp_array[curr_idx] =
(MPI_Aint)piece_info->dset_info->buf.cvp - (MPI_Aint)base_buf_addr.cvp;
}
else if (io_info->op_type == H5D_IO_OP_READ) {
chunk_mem_disp_array[curr_idx] =
(MPI_Aint)piece_info->dset_info->buf.vp - (MPI_Aint)base_buf_addr.vp;
}
curr_idx++;
} /* end for */
/* Create final MPI derived datatype for the file */
if (MPI_SUCCESS !=
(mpi_code = MPI_Type_create_struct((int)num_chunk, chunk_mpi_file_counts,
chunk_file_disp_array, chunk_ftype, &chunk_final_ftype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&chunk_final_ftype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
chunk_final_ftype_is_derived = true;
/* Create final MPI derived datatype for memory */
if (MPI_SUCCESS !=
(mpi_code = MPI_Type_create_struct((int)num_chunk, chunk_mpi_mem_counts, chunk_mem_disp_array,
chunk_mtype, &chunk_final_mtype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(&chunk_final_mtype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
chunk_final_mtype_is_derived = true;
/* Free the file & memory MPI datatypes for each chunk */
for (size_t i = 0; i < num_chunk; i++) {
if (chunk_mbt_is_derived_array[i])
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(chunk_mtype + i)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
if (chunk_mft_is_derived_array[i])
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(chunk_ftype + i)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
} /* end for */
/* We have a single, complicated MPI datatype for both memory & file */
mpi_buf_count = (hsize_t)1;
} /* end if */
else { /* no selection at all for this process */
ctg_store.contig.dset_addr = 0;
/* just provide a valid mem address. no actual IO occur */
base_buf_addr = io_info->dsets_info[0].buf;
/* Set the MPI datatype */
chunk_final_ftype = MPI_BYTE;
chunk_final_mtype = MPI_BYTE;
/* No chunks selected for this process */
mpi_buf_count = (hsize_t)0;
} /* end else */
#ifdef H5Dmpio_DEBUG
H5D_MPIO_DEBUG(mpi_rank, "before coming to final collective I/O");
#endif
/* Set up the base storage address for this piece */
io_info->store_faddr = ctg_store.contig.dset_addr;
io_info->base_maddr = base_buf_addr;
/* Perform final collective I/O operation */
if (H5D__final_collective_io(io_info, mpi_buf_count, chunk_final_ftype, chunk_final_mtype) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish MPI-IO");
}
done:
#ifdef H5Dmpio_DEBUG
H5D_MPIO_DEBUG_VA(mpi_rank, "before freeing memory inside H5D_link_collective_io ret_value = %d",
ret_value);
#endif
if (ret_value < 0)
H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_NO_CHUNK_OPTIMIZATION);
/* Release resources */
if (chunk_mtype)
H5MM_xfree(chunk_mtype);
if (chunk_ftype)
H5MM_xfree(chunk_ftype);
if (chunk_file_disp_array)
H5MM_xfree(chunk_file_disp_array);
if (chunk_mem_disp_array)
H5MM_xfree(chunk_mem_disp_array);
if (chunk_mpi_mem_counts)
H5MM_xfree(chunk_mpi_mem_counts);
if (chunk_mpi_file_counts)
H5MM_xfree(chunk_mpi_file_counts);
if (chunk_mbt_is_derived_array)
H5MM_xfree(chunk_mbt_is_derived_array);
if (chunk_mft_is_derived_array)
H5MM_xfree(chunk_mft_is_derived_array);
/* Free the MPI buf and file types, if they were derived */
if (chunk_final_mtype_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_final_mtype)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
if (chunk_final_ftype_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_final_ftype)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__link_piece_collective_io */
/*-------------------------------------------------------------------------
* Function: H5D__link_chunk_filtered_collective_io
*
* Purpose: Performs collective I/O on filtered chunks by creating a
* single MPI derived datatype to link with all filtered
* chunks. The general algorithm is as follows:
*
* 1. Construct a list of selected chunks in the collective
* I/O operation
* 2. If the operation is a read operation
* A. Ensure that the list of chunks is sorted in
* monotonically non-decreasing order of chunk offset
* in the file
* B. Participate in a collective read of chunks from
* the file
* C. Loop through each selected chunk, unfiltering it and
* scattering the data to the application's read buffer
* 3. If the operation is a write operation
* A. Redistribute any chunks being written by more than 1
* MPI rank, such that the chunk is only owned by 1 MPI
* rank. The rank writing to the chunk which currently
* has the least amount of chunks assigned to it becomes
* the new owner (in the case of ties, the lowest MPI
* rank becomes the new owner)
* B. Participate in a collective read of chunks from the
* file
* C. Loop through each chunk selected in the operation
* and for each chunk:
* I. If we actually read the chunk from the file (if
* a chunk is being fully overwritten, we skip
* reading it), pass the chunk through the filter
* pipeline in reverse order (unfilter the chunk)
* II. Update the chunk data with the modifications from
* the owning MPI rank
* III. Receive any modification data from other
* ranks and update the chunk data with those
* modifications
* IV. Filter the chunk
* D. Contribute the modified chunks to an array gathered
* by all ranks which contains information for
* re-allocating space in the file for every chunk
* modified. Then, each rank collectively re-allocates
* each chunk from the gathered array with their new
* sizes after the filter operation
* E. Proceed with the collective write operation for all
* the modified chunks
* F. Contribute the modified chunks to an array gathered
* by all ranks which contains information for
* re-inserting every chunk modified into the chunk
* index. Then, each rank collectively re-inserts each
* chunk from the gathered array into the chunk index
*
* TODO: Note that steps D. and F. here are both collective
* operations that partially share data from the
* H5D_filtered_collective_chunk_info_t structure. To
* try to conserve on memory a bit, the distributed
* arrays these operations create are discarded after
* each operation is performed. If memory consumption
* here proves to not be an issue, the necessary data
* for both operations could be combined into a single
* structure so that only one collective MPI operation
* is needed to carry out both operations, rather than
* two.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_infos,
size_t num_dset_infos, int mpi_rank, int mpi_size)
{
H5D_filtered_collective_io_info_t chunk_list = {0};
unsigned char **chunk_msg_bufs = NULL;
size_t *rank_chunks_assigned_map = NULL;
int chunk_msg_bufs_len = 0;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(io_info);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_DEBUG_VA(mpi_rank, "Performing Linked-chunk I/O (%s) with MPI Comm size of %d",
io_info->op_type == H5D_IO_OP_WRITE ? "write" : "read", mpi_size);
H5D_MPIO_TIME_START(mpi_rank, "Linked-chunk I/O");
#endif
/* Set the actual-chunk-opt-mode property. */
H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_LINK_CHUNK);
/* Set the actual-io-mode property.
* Link chunk filtered I/O does not break to independent, so can set right away
*/
H5CX_set_mpio_actual_io_mode(H5D_MPIO_CHUNK_COLLECTIVE);
/* Build a list of selected chunks in the collective io operation */
if (H5D__mpio_collective_filtered_chunk_io_setup(io_info, dset_infos, num_dset_infos, mpi_rank,
&chunk_list) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't construct filtered I/O info list");
if (io_info->op_type == H5D_IO_OP_READ) { /* Filtered collective read */
if (H5D__mpio_collective_filtered_chunk_read(&chunk_list, io_info, num_dset_infos, mpi_rank) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't read filtered chunks");
}
else { /* Filtered collective write */
if (mpi_size > 1) {
/* Redistribute shared chunks being written to */
if (H5D__mpio_redistribute_shared_chunks(&chunk_list, io_info, mpi_rank, mpi_size,
&rank_chunks_assigned_map) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to redistribute shared chunks");
/* Send any chunk modification messages for chunks this rank no longer owns */
if (H5D__mpio_share_chunk_modification_data(&chunk_list, io_info, mpi_rank, mpi_size,
&chunk_msg_bufs, &chunk_msg_bufs_len) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"unable to send chunk modification data between MPI ranks");
/* Make sure the local chunk list was updated correctly */
assert(chunk_list.num_chunk_infos == rank_chunks_assigned_map[mpi_rank]);
}
/* Proceed to update all the chunks this rank owns with its own
* modification data and data from other ranks, before re-filtering
* the chunks. As chunk reads are done collectively here, all ranks
* must participate.
*/
if (H5D__mpio_collective_filtered_chunk_update(&chunk_list, chunk_msg_bufs, chunk_msg_bufs_len,
io_info, num_dset_infos, mpi_rank) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't update modified chunks");
/* Free up resources used by chunk hash table now that we're done updating chunks */
HASH_CLEAR(hh, chunk_list.chunk_hash_table);
/* All ranks now collectively re-allocate file space for all chunks */
if (H5D__mpio_collective_filtered_chunk_reallocate(&chunk_list, rank_chunks_assigned_map, io_info,
num_dset_infos, mpi_rank, mpi_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"couldn't collectively re-allocate file space for chunks");
/* Perform vector I/O on chunks */
if (H5D__mpio_collective_filtered_vec_io(&chunk_list, io_info->f_sh, io_info->op_type) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't perform vector I/O on filtered chunks");
/* Free up resources in anticipation of following collective operation */
for (size_t i = 0; i < chunk_list.num_chunk_infos; i++) {
if (chunk_list.chunk_infos[i].buf) {
H5MM_free(chunk_list.chunk_infos[i].buf);
chunk_list.chunk_infos[i].buf = NULL;
}
}
/* Participate in the collective re-insertion of all chunks modified
* into the chunk index
*/
if (H5D__mpio_collective_filtered_chunk_reinsert(&chunk_list, rank_chunks_assigned_map, io_info,
num_dset_infos, mpi_rank, mpi_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"couldn't collectively re-insert modified chunks into chunk index");
}
done:
if (ret_value < 0)
H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_NO_CHUNK_OPTIMIZATION);
if (chunk_msg_bufs) {
for (size_t i = 0; i < (size_t)chunk_msg_bufs_len; i++)
H5MM_free(chunk_msg_bufs[i]);
H5MM_free(chunk_msg_bufs);
}
HASH_CLEAR(hh, chunk_list.chunk_hash_table);
if (rank_chunks_assigned_map)
H5MM_free(rank_chunks_assigned_map);
/* Free resources used by a rank which had some selection */
if (chunk_list.chunk_infos) {
for (size_t i = 0; i < chunk_list.num_chunk_infos; i++)
if (chunk_list.chunk_infos[i].buf)
H5MM_free(chunk_list.chunk_infos[i].buf);
H5MM_free(chunk_list.chunk_infos);
} /* end if */
/* Free resources used by cached dataset info */
if ((num_dset_infos == 1) && (chunk_list.dset_info.single_dset_info)) {
H5D_mpio_filtered_dset_info_t *curr_dset_info = chunk_list.dset_info.single_dset_info;
if (curr_dset_info->fb_info_init && H5D__fill_term(&curr_dset_info->fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release fill buffer info");
if (curr_dset_info->fill_space && H5S_close(curr_dset_info->fill_space) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close fill space");
H5MM_free(chunk_list.dset_info.single_dset_info);
chunk_list.dset_info.single_dset_info = NULL;
}
else if ((num_dset_infos > 1) && (chunk_list.dset_info.dset_info_hash_table)) {
H5D_mpio_filtered_dset_info_t *curr_dset_info;
H5D_mpio_filtered_dset_info_t *tmp;
HASH_ITER(hh, chunk_list.dset_info.dset_info_hash_table, curr_dset_info, tmp)
{
HASH_DELETE(hh, chunk_list.dset_info.dset_info_hash_table, curr_dset_info);
if (curr_dset_info->fb_info_init && H5D__fill_term(&curr_dset_info->fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release fill buffer info");
if (curr_dset_info->fill_space && H5S_close(curr_dset_info->fill_space) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close fill space");
H5MM_free(curr_dset_info);
curr_dset_info = NULL;
}
}
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__link_chunk_filtered_collective_io() */
/*-------------------------------------------------------------------------
* Function: H5D__multi_chunk_collective_io
*
* Purpose: To do IO per chunk according to IO mode(collective/independent/none)
*
* 1. Use MPI_gather and MPI_Bcast to obtain IO mode in each chunk(collective/independent/none)
* 2. Depending on whether the IO mode is collective or independent or none,
* Create either MPI derived datatype for each chunk or just do independent IO
* 3. Use common collective IO routine to do MPI-IO
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__multi_chunk_collective_io(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_info, int mpi_rank,
int mpi_size)
{
uint8_t *chunk_io_option = NULL;
haddr_t *chunk_addr = NULL;
H5D_storage_t store; /* union of EFL and chunk pointer in file space */
H5FD_mpio_collective_opt_t last_coll_opt_mode =
H5FD_MPIO_COLLECTIVE_IO; /* Last parallel transfer with independent IO or collective IO with this mode
*/
H5FD_mpio_collective_opt_t orig_coll_opt_mode =
H5FD_MPIO_COLLECTIVE_IO; /* Original parallel transfer property on entering this function */
size_t total_chunk; /* Total # of chunks in dataset */
size_t num_chunk; /* Number of chunks for this process */
H5SL_node_t *piece_node = NULL; /* Current node in chunk skip list */
H5D_piece_info_t *next_chunk_info = NULL; /* Chunk info for next selected chunk */
size_t u; /* Local index variable */
H5D_mpio_actual_io_mode_t actual_io_mode =
H5D_MPIO_NO_COLLECTIVE; /* Local variable for tracking the I/O mode used. */
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE_TAG(dset_info->dset->oloc.addr)
assert(dset_info->layout->type == H5D_CHUNKED);
/* Get the current I/O collective opt mode so we can restore it later */
if (H5CX_get_mpio_coll_opt(&orig_coll_opt_mode) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get MPI-I/O collective_op property");
/* Set the actual chunk opt mode property */
H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_MULTI_CHUNK);
/* Retrieve total # of chunks in dataset */
H5_CHECKED_ASSIGN(total_chunk, size_t, dset_info->layout->u.chunk.nchunks, hsize_t);
assert(total_chunk != 0);
/* Allocate memories */
chunk_io_option = (uint8_t *)H5MM_calloc(total_chunk);
chunk_addr = (haddr_t *)H5MM_calloc(total_chunk * sizeof(haddr_t));
#ifdef H5Dmpio_DEBUG
H5D_MPIO_DEBUG_VA(mpi_rank, "total_chunk %zu", total_chunk);
#endif
/* Obtain IO option for each chunk */
if (H5D__obtain_mpio_mode(io_info, dset_info, chunk_io_option, chunk_addr, mpi_rank, mpi_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTRECV, FAIL, "unable to obtain MPIO mode");
/* Set memory buffers */
io_info->base_maddr = dset_info->buf;
/* Set dataset storage for I/O info */
dset_info->store = &store;
/* Get the number of chunks with a selection */
num_chunk = H5SL_count(dset_info->layout_io_info.chunk_map->dset_sel_pieces);
if (num_chunk) {
/* Start at the beginning of the chunk map skiplist. Since these chunks are
* stored in index order and since we're iterating in index order we can
* just check for each chunk being selected in order */
if (NULL == (piece_node = H5SL_first(dset_info->layout_io_info.chunk_map->dset_sel_pieces)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't get piece node from skip list");
if (NULL == (next_chunk_info = (H5D_piece_info_t *)H5SL_item(piece_node)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't get piece info from skip list");
}
/* Loop over _all_ the chunks */
for (u = 0; u < total_chunk; u++) {
H5D_piece_info_t *chunk_info; /* Chunk info for current chunk */
H5S_t *fspace; /* Dataspace describing chunk & selection in it */
H5S_t *mspace; /* Dataspace describing selection in memory corresponding to this chunk */
#ifdef H5Dmpio_DEBUG
H5D_MPIO_DEBUG_VA(mpi_rank, "mpi_rank = %d, chunk index = %zu", mpi_rank, u);
#endif
/* Check if this chunk is the next chunk in the skip list, if there are
* selected chunks left to process */
assert(!num_chunk || next_chunk_info);
assert(!num_chunk || next_chunk_info->index >= u);
if (num_chunk && next_chunk_info->index == u) {
/* Next chunk is this chunk */
chunk_info = next_chunk_info;
/* One less chunk to process */
num_chunk--;
/* Advance next chunk to next node in skip list, if there are more chunks selected */
if (num_chunk) {
if (NULL == (piece_node = H5SL_next(piece_node)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk skip list terminated early");
if (NULL == (next_chunk_info = (H5D_piece_info_t *)H5SL_item(piece_node)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't get piece info from skip list");
}
/* Pass in chunk's coordinates in a union. */
store.chunk.scaled = chunk_info->scaled;
}
else
chunk_info = NULL;
/* Collective IO for this chunk,
* Note: even there is no selection for this process, the process still
* needs to contribute MPI NONE TYPE.
*/
if (chunk_io_option[u] == H5D_CHUNK_IO_MODE_COL) {
#ifdef H5Dmpio_DEBUG
H5D_MPIO_DEBUG_VA(mpi_rank, "inside collective chunk IO mpi_rank = %d, chunk index = %zu",
mpi_rank, u);
#endif
/* Set the file & memory dataspaces */
if (chunk_info) {
fspace = chunk_info->fspace;
mspace = chunk_info->mspace;
/* Update the local variable tracking the actual io mode property.
*
* Note: H5D_MPIO_COLLECTIVE_MULTI | H5D_MPIO_INDEPENDENT = H5D_MPIO_MIXED
* to ease switching between to mixed I/O without checking the current
* value of the property. You can see the definition in H5Ppublic.h
*/
actual_io_mode = (H5D_mpio_actual_io_mode_t)(actual_io_mode | H5D_MPIO_CHUNK_COLLECTIVE);
} /* end if */
else {
fspace = mspace = NULL;
} /* end else */
/* Switch back to collective I/O */
if (last_coll_opt_mode != H5FD_MPIO_COLLECTIVE_IO) {
if (H5CX_set_mpio_coll_opt(H5FD_MPIO_COLLECTIVE_IO) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't switch to collective I/O");
last_coll_opt_mode = H5FD_MPIO_COLLECTIVE_IO;
} /* end if */
/* Initialize temporary contiguous storage address */
io_info->store_faddr = chunk_addr[u];
/* Perform the I/O */
if (H5D__inter_collective_io(io_info, dset_info, fspace, mspace) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish shared collective MPI-IO");
} /* end if */
else { /* possible independent IO for this chunk */
#ifdef H5Dmpio_DEBUG
H5D_MPIO_DEBUG_VA(mpi_rank, "inside independent IO mpi_rank = %d, chunk index = %zu", mpi_rank,
u);
#endif
assert(chunk_io_option[u] == 0);
/* Set the file & memory dataspaces */
if (chunk_info) {
fspace = chunk_info->fspace;
mspace = chunk_info->mspace;
/* Update the local variable tracking the actual io mode. */
actual_io_mode = (H5D_mpio_actual_io_mode_t)(actual_io_mode | H5D_MPIO_CHUNK_INDEPENDENT);
} /* end if */
else {
fspace = mspace = NULL;
} /* end else */
/* Using independent I/O with file setview.*/
if (last_coll_opt_mode != H5FD_MPIO_INDIVIDUAL_IO) {
if (H5CX_set_mpio_coll_opt(H5FD_MPIO_INDIVIDUAL_IO) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't switch to individual I/O");
last_coll_opt_mode = H5FD_MPIO_INDIVIDUAL_IO;
} /* end if */
/* Initialize temporary contiguous storage address */
io_info->store_faddr = chunk_addr[u];
/* Perform the I/O */
if (H5D__inter_collective_io(io_info, dset_info, fspace, mspace) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish shared collective MPI-IO");
#ifdef H5Dmpio_DEBUG
H5D_MPIO_DEBUG(mpi_rank, "after inter collective IO");
#endif
} /* end else */
} /* end for */
/* Write the local value of actual io mode to the API context. */
H5CX_set_mpio_actual_io_mode(actual_io_mode);
done:
if (ret_value < 0)
H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_NO_CHUNK_OPTIMIZATION);
/* Reset collective opt mode */
if (H5CX_set_mpio_coll_opt(orig_coll_opt_mode) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't reset MPI-I/O collective_op property");
/* Free memory */
if (chunk_io_option)
H5MM_xfree(chunk_io_option);
if (chunk_addr)
H5MM_xfree(chunk_addr);
FUNC_LEAVE_NOAPI_TAG(ret_value)
} /* end H5D__multi_chunk_collective_io */
/*-------------------------------------------------------------------------
* Function: H5D__multi_chunk_filtered_collective_io
*
* Purpose: Performs collective I/O on filtered chunks iteratively to
* save on memory and potentially get better performance
* depending on the average number of chunks per rank. While
* linked-chunk I/O will construct and work on a list of all
* of the chunks selected in the I/O operation at once, this
* function works iteratively on a set of chunks at a time; at
* most one chunk per rank per iteration. The general
* algorithm is as follows:
*
* 1. Construct a list of selected chunks in the collective
* I/O operation
* 2. If the operation is a read operation, loop an amount of
* times equal to the maximum number of chunks selected on
* any particular rank and on each iteration:
* A. Participate in a collective read of chunks from
* the file (ranks that run out of chunks still need
* to participate)
* B. Unfilter the chunk that was read (if any)
* C. Scatter the read chunk's data to the application's
* read buffer
* 3. If the operation is a write operation, redistribute any
* chunks being written to by more than 1 MPI rank, such
* that the chunk is only owned by 1 MPI rank. The rank
* writing to the chunk which currently has the least
* amount of chunks assigned to it becomes the new owner
* (in the case of ties, the lowest MPI rank becomes the
* new owner). Then, loop an amount of times equal to the
* maximum number of chunks selected on any particular
* rank and on each iteration:
* A. Participate in a collective read of chunks from
* the file (ranks that run out of chunks still need
* to participate)
* I. If we actually read a chunk from the file (if
* a chunk is being fully overwritten, we skip
* reading it), pass the chunk through the filter
* pipeline in reverse order (unfilter the chunk)
* B. Update the chunk data with the modifications from
* the owning rank
* C. Receive any modification data from other ranks and
* update the chunk data with those modifications
* D. Filter the chunk
* E. Contribute the chunk to an array gathered by
* all ranks which contains information for
* re-allocating space in the file for every chunk
* modified in this iteration (up to one chunk per
* rank; some ranks may not have a selection/may have
* less chunks to work on than other ranks). Then,
* each rank collectively re-allocates each chunk
* from the gathered array with their new sizes
* after the filter operation
* F. Proceed with the collective write operation
* for the chunks modified on this iteration
* G. Contribute the chunk to an array gathered by
* all ranks which contains information for
* re-inserting every chunk modified on this
* iteration into the chunk index. Then, each rank
* collectively re-inserts each chunk from the
* gathered array into the chunk index
*
* TODO: Note that steps E. and G. here are both collective
* operations that partially share data from the
* H5D_filtered_collective_chunk_info_t structure. To
* try to conserve on memory a bit, the distributed
* arrays these operations create are discarded after
* each operation is performed. If memory consumption
* here proves to not be an issue, the necessary data
* for both operations could be combined into a single
* structure so that only one collective MPI operation
* is needed to carry out both operations, rather than
* two.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, H5D_dset_io_info_t *dset_infos,
size_t num_dset_infos, int mpi_rank, int mpi_size)
{
H5D_filtered_collective_io_info_t chunk_list = {0};
unsigned char **chunk_msg_bufs = NULL;
bool have_chunk_to_process;
size_t max_num_chunks;
int chunk_msg_bufs_len = 0;
int mpi_code;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE_TAG(dset_infos->dset->oloc.addr)
assert(io_info);
assert(num_dset_infos == 1); /* Currently only supported with 1 dataset at a time */
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_DEBUG_VA(mpi_rank, "Performing Multi-chunk I/O (%s) with MPI Comm size of %d",
io_info->op_type == H5D_IO_OP_WRITE ? "write" : "read", mpi_size);
H5D_MPIO_TIME_START(mpi_rank, "Multi-chunk I/O");
#endif
/* Set the actual chunk opt mode property */
H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_MULTI_CHUNK);
/* Set the actual_io_mode property.
* Multi chunk I/O does not break to independent, so can set right away
*/
H5CX_set_mpio_actual_io_mode(H5D_MPIO_CHUNK_COLLECTIVE);
/* Build a list of selected chunks in the collective IO operation */
if (H5D__mpio_collective_filtered_chunk_io_setup(io_info, dset_infos, 1, mpi_rank, &chunk_list) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "couldn't construct filtered I/O info list");
/* Retrieve the maximum number of chunks selected for any rank */
if (MPI_SUCCESS != (mpi_code = MPI_Allreduce(&chunk_list.num_chunk_infos, &max_num_chunks, 1,
MPI_UNSIGNED_LONG_LONG, MPI_MAX, io_info->comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code)
/* If no one has anything selected at all, end the operation */
if (0 == max_num_chunks)
HGOTO_DONE(SUCCEED);
if (io_info->op_type == H5D_IO_OP_READ) { /* Filtered collective read */
for (size_t i = 0; i < max_num_chunks; i++) {
H5D_filtered_collective_io_info_t single_chunk_list = chunk_list;
/* Check if this rank has a chunk to work on for this iteration */
have_chunk_to_process = (i < chunk_list.num_chunk_infos);
/*
* Setup a chunk list structure for either 1 or 0 chunks, depending
* on whether this rank has a chunk to work on for this iteration
*/
if (have_chunk_to_process) {
single_chunk_list.chunk_infos = &chunk_list.chunk_infos[i];
single_chunk_list.num_chunk_infos = 1;
single_chunk_list.num_chunks_to_read = chunk_list.chunk_infos[i].need_read ? 1 : 0;
}
else {
single_chunk_list.chunk_infos = NULL;
single_chunk_list.num_chunk_infos = 0;
single_chunk_list.num_chunks_to_read = 0;
}
if (H5D__mpio_collective_filtered_chunk_read(&single_chunk_list, io_info, 1, mpi_rank) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't read filtered chunks");
if (have_chunk_to_process && chunk_list.chunk_infos[i].buf) {
H5MM_free(chunk_list.chunk_infos[i].buf);
chunk_list.chunk_infos[i].buf = NULL;
}
}
}
else { /* Filtered collective write */
if (mpi_size > 1) {
/* Redistribute shared chunks being written to */
if (H5D__mpio_redistribute_shared_chunks(&chunk_list, io_info, mpi_rank, mpi_size, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to redistribute shared chunks");
/* Send any chunk modification messages for chunks this rank no longer owns */
if (H5D__mpio_share_chunk_modification_data(&chunk_list, io_info, mpi_rank, mpi_size,
&chunk_msg_bufs, &chunk_msg_bufs_len) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"unable to send chunk modification data between MPI ranks");
}
/* Iterate over the max number of chunks among all ranks, as this rank could
* have no chunks left to work on, but it still needs to participate in the
* collective re-allocation and re-insertion of chunks modified by other ranks.
*/
for (size_t i = 0; i < max_num_chunks; i++) {
H5D_filtered_collective_io_info_t single_chunk_list = chunk_list;
/* Check if this rank has a chunk to work on for this iteration */
have_chunk_to_process =
(i < chunk_list.num_chunk_infos) && (mpi_rank == chunk_list.chunk_infos[i].new_owner);
/*
* Setup a chunk list structure for either 1 or 0 chunks, depending
* on whether this rank has a chunk to work on for this iteration
*/
if (have_chunk_to_process) {
single_chunk_list.chunk_infos = &chunk_list.chunk_infos[i];
single_chunk_list.num_chunk_infos = 1;
single_chunk_list.num_chunks_to_read = chunk_list.chunk_infos[i].need_read ? 1 : 0;
}
else {
single_chunk_list.chunk_infos = NULL;
single_chunk_list.num_chunk_infos = 0;
single_chunk_list.num_chunks_to_read = 0;
}
/* Proceed to update the chunk this rank owns (if any left) with its
* own modification data and data from other ranks, before re-filtering
* the chunks. As chunk reads are done collectively here, all ranks
* must participate.
*/
if (H5D__mpio_collective_filtered_chunk_update(&single_chunk_list, chunk_msg_bufs,
chunk_msg_bufs_len, io_info, 1, mpi_rank) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't update modified chunks");
/* All ranks now collectively re-allocate file space for all chunks */
if (H5D__mpio_collective_filtered_chunk_reallocate(&single_chunk_list, NULL, io_info, 1, mpi_rank,
mpi_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"couldn't collectively re-allocate file space for chunks");
/* Perform vector I/O on chunks */
if (H5D__mpio_collective_filtered_vec_io(&single_chunk_list, io_info->f_sh, io_info->op_type) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"couldn't perform vector I/O on filtered chunks");
/* Free up resources in anticipation of following collective operation */
if (have_chunk_to_process && chunk_list.chunk_infos[i].buf) {
H5MM_free(chunk_list.chunk_infos[i].buf);
chunk_list.chunk_infos[i].buf = NULL;
}
/* Participate in the collective re-insertion of all chunks modified
* in this iteration into the chunk index
*/
if (H5D__mpio_collective_filtered_chunk_reinsert(&single_chunk_list, NULL, io_info, 1, mpi_rank,
mpi_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"couldn't collectively re-insert modified chunks into chunk index");
} /* end for */
}
done:
if (ret_value < 0)
H5CX_set_mpio_actual_chunk_opt(H5D_MPIO_NO_CHUNK_OPTIMIZATION);
if (chunk_msg_bufs) {
for (size_t i = 0; i < (size_t)chunk_msg_bufs_len; i++)
H5MM_free(chunk_msg_bufs[i]);
H5MM_free(chunk_msg_bufs);
}
HASH_CLEAR(hh, chunk_list.chunk_hash_table);
/* Free resources used by a rank which had some selection */
if (chunk_list.chunk_infos) {
for (size_t i = 0; i < chunk_list.num_chunk_infos; i++)
if (chunk_list.chunk_infos[i].buf)
H5MM_free(chunk_list.chunk_infos[i].buf);
H5MM_free(chunk_list.chunk_infos);
} /* end if */
/* Free resources used by cached dataset info */
if ((num_dset_infos == 1) && (chunk_list.dset_info.single_dset_info)) {
H5D_mpio_filtered_dset_info_t *curr_dset_info = chunk_list.dset_info.single_dset_info;
if (curr_dset_info->fb_info_init && H5D__fill_term(&curr_dset_info->fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release fill buffer info");
if (curr_dset_info->fill_space && H5S_close(curr_dset_info->fill_space) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close fill space");
H5MM_free(chunk_list.dset_info.single_dset_info);
chunk_list.dset_info.single_dset_info = NULL;
}
else if ((num_dset_infos > 1) && (chunk_list.dset_info.dset_info_hash_table)) {
H5D_mpio_filtered_dset_info_t *curr_dset_info;
H5D_mpio_filtered_dset_info_t *tmp;
HASH_ITER(hh, chunk_list.dset_info.dset_info_hash_table, curr_dset_info, tmp)
{
HASH_DELETE(hh, chunk_list.dset_info.dset_info_hash_table, curr_dset_info);
if (curr_dset_info->fb_info_init && H5D__fill_term(&curr_dset_info->fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release fill buffer info");
if (curr_dset_info->fill_space && H5S_close(curr_dset_info->fill_space) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close fill space");
H5MM_free(curr_dset_info);
curr_dset_info = NULL;
}
}
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI_TAG(ret_value)
} /* end H5D__multi_chunk_filtered_collective_io() */
/*-------------------------------------------------------------------------
* Function: H5D__inter_collective_io
*
* Purpose: Routine for the shared part of collective IO between multiple chunk
* collective IO and contiguous collective IO
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__inter_collective_io(H5D_io_info_t *io_info, const H5D_dset_io_info_t *di, H5S_t *file_space,
H5S_t *mem_space)
{
int mpi_buf_count; /* # of MPI types */
bool mbt_is_derived = false;
bool mft_is_derived = false;
MPI_Datatype mpi_file_type, mpi_buf_type;
int mpi_code; /* MPI return code */
#ifdef H5Dmpio_DEBUG
int mpi_rank;
#endif
herr_t ret_value = SUCCEED; /* return value */
FUNC_ENTER_PACKAGE
#ifdef H5Dmpio_DEBUG
mpi_rank = H5F_mpi_get_rank(di->dset->oloc.file);
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_TIME_START(mpi_rank, "Inter collective I/O");
if (mpi_rank < 0)
HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain MPI rank");
#endif
assert(io_info);
if ((file_space != NULL) && (mem_space != NULL)) {
int mpi_file_count; /* Number of file "objects" to transfer */
hsize_t *permute_map = NULL; /* array that holds the mapping from the old,
out-of-order displacements to the in-order
displacements of the MPI datatypes of the
point selection of the file space */
bool is_permuted = false;
assert(di);
/* Obtain disk and memory MPI derived datatype */
/* NOTE: The permute_map array can be allocated within H5S_mpio_space_type
* and will be fed into the next call to H5S_mpio_space_type
* where it will be freed.
*/
if (H5S_mpio_space_type(file_space, di->type_info.src_type_size, &mpi_file_type, &mpi_file_count,
&mft_is_derived, /* OUT: datatype created */
true, /* this is a file space, so
permute the datatype if the
point selection is out of
order */
&permute_map, /* OUT: a map to indicate
the permutation of
points selected in
case they are out of
order */
&is_permuted /* OUT */) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI file type");
/* Sanity check */
if (is_permuted)
assert(permute_map);
if (H5S_mpio_space_type(mem_space, di->type_info.src_type_size, &mpi_buf_type, &mpi_buf_count,
&mbt_is_derived, /* OUT: datatype created */
false, /* this is a memory space, so if
the file space is not
permuted, there is no need to
permute the datatype if the
point selections are out of
order*/
&permute_map /* IN: the permutation map
generated by the
file_space selection
and applied to the
memory selection */
,
&is_permuted /* IN */) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "couldn't create MPI buffer type");
/* Sanity check */
if (is_permuted)
assert(!permute_map);
} /* end if */
else {
/* For non-selection, participate with a none MPI derived datatype, the count is 0. */
mpi_buf_type = MPI_BYTE;
mpi_file_type = MPI_BYTE;
mpi_buf_count = 0;
mbt_is_derived = false;
mft_is_derived = false;
} /* end else */
#ifdef H5Dmpio_DEBUG
H5D_MPIO_DEBUG(mpi_rank, "before final collective I/O");
#endif
/* Perform final collective I/O operation */
if (H5D__final_collective_io(io_info, (hsize_t)mpi_buf_count, mpi_file_type, mpi_buf_type) < 0)
HGOTO_ERROR(H5E_IO, H5E_CANTGET, FAIL, "couldn't finish collective MPI-IO");
done:
/* Free the MPI buf and file types, if they were derived */
if (mbt_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mpi_buf_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
if (mft_is_derived && MPI_SUCCESS != (mpi_code = MPI_Type_free(&mpi_file_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_DEBUG_VA(mpi_rank, "before leaving inter_collective_io ret_value = %d", ret_value);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__inter_collective_io() */
/*-------------------------------------------------------------------------
* Function: H5D__final_collective_io
*
* Purpose: Routine for the common part of collective IO with different storages.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__final_collective_io(H5D_io_info_t *io_info, hsize_t mpi_buf_count, MPI_Datatype mpi_file_type,
MPI_Datatype mpi_buf_type)
{
#ifdef H5Dmpio_DEBUG
int mpi_rank;
#endif
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
#ifdef H5Dmpio_DEBUG
mpi_rank = H5F_mpi_get_rank(io_info->dsets_info[0].dset->oloc.file);
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_TIME_START(mpi_rank, "Final collective I/O");
if (mpi_rank < 0)
HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain MPI rank");
#endif
/* Pass buf type, file type to the file driver. */
if (H5CX_set_mpi_coll_datatypes(mpi_buf_type, mpi_file_type) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set MPI-I/O collective I/O datatypes");
if (io_info->op_type == H5D_IO_OP_WRITE) {
if ((io_info->md_io_ops.single_write_md)(io_info, mpi_buf_count, NULL, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed");
} /* end if */
else {
if ((io_info->md_io_ops.single_read_md)(io_info, mpi_buf_count, NULL, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "optimized read failed");
} /* end else */
done:
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_DEBUG_VA(mpi_rank, "ret_value before leaving final_collective_io=%d", ret_value);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__final_collective_io */
/*-------------------------------------------------------------------------
* Function: H5D__cmp_piece_addr
*
* Purpose: Routine to compare piece addresses
*
* Description: Callback for qsort() to compare piece addresses
*
* Return: -1, 0, 1
*
*-------------------------------------------------------------------------
*/
static int
H5D__cmp_piece_addr(const void *piece_info1, const void *piece_info2)
{
haddr_t addr1;
haddr_t addr2;
FUNC_ENTER_PACKAGE_NOERR
addr1 = (*((const H5D_piece_info_t *const *)piece_info1))->faddr;
addr2 = (*((const H5D_piece_info_t *const *)piece_info2))->faddr;
FUNC_LEAVE_NOAPI(H5_addr_cmp(addr1, addr2))
} /* end H5D__cmp_chunk_addr() */
/*-------------------------------------------------------------------------
* Function: H5D__cmp_filtered_collective_io_info_entry
*
* Purpose: Routine to compare filtered collective chunk io info
* entries
*
* Description: Callback for qsort() to compare filtered collective chunk
* io info entries
*
* Return: -1, 0, 1
*
*-------------------------------------------------------------------------
*/
static int
H5D__cmp_filtered_collective_io_info_entry(const void *filtered_collective_io_info_entry1,
const void *filtered_collective_io_info_entry2)
{
const H5D_filtered_collective_chunk_info_t *entry1;
const H5D_filtered_collective_chunk_info_t *entry2;
haddr_t addr1 = HADDR_UNDEF;
haddr_t addr2 = HADDR_UNDEF;
int ret_value;
FUNC_ENTER_PACKAGE_NOERR
entry1 = (const H5D_filtered_collective_chunk_info_t *)filtered_collective_io_info_entry1;
entry2 = (const H5D_filtered_collective_chunk_info_t *)filtered_collective_io_info_entry2;
addr1 = entry1->chunk_new.offset;
addr2 = entry2->chunk_new.offset;
/*
* If both chunk's file addresses are defined, H5_addr_cmp is safe to use.
* If only one chunk's file address is defined, return the appropriate
* value based on which is defined. If neither chunk's file address is
* defined, compare chunk entries based on their dataset object header
* address, then by their chunk index value.
*/
if (H5_addr_defined(addr1) && H5_addr_defined(addr2)) {
ret_value = H5_addr_cmp(addr1, addr2);
}
else if (!H5_addr_defined(addr1) && !H5_addr_defined(addr2)) {
haddr_t oloc_addr1 = entry1->index_info.dset_oloc_addr;
haddr_t oloc_addr2 = entry2->index_info.dset_oloc_addr;
if (0 == (ret_value = H5_addr_cmp(oloc_addr1, oloc_addr2))) {
hsize_t chunk_idx1 = entry1->index_info.chunk_idx;
hsize_t chunk_idx2 = entry2->index_info.chunk_idx;
ret_value = (chunk_idx1 > chunk_idx2) - (chunk_idx1 < chunk_idx2);
}
}
else
ret_value = H5_addr_defined(addr1) ? 1 : -1;
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__cmp_filtered_collective_io_info_entry() */
/*-------------------------------------------------------------------------
* Function: H5D__cmp_chunk_redistribute_info
*
* Purpose: Routine to compare two H5D_chunk_redistribute_info_t
* structures
*
* Description: Callback for qsort() to compare two
* H5D_chunk_redistribute_info_t structures
*
* Return: -1, 0, 1
*
*-------------------------------------------------------------------------
*/
static int
H5D__cmp_chunk_redistribute_info(const void *_entry1, const void *_entry2)
{
const H5D_chunk_redistribute_info_t *entry1;
const H5D_chunk_redistribute_info_t *entry2;
haddr_t oloc_addr1;
haddr_t oloc_addr2;
int ret_value;
FUNC_ENTER_PACKAGE_NOERR
entry1 = (const H5D_chunk_redistribute_info_t *)_entry1;
entry2 = (const H5D_chunk_redistribute_info_t *)_entry2;
oloc_addr1 = entry1->dset_oloc_addr;
oloc_addr2 = entry2->dset_oloc_addr;
/* Sort first by dataset object header address */
if (0 == (ret_value = H5_addr_cmp(oloc_addr1, oloc_addr2))) {
hsize_t chunk_index1 = entry1->chunk_idx;
hsize_t chunk_index2 = entry2->chunk_idx;
/* Then by chunk index value */
if (chunk_index1 == chunk_index2) {
int orig_owner1 = entry1->orig_owner;
int orig_owner2 = entry2->orig_owner;
/* And finally by original owning MPI rank for the chunk */
ret_value = (orig_owner1 > orig_owner2) - (orig_owner1 < orig_owner2);
}
else
ret_value = (chunk_index1 > chunk_index2) - (chunk_index1 < chunk_index2);
}
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__cmp_chunk_redistribute_info() */
/*-------------------------------------------------------------------------
* Function: H5D__cmp_chunk_redistribute_info_orig_owner
*
* Purpose: Routine to compare the original owning MPI rank for two
* H5D_chunk_redistribute_info_t structures
*
* Description: Callback for qsort() to compare the original owning MPI
* rank for two H5D_chunk_redistribute_info_t
* structures
*
* NOTE: The inner logic used in this sorting callback (inside the
* block where the original owners are equal) is intended to
* cause the given array of H5D_chunk_redistribute_info_t
* structures to be sorted back exactly as it was sorted
* before a shared chunks redistribution operation, according
* to the logic in H5D__cmp_filtered_collective_io_info_entry.
* Since the two sorting callbacks are currently tied directly
* to each other, both should be updated in the same way when
* changes are made.
*
* Return: -1, 0, 1
*
*-------------------------------------------------------------------------
*/
static int
H5D__cmp_chunk_redistribute_info_orig_owner(const void *_entry1, const void *_entry2)
{
const H5D_chunk_redistribute_info_t *entry1;
const H5D_chunk_redistribute_info_t *entry2;
int owner1 = -1;
int owner2 = -1;
int ret_value;
FUNC_ENTER_PACKAGE_NOERR
entry1 = (const H5D_chunk_redistribute_info_t *)_entry1;
entry2 = (const H5D_chunk_redistribute_info_t *)_entry2;
owner1 = entry1->orig_owner;
owner2 = entry2->orig_owner;
if (owner1 == owner2) {
haddr_t addr1 = entry1->chunk_block.offset;
haddr_t addr2 = entry2->chunk_block.offset;
/*
* If both chunk's file addresses are defined, H5_addr_cmp is safe to use.
* If only one chunk's file address is defined, return the appropriate
* value based on which is defined. If neither chunk's file address is
* defined, compare chunk entries based on their dataset object header
* address, then by their chunk index value.
*/
if (H5_addr_defined(addr1) && H5_addr_defined(addr2)) {
ret_value = H5_addr_cmp(addr1, addr2);
}
else if (!H5_addr_defined(addr1) && !H5_addr_defined(addr2)) {
haddr_t oloc_addr1 = entry1->dset_oloc_addr;
haddr_t oloc_addr2 = entry2->dset_oloc_addr;
if (0 == (ret_value = H5_addr_cmp(oloc_addr1, oloc_addr2))) {
hsize_t chunk_idx1 = entry1->chunk_idx;
hsize_t chunk_idx2 = entry2->chunk_idx;
ret_value = (chunk_idx1 > chunk_idx2) - (chunk_idx1 < chunk_idx2);
}
}
else
ret_value = H5_addr_defined(addr1) ? 1 : -1;
}
else
ret_value = (owner1 > owner2) - (owner1 < owner2);
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__cmp_chunk_redistribute_info_orig_owner() */
/*-------------------------------------------------------------------------
* Function: H5D__obtain_mpio_mode
*
* Purpose: Routine to obtain each io mode(collective,independent or none) for each chunk;
* Each chunk address is also obtained.
*
* Description:
*
* 1) Each process provides two piece of information for all chunks having selection
* a) chunk index
* b) whether this chunk is regular(for MPI derived datatype not working case)
*
* 2) Gather all the information to the root process
*
* 3) Root process will do the following:
* a) Obtain chunk addresses for all chunks in this dataspace
* b) With the consideration of the user option, calculate IO mode for each chunk
* c) Build MPI derived datatype to combine "chunk address" and "assign_io" information
* in order to do MPI Bcast only once
* d) MPI Bcast the IO mode and chunk address information for each chunk.
* 4) Each process then retrieves IO mode and chunk address information to assign_io_mode and
*chunk_addr.
*
* Parameters:
*
* Input: H5D_io_info_t* io_info,
* H5D_dset_io_info_t *di,(dataset info struct)
* Output: uint8_t assign_io_mode[], : IO mode, collective, independent or none
* haddr_t chunk_addr[], : chunk address array for each chunk
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__obtain_mpio_mode(H5D_io_info_t *io_info, H5D_dset_io_info_t *di, uint8_t assign_io_mode[],
haddr_t chunk_addr[], int mpi_rank, int mpi_size)
{
size_t total_chunks;
unsigned percent_nproc_per_chunk, threshold_nproc_per_chunk;
uint8_t *io_mode_info = NULL;
uint8_t *recv_io_mode_info = NULL;
uint8_t *mergebuf = NULL;
uint8_t *tempbuf;
H5SL_node_t *chunk_node;
H5D_piece_info_t *chunk_info;
H5P_coll_md_read_flag_t md_reads_file_flag;
bool md_reads_context_flag;
bool restore_md_reads_state = false;
MPI_Comm comm;
int root;
size_t ic;
int mpi_code;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(di->layout->type == H5D_CHUNKED);
/* Assign the rank 0 to the root */
root = 0;
comm = io_info->comm;
/* Setup parameters */
H5_CHECKED_ASSIGN(total_chunks, size_t, di->layout->u.chunk.nchunks, hsize_t);
if (H5CX_get_mpio_chunk_opt_ratio(&percent_nproc_per_chunk) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't get percent nproc per chunk");
/* if ratio is 0, perform collective io */
if (0 == percent_nproc_per_chunk) {
if (H5D__chunk_addrmap(di->dset, chunk_addr) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address");
for (ic = 0; ic < total_chunks; ic++)
assign_io_mode[ic] = H5D_CHUNK_IO_MODE_COL;
HGOTO_DONE(SUCCEED);
} /* end if */
threshold_nproc_per_chunk = (unsigned)mpi_size * percent_nproc_per_chunk / 100;
/* Allocate memory */
if (NULL == (io_mode_info = (uint8_t *)H5MM_calloc(total_chunks)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate I/O mode info buffer");
if (NULL == (mergebuf = (uint8_t *)H5MM_malloc((sizeof(haddr_t) + 1) * total_chunks)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate mergebuf buffer");
tempbuf = mergebuf + total_chunks;
if (mpi_rank == root)
if (NULL == (recv_io_mode_info = (uint8_t *)H5MM_malloc(total_chunks * (size_t)mpi_size)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate recv I/O mode info buffer");
/* Obtain the regularity and selection information for all chunks in this process. */
chunk_node = H5SL_first(di->layout_io_info.chunk_map->dset_sel_pieces);
while (chunk_node) {
chunk_info = (H5D_piece_info_t *)H5SL_item(chunk_node);
io_mode_info[chunk_info->index] = H5D_CHUNK_SELECT_REG; /* this chunk is selected and is "regular" */
chunk_node = H5SL_next(chunk_node);
} /* end while */
/* Gather all the information */
H5_CHECK_OVERFLOW(total_chunks, size_t, int);
if (MPI_SUCCESS != (mpi_code = MPI_Gather(io_mode_info, (int)total_chunks, MPI_BYTE, recv_io_mode_info,
(int)total_chunks, MPI_BYTE, root, comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Gather failed", mpi_code)
/* Calculate the mode for IO(collective, independent or none) at root process */
if (mpi_rank == root) {
size_t nproc;
unsigned *nproc_per_chunk;
/*
* If enabled, disable collective metadata reads here.
* Since the chunk address mapping is done on rank 0
* only here, it will cause problems if collective
* metadata reads are enabled.
*/
if (H5F_get_coll_metadata_reads(di->dset->oloc.file)) {
#ifndef NDEBUG
{
H5D_chk_idx_info_t idx_info;
bool index_is_open;
idx_info.f = di->dset->oloc.file;
idx_info.pline = &di->dset->shared->dcpl_cache.pline;
idx_info.layout = &di->dset->shared->layout.u.chunk;
idx_info.storage = &di->dset->shared->layout.storage.u.chunk;
/*
* The dataset's chunk index should be open at this point.
* Otherwise, we will end up reading it in independently,
* which may not be desired.
*/
idx_info.storage->ops->is_open(&idx_info, &index_is_open);
assert(index_is_open);
}
#endif
md_reads_file_flag = H5P_FORCE_FALSE;
md_reads_context_flag = false;
H5F_set_coll_metadata_reads(di->dset->oloc.file, &md_reads_file_flag, &md_reads_context_flag);
restore_md_reads_state = true;
}
/* pre-computing: calculate number of processes and
regularity of the selection occupied in each chunk */
if (NULL == (nproc_per_chunk = (unsigned *)H5MM_calloc(total_chunks * sizeof(unsigned))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate nproc_per_chunk buffer");
/* calculating the chunk address */
if (H5D__chunk_addrmap(di->dset, chunk_addr) < 0) {
H5MM_free(nproc_per_chunk);
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk address");
} /* end if */
/* checking for number of process per chunk and regularity of the selection*/
for (nproc = 0; nproc < (size_t)mpi_size; nproc++) {
uint8_t *tmp_recv_io_mode_info = recv_io_mode_info + (nproc * total_chunks);
/* Calculate the number of process per chunk and adding irregular selection option */
for (ic = 0; ic < total_chunks; ic++, tmp_recv_io_mode_info++) {
if (*tmp_recv_io_mode_info != 0) {
nproc_per_chunk[ic]++;
} /* end if */
} /* end for */
} /* end for */
/* Calculating MPIO mode for each chunk (collective, independent, none) */
for (ic = 0; ic < total_chunks; ic++) {
if (nproc_per_chunk[ic] > MAX(1, threshold_nproc_per_chunk)) {
assign_io_mode[ic] = H5D_CHUNK_IO_MODE_COL;
} /* end if */
} /* end for */
/* merge buffer io_mode info and chunk addr into one */
H5MM_memcpy(mergebuf, assign_io_mode, total_chunks);
H5MM_memcpy(tempbuf, chunk_addr, sizeof(haddr_t) * total_chunks);
H5MM_free(nproc_per_chunk);
} /* end if */
/* Broadcasting the MPI_IO option info. and chunk address info. */
if ((sizeof(haddr_t) + 1) * total_chunks > INT_MAX)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "result overflow");
if (MPI_SUCCESS !=
(mpi_code = MPI_Bcast(mergebuf, (int)((sizeof(haddr_t) + 1) * total_chunks), MPI_BYTE, root, comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_BCast failed", mpi_code)
H5MM_memcpy(assign_io_mode, mergebuf, total_chunks);
H5MM_memcpy(chunk_addr, tempbuf, sizeof(haddr_t) * total_chunks);
#ifdef H5_HAVE_INSTRUMENTED_LIBRARY
{
bool coll_op = false;
for (ic = 0; ic < total_chunks; ic++)
if (assign_io_mode[ic] == H5D_CHUNK_IO_MODE_COL) {
if (H5CX_test_set_mpio_coll_chunk_multi_ratio_coll(0) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value");
coll_op = true;
break;
} /* end if */
if (!coll_op)
if (H5CX_test_set_mpio_coll_chunk_multi_ratio_ind(0) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to set property value");
}
#endif
done:
/* Re-enable collective metadata reads if we disabled them */
if (restore_md_reads_state)
H5F_set_coll_metadata_reads(di->dset->oloc.file, &md_reads_file_flag, &md_reads_context_flag);
if (io_mode_info)
H5MM_free(io_mode_info);
if (mergebuf)
H5MM_free(mergebuf);
if (recv_io_mode_info) {
assert(mpi_rank == root);
H5MM_free(recv_io_mode_info);
} /* end if */
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__obtain_mpio_mode() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_collective_filtered_chunk_io_setup
*
* Purpose: Constructs a list of entries which contain the necessary
* information for inter-process communication when performing
* collective io on filtered chunks. This list is used by
* each MPI rank when performing I/O on locally selected
* chunks and also in operations that must be collectively
* done on every chunk, such as chunk re-allocation, insertion
* of chunks into the chunk index, etc.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_collective_filtered_chunk_io_setup(const H5D_io_info_t *io_info, const H5D_dset_io_info_t *di,
size_t num_dset_infos, int mpi_rank,
H5D_filtered_collective_io_info_t *chunk_list)
{
H5D_filtered_collective_chunk_info_t *local_info_array = NULL;
H5D_mpio_filtered_dset_info_t *curr_dset_info = NULL;
size_t num_chunks_selected = 0;
size_t num_chunks_to_read = 0;
size_t buf_idx = 0;
bool need_sort = false;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(io_info);
assert(di);
assert(chunk_list);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_TIME_START(mpi_rank, "Filtered Collective I/O Setup");
#endif
/* Calculate hash key length for chunk hash table */
if (num_dset_infos > 1) {
/* Just in case the structure changes... */
HDcompile_assert(offsetof(H5D_chunk_index_info_t, dset_oloc_addr) >
offsetof(H5D_chunk_index_info_t, chunk_idx));
/* Calculate key length using uthash compound key example */
chunk_list->chunk_hash_table_keylen = offsetof(H5D_chunk_index_info_t, dset_oloc_addr) +
sizeof(haddr_t) - offsetof(H5D_chunk_index_info_t, chunk_idx);
}
else
chunk_list->chunk_hash_table_keylen = sizeof(hsize_t);
chunk_list->all_dset_indices_empty = true;
chunk_list->no_dset_index_insert_methods = true;
/* Calculate size needed for total chunk list */
for (size_t dset_idx = 0; dset_idx < num_dset_infos; dset_idx++) {
/* Skip this dataset if no I/O is being performed */
if (di[dset_idx].skip_io)
continue;
/* Only process filtered, chunked datasets. A contiguous dataset
* could possibly have filters in the DCPL pipeline, but the library
* will currently ignore optional filters in that case.
*/
if ((di[dset_idx].dset->shared->dcpl_cache.pline.nused == 0) ||
(di[dset_idx].layout->type == H5D_CONTIGUOUS))
continue;
assert(di[dset_idx].layout->type == H5D_CHUNKED);
assert(di[dset_idx].layout->storage.type == H5D_CHUNKED);
num_chunks_selected += H5SL_count(di[dset_idx].layout_io_info.chunk_map->dset_sel_pieces);
}
if (num_chunks_selected)
if (NULL == (local_info_array = H5MM_malloc(num_chunks_selected * sizeof(*local_info_array))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate local io info array buffer");
for (size_t dset_idx = 0; dset_idx < num_dset_infos; dset_idx++) {
H5D_chunk_ud_t udata;
H5O_fill_t *fill_msg;
haddr_t prev_tag = HADDR_UNDEF;
/* Skip this dataset if no I/O is being performed */
if (di[dset_idx].skip_io)
continue;
/* Only process filtered, chunked datasets. A contiguous dataset
* could possibly have filters in the DCPL pipeline, but the library
* will currently ignore optional filters in that case.
*/
if ((di[dset_idx].dset->shared->dcpl_cache.pline.nused == 0) ||
(di[dset_idx].layout->type == H5D_CONTIGUOUS))
continue;
assert(di[dset_idx].layout->storage.type == H5D_CHUNKED);
assert(di[dset_idx].layout->storage.u.chunk.idx_type != H5D_CHUNK_IDX_NONE);
/*
* To support the multi-dataset I/O case, cache some info (chunk size,
* fill buffer and fill dataspace, etc.) about each dataset involved
* in the I/O operation for use when processing chunks. If only one
* dataset is involved, this information is the same for every chunk
* processed. Otherwise, if multiple datasets are involved, a hash
* table is used to quickly match a particular chunk with the cached
* information pertaining to the dataset it resides in.
*/
if (NULL == (curr_dset_info = H5MM_malloc(sizeof(H5D_mpio_filtered_dset_info_t))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate space for dataset info");
memset(&curr_dset_info->fb_info, 0, sizeof(H5D_fill_buf_info_t));
H5D_MPIO_INIT_CHUNK_IDX_INFO(curr_dset_info->chunk_idx_info, di[dset_idx].dset);
curr_dset_info->dset_io_info = &di[dset_idx];
curr_dset_info->file_chunk_size = di[dset_idx].dset->shared->layout.u.chunk.size;
curr_dset_info->dset_oloc_addr = di[dset_idx].dset->oloc.addr;
curr_dset_info->fill_space = NULL;
curr_dset_info->fb_info_init = false;
curr_dset_info->index_empty = false;
/* Determine if fill values should be written to chunks */
fill_msg = &di[dset_idx].dset->shared->dcpl_cache.fill;
curr_dset_info->should_fill =
(fill_msg->fill_time == H5D_FILL_TIME_ALLOC) ||
((fill_msg->fill_time == H5D_FILL_TIME_IFSET) && fill_msg->fill_defined);
if (curr_dset_info->should_fill) {
hsize_t chunk_dims[H5S_MAX_RANK];
assert(di[dset_idx].dset->shared->ndims == di[dset_idx].dset->shared->layout.u.chunk.ndims - 1);
for (size_t dim_idx = 0; dim_idx < di[dset_idx].dset->shared->layout.u.chunk.ndims - 1; dim_idx++)
chunk_dims[dim_idx] = (hsize_t)di[dset_idx].dset->shared->layout.u.chunk.dim[dim_idx];
/* Get a dataspace for filling chunk memory buffers */
if (NULL == (curr_dset_info->fill_space = H5S_create_simple(
di[dset_idx].dset->shared->layout.u.chunk.ndims - 1, chunk_dims, NULL)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create chunk fill dataspace");
/* Initialize fill value buffer */
if (H5D__fill_init(&curr_dset_info->fb_info, NULL, (H5MM_allocate_t)H5D__chunk_mem_alloc,
(void *)&di[dset_idx].dset->shared->dcpl_cache.pline,
(H5MM_free_t)H5D__chunk_mem_free,
(void *)&di[dset_idx].dset->shared->dcpl_cache.pline,
&di[dset_idx].dset->shared->dcpl_cache.fill, di[dset_idx].dset->shared->type,
0, curr_dset_info->file_chunk_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "can't initialize fill value buffer");
curr_dset_info->fb_info_init = true;
}
/*
* If the dataset is incrementally allocated and hasn't been written
* to yet, the chunk index should be empty. In this case, a collective
* read of its chunks is essentially a no-op, so we can avoid that read
* later. If all datasets have empty chunk indices, we can skip the
* collective read entirely.
*/
if (fill_msg->alloc_time == H5D_ALLOC_TIME_INCR)
if (H5D__chunk_index_empty(di[dset_idx].dset, &curr_dset_info->index_empty) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "couldn't determine if chunk index is empty");
if ((fill_msg->alloc_time != H5D_ALLOC_TIME_INCR) || !curr_dset_info->index_empty)
chunk_list->all_dset_indices_empty = false;
if (curr_dset_info->chunk_idx_info.storage->ops->insert)
chunk_list->no_dset_index_insert_methods = false;
/*
* For multi-dataset I/O, use a hash table to keep a mapping between
* chunks and the cached info for the dataset that they're in. Otherwise,
* we can just use the info object directly if only one dataset is being
* worked on.
*/
if (num_dset_infos > 1) {
HASH_ADD(hh, chunk_list->dset_info.dset_info_hash_table, dset_oloc_addr, sizeof(haddr_t),
curr_dset_info);
}
else
chunk_list->dset_info.single_dset_info = curr_dset_info;
curr_dset_info = NULL;
/*
* Now, each rank builds a local list of info about the chunks
* they have selected among the chunks in the current dataset
*/
/* Set metadata tagging with dataset oheader addr */
H5AC_tag(di[dset_idx].dset->oloc.addr, &prev_tag);
if (H5SL_count(di[dset_idx].layout_io_info.chunk_map->dset_sel_pieces)) {
H5SL_node_t *chunk_node;
bool filter_partial_edge_chunks;
/* Determine whether partial edge chunks should be filtered */
filter_partial_edge_chunks = !(di[dset_idx].dset->shared->layout.u.chunk.flags &
H5O_LAYOUT_CHUNK_DONT_FILTER_PARTIAL_BOUND_CHUNKS);
chunk_node = H5SL_first(di[dset_idx].layout_io_info.chunk_map->dset_sel_pieces);
while (chunk_node) {
H5D_piece_info_t *chunk_info;
hsize_t select_npoints;
chunk_info = (H5D_piece_info_t *)H5SL_item(chunk_node);
assert(chunk_info->filtered_dset);
/* Obtain this chunk's address */
if (H5D__chunk_lookup(di[dset_idx].dset, chunk_info->scaled, &udata) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address");
/* Initialize rank-local chunk info */
local_info_array[buf_idx].chunk_info = chunk_info;
local_info_array[buf_idx].chunk_buf_size = 0;
local_info_array[buf_idx].num_writers = 0;
local_info_array[buf_idx].orig_owner = mpi_rank;
local_info_array[buf_idx].new_owner = mpi_rank;
local_info_array[buf_idx].buf = NULL;
select_npoints = H5S_GET_SELECT_NPOINTS(chunk_info->fspace);
local_info_array[buf_idx].io_size =
(size_t)select_npoints * di[dset_idx].type_info.dst_type_size;
/*
* Determine whether this chunk will need to be read from the file. If this is
* a read operation, the chunk will be read. If this is a write operation, we
* generally need to read a filtered chunk from the file before modifying it,
* unless the chunk is being fully overwritten.
*
* TODO: Currently the full overwrite status of a chunk is only obtained on a
* per-rank basis. This means that if the total selection in the chunk, as
* determined by the combination of selections of all of the ranks interested in
* the chunk, covers the entire chunk, the performance optimization of not reading
* the chunk from the file is still valid, but is not applied in the current
* implementation.
*
* To implement this case, a few approaches were considered:
*
* - Keep a running total (distributed to each rank) of the number of chunk
* elements selected during chunk redistribution and compare that to the total
* number of elements in the chunk once redistribution is finished
*
* - Process all incoming chunk messages before doing I/O (these are currently
* processed AFTER doing I/O), combine the owning rank's selection in a chunk
* with the selections received from other ranks and check to see whether that
* combined selection covers the entire chunk
*
* The first approach will be dangerous if the application performs an overlapping
* write to a chunk, as the number of selected elements can equal or exceed the
* number of elements in the chunk without the whole chunk selection being covered.
* While it might be considered erroneous for an application to do an overlapping
* write, we don't explicitly disallow it.
*
* The second approach contains a bit of complexity in that part of the chunk
* messages will be needed before doing I/O and part will be needed after doing I/O.
* Since modification data from chunk messages can't be applied until after any I/O
* is performed (otherwise, we'll overwrite any applied modification data), chunk
* messages are currently entirely processed after I/O. However, in order to determine
* if a chunk is being fully overwritten, we need the dataspace portion of the chunk
* messages before doing I/O. The naive way to do this is to process chunk messages
* twice, using just the relevant information from the message before and after I/O.
* The better way would be to avoid processing chunk messages twice by extracting (and
* keeping around) the dataspace portion of the message before I/O and processing the
* rest of the chunk message after I/O. Note that the dataspace portion of each chunk
* message is used to correctly apply chunk modification data from the message, so
* must be kept around both before and after I/O in this case.
*/
if (io_info->op_type == H5D_IO_OP_READ)
local_info_array[buf_idx].need_read = true;
else {
local_info_array[buf_idx].need_read =
local_info_array[buf_idx].io_size <
(size_t)di[dset_idx].dset->shared->layout.u.chunk.size;
}
if (local_info_array[buf_idx].need_read)
num_chunks_to_read++;
local_info_array[buf_idx].skip_filter_pline = false;
if (!filter_partial_edge_chunks) {
/*
* If this is a partial edge chunk and the "don't filter partial edge
* chunks" flag is set, make sure not to apply filters to the chunk.
*/
if (H5D__chunk_is_partial_edge_chunk(
di[dset_idx].dset->shared->ndims, di[dset_idx].dset->shared->layout.u.chunk.dim,
chunk_info->scaled, di[dset_idx].dset->shared->curr_dims))
local_info_array[buf_idx].skip_filter_pline = true;
}
/* Initialize the chunk's shared info */
local_info_array[buf_idx].chunk_current = udata.chunk_block;
local_info_array[buf_idx].chunk_new = udata.chunk_block;
/*
* Check if the list is not in ascending order of offset in the file
* or has unallocated chunks. In either case, the list should get
* sorted.
*/
if (!need_sort && buf_idx) {
haddr_t curr_chunk_offset = local_info_array[buf_idx].chunk_current.offset;
haddr_t prev_chunk_offset = local_info_array[buf_idx - 1].chunk_current.offset;
if (!H5_addr_defined(prev_chunk_offset) || !H5_addr_defined(curr_chunk_offset) ||
(curr_chunk_offset < prev_chunk_offset))
need_sort = true;
}
/* Needed for proper hashing later on */
memset(&local_info_array[buf_idx].index_info, 0, sizeof(H5D_chunk_index_info_t));
/*
* Extensible arrays may calculate a chunk's index a little differently
* than normal when the dataset's unlimited dimension is not the
* slowest-changing dimension, so set the index here based on what the
* extensible array code calculated instead of what was calculated
* in the chunk file mapping.
*/
if (di[dset_idx].dset->shared->layout.u.chunk.idx_type == H5D_CHUNK_IDX_EARRAY)
local_info_array[buf_idx].index_info.chunk_idx = udata.chunk_idx;
else
local_info_array[buf_idx].index_info.chunk_idx = chunk_info->index;
assert(H5_addr_defined(di[dset_idx].dset->oloc.addr));
local_info_array[buf_idx].index_info.dset_oloc_addr = di[dset_idx].dset->oloc.addr;
local_info_array[buf_idx].index_info.filter_mask = udata.filter_mask;
local_info_array[buf_idx].index_info.need_insert = false;
buf_idx++;
chunk_node = H5SL_next(chunk_node);
}
}
/* Reset metadata tagging */
H5AC_tag(prev_tag, NULL);
}
/* Ensure the chunk list is sorted in ascending order of offset in the file */
if (local_info_array && need_sort)
qsort(local_info_array, num_chunks_selected, sizeof(H5D_filtered_collective_chunk_info_t),
H5D__cmp_filtered_collective_io_info_entry);
chunk_list->chunk_infos = local_info_array;
chunk_list->num_chunk_infos = num_chunks_selected;
chunk_list->num_chunks_to_read = num_chunks_to_read;
#ifdef H5Dmpio_DEBUG
H5D__mpio_dump_collective_filtered_chunk_list(chunk_list, mpi_rank);
#endif
done:
if (ret_value < 0) {
/* Free temporary cached dataset info object */
if (curr_dset_info) {
if (curr_dset_info->fb_info_init && H5D__fill_term(&curr_dset_info->fb_info) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't release fill buffer info");
if (curr_dset_info->fill_space && H5S_close(curr_dset_info->fill_space) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CLOSEERROR, FAIL, "can't close fill space");
H5MM_free(curr_dset_info);
curr_dset_info = NULL;
if (num_dset_infos == 1)
chunk_list->dset_info.single_dset_info = NULL;
}
/* Free resources used by cached dataset info hash table */
if (num_dset_infos > 1) {
H5D_mpio_filtered_dset_info_t *tmp;
HASH_ITER(hh, chunk_list->dset_info.dset_info_hash_table, curr_dset_info, tmp)
{
HASH_DELETE(hh, chunk_list->dset_info.dset_info_hash_table, curr_dset_info);
H5MM_free(curr_dset_info);
curr_dset_info = NULL;
}
}
if (num_dset_infos == 1)
chunk_list->dset_info.single_dset_info = NULL;
else
chunk_list->dset_info.dset_info_hash_table = NULL;
H5MM_free(local_info_array);
}
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_collective_filtered_chunk_io_setup() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_redistribute_shared_chunks
*
* Purpose: When performing a parallel write on a chunked Dataset with
* filters applied, we must ensure that any particular chunk
* is only written to by a single MPI rank in order to avoid
* potential data races on the chunk. This function is used to
* redistribute (by assigning ownership to a single rank) any
* chunks which are selected by more than one MPI rank.
*
* An initial Allgather is performed to determine how many
* chunks each rank has selected in the write operation and
* then that number is compared against a threshold value to
* determine whether chunk redistribution should be done on
* MPI rank 0 only, or on all MPI ranks.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_redistribute_shared_chunks(H5D_filtered_collective_io_info_t *chunk_list,
const H5D_io_info_t *io_info, int mpi_rank, int mpi_size,
size_t **rank_chunks_assigned_map)
{
bool redistribute_on_all_ranks;
size_t *num_chunks_map = NULL;
size_t coll_chunk_list_size = 0;
int mpi_code;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(chunk_list);
assert(io_info);
assert(mpi_size > 1); /* No chunk sharing is possible for MPI Comm size of 1 */
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_TIME_START(mpi_rank, "Redistribute shared chunks");
#endif
/*
* Allocate an array for each rank to keep track of the number of
* chunks assigned to any other rank in order to cut down on future
* MPI communication.
*/
if (NULL == (num_chunks_map = H5MM_malloc((size_t)mpi_size * sizeof(*num_chunks_map))))
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "couldn't allocate assigned chunks array");
/* Perform initial Allgather to determine the collective chunk list size */
if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&chunk_list->num_chunk_infos, 1, H5_SIZE_T_AS_MPI_TYPE,
num_chunks_map, 1, H5_SIZE_T_AS_MPI_TYPE, io_info->comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code)
for (int curr_rank = 0; curr_rank < mpi_size; curr_rank++)
coll_chunk_list_size += num_chunks_map[curr_rank];
/*
* Determine whether we should perform chunk redistribution on all
* ranks or just rank 0. For a relatively small number of chunks,
* we redistribute on all ranks to cut down on MPI communication
* overhead. For a larger number of chunks, we redistribute on
* rank 0 only to cut down on memory usage.
*/
redistribute_on_all_ranks = coll_chunk_list_size < H5D_CHUNK_REDISTRIBUTE_THRES;
if (H5D__mpio_redistribute_shared_chunks_int(chunk_list, num_chunks_map, redistribute_on_all_ranks,
io_info, mpi_rank, mpi_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTREDISTRIBUTE, FAIL, "can't redistribute shared chunks");
/*
* If the caller provided a pointer for the mapping from
* rank value -> number of chunks assigned, return that
* mapping here.
*/
if (rank_chunks_assigned_map) {
/*
* If we performed chunk redistribution on rank 0 only, distribute
* the rank value -> number of chunks assigned mapping back to all
* ranks.
*/
if (!redistribute_on_all_ranks) {
if (MPI_SUCCESS !=
(mpi_code = MPI_Bcast(num_chunks_map, mpi_size, H5_SIZE_T_AS_MPI_TYPE, 0, io_info->comm)))
HMPI_GOTO_ERROR(FAIL, "couldn't broadcast chunk mapping to other ranks", mpi_code)
}
*rank_chunks_assigned_map = num_chunks_map;
}
done:
if (!rank_chunks_assigned_map || (ret_value < 0)) {
num_chunks_map = H5MM_xfree(num_chunks_map);
}
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_redistribute_shared_chunks() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_redistribute_shared_chunks_int
*
* Purpose: Routine to perform redistribution of shared chunks during
* parallel writes to datasets with filters applied.
*
* If `all_ranks_involved` is true, chunk redistribution
* occurs on all MPI ranks. This is usually done when there
* is a relatively small number of chunks involved in order to
* cut down on MPI communication overhead while increasing
* total memory usage a bit.
*
* If `all_ranks_involved` is false, only rank 0 will perform
* chunk redistribution. This is usually done when there is
* a relatively large number of chunks involved in order to
* cut down on total memory usage at the cost of increased
* overhead from MPI communication.
*
* This implementation is as follows:
*
* - All MPI ranks send their list of selected chunks to the
* ranks involved in chunk redistribution. Then, the
* involved ranks sort this new list in order of:
*
* dataset object header address -> chunk index value ->
* original owning MPI rank for chunk
*
* - The involved ranks scan the list looking for matching
* runs of (dataset object header address, chunk index value)
* pairs (corresponding to a shared chunk which has been
* selected by more than one rank in the I/O operation) and
* for each shared chunk, redistribute the chunk to the MPI
* rank writing to the chunk which currently has the least
* amount of chunks assigned to it. This is done by modifying
* the "new_owner" field in each of the list entries
* corresponding to that chunk. The involved ranks then
* re-sort the list in order of original chunk owner so that
* each rank's section of contributed chunks is contiguous
* in the collective chunk list.
*
* - If chunk redistribution occurred on all ranks, each rank
* scans through the collective chunk list to find their
* contributed section of chunks and uses that to update
* their local chunk list with the newly-updated "new_owner"
* and "num_writers" fields. If chunk redistribution
* occurred only on rank 0, an MPI_Scatterv operation will
* be used to scatter the segments of the collective chunk
* list from rank 0 back to the corresponding ranks.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_redistribute_shared_chunks_int(H5D_filtered_collective_io_info_t *chunk_list,
size_t *num_chunks_assigned_map, bool all_ranks_involved,
const H5D_io_info_t *io_info, int mpi_rank, int mpi_size)
{
MPI_Datatype struct_type;
MPI_Datatype packed_type;
bool struct_type_derived = false;
bool packed_type_derived = false;
size_t coll_chunk_list_num_entries = 0;
void *coll_chunk_list = NULL;
int *counts_disps_array = NULL;
int *counts_ptr = NULL;
int *displacements_ptr = NULL;
int num_chunks_int;
int mpi_code;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(chunk_list);
assert(num_chunks_assigned_map);
assert(io_info);
assert(mpi_size > 1);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_TIME_START(mpi_rank, "Redistribute shared chunks (internal)");
#endif
/*
* Make sure it's safe to cast this rank's number
* of chunks to be sent into an int for MPI
*/
H5_CHECKED_ASSIGN(num_chunks_int, int, num_chunks_assigned_map[mpi_rank], size_t);
/*
* Phase 1 - Participate in collective gathering of every rank's
* list of chunks to the ranks which are performing the redistribution
* operation.
*/
if (all_ranks_involved || (mpi_rank == 0)) {
/*
* Allocate array to store the receive counts of each rank, as well as
* the displacements into the final array where each rank will place
* their data. The first half of the array contains the receive counts
* (in rank order), while the latter half contains the displacements
* (also in rank order).
*/
if (NULL == (counts_disps_array = H5MM_malloc(2 * (size_t)mpi_size * sizeof(*counts_disps_array)))) {
/* Push an error, but still participate in collective gather operation */
HDONE_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL,
"couldn't allocate receive counts and displacements array");
}
else {
/* Set the receive counts from the assigned chunks map */
counts_ptr = counts_disps_array;
for (int curr_rank = 0; curr_rank < mpi_size; curr_rank++)
H5_CHECKED_ASSIGN(counts_ptr[curr_rank], int, num_chunks_assigned_map[curr_rank], size_t);
/* Set the displacements into the receive buffer for the gather operation */
displacements_ptr = &counts_disps_array[mpi_size];
*displacements_ptr = 0;
for (int curr_rank = 1; curr_rank < mpi_size; curr_rank++)
displacements_ptr[curr_rank] = displacements_ptr[curr_rank - 1] + counts_ptr[curr_rank - 1];
}
}
/*
* Construct MPI derived types for extracting information
* necessary for MPI communication
*/
if (H5D__mpio_get_chunk_redistribute_info_types(&packed_type, &packed_type_derived, &struct_type,
&struct_type_derived) < 0) {
/* Push an error, but still participate in collective gather operation */
HDONE_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,
"can't create derived datatypes for chunk redistribution info");
}
/* Perform gather operation */
if (H5_mpio_gatherv_alloc(chunk_list->chunk_infos, num_chunks_int, struct_type, counts_ptr,
displacements_ptr, packed_type, all_ranks_involved, 0, io_info->comm, mpi_rank,
mpi_size, &coll_chunk_list, &coll_chunk_list_num_entries) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL,
"can't gather chunk redistribution info to involved ranks");
/*
* If all ranks are redistributing shared chunks, we no
* longer need the receive counts and displacements array
*/
if (all_ranks_involved) {
counts_disps_array = H5MM_xfree(counts_disps_array);
}
/* No useful work to do - exit */
if (coll_chunk_list_num_entries == 0)
HGOTO_DONE(SUCCEED);
/*
* Phase 2 - Involved ranks now redistribute any shared chunks to new
* owners as necessary.
*/
if (all_ranks_involved || (mpi_rank == 0)) {
H5D_chunk_redistribute_info_t *chunk_entry;
/* Clear the mapping from rank value -> number of assigned chunks */
memset(num_chunks_assigned_map, 0, (size_t)mpi_size * sizeof(*num_chunks_assigned_map));
/*
* Sort collective chunk list according to:
* dataset object header address -> chunk index value -> original owning MPI rank for chunk
*/
qsort(coll_chunk_list, coll_chunk_list_num_entries, sizeof(H5D_chunk_redistribute_info_t),
H5D__cmp_chunk_redistribute_info);
/*
* Process all chunks in the collective chunk list.
* Note that the loop counter is incremented by both
* the outer loop (while processing each entry in
* the collective chunk list) and the inner loop
* (while processing duplicate entries for shared
* chunks).
*/
chunk_entry = &((H5D_chunk_redistribute_info_t *)coll_chunk_list)[0];
for (size_t entry_idx = 0; entry_idx < coll_chunk_list_num_entries;) {
haddr_t curr_oloc_addr;
hsize_t curr_chunk_idx;
size_t set_begin_index;
bool keep_processing;
int num_writers;
int new_chunk_owner;
/* Set chunk's initial new owner to its original owner */
new_chunk_owner = chunk_entry->orig_owner;
/*
* Set the current dataset object header address and chunk
* index value so we know when we've processed all duplicate
* entries for a particular shared chunk
*/
curr_oloc_addr = chunk_entry->dset_oloc_addr;
curr_chunk_idx = chunk_entry->chunk_idx;
/* Reset the initial number of writers to this chunk */
num_writers = 0;
/* Set index for the beginning of this section of duplicate chunk entries */
set_begin_index = entry_idx;
/*
* Process each chunk entry in the set for the current
* (possibly shared) chunk and increment the loop counter
* while doing so.
*/
do {
/*
* The new owner of the chunk is determined by the rank
* writing to the chunk which currently has the least amount
* of chunks assigned to it
*/
if (num_chunks_assigned_map[chunk_entry->orig_owner] <
num_chunks_assigned_map[new_chunk_owner])
new_chunk_owner = chunk_entry->orig_owner;
/* Update the number of writers to this particular chunk */
num_writers++;
chunk_entry++;
keep_processing =
/* Make sure we haven't run out of chunks in the chunk list */
(++entry_idx < coll_chunk_list_num_entries) &&
/* Make sure the chunk we're looking at is in the same dataset */
(H5_addr_eq(chunk_entry->dset_oloc_addr, curr_oloc_addr)) &&
/* Make sure the chunk we're looking at is the same chunk */
(chunk_entry->chunk_idx == curr_chunk_idx);
} while (keep_processing);
/* We should never have more writers to a chunk than the number of MPI ranks */
assert(num_writers <= mpi_size);
/* Set all processed chunk entries' "new_owner" and "num_writers" fields */
for (; set_begin_index < entry_idx; set_begin_index++) {
H5D_chunk_redistribute_info_t *entry;
entry = &((H5D_chunk_redistribute_info_t *)coll_chunk_list)[set_begin_index];
entry->new_owner = new_chunk_owner;
entry->num_writers = num_writers;
}
/* Update the number of chunks assigned to the MPI rank that now owns this chunk */
num_chunks_assigned_map[new_chunk_owner]++;
}
/*
* Re-sort the collective chunk list in order of original chunk owner
* so that each rank's section of contributed chunks is contiguous in
* the collective chunk list.
*
* NOTE: this re-sort is frail in that it needs to sort the collective
* chunk list so that each rank's section of contributed chunks
* is in the exact order it was contributed in, or things will
* be scrambled when each rank's local chunk list is updated.
* Therefore, the sorting algorithm here is tied to the one
* used during the I/O setup operation. Specifically, chunks
* are first sorted by ascending order of offset in the file and
* then by chunk index. In the future, a better redistribution
* algorithm may be devised that doesn't rely on frail sorting,
* but the current implementation is a quick and naive approach.
*/
qsort(coll_chunk_list, coll_chunk_list_num_entries, sizeof(H5D_chunk_redistribute_info_t),
H5D__cmp_chunk_redistribute_info_orig_owner);
}
if (all_ranks_involved) {
size_t entry_idx;
/*
* If redistribution occurred on all ranks, search for the section
* in the collective chunk list corresponding to this rank's locally
* selected chunks and update the local list after redistribution.
*/
for (entry_idx = 0; entry_idx < coll_chunk_list_num_entries; entry_idx++)
if (mpi_rank == ((H5D_chunk_redistribute_info_t *)coll_chunk_list)[entry_idx].orig_owner)
break;
for (size_t info_idx = 0; info_idx < (size_t)num_chunks_int; info_idx++) {
H5D_chunk_redistribute_info_t *coll_entry;
coll_entry = &((H5D_chunk_redistribute_info_t *)coll_chunk_list)[entry_idx++];
chunk_list->chunk_infos[info_idx].new_owner = coll_entry->new_owner;
chunk_list->chunk_infos[info_idx].num_writers = coll_entry->num_writers;
/*
* Check if the chunk list struct's `num_chunks_to_read` field
* needs to be updated
*/
if (chunk_list->chunk_infos[info_idx].need_read &&
(chunk_list->chunk_infos[info_idx].new_owner != mpi_rank)) {
chunk_list->chunk_infos[info_idx].need_read = false;
assert(chunk_list->num_chunks_to_read > 0);
chunk_list->num_chunks_to_read--;
}
}
}
else {
/*
* If redistribution occurred only on rank 0, scatter the segments
* of the collective chunk list back to each rank so that their
* local chunk lists get updated
*/
if (MPI_SUCCESS !=
(mpi_code = MPI_Scatterv(coll_chunk_list, counts_ptr, displacements_ptr, packed_type,
chunk_list->chunk_infos, num_chunks_int, struct_type, 0, io_info->comm)))
HMPI_GOTO_ERROR(FAIL, "unable to scatter shared chunks info buffer", mpi_code)
/*
* Now that chunks have been redistributed, each rank must update
* their chunk list struct's `num_chunks_to_read` field since it
* may now be out of date.
*/
for (size_t info_idx = 0; info_idx < chunk_list->num_chunk_infos; info_idx++) {
if ((chunk_list->chunk_infos[info_idx].new_owner != mpi_rank) &&
chunk_list->chunk_infos[info_idx].need_read) {
chunk_list->chunk_infos[info_idx].need_read = false;
assert(chunk_list->num_chunks_to_read > 0);
chunk_list->num_chunks_to_read--;
}
}
}
#ifdef H5Dmpio_DEBUG
H5D__mpio_dump_collective_filtered_chunk_list(chunk_list, mpi_rank);
#endif
done:
H5MM_free(coll_chunk_list);
if (struct_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&struct_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
if (packed_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&packed_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
H5MM_free(counts_disps_array);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_redistribute_shared_chunks_int() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_share_chunk_modification_data
*
* Purpose: When performing a parallel write on a chunked dataset with
* filters applied, we must first ensure that any particular
* chunk is only written to by a single MPI rank in order to
* avoid potential data races on the chunk. Once dataset
* chunks have been redistributed in a suitable manner, each
* MPI rank must send its chunk data to other ranks for each
* chunk it no longer owns.
*
* The current implementation here follows the Nonblocking
* Consensus algorithm described in:
* http://unixer.de/publications/img/hoefler-dsde-protocols.pdf
*
* First, each MPI rank scans through its list of selected
* chunks and does the following for each chunk:
*
* * If a chunk in the MPI rank's chunk list is still owned
* by that rank, the rank checks how many messages are
* incoming for that chunk and adds that to its running
* total. Then, the rank updates its local chunk list so
* that any previous chunk entries for chunks that are no
* longer owned by the rank get overwritten by chunk
* entries for chunks the rank still owns. Since the data
* for the chunks no longer owned will have already been
* sent, those chunks can effectively be discarded.
* * If a chunk in the MPI rank's chunk list is no longer
* owned by that rank, the rank sends the data it wishes to
* update the chunk with to the MPI rank that now has
* ownership of that chunk. To do this, it encodes the
* chunk's index value, the dataset's object header address
* (only for the multi-dataset I/O case), its selection in
* the chunk and its modification data into a buffer and
* then posts a non-blocking MPI_Issend to the owning rank.
*
* Once this step is complete, all MPI ranks allocate arrays
* to hold chunk message receive buffers and MPI request
* objects for each non-blocking receive they will post for
* incoming chunk modification messages. Then, all MPI ranks
* enter a loop that alternates between non-blocking
* MPI_Iprobe calls to probe for incoming messages and
* MPI_Testall calls to see if all send requests have
* completed. As chunk modification messages arrive,
* non-blocking MPI_Irecv calls will be posted for each
* message.
*
* Once all send requests have completed, an MPI_Ibarrier is
* posted and the loop then alternates between MPI_Iprobe
* calls and MPI_Test calls to check if all ranks have reached
* the non-blocking barrier. Once all ranks have reached the
* barrier, processing can move on to updating the selected
* chunks that are owned in the operation.
*
* Any chunk messages that were received from other ranks
* will be returned through the `chunk_msg_bufs` array and
* `chunk_msg_bufs_len` will be set appropriately.
*
* NOTE: The use of non-blocking sends and receives of chunk
* data here may contribute to large amounts of memory
* usage/MPI request overhead if the number of shared
* chunks is high. If this becomes a problem, it may be
* useful to split the message receiving loop away so
* that chunk modification messages can be received and
* processed immediately (MPI_Recv) using a single chunk
* message buffer. However, it's possible this may
* degrade performance since the chunk message sends
* are synchronous (MPI_Issend) in the Nonblocking
* Consensus algorithm.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_share_chunk_modification_data(H5D_filtered_collective_io_info_t *chunk_list, H5D_io_info_t *io_info,
int mpi_rank, int H5_ATTR_NDEBUG_UNUSED mpi_size,
unsigned char ***chunk_msg_bufs, int *chunk_msg_bufs_len)
{
H5D_filtered_collective_chunk_info_t *chunk_table = NULL;
H5S_sel_iter_t *mem_iter = NULL;
unsigned char **msg_send_bufs = NULL;
unsigned char **msg_recv_bufs = NULL;
MPI_Request *send_requests = NULL;
MPI_Request *recv_requests = NULL;
MPI_Request ibarrier = MPI_REQUEST_NULL;
bool mem_iter_init = false;
bool ibarrier_posted = false;
size_t send_bufs_nalloc = 0;
size_t num_send_requests = 0;
size_t num_recv_requests = 0;
size_t num_msgs_incoming = 0;
size_t hash_keylen = 0;
size_t last_assigned_idx;
int mpi_code;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(chunk_list);
assert(io_info);
assert(mpi_size > 1);
assert(chunk_msg_bufs);
assert(chunk_msg_bufs_len);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_TIME_START(mpi_rank, "Share chunk modification data");
#endif
/* Set to latest format for encoding dataspace */
H5CX_set_libver_bounds(NULL);
if (chunk_list->num_chunk_infos > 0) {
hash_keylen = chunk_list->chunk_hash_table_keylen;
assert(hash_keylen > 0);
/* Allocate a selection iterator for iterating over chunk dataspaces */
if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate dataspace selection iterator");
/*
* Allocate send buffer and MPI_Request arrays for non-blocking
* sends of outgoing chunk messages
*/
send_bufs_nalloc = H5D_CHUNK_NUM_SEND_MSGS_INIT;
if (NULL == (msg_send_bufs = H5MM_malloc(send_bufs_nalloc * sizeof(*msg_send_bufs))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"couldn't allocate chunk modification message buffer array");
if (NULL == (send_requests = H5MM_malloc(send_bufs_nalloc * sizeof(*send_requests))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate send requests array");
}
/*
* For each chunk this rank owns, add to the total number of
* incoming MPI messages, then update the local chunk list to
* overwrite any previous chunks no longer owned by this rank.
* Since the data for those chunks will have already been sent,
* this rank should no longer be interested in them and they
* can effectively be discarded. This bookkeeping also makes
* the code for the collective file space re-allocation and
* chunk re-insertion operations a bit simpler.
*
* For each chunk this rank doesn't own, use non-blocking
* synchronous sends to send the data this rank is writing to
* the rank that does own the chunk.
*/
last_assigned_idx = 0;
for (size_t info_idx = 0; info_idx < chunk_list->num_chunk_infos; info_idx++) {
H5D_filtered_collective_chunk_info_t *chunk_entry = &chunk_list->chunk_infos[info_idx];
if (mpi_rank == chunk_entry->new_owner) {
num_msgs_incoming += (size_t)(chunk_entry->num_writers - 1);
/*
* Overwrite chunk entries this rank doesn't own with entries that it
* does own, since it has sent the necessary data and is no longer
* interested in the chunks it doesn't own.
*/
chunk_list->chunk_infos[last_assigned_idx] = chunk_list->chunk_infos[info_idx];
/*
* Since, at large scale, a chunk's index value may be larger than
* the maximum value that can be stored in an int, we cannot rely
* on using a chunk's index value as the tag for the MPI messages
* sent/received for a chunk. Further, to support the multi-dataset
* I/O case, we can't rely on being able to distinguish between
* chunks by their chunk index value alone since two chunks from
* different datasets could have the same chunk index value.
* Therefore, add this chunk to a hash table with the dataset's
* object header address + the chunk's index value as a key so that
* we can quickly find the chunk when processing chunk messages that
* were received. The message itself will contain the dataset's
* object header address and the chunk's index value so we can
* update the correct chunk with the received data.
*/
HASH_ADD(hh, chunk_table, index_info.chunk_idx, hash_keylen,
&chunk_list->chunk_infos[last_assigned_idx]);
last_assigned_idx++;
}
else {
H5D_piece_info_t *chunk_info = chunk_entry->chunk_info;
unsigned char *mod_data_p = NULL;
hsize_t iter_nelmts;
size_t mod_data_size = 0;
size_t space_size = 0;
/* Add the size of the chunk hash table key to the encoded size */
mod_data_size += hash_keylen;
/* Determine size of serialized chunk file dataspace */
if (H5S_encode(chunk_info->fspace, &mod_data_p, &space_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get encoded dataspace size");
mod_data_size += space_size;
/* Determine size of data being written */
iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace);
H5_CHECK_OVERFLOW(iter_nelmts, hsize_t, size_t);
mod_data_size += (size_t)iter_nelmts * chunk_info->dset_info->type_info.src_type_size;
if (NULL == (msg_send_bufs[num_send_requests] = H5MM_malloc(mod_data_size)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"couldn't allocate chunk modification message buffer");
mod_data_p = msg_send_bufs[num_send_requests];
/*
* Add the chunk hash table key (chunk index value + possibly
* dataset object header address) into the buffer
*/
H5MM_memcpy(mod_data_p, &chunk_entry->index_info.chunk_idx, hash_keylen);
mod_data_p += hash_keylen;
/* Serialize the chunk's file dataspace into the buffer */
if (H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to encode dataspace");
/* Initialize iterator for memory selection */
if (H5S_select_iter_init(mem_iter, chunk_info->mspace,
chunk_info->dset_info->type_info.src_type_size,
H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize memory selection information");
mem_iter_init = true;
/* Collect the modification data into the buffer */
if (0 ==
H5D__gather_mem(chunk_info->dset_info->buf.cvp, mem_iter, (size_t)iter_nelmts, mod_data_p))
HGOTO_ERROR(H5E_IO, H5E_CANTGATHER, FAIL, "couldn't gather from write buffer");
/*
* Ensure that the size of the chunk data being sent can be
* safely cast to an int for MPI. Note that this should
* generally be OK for now (unless a rank is sending a
* whole 32-bit-sized chunk of data + its encoded selection),
* but if we allow larger than 32-bit-sized chunks in the
* future, this may become a problem and derived datatypes
* will need to be used.
*/
H5_CHECK_OVERFLOW(mod_data_size, size_t, int);
/* Send modification data to new owner */
if (MPI_SUCCESS !=
(mpi_code = MPI_Issend(msg_send_bufs[num_send_requests], (int)mod_data_size, MPI_BYTE,
chunk_entry->new_owner, H5D_CHUNK_MOD_DATA_TAG, io_info->comm,
&send_requests[num_send_requests])))
HMPI_GOTO_ERROR(FAIL, "MPI_Issend failed", mpi_code)
num_send_requests++;
/* Resize send buffer and send request arrays if necessary */
if (num_send_requests == send_bufs_nalloc) {
void *tmp_alloc;
send_bufs_nalloc = (size_t)((double)send_bufs_nalloc * 1.5);
if (NULL ==
(tmp_alloc = H5MM_realloc(msg_send_bufs, send_bufs_nalloc * sizeof(*msg_send_bufs))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"couldn't resize chunk modification message buffer array");
msg_send_bufs = tmp_alloc;
if (NULL ==
(tmp_alloc = H5MM_realloc(send_requests, send_bufs_nalloc * sizeof(*send_requests))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't resize send requests array");
send_requests = tmp_alloc;
}
if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release memory selection iterator");
mem_iter_init = false;
}
}
/* Check if the number of send or receive requests will overflow an int (MPI requirement) */
if (num_send_requests > INT_MAX || num_msgs_incoming > INT_MAX)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
"too many shared chunks in parallel filtered write operation");
H5_CHECK_OVERFLOW(num_send_requests, size_t, int);
H5_CHECK_OVERFLOW(num_msgs_incoming, size_t, int);
/*
* Allocate receive buffer and MPI_Request arrays for non-blocking
* receives of incoming chunk messages
*/
if (num_msgs_incoming) {
if (NULL == (msg_recv_bufs = H5MM_malloc(num_msgs_incoming * sizeof(*msg_recv_bufs))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"couldn't allocate chunk modification message buffer array");
if (NULL == (recv_requests = H5MM_malloc(num_msgs_incoming * sizeof(*recv_requests))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive requests array");
}
/* Process any incoming messages until everyone is done */
do {
MPI_Status status;
int msg_flag;
/* Probe for an incoming message from any rank */
if (MPI_SUCCESS != (mpi_code = MPI_Iprobe(MPI_ANY_SOURCE, H5D_CHUNK_MOD_DATA_TAG, io_info->comm,
&msg_flag, &status)))
HMPI_GOTO_ERROR(FAIL, "MPI_Iprobe failed", mpi_code)
/*
* If a message was found, allocate a buffer for the message and
* post a non-blocking receive to receive it
*/
if (msg_flag) {
MPI_Count msg_size = 0;
if (MPI_SUCCESS != (mpi_code = MPI_Get_elements_x(&status, MPI_BYTE, &msg_size)))
HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements_x failed", mpi_code)
H5_CHECK_OVERFLOW(msg_size, MPI_Count, int);
if (msg_size <= 0)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "invalid chunk modification message size");
assert((num_recv_requests + 1) <= num_msgs_incoming);
if (NULL ==
(msg_recv_bufs[num_recv_requests] = H5MM_malloc((size_t)msg_size * sizeof(unsigned char))))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL,
"couldn't allocate chunk modification message receive buffer");
if (MPI_SUCCESS != (mpi_code = MPI_Irecv(msg_recv_bufs[num_recv_requests], (int)msg_size,
MPI_BYTE, status.MPI_SOURCE, H5D_CHUNK_MOD_DATA_TAG,
io_info->comm, &recv_requests[num_recv_requests])))
HMPI_GOTO_ERROR(FAIL, "MPI_Irecv failed", mpi_code)
num_recv_requests++;
}
if (ibarrier_posted) {
int ibarrier_completed;
if (MPI_SUCCESS != (mpi_code = MPI_Test(&ibarrier, &ibarrier_completed, MPI_STATUS_IGNORE)))
HMPI_GOTO_ERROR(FAIL, "MPI_Test failed", mpi_code)
if (ibarrier_completed)
break;
}
else {
int all_sends_completed;
/* Determine if all send requests have completed
*
* gcc 11 complains about passing MPI_STATUSES_IGNORE as an MPI_Status
* array. See the discussion here:
*
* https://github.com/pmodels/mpich/issues/5687
*/
H5_GCC_DIAG_OFF("stringop-overflow")
if (MPI_SUCCESS != (mpi_code = MPI_Testall((int)num_send_requests, send_requests,
&all_sends_completed, MPI_STATUSES_IGNORE)))
HMPI_GOTO_ERROR(FAIL, "MPI_Testall failed", mpi_code)
H5_GCC_DIAG_ON("stringop-overflow")
if (all_sends_completed) {
/* Post non-blocking barrier */
if (MPI_SUCCESS != (mpi_code = MPI_Ibarrier(io_info->comm, &ibarrier)))
HMPI_GOTO_ERROR(FAIL, "MPI_Ibarrier failed", mpi_code)
ibarrier_posted = true;
/*
* Now that all send requests have completed, free up the
* send buffers used in the non-blocking operations
*/
if (msg_send_bufs) {
for (size_t i = 0; i < num_send_requests; i++) {
if (msg_send_bufs[i])
H5MM_free(msg_send_bufs[i]);
}
msg_send_bufs = H5MM_xfree(msg_send_bufs);
}
}
}
} while (1);
/*
* Ensure all receive requests have completed before moving on.
* For linked-chunk I/O, more overlap with computation could
* theoretically be achieved by returning the receive requests
* array and postponing this wait until during chunk updating
* when the data is really needed. However, multi-chunk I/O
* only updates a chunk at a time and the messages may not come
* in the order that chunks are processed. So, the safest way to
* support both I/O modes is to simply make sure all messages
* are available.
*
* gcc 11 complains about passing MPI_STATUSES_IGNORE as an MPI_Status
* array. See the discussion here:
*
* https://github.com/pmodels/mpich/issues/5687
*/
H5_GCC_DIAG_OFF("stringop-overflow")
if (MPI_SUCCESS != (mpi_code = MPI_Waitall((int)num_recv_requests, recv_requests, MPI_STATUSES_IGNORE)))
HMPI_GOTO_ERROR(FAIL, "MPI_Waitall failed", mpi_code)
H5_GCC_DIAG_ON("stringop-overflow")
/* Set the new number of locally-selected chunks */
chunk_list->num_chunk_infos = last_assigned_idx;
/* Set chunk hash table information for future use */
chunk_list->chunk_hash_table = chunk_table;
/* Return chunk message buffers if any were received */
*chunk_msg_bufs = msg_recv_bufs;
*chunk_msg_bufs_len = (int)num_recv_requests;
done:
if (ret_value < 0) {
/* If this rank failed, make sure to participate in collective barrier */
if (!ibarrier_posted) {
if (MPI_SUCCESS != (mpi_code = MPI_Ibarrier(io_info->comm, &ibarrier)))
HMPI_GOTO_ERROR(FAIL, "MPI_Ibarrier failed", mpi_code)
}
if (num_send_requests) {
for (size_t i = 0; i < num_send_requests; i++) {
MPI_Cancel(&send_requests[i]);
}
}
if (recv_requests) {
for (size_t i = 0; i < num_recv_requests; i++) {
MPI_Cancel(&recv_requests[i]);
}
}
if (msg_recv_bufs) {
for (size_t i = 0; i < num_recv_requests; i++) {
H5MM_free(msg_recv_bufs[i]);
}
H5MM_free(msg_recv_bufs);
}
HASH_CLEAR(hh, chunk_table);
}
if (recv_requests)
H5MM_free(recv_requests);
if (send_requests)
H5MM_free(send_requests);
if (msg_send_bufs) {
for (size_t i = 0; i < num_send_requests; i++) {
if (msg_send_bufs[i])
H5MM_free(msg_send_bufs[i]);
}
H5MM_free(msg_send_bufs);
}
if (mem_iter) {
if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release dataspace selection iterator");
mem_iter = H5FL_FREE(H5S_sel_iter_t, mem_iter);
}
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_share_chunk_modification_data() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_collective_filtered_chunk_read
*
* Purpose: This routine coordinates a collective read across all ranks
* of the chunks they have selected. Each rank will then go
* and unfilter their read chunks as necessary and scatter
* the data into the provided read buffer.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_collective_filtered_chunk_read(H5D_filtered_collective_io_info_t *chunk_list,
const H5D_io_info_t *io_info, size_t num_dset_infos, int mpi_rank)
{
H5Z_EDC_t err_detect; /* Error detection info */
H5Z_cb_t filter_cb; /* I/O filter callback function */
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(chunk_list);
assert(io_info);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_TIME_START(mpi_rank, "Filtered collective chunk read");
#else
(void)mpi_rank;
#endif
/*
* Allocate memory buffers for all chunks being read. Chunk data buffers are of
* the largest size between the chunk's current filtered size and the chunk's true
* size, as calculated by the number of elements in the chunk's file space extent
* multiplied by the datatype size. This tries to ensure that:
*
* * If we're reading the chunk and the filter normally reduces the chunk size,
* the unfiltering operation won't need to grow the buffer.
* * If we're reading the chunk and the filter normally grows the chunk size,
* we make sure to read into a buffer of size equal to the filtered chunk's
* size; reading into a (smaller) buffer of size equal to the unfiltered
* chunk size would of course be bad.
*/
for (size_t info_idx = 0; info_idx < chunk_list->num_chunk_infos; info_idx++) {
H5D_filtered_collective_chunk_info_t *chunk_entry = &chunk_list->chunk_infos[info_idx];
H5D_mpio_filtered_dset_info_t *cached_dset_info;
hsize_t file_chunk_size;
assert(chunk_entry->need_read);
/* Find the cached dataset info for the dataset this chunk is in */
if (num_dset_infos > 1) {
HASH_FIND(hh, chunk_list->dset_info.dset_info_hash_table, &chunk_entry->index_info.dset_oloc_addr,
sizeof(haddr_t), cached_dset_info);
if (cached_dset_info == NULL) {
if (chunk_list->all_dset_indices_empty)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFIND, FAIL, "unable to find cached dataset info entry");
else {
/* Push an error, but participate in collective read */
HDONE_ERROR(H5E_DATASET, H5E_CANTFIND, FAIL, "unable to find cached dataset info entry");
break;
}
}
}
else
cached_dset_info = chunk_list->dset_info.single_dset_info;
assert(cached_dset_info);
file_chunk_size = cached_dset_info->file_chunk_size;
chunk_entry->chunk_buf_size = MAX(chunk_entry->chunk_current.length, file_chunk_size);
if (NULL == (chunk_entry->buf = H5MM_malloc(chunk_entry->chunk_buf_size))) {
if (chunk_list->all_dset_indices_empty)
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk data buffer");
else {
/* Push an error, but participate in collective read */
HDONE_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk data buffer");
break;
}
}
/*
* Check whether the chunk needs to be read from the file, based
* on whether the dataset's chunk index is empty or the chunk has
* a defined address in the file. If the chunk doesn't need to be
* read from the file, just fill the chunk buffer with the fill
* value if necessary.
*/
if (cached_dset_info->index_empty || !H5_addr_defined(chunk_entry->chunk_current.offset)) {
chunk_entry->need_read = false;
/* Update field keeping track of number of chunks to read */
assert(chunk_list->num_chunks_to_read > 0);
chunk_list->num_chunks_to_read--;
}
if (chunk_entry->need_read) {
/* Set chunk's new length for eventual filter pipeline calls */
if (chunk_entry->skip_filter_pline)
chunk_entry->chunk_new.length = file_chunk_size;
else
chunk_entry->chunk_new.length = chunk_entry->chunk_current.length;
}
else {
/* Set chunk's new length for eventual filter pipeline calls */
chunk_entry->chunk_new.length = file_chunk_size;
/* Determine if fill values should be "read" for this unallocated chunk */
if (cached_dset_info->should_fill) {
assert(cached_dset_info->fb_info_init);
assert(cached_dset_info->fb_info.fill_buf);
/* Write fill value to memory buffer */
if (H5D__fill(cached_dset_info->fb_info.fill_buf,
cached_dset_info->dset_io_info->type_info.dset_type, chunk_entry->buf,
cached_dset_info->dset_io_info->type_info.mem_type,
cached_dset_info->fill_space) < 0) {
if (chunk_list->all_dset_indices_empty)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"couldn't fill chunk buffer with fill value");
else {
/* Push an error, but participate in collective read */
HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"couldn't fill chunk buffer with fill value");
break;
}
}
}
}
}
/* Perform collective vector read if necessary */
if (!chunk_list->all_dset_indices_empty)
if (H5D__mpio_collective_filtered_vec_io(chunk_list, io_info->f_sh, H5D_IO_OP_READ) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't perform vector I/O on filtered chunks");
if (chunk_list->num_chunk_infos) {
/* Retrieve filter settings from API context */
if (H5CX_get_err_detect(&err_detect) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get error detection info");
if (H5CX_get_filter_cb(&filter_cb) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get I/O filter callback function");
}
/*
* Iterate through all the read chunks, unfiltering them and scattering their
* data out to the application's read buffer.
*/
for (size_t info_idx = 0; info_idx < chunk_list->num_chunk_infos; info_idx++) {
H5D_filtered_collective_chunk_info_t *chunk_entry = &chunk_list->chunk_infos[info_idx];
H5D_piece_info_t *chunk_info = chunk_entry->chunk_info;
hsize_t iter_nelmts;
/* Unfilter the chunk, unless we didn't read it from the file */
if (chunk_entry->need_read && !chunk_entry->skip_filter_pline) {
if (H5Z_pipeline(&chunk_info->dset_info->dset->shared->dcpl_cache.pline, H5Z_FLAG_REVERSE,
&(chunk_entry->index_info.filter_mask), err_detect, filter_cb,
(size_t *)&chunk_entry->chunk_new.length, &chunk_entry->chunk_buf_size,
&chunk_entry->buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFILTER, FAIL, "couldn't unfilter chunk for modifying");
}
/* Scatter the chunk data to the read buffer */
iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace);
if (H5D_select_io_mem(chunk_info->dset_info->buf.vp, chunk_info->mspace, chunk_entry->buf,
chunk_info->fspace, chunk_info->dset_info->type_info.src_type_size,
(size_t)iter_nelmts) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't copy chunk data to read buffer");
}
done:
/* Free all resources used by entries in the chunk list */
for (size_t info_idx = 0; info_idx < chunk_list->num_chunk_infos; info_idx++) {
if (chunk_list->chunk_infos[info_idx].buf) {
H5MM_free(chunk_list->chunk_infos[info_idx].buf);
chunk_list->chunk_infos[info_idx].buf = NULL;
}
}
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_collective_filtered_chunk_read() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_collective_filtered_chunk_update
*
* Purpose: When performing a parallel write on a chunked dataset with
* filters applied, all ranks must update their owned chunks
* with their own modification data and data from other ranks.
* This routine is responsible for coordinating that process.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_collective_filtered_chunk_update(H5D_filtered_collective_io_info_t *chunk_list,
unsigned char **chunk_msg_bufs, int chunk_msg_bufs_len,
const H5D_io_info_t *io_info, size_t num_dset_infos, int mpi_rank)
{
H5S_sel_iter_t *sel_iter = NULL; /* Dataspace selection iterator for H5D__scatter_mem */
H5Z_EDC_t err_detect; /* Error detection info */
H5Z_cb_t filter_cb; /* I/O filter callback function */
uint8_t *key_buf = NULL;
H5S_t *dataspace = NULL;
bool sel_iter_init = false;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(chunk_list);
assert((chunk_msg_bufs && chunk_list->chunk_hash_table) || 0 == chunk_msg_bufs_len);
assert(io_info);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_TIME_START(mpi_rank, "Filtered collective chunk update");
#endif
/*
* Allocate memory buffers for all owned chunks. Chunk data buffers are of the
* largest size between the chunk's current filtered size and the chunk's true
* size, as calculated by the number of elements in the chunk's file space extent
* multiplied by the datatype size. This tries to ensure that:
*
* * If we're fully overwriting the chunk and the filter normally reduces the
* chunk size, we simply have the exact buffer size required to hold the
* unfiltered chunk data.
* * If we're fully overwriting the chunk and the filter normally grows the
* chunk size (e.g., fletcher32 filter), the final filtering operation
* (hopefully) won't need to grow the buffer.
* * If we're reading the chunk and the filter normally reduces the chunk size,
* the unfiltering operation won't need to grow the buffer.
* * If we're reading the chunk and the filter normally grows the chunk size,
* we make sure to read into a buffer of size equal to the filtered chunk's
* size; reading into a (smaller) buffer of size equal to the unfiltered
* chunk size would of course be bad.
*/
for (size_t info_idx = 0; info_idx < chunk_list->num_chunk_infos; info_idx++) {
H5D_filtered_collective_chunk_info_t *chunk_entry = &chunk_list->chunk_infos[info_idx];
H5D_mpio_filtered_dset_info_t *cached_dset_info;
hsize_t file_chunk_size;
assert(mpi_rank == chunk_entry->new_owner);
/* Find the cached dataset info for the dataset this chunk is in */
if (num_dset_infos > 1) {
HASH_FIND(hh, chunk_list->dset_info.dset_info_hash_table, &chunk_entry->index_info.dset_oloc_addr,
sizeof(haddr_t), cached_dset_info);
if (cached_dset_info == NULL) {
if (chunk_list->all_dset_indices_empty)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFIND, FAIL, "unable to find cached dataset info entry");
else {
/* Push an error, but participate in collective read */
HDONE_ERROR(H5E_DATASET, H5E_CANTFIND, FAIL, "unable to find cached dataset info entry");
break;
}
}
}
else
cached_dset_info = chunk_list->dset_info.single_dset_info;
assert(cached_dset_info);
file_chunk_size = cached_dset_info->file_chunk_size;
chunk_entry->chunk_buf_size = MAX(chunk_entry->chunk_current.length, file_chunk_size);
/*
* If this chunk hasn't been allocated yet and we aren't writing
* out fill values to it, make sure to 0-fill its memory buffer
* so we don't use uninitialized memory.
*/
if (!H5_addr_defined(chunk_entry->chunk_current.offset) && !cached_dset_info->should_fill)
chunk_entry->buf = H5MM_calloc(chunk_entry->chunk_buf_size);
else
chunk_entry->buf = H5MM_malloc(chunk_entry->chunk_buf_size);
if (NULL == chunk_entry->buf) {
if (chunk_list->all_dset_indices_empty)
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk data buffer");
else {
/* Push an error, but participate in collective read */
HDONE_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate chunk data buffer");
break;
}
}
if (!chunk_entry->need_read)
/* Set chunk's new length for eventual filter pipeline calls */
chunk_entry->chunk_new.length = file_chunk_size;
else {
/*
* Check whether the chunk needs to be read from the file, based
* on whether the dataset's chunk index is empty or the chunk has
* a defined address in the file. If the chunk doesn't need to be
* read from the file, just fill the chunk buffer with the fill
* value if necessary.
*/
if (cached_dset_info->index_empty || !H5_addr_defined(chunk_entry->chunk_current.offset)) {
chunk_entry->need_read = false;
/* Update field keeping track of number of chunks to read */
assert(chunk_list->num_chunks_to_read > 0);
chunk_list->num_chunks_to_read--;
}
if (chunk_entry->need_read) {
/* Set chunk's new length for eventual filter pipeline calls */
if (chunk_entry->skip_filter_pline)
chunk_entry->chunk_new.length = file_chunk_size;
else
chunk_entry->chunk_new.length = chunk_entry->chunk_current.length;
}
else {
/* Set chunk's new length for eventual filter pipeline calls */
chunk_entry->chunk_new.length = file_chunk_size;
/* Determine if fill values should be "read" for this unallocated chunk */
if (cached_dset_info->should_fill) {
assert(cached_dset_info->fb_info_init);
assert(cached_dset_info->fb_info.fill_buf);
/* Write fill value to memory buffer */
if (H5D__fill(cached_dset_info->fb_info.fill_buf,
cached_dset_info->dset_io_info->type_info.dset_type, chunk_entry->buf,
cached_dset_info->dset_io_info->type_info.mem_type,
cached_dset_info->fill_space) < 0) {
if (chunk_list->all_dset_indices_empty)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"couldn't fill chunk buffer with fill value");
else {
/* Push an error, but participate in collective read */
HDONE_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"couldn't fill chunk buffer with fill value");
break;
}
}
}
}
}
}
/* Perform collective vector read if necessary */
if (!chunk_list->all_dset_indices_empty)
if (H5D__mpio_collective_filtered_vec_io(chunk_list, io_info->f_sh, H5D_IO_OP_READ) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't perform vector I/O on filtered chunks");
/*
* Now that all owned chunks have been read, update the chunks
* with modification data from the owning rank and other ranks.
*/
if (chunk_list->num_chunk_infos > 0) {
/* Retrieve filter settings from API context */
if (H5CX_get_err_detect(&err_detect) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get error detection info");
if (H5CX_get_filter_cb(&filter_cb) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get I/O filter callback function");
}
/* Process all chunks with data from the owning rank first */
for (size_t info_idx = 0; info_idx < chunk_list->num_chunk_infos; info_idx++) {
H5D_filtered_collective_chunk_info_t *chunk_entry = &chunk_list->chunk_infos[info_idx];
H5D_piece_info_t *chunk_info = chunk_entry->chunk_info;
hsize_t iter_nelmts;
assert(mpi_rank == chunk_entry->new_owner);
/*
* If this chunk wasn't being fully overwritten, we read it from
* the file, so we need to unfilter it
*/
if (chunk_entry->need_read && !chunk_entry->skip_filter_pline) {
if (H5Z_pipeline(&chunk_info->dset_info->dset->shared->dcpl_cache.pline, H5Z_FLAG_REVERSE,
&(chunk_entry->index_info.filter_mask), err_detect, filter_cb,
(size_t *)&chunk_entry->chunk_new.length, &chunk_entry->chunk_buf_size,
&chunk_entry->buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFILTER, FAIL, "couldn't unfilter chunk for modifying");
}
iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace);
if (H5D_select_io_mem(chunk_entry->buf, chunk_info->fspace, chunk_info->dset_info->buf.cvp,
chunk_info->mspace, chunk_info->dset_info->type_info.dst_type_size,
(size_t)iter_nelmts) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't copy chunk data to write buffer");
}
/* Allocate iterator for memory selection */
if (chunk_msg_bufs_len > 0) {
assert(chunk_list->chunk_hash_table_keylen > 0);
if (NULL == (key_buf = H5MM_malloc(chunk_list->chunk_hash_table_keylen)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate hash table key buffer");
if (NULL == (sel_iter = H5FL_MALLOC(H5S_sel_iter_t)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate memory iterator");
}
/* Now process all received chunk message buffers */
for (size_t buf_idx = 0; buf_idx < (size_t)chunk_msg_bufs_len; buf_idx++) {
H5D_filtered_collective_chunk_info_t *chunk_entry = NULL;
const unsigned char *msg_ptr = chunk_msg_bufs[buf_idx];
if (msg_ptr) {
/* Retrieve the chunk hash table key from the chunk message buffer */
H5MM_memcpy(key_buf, msg_ptr, chunk_list->chunk_hash_table_keylen);
msg_ptr += chunk_list->chunk_hash_table_keylen;
/* Find the chunk entry according to its chunk hash table key */
HASH_FIND(hh, chunk_list->chunk_hash_table, key_buf, chunk_list->chunk_hash_table_keylen,
chunk_entry);
if (chunk_entry == NULL)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFIND, FAIL, "unable to find chunk entry");
if (mpi_rank != chunk_entry->new_owner)
HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk owner set to incorrect MPI rank");
/*
* Only process the chunk if its data buffer is allocated.
* In the case of multi-chunk I/O, we're only working on
* a chunk at a time, so we need to skip over messages
* that aren't for the chunk we're currently working on.
*/
if (!chunk_entry->buf)
continue;
else {
hsize_t iter_nelmts;
/* Decode the chunk file dataspace from the message */
if (NULL == (dataspace = H5S_decode(&msg_ptr)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTDECODE, FAIL, "unable to decode dataspace");
if (H5S_select_iter_init(sel_iter, dataspace,
chunk_entry->chunk_info->dset_info->type_info.dst_type_size,
H5S_SEL_ITER_SHARE_WITH_DATASPACE) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL,
"unable to initialize memory selection information");
sel_iter_init = true;
iter_nelmts = H5S_GET_SELECT_NPOINTS(dataspace);
/* Update the chunk data with the received modification data */
if (H5D__scatter_mem(msg_ptr, sel_iter, (size_t)iter_nelmts, chunk_entry->buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "couldn't scatter to write buffer");
if (H5S_SELECT_ITER_RELEASE(sel_iter) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator");
sel_iter_init = false;
if (dataspace) {
if (H5S_close(dataspace) < 0)
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace");
dataspace = NULL;
}
H5MM_free(chunk_msg_bufs[buf_idx]);
chunk_msg_bufs[buf_idx] = NULL;
}
}
}
/* Finally, filter all the chunks */
for (size_t info_idx = 0; info_idx < chunk_list->num_chunk_infos; info_idx++) {
if (!chunk_list->chunk_infos[info_idx].skip_filter_pline) {
if (H5Z_pipeline(
&chunk_list->chunk_infos[info_idx].chunk_info->dset_info->dset->shared->dcpl_cache.pline,
0, &(chunk_list->chunk_infos[info_idx].index_info.filter_mask), err_detect, filter_cb,
(size_t *)&chunk_list->chunk_infos[info_idx].chunk_new.length,
&chunk_list->chunk_infos[info_idx].chunk_buf_size,
&chunk_list->chunk_infos[info_idx].buf) < 0)
HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "output pipeline failed");
}
#if H5_SIZEOF_SIZE_T > 4
/* Check for the chunk expanding too much to encode in a 32-bit value */
if (chunk_list->chunk_infos[info_idx].chunk_new.length > ((size_t)0xffffffff))
HGOTO_ERROR(H5E_DATASET, H5E_BADRANGE, FAIL, "chunk too large for 32-bit length");
#endif
}
done:
if (dataspace && (H5S_close(dataspace) < 0))
HDONE_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "can't close dataspace");
if (sel_iter) {
if (sel_iter_init && H5S_SELECT_ITER_RELEASE(sel_iter) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator");
sel_iter = H5FL_FREE(H5S_sel_iter_t, sel_iter);
}
H5MM_free(key_buf);
/* On failure, try to free all resources used by entries in the chunk list */
if (ret_value < 0) {
for (size_t info_idx = 0; info_idx < chunk_list->num_chunk_infos; info_idx++) {
if (chunk_list->chunk_infos[info_idx].buf) {
H5MM_free(chunk_list->chunk_infos[info_idx].buf);
chunk_list->chunk_infos[info_idx].buf = NULL;
}
}
}
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_collective_filtered_chunk_update() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_collective_filtered_chunk_reallocate
*
* Purpose: When performing a parallel write on a chunked dataset with
* filters applied, all ranks must eventually get together and
* perform a collective reallocation of space in the file for
* all chunks that were modified on all ranks. This routine is
* responsible for coordinating that process.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_collective_filtered_chunk_reallocate(H5D_filtered_collective_io_info_t *chunk_list,
size_t *num_chunks_assigned_map, H5D_io_info_t *io_info,
size_t num_dset_infos, int mpi_rank, int mpi_size)
{
H5D_chunk_alloc_info_t *collective_list = NULL;
MPI_Datatype send_type;
MPI_Datatype recv_type;
bool send_type_derived = false;
bool recv_type_derived = false;
bool need_sort = false;
size_t collective_num_entries = 0;
size_t num_local_chunks_processed = 0;
void *gathered_array = NULL;
int *counts_disps_array = NULL;
int *counts_ptr = NULL;
int *displacements_ptr = NULL;
int mpi_code;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(chunk_list);
assert(io_info);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_TIME_START(mpi_rank, "Reallocation of chunk file space");
#endif
/*
* Make sure it's safe to cast this rank's number
* of chunks to be sent into an int for MPI
*/
H5_CHECK_OVERFLOW(chunk_list->num_chunk_infos, size_t, int);
/* Create derived datatypes for the chunk file space info needed */
if (H5D__mpio_get_chunk_alloc_info_types(&recv_type, &recv_type_derived, &send_type, &send_type_derived) <
0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,
"can't create derived datatypes for chunk file space info");
/*
* Gather the new chunk sizes to all ranks for a collective reallocation
* of the chunks in the file.
*/
if (num_chunks_assigned_map) {
/*
* If a mapping between rank value -> number of assigned chunks has
* been provided (usually during linked-chunk I/O), we can use this
* to optimize MPI overhead a bit since MPI ranks won't need to
* first inform each other about how many chunks they're contributing.
*/
if (NULL == (counts_disps_array = H5MM_malloc(2 * (size_t)mpi_size * sizeof(*counts_disps_array)))) {
/* Push an error, but still participate in collective gather operation */
HDONE_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL,
"couldn't allocate receive counts and displacements array");
}
else {
/* Set the receive counts from the assigned chunks map */
counts_ptr = counts_disps_array;
for (int curr_rank = 0; curr_rank < mpi_size; curr_rank++)
H5_CHECKED_ASSIGN(counts_ptr[curr_rank], int, num_chunks_assigned_map[curr_rank], size_t);
/* Set the displacements into the receive buffer for the gather operation */
displacements_ptr = &counts_disps_array[mpi_size];
*displacements_ptr = 0;
for (int curr_rank = 1; curr_rank < mpi_size; curr_rank++)
displacements_ptr[curr_rank] = displacements_ptr[curr_rank - 1] + counts_ptr[curr_rank - 1];
}
/* Perform gather operation */
if (H5_mpio_gatherv_alloc(chunk_list->chunk_infos, (int)chunk_list->num_chunk_infos, send_type,
counts_ptr, displacements_ptr, recv_type, true, 0, io_info->comm, mpi_rank,
mpi_size, &gathered_array, &collective_num_entries) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL,
"can't gather chunk file space info to/from ranks");
}
else {
/*
* If no mapping between rank value -> number of assigned chunks has
* been provided (usually during multi-chunk I/O), all MPI ranks will
* need to first inform other ranks about how many chunks they're
* contributing before performing the actual gather operation. Use
* the 'simple' MPI_Allgatherv wrapper for this.
*/
if (H5_mpio_gatherv_alloc_simple(chunk_list->chunk_infos, (int)chunk_list->num_chunk_infos, send_type,
recv_type, true, 0, io_info->comm, mpi_rank, mpi_size,
&gathered_array, &collective_num_entries) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL,
"can't gather chunk file space info to/from ranks");
}
/* Collectively re-allocate the modified chunks (from each rank) in the file */
collective_list = (H5D_chunk_alloc_info_t *)gathered_array;
num_local_chunks_processed = 0;
for (size_t entry_idx = 0; entry_idx < collective_num_entries; entry_idx++) {
H5D_mpio_filtered_dset_info_t *cached_dset_info;
H5D_chunk_alloc_info_t *coll_entry = &collective_list[entry_idx];
bool need_insert;
bool update_local_chunk;
/* Find the cached dataset info for the dataset this chunk is in */
if (num_dset_infos > 1) {
HASH_FIND(hh, chunk_list->dset_info.dset_info_hash_table, &coll_entry->dset_oloc_addr,
sizeof(haddr_t), cached_dset_info);
if (cached_dset_info == NULL)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFIND, FAIL, "unable to find cached dataset info entry");
}
else
cached_dset_info = chunk_list->dset_info.single_dset_info;
assert(cached_dset_info);
if (H5D__chunk_file_alloc(&cached_dset_info->chunk_idx_info, &coll_entry->chunk_current,
&coll_entry->chunk_new, &need_insert, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "unable to allocate chunk");
/*
* If we just re-allocated a chunk that is local to this
* rank, make sure to update the chunk entry in the local
* chunk list
*/
update_local_chunk =
(num_local_chunks_processed < chunk_list->num_chunk_infos) &&
(coll_entry->dset_oloc_addr ==
chunk_list->chunk_infos[num_local_chunks_processed].index_info.dset_oloc_addr) &&
(coll_entry->chunk_idx ==
chunk_list->chunk_infos[num_local_chunks_processed].index_info.chunk_idx);
if (update_local_chunk) {
H5D_filtered_collective_chunk_info_t *local_chunk;
local_chunk = &chunk_list->chunk_infos[num_local_chunks_processed];
/* Sanity check that this chunk is actually local */
assert(mpi_rank == local_chunk->orig_owner);
assert(mpi_rank == local_chunk->new_owner);
local_chunk->chunk_new = coll_entry->chunk_new;
local_chunk->index_info.need_insert = need_insert;
/*
* Since chunk reallocation can move chunks around, check if
* the local chunk list is still in ascending offset of order
* in the file
*/
if (num_local_chunks_processed) {
haddr_t curr_chunk_offset = local_chunk->chunk_new.offset;
haddr_t prev_chunk_offset =
chunk_list->chunk_infos[num_local_chunks_processed - 1].chunk_new.offset;
assert(H5_addr_defined(prev_chunk_offset) && H5_addr_defined(curr_chunk_offset));
if (curr_chunk_offset < prev_chunk_offset)
need_sort = true;
}
num_local_chunks_processed++;
}
}
assert(chunk_list->num_chunk_infos == num_local_chunks_processed);
/*
* Ensure this rank's local chunk list is sorted in
* ascending order of offset in the file
*/
if (need_sort)
qsort(chunk_list->chunk_infos, chunk_list->num_chunk_infos,
sizeof(H5D_filtered_collective_chunk_info_t), H5D__cmp_filtered_collective_io_info_entry);
done:
H5MM_free(gathered_array);
H5MM_free(counts_disps_array);
if (send_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&send_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
if (recv_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&recv_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* H5D__mpio_collective_filtered_chunk_reallocate() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_collective_filtered_chunk_reinsert
*
* Purpose: When performing a parallel write on a chunked dataset with
* filters applied, all ranks must eventually get together and
* perform a collective reinsertion into the dataset's chunk
* index of chunks that were modified. This routine is
* responsible for coordinating that process.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_collective_filtered_chunk_reinsert(H5D_filtered_collective_io_info_t *chunk_list,
size_t *num_chunks_assigned_map, H5D_io_info_t *io_info,
size_t num_dset_infos, int mpi_rank, int mpi_size)
{
MPI_Datatype send_type;
MPI_Datatype recv_type;
size_t collective_num_entries = 0;
bool send_type_derived = false;
bool recv_type_derived = false;
void *gathered_array = NULL;
int *counts_disps_array = NULL;
int *counts_ptr = NULL;
int *displacements_ptr = NULL;
int mpi_code;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(chunk_list);
assert(io_info);
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TRACE_ENTER(mpi_rank);
H5D_MPIO_TIME_START(mpi_rank, "Reinsertion of modified chunks into chunk index");
#endif
/*
* If no datasets involved have a chunk index 'insert'
* operation, this function is a no-op
*/
if (chunk_list->no_dset_index_insert_methods)
HGOTO_DONE(SUCCEED);
/*
* Make sure it's safe to cast this rank's number
* of chunks to be sent into an int for MPI
*/
H5_CHECK_OVERFLOW(chunk_list->num_chunk_infos, size_t, int);
/* Create derived datatypes for the chunk re-insertion info needed */
if (H5D__mpio_get_chunk_insert_info_types(&recv_type, &recv_type_derived, &send_type,
&send_type_derived) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL,
"can't create derived datatypes for chunk re-insertion info");
/*
* Gather information to all ranks for a collective re-insertion
* of the modified chunks into the chunk index
*/
if (num_chunks_assigned_map) {
/*
* If a mapping between rank value -> number of assigned chunks has
* been provided (usually during linked-chunk I/O), we can use this
* to optimize MPI overhead a bit since MPI ranks won't need to
* first inform each other about how many chunks they're contributing.
*/
if (NULL == (counts_disps_array = H5MM_malloc(2 * (size_t)mpi_size * sizeof(*counts_disps_array)))) {
/* Push an error, but still participate in collective gather operation */
HDONE_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL,
"couldn't allocate receive counts and displacements array");
}
else {
/* Set the receive counts from the assigned chunks map */
counts_ptr = counts_disps_array;
for (int curr_rank = 0; curr_rank < mpi_size; curr_rank++)
H5_CHECKED_ASSIGN(counts_ptr[curr_rank], int, num_chunks_assigned_map[curr_rank], size_t);
/* Set the displacements into the receive buffer for the gather operation */
displacements_ptr = &counts_disps_array[mpi_size];
*displacements_ptr = 0;
for (int curr_rank = 1; curr_rank < mpi_size; curr_rank++)
displacements_ptr[curr_rank] = displacements_ptr[curr_rank - 1] + counts_ptr[curr_rank - 1];
}
/* Perform gather operation */
if (H5_mpio_gatherv_alloc(chunk_list->chunk_infos, (int)chunk_list->num_chunk_infos, send_type,
counts_ptr, displacements_ptr, recv_type, true, 0, io_info->comm, mpi_rank,
mpi_size, &gathered_array, &collective_num_entries) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL,
"can't gather chunk index re-insertion info to/from ranks");
}
else {
/*
* If no mapping between rank value -> number of assigned chunks has
* been provided (usually during multi-chunk I/O), all MPI ranks will
* need to first inform other ranks about how many chunks they're
* contributing before performing the actual gather operation. Use
* the 'simple' MPI_Allgatherv wrapper for this.
*/
if (H5_mpio_gatherv_alloc_simple(chunk_list->chunk_infos, (int)chunk_list->num_chunk_infos, send_type,
recv_type, true, 0, io_info->comm, mpi_rank, mpi_size,
&gathered_array, &collective_num_entries) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL,
"can't gather chunk index re-insertion info to/from ranks");
}
for (size_t entry_idx = 0; entry_idx < collective_num_entries; entry_idx++) {
H5D_mpio_filtered_dset_info_t *cached_dset_info;
H5D_chunk_insert_info_t *coll_entry = &((H5D_chunk_insert_info_t *)gathered_array)[entry_idx];
H5D_chunk_ud_t chunk_ud;
haddr_t prev_tag = HADDR_UNDEF;
hsize_t scaled_coords[H5O_LAYOUT_NDIMS];
/*
* We only need to reinsert this chunk if we had to actually
* allocate or reallocate space in the file for it
*/
if (!coll_entry->index_info.need_insert)
continue;
/* Find the cached dataset info for the dataset this chunk is in */
if (num_dset_infos > 1) {
HASH_FIND(hh, chunk_list->dset_info.dset_info_hash_table, &coll_entry->index_info.dset_oloc_addr,
sizeof(haddr_t), cached_dset_info);
if (cached_dset_info == NULL)
HGOTO_ERROR(H5E_DATASET, H5E_CANTFIND, FAIL, "unable to find cached dataset info entry");
}
else
cached_dset_info = chunk_list->dset_info.single_dset_info;
assert(cached_dset_info);
chunk_ud.common.layout = cached_dset_info->chunk_idx_info.layout;
chunk_ud.common.storage = cached_dset_info->chunk_idx_info.storage;
chunk_ud.common.scaled = scaled_coords;
chunk_ud.chunk_block = coll_entry->chunk_block;
chunk_ud.chunk_idx = coll_entry->index_info.chunk_idx;
chunk_ud.filter_mask = coll_entry->index_info.filter_mask;
/* Calculate scaled coordinates for the chunk */
if (cached_dset_info->chunk_idx_info.layout->idx_type == H5D_CHUNK_IDX_EARRAY &&
cached_dset_info->chunk_idx_info.layout->u.earray.unlim_dim > 0) {
/*
* Extensible arrays where the unlimited dimension is not
* the slowest-changing dimension "swizzle" the coordinates
* to move the unlimited dimension value to offset 0. Therefore,
* we use the "swizzled" down chunks to calculate the "swizzled"
* scaled coordinates and then we undo the "swizzle" operation.
*
* TODO: In the future, this is something that should be handled
* by the particular chunk index rather than manually
* here. Likely, the chunk index ops should get a new
* callback that accepts a chunk index and provides the
* caller with the scaled coordinates for that chunk.
*/
H5VM_array_calc_pre(chunk_ud.chunk_idx, cached_dset_info->dset_io_info->dset->shared->ndims,
cached_dset_info->chunk_idx_info.layout->u.earray.swizzled_down_chunks,
scaled_coords);
H5VM_unswizzle_coords(hsize_t, scaled_coords,
cached_dset_info->chunk_idx_info.layout->u.earray.unlim_dim);
}
else {
H5VM_array_calc_pre(chunk_ud.chunk_idx, cached_dset_info->dset_io_info->dset->shared->ndims,
cached_dset_info->dset_io_info->dset->shared->layout.u.chunk.down_chunks,
scaled_coords);
}
scaled_coords[cached_dset_info->dset_io_info->dset->shared->ndims] = 0;
#ifndef NDEBUG
/*
* If a matching local chunk entry is found, the
* `chunk_info` structure (which contains the chunk's
* pre-computed scaled coordinates) will be valid
* for this rank. Compare those coordinates against
* the calculated coordinates above to make sure
* they match.
*/
for (size_t dbg_idx = 0; dbg_idx < chunk_list->num_chunk_infos; dbg_idx++) {
bool same_chunk;
/* Chunks must have the same index and reside in the same dataset */
same_chunk = (0 == H5_addr_cmp(coll_entry->index_info.dset_oloc_addr,
chunk_list->chunk_infos[dbg_idx].index_info.dset_oloc_addr));
same_chunk = same_chunk && (coll_entry->index_info.chunk_idx ==
chunk_list->chunk_infos[dbg_idx].index_info.chunk_idx);
if (same_chunk) {
bool coords_match =
!memcmp(scaled_coords, chunk_list->chunk_infos[dbg_idx].chunk_info->scaled,
cached_dset_info->dset_io_info->dset->shared->ndims * sizeof(hsize_t));
assert(coords_match && "Calculated scaled coordinates for chunk didn't match "
"chunk's actual scaled coordinates!");
break;
}
}
#endif
/* Set metadata tagging with dataset oheader addr */
H5AC_tag(cached_dset_info->dset_io_info->dset->oloc.addr, &prev_tag);
if ((cached_dset_info->chunk_idx_info.storage->ops->insert)(
&cached_dset_info->chunk_idx_info, &chunk_ud, cached_dset_info->dset_io_info->dset) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert chunk address into index");
/* Reset metadata tagging */
H5AC_tag(prev_tag, NULL);
}
done:
H5MM_free(gathered_array);
H5MM_free(counts_disps_array);
if (send_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&send_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
if (recv_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&recv_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
#ifdef H5Dmpio_DEBUG
H5D_MPIO_TIME_STOP(mpi_rank);
H5D_MPIO_TRACE_EXIT(mpi_rank);
#endif
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_collective_filtered_chunk_reinsert() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_get_chunk_redistribute_info_types
*
* Purpose: Constructs MPI derived datatypes for communicating the
* info from a H5D_filtered_collective_chunk_info_t structure
* that is necessary for redistributing shared chunks during a
* collective write of filtered chunks.
*
* The datatype returned through `contig_type` has an extent
* equal to the size of an H5D_chunk_redistribute_info_t
* structure and is suitable for communicating that structure
* type.
*
* The datatype returned through `resized_type` has an extent
* equal to the size of an H5D_filtered_collective_chunk_info_t
* structure. This makes it suitable for sending an array of
* those structures, while extracting out just the info
* necessary for the chunk redistribution operation during
* communication.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_get_chunk_redistribute_info_types(MPI_Datatype *contig_type, bool *contig_type_derived,
MPI_Datatype *resized_type, bool *resized_type_derived)
{
MPI_Datatype struct_type = MPI_DATATYPE_NULL;
bool struct_type_derived = false;
MPI_Datatype chunk_block_type = MPI_DATATYPE_NULL;
bool chunk_block_type_derived = false;
MPI_Datatype types[6];
MPI_Aint displacements[6];
int block_lengths[6];
int field_count;
int mpi_code;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(contig_type);
assert(contig_type_derived);
assert(resized_type);
assert(resized_type_derived);
*contig_type_derived = false;
*resized_type_derived = false;
/* Create struct type for the inner H5F_block_t structure */
if (H5F_mpi_get_file_block_type(false, &chunk_block_type, &chunk_block_type_derived) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't create derived type for chunk file description");
field_count = 6;
assert(field_count == (sizeof(types) / sizeof(MPI_Datatype)));
/*
* Create structure type to pack chunk H5F_block_t structure
* next to chunk_idx, dset_oloc_addr, orig_owner, new_owner
* and num_writers fields
*/
block_lengths[0] = 1;
block_lengths[1] = 1;
block_lengths[2] = 1;
block_lengths[3] = 1;
block_lengths[4] = 1;
block_lengths[5] = 1;
displacements[0] = offsetof(H5D_chunk_redistribute_info_t, chunk_block);
displacements[1] = offsetof(H5D_chunk_redistribute_info_t, chunk_idx);
displacements[2] = offsetof(H5D_chunk_redistribute_info_t, dset_oloc_addr);
displacements[3] = offsetof(H5D_chunk_redistribute_info_t, orig_owner);
displacements[4] = offsetof(H5D_chunk_redistribute_info_t, new_owner);
displacements[5] = offsetof(H5D_chunk_redistribute_info_t, num_writers);
types[0] = chunk_block_type;
types[1] = HSIZE_AS_MPI_TYPE;
types[2] = HADDR_AS_MPI_TYPE;
types[3] = MPI_INT;
types[4] = MPI_INT;
types[5] = MPI_INT;
if (MPI_SUCCESS !=
(mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, contig_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
*contig_type_derived = true;
if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(contig_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
/* Create struct type to extract the chunk_current, chunk_idx,
* dset_oloc_addr, orig_owner, new_owner and num_writers fields
* from a H5D_filtered_collective_chunk_info_t structure
*/
block_lengths[0] = 1;
block_lengths[1] = 1;
block_lengths[2] = 1;
block_lengths[3] = 1;
block_lengths[4] = 1;
block_lengths[5] = 1;
displacements[0] = offsetof(H5D_filtered_collective_chunk_info_t, chunk_current);
displacements[1] = offsetof(H5D_filtered_collective_chunk_info_t, index_info.chunk_idx);
displacements[2] = offsetof(H5D_filtered_collective_chunk_info_t, index_info.dset_oloc_addr);
displacements[3] = offsetof(H5D_filtered_collective_chunk_info_t, orig_owner);
displacements[4] = offsetof(H5D_filtered_collective_chunk_info_t, new_owner);
displacements[5] = offsetof(H5D_filtered_collective_chunk_info_t, num_writers);
types[0] = chunk_block_type;
types[1] = HSIZE_AS_MPI_TYPE;
types[2] = HADDR_AS_MPI_TYPE;
types[3] = MPI_INT;
types[4] = MPI_INT;
types[5] = MPI_INT;
if (MPI_SUCCESS !=
(mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, &struct_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
struct_type_derived = true;
if (MPI_SUCCESS != (mpi_code = MPI_Type_create_resized(
struct_type, 0, sizeof(H5D_filtered_collective_chunk_info_t), resized_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_resized failed", mpi_code)
*resized_type_derived = true;
if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(resized_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
done:
if (struct_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&struct_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
if (chunk_block_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_block_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
if (ret_value < 0) {
if (*resized_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(resized_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
*resized_type_derived = false;
}
if (*contig_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(contig_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
*contig_type_derived = false;
}
}
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_get_chunk_redistribute_info_types() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_get_chunk_alloc_info_types
*
* Purpose: Constructs MPI derived datatypes for communicating the info
* from a H5D_filtered_collective_chunk_info_t structure that
* is necessary for re-allocating file space during a
* collective write of filtered chunks.
*
* The datatype returned through `contig_type` has an extent
* equal to the size of an H5D_chunk_alloc_info_t structure
* and is suitable for communicating that structure type.
*
* The datatype returned through `resized_type` has an extent
* equal to the size of an H5D_filtered_collective_chunk_info_t
* structure. This makes it suitable for sending an array of
* those structures, while extracting out just the info
* necessary for the chunk file space reallocation operation
* during communication.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_get_chunk_alloc_info_types(MPI_Datatype *contig_type, bool *contig_type_derived,
MPI_Datatype *resized_type, bool *resized_type_derived)
{
MPI_Datatype struct_type = MPI_DATATYPE_NULL;
bool struct_type_derived = false;
MPI_Datatype chunk_block_type = MPI_DATATYPE_NULL;
bool chunk_block_type_derived = false;
MPI_Datatype types[4];
MPI_Aint displacements[4];
int block_lengths[4];
int field_count;
int mpi_code;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(contig_type);
assert(contig_type_derived);
assert(resized_type);
assert(resized_type_derived);
*contig_type_derived = false;
*resized_type_derived = false;
/* Create struct type for the inner H5F_block_t structure */
if (H5F_mpi_get_file_block_type(false, &chunk_block_type, &chunk_block_type_derived) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't create derived type for chunk file description");
field_count = 4;
assert(field_count == (sizeof(types) / sizeof(MPI_Datatype)));
/*
* Create structure type to pack both chunk H5F_block_t structures
* next to chunk_idx and dset_oloc_addr fields
*/
block_lengths[0] = 1;
block_lengths[1] = 1;
block_lengths[2] = 1;
block_lengths[3] = 1;
displacements[0] = offsetof(H5D_chunk_alloc_info_t, chunk_current);
displacements[1] = offsetof(H5D_chunk_alloc_info_t, chunk_new);
displacements[2] = offsetof(H5D_chunk_alloc_info_t, chunk_idx);
displacements[3] = offsetof(H5D_chunk_alloc_info_t, dset_oloc_addr);
types[0] = chunk_block_type;
types[1] = chunk_block_type;
types[2] = HSIZE_AS_MPI_TYPE;
types[3] = HADDR_AS_MPI_TYPE;
if (MPI_SUCCESS !=
(mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, contig_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
*contig_type_derived = true;
if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(contig_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
/*
* Create struct type to extract the chunk_current, chunk_new, chunk_idx
* and dset_oloc_addr fields from a H5D_filtered_collective_chunk_info_t
* structure
*/
block_lengths[0] = 1;
block_lengths[1] = 1;
block_lengths[2] = 1;
block_lengths[3] = 1;
displacements[0] = offsetof(H5D_filtered_collective_chunk_info_t, chunk_current);
displacements[1] = offsetof(H5D_filtered_collective_chunk_info_t, chunk_new);
displacements[2] = offsetof(H5D_filtered_collective_chunk_info_t, index_info.chunk_idx);
displacements[3] = offsetof(H5D_filtered_collective_chunk_info_t, index_info.dset_oloc_addr);
types[0] = chunk_block_type;
types[1] = chunk_block_type;
types[2] = HSIZE_AS_MPI_TYPE;
types[3] = HADDR_AS_MPI_TYPE;
if (MPI_SUCCESS !=
(mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, &struct_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
struct_type_derived = true;
if (MPI_SUCCESS != (mpi_code = MPI_Type_create_resized(
struct_type, 0, sizeof(H5D_filtered_collective_chunk_info_t), resized_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_resized failed", mpi_code)
*resized_type_derived = true;
if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(resized_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
done:
if (struct_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&struct_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
if (chunk_block_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_block_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
if (ret_value < 0) {
if (*resized_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(resized_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
*resized_type_derived = false;
}
if (*contig_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(contig_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
*contig_type_derived = false;
}
}
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_get_chunk_alloc_info_types() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_get_chunk_insert_info_types
*
* Purpose: Constructs MPI derived datatypes for communicating the
* information necessary when reinserting chunks into a
* dataset's chunk index. This includes the chunk's new offset
* and size (H5F_block_t) and the inner `index_info` structure
* of a H5D_filtered_collective_chunk_info_t structure.
*
* The datatype returned through `contig_type` has an extent
* equal to the size of an H5D_chunk_insert_info_t structure
* and is suitable for communicating that structure type.
*
* The datatype returned through `resized_type` has an extent
* equal to the size of the encompassing
* H5D_filtered_collective_chunk_info_t structure. This makes
* it suitable for sending an array of
* H5D_filtered_collective_chunk_info_t structures, while
* extracting out just the information needed during
* communication.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_get_chunk_insert_info_types(MPI_Datatype *contig_type, bool *contig_type_derived,
MPI_Datatype *resized_type, bool *resized_type_derived)
{
MPI_Datatype struct_type = MPI_DATATYPE_NULL;
bool struct_type_derived = false;
MPI_Datatype chunk_block_type = MPI_DATATYPE_NULL;
bool chunk_block_type_derived = false;
MPI_Aint contig_type_extent;
MPI_Datatype types[5];
MPI_Aint displacements[5];
int block_lengths[5];
int field_count;
int mpi_code;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(contig_type);
assert(contig_type_derived);
assert(resized_type);
assert(resized_type_derived);
*contig_type_derived = false;
*resized_type_derived = false;
/* Create struct type for an H5F_block_t structure */
if (H5F_mpi_get_file_block_type(false, &chunk_block_type, &chunk_block_type_derived) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't create derived type for chunk file description");
field_count = 5;
assert(field_count == (sizeof(types) / sizeof(MPI_Datatype)));
/*
* Create struct type to pack information into memory as follows:
*
* Chunk's new Offset/Size (H5F_block_t) ->
* Chunk Index Info (H5D_chunk_index_info_t)
*/
block_lengths[0] = 1;
block_lengths[1] = 1;
block_lengths[2] = 1;
block_lengths[3] = 1;
block_lengths[4] = 1;
displacements[0] = offsetof(H5D_chunk_insert_info_t, chunk_block);
displacements[1] = offsetof(H5D_chunk_insert_info_t, index_info.chunk_idx);
displacements[2] = offsetof(H5D_chunk_insert_info_t, index_info.dset_oloc_addr);
displacements[3] = offsetof(H5D_chunk_insert_info_t, index_info.filter_mask);
displacements[4] = offsetof(H5D_chunk_insert_info_t, index_info.need_insert);
types[0] = chunk_block_type;
types[1] = HSIZE_AS_MPI_TYPE;
types[2] = HADDR_AS_MPI_TYPE;
types[3] = MPI_UNSIGNED;
types[4] = MPI_C_BOOL;
if (MPI_SUCCESS !=
(mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, &struct_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
struct_type_derived = true;
contig_type_extent = (MPI_Aint)(sizeof(H5F_block_t) + sizeof(H5D_chunk_index_info_t));
if (MPI_SUCCESS != (mpi_code = MPI_Type_create_resized(struct_type, 0, contig_type_extent, contig_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_resized failed", mpi_code)
*contig_type_derived = true;
if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(contig_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
struct_type_derived = false;
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&struct_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
/*
* Create struct type to correctly extract all needed
* information from a H5D_filtered_collective_chunk_info_t
* structure.
*/
displacements[0] = offsetof(H5D_filtered_collective_chunk_info_t, chunk_new);
displacements[1] = offsetof(H5D_filtered_collective_chunk_info_t, index_info.chunk_idx);
displacements[2] = offsetof(H5D_filtered_collective_chunk_info_t, index_info.dset_oloc_addr);
displacements[3] = offsetof(H5D_filtered_collective_chunk_info_t, index_info.filter_mask);
displacements[4] = offsetof(H5D_filtered_collective_chunk_info_t, index_info.need_insert);
if (MPI_SUCCESS !=
(mpi_code = MPI_Type_create_struct(field_count, block_lengths, displacements, types, &struct_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_struct failed", mpi_code)
struct_type_derived = true;
if (MPI_SUCCESS != (mpi_code = MPI_Type_create_resized(
struct_type, 0, sizeof(H5D_filtered_collective_chunk_info_t), resized_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_resized failed", mpi_code)
*resized_type_derived = true;
if (MPI_SUCCESS != (mpi_code = MPI_Type_commit(resized_type)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
done:
if (struct_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&struct_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
if (chunk_block_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(&chunk_block_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
}
if (ret_value < 0) {
if (*resized_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(resized_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
*resized_type_derived = false;
}
if (*contig_type_derived) {
if (MPI_SUCCESS != (mpi_code = MPI_Type_free(contig_type)))
HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code)
*contig_type_derived = false;
}
}
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_get_chunk_insert_info_types() */
/*-------------------------------------------------------------------------
* Function: H5D__mpio_collective_filtered_vec_io
*
* Purpose: Given a pointer to a H5D_filtered_collective_io_info_t
* structure with information about collective filtered chunk
* I/O, populates I/O vectors and performs vector I/O on those
* chunks.
*
* Return: Non-negative on success/Negative on failure
*
*-------------------------------------------------------------------------
*/
static herr_t
H5D__mpio_collective_filtered_vec_io(const H5D_filtered_collective_io_info_t *chunk_list, H5F_shared_t *f_sh,
H5D_io_op_type_t op_type)
{
const void **io_wbufs = NULL;
void **io_rbufs = NULL;
H5FD_mem_t io_types[2];
uint32_t iovec_count = 0;
haddr_t *io_addrs = NULL;
size_t *io_sizes = NULL;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE
assert(chunk_list);
assert(f_sh);
if (op_type == H5D_IO_OP_WRITE)
iovec_count = (uint32_t)chunk_list->num_chunk_infos;
else {
assert(chunk_list->num_chunks_to_read <= chunk_list->num_chunk_infos);
iovec_count = (uint32_t)chunk_list->num_chunks_to_read;
}
if (iovec_count > 0) {
if (chunk_list->num_chunk_infos > UINT32_MAX)
HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL,
"number of chunk entries in I/O operation exceeds UINT32_MAX");
if (NULL == (io_addrs = H5MM_malloc(iovec_count * sizeof(*io_addrs))))
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL,
"couldn't allocate space for I/O addresses vector");
if (NULL == (io_sizes = H5MM_malloc(iovec_count * sizeof(*io_sizes))))
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL, "couldn't allocate space for I/O sizes vector");
if (op_type == H5D_IO_OP_WRITE) {
if (NULL == (io_wbufs = H5MM_malloc(iovec_count * sizeof(*io_wbufs))))
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL,
"couldn't allocate space for I/O buffers vector");
}
else {
if (NULL == (io_rbufs = H5MM_malloc(iovec_count * sizeof(*io_rbufs))))
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTALLOC, FAIL,
"couldn't allocate space for I/O buffers vector");
}
/*
* Since all I/O will be raw data, we can save on memory a bit by
* making use of H5FD_MEM_NOLIST to signal that all the memory types
* are the same across the I/O vectors
*/
io_types[0] = H5FD_MEM_DRAW;
io_types[1] = H5FD_MEM_NOLIST;
for (size_t i = 0, vec_idx = 0; i < chunk_list->num_chunk_infos; i++) {
H5F_block_t *chunk_block;
if (op_type == H5D_IO_OP_READ && !chunk_list->chunk_infos[i].need_read)
continue;
/*
* Check that we aren't going to accidentally try to write past the
* allocated memory for the I/O vector buffers in case bookkeeping
* wasn't done properly for the chunk list struct's `num_chunks_to_read`
* field.
*/
assert(vec_idx < iovec_count);
/* Set convenience pointer for current chunk block */
chunk_block = (op_type == H5D_IO_OP_READ) ? &chunk_list->chunk_infos[i].chunk_current
: &chunk_list->chunk_infos[i].chunk_new;
assert(H5_addr_defined(chunk_block->offset));
io_addrs[vec_idx] = chunk_block->offset;
/*
* Ensure the chunk list is sorted in ascending ordering of
* offset in the file. Note that we only compare that the
* current address is greater than the previous address and
* not equal to it; file addresses should only appear in the
* chunk list once.
*/
#ifndef NDEBUG
if (vec_idx > 0)
assert(io_addrs[vec_idx] > io_addrs[vec_idx - 1]);
#endif
io_sizes[vec_idx] = (size_t)chunk_block->length;
if (op_type == H5D_IO_OP_WRITE)
io_wbufs[vec_idx] = chunk_list->chunk_infos[i].buf;
else
io_rbufs[vec_idx] = chunk_list->chunk_infos[i].buf;
vec_idx++;
}
}
if (op_type == H5D_IO_OP_WRITE) {
if (H5F_shared_vector_write(f_sh, iovec_count, io_types, io_addrs, io_sizes, io_wbufs) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "vector write call failed");
}
else {
if (H5F_shared_vector_read(f_sh, iovec_count, io_types, io_addrs, io_sizes, io_rbufs) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "vector read call failed");
}
done:
H5MM_free(io_wbufs);
H5MM_free(io_rbufs);
H5MM_free(io_sizes);
H5MM_free(io_addrs);
FUNC_LEAVE_NOAPI(ret_value)
}
#ifdef H5Dmpio_DEBUG
static herr_t
H5D__mpio_dump_collective_filtered_chunk_list(H5D_filtered_collective_io_info_t *chunk_list, int mpi_rank)
{
H5D_filtered_collective_chunk_info_t *chunk_entry;
size_t i;
herr_t ret_value = SUCCEED;
FUNC_ENTER_PACKAGE_NOERR
H5D_MPIO_DEBUG(mpi_rank, "CHUNK LIST: [");
for (i = 0; i < chunk_list->num_chunk_infos; i++) {
unsigned chunk_rank;
chunk_entry = &chunk_list->chunk_infos[i];
assert(chunk_entry->chunk_info);
chunk_rank = (unsigned)H5S_GET_EXTENT_NDIMS(chunk_entry->chunk_info->fspace);
H5D_MPIO_DEBUG(mpi_rank, " {");
H5D_MPIO_DEBUG_VA(mpi_rank, " - Entry %zu -", i);
H5D_MPIO_DEBUG(mpi_rank, " - Chunk Fspace Info -");
H5D_MPIO_DEBUG_VA(mpi_rank,
" Chunk Current Info: { Offset: %" PRIuHADDR ", Length: %" PRIuHADDR " }",
chunk_entry->chunk_current.offset, chunk_entry->chunk_current.length);
H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk New Info: { Offset: %" PRIuHADDR ", Length: %" PRIuHADDR " }",
chunk_entry->chunk_new.offset, chunk_entry->chunk_new.length);
H5D_MPIO_DEBUG(mpi_rank, " - Chunk Insert Info -");
H5D_MPIO_DEBUG_VA(mpi_rank,
" Chunk Scaled Coords (4-d): { %" PRIuHSIZE ", %" PRIuHSIZE ", %" PRIuHSIZE
", %" PRIuHSIZE " }",
chunk_rank < 1 ? 0 : chunk_entry->chunk_info->scaled[0],
chunk_rank < 2 ? 0 : chunk_entry->chunk_info->scaled[1],
chunk_rank < 3 ? 0 : chunk_entry->chunk_info->scaled[2],
chunk_rank < 4 ? 0 : chunk_entry->chunk_info->scaled[3]);
H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk Index: %" PRIuHSIZE, chunk_entry->index_info.chunk_idx);
H5D_MPIO_DEBUG_VA(mpi_rank, " Dataset Object Header Address: %" PRIuHADDR,
chunk_entry->index_info.dset_oloc_addr);
H5D_MPIO_DEBUG_VA(mpi_rank, " Filter Mask: %u", chunk_entry->index_info.filter_mask);
H5D_MPIO_DEBUG_VA(mpi_rank, " Need Insert: %s",
chunk_entry->index_info.need_insert ? "YES" : "NO");
H5D_MPIO_DEBUG(mpi_rank, " - Other Info -");
H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk Info Ptr: %p", (void *)chunk_entry->chunk_info);
H5D_MPIO_DEBUG_VA(mpi_rank, " Need Read: %s", chunk_entry->need_read ? "YES" : "NO");
H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk I/O Size: %zu", chunk_entry->io_size);
H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk Buffer Size: %zu", chunk_entry->chunk_buf_size);
H5D_MPIO_DEBUG_VA(mpi_rank, " Original Owner: %d", chunk_entry->orig_owner);
H5D_MPIO_DEBUG_VA(mpi_rank, " New Owner: %d", chunk_entry->new_owner);
H5D_MPIO_DEBUG_VA(mpi_rank, " # of Writers: %d", chunk_entry->num_writers);
H5D_MPIO_DEBUG_VA(mpi_rank, " Chunk Data Buffer Ptr: %p", (void *)chunk_entry->buf);
H5D_MPIO_DEBUG(mpi_rank, " }");
}
H5D_MPIO_DEBUG(mpi_rank, "]");
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__mpio_dump_collective_filtered_chunk_list() */
#endif
#endif /* H5_HAVE_PARALLEL */
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