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ph5_concat.cpp
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/*
* Copyright (C) 2019, Northwestern University and Fermi National Accelerator Laboratory
* See COPYRIGHT notice in top-level directory.
*/
#ifdef HAVE_CONFIG_H
# include <config.h>
#endif
#include <iostream>
#include <cstring>
#include <numeric>
#include <algorithm>
#include <math.h>
#include <unordered_map>
#include <functional>
#include <assert.h>
#include <sys/time.h>
#include <stdio.h>
#include <stdlib.h>
#ifdef HAVE_ACCESS
#include <unistd.h> /* access() */
#endif
#include "ph5_concat.hpp"
/*----< Concatenator() >-----------------------------------------------------*/
Concatenator::Concatenator(int nprocs,
int rank,
MPI_Comm comm,
MPI_Info info,
size_t num_input_files,
string const& output,
bool append_mode,
bool posix_open,
bool in_memory_io,
bool chunk_caching,
size_t compress_threshold,
bool one_process_create,
unsigned int zip_level,
bool enforce_contiguous,
size_t buffer_size,
int io_strategy,
string const& part_key_base) :
comm(comm),
info(info),
nprocs(nprocs),
rank(rank),
num_input_files(num_input_files),
io_buffer_size(buffer_size),
zip(zip_level),
enforce_contiguous(enforce_contiguous),
posix_open(posix_open),
in_memory_io(in_memory_io),
chunk_caching(chunk_caching),
compress_threshold(compress_threshold * 1048576),
one_process_create(one_process_create),
io_strategy(io_strategy),
output_file_name(output),
part_key_base(part_key_base)
{
// chunk_size_threshold = 1*1024*1024; // Chunk size threshold (1 MiB or 1 M elements)
chunk_size_threshold = 256*1024; // Chunk size threshold (256K elements)
in_memory_cache_size = 512*1024*1024ull; // In-memory buffer increase (512 MiB)
output_meta_cache_size = 128*1024*1024; // metadata cache size (128 MiB)
raw_chunk_cache_size = 64*1024*1024; // raw chunk cache size (64 MiB)
max_local_size_in_bytes = 0;
original_num_groups = 0;
num_groups_have_key = 0;
num_groups = 0;
original_total_num_datasets = 0;
total_num_datasets = 0;
/* whether to create a partition key dataset in each group */
if (part_key_base.compare("") == 0)
add_partition_key = false;
else
add_partition_key = true;
/* spill's group index in groups[] array */
spill_grp_no = -1;
/* hash lookup tables, one per input file, built based on the user
* indicated key base dataset in group /spill
*/
lookup_table = new table[num_input_files];
async_reqs = new MPI_Request[nprocs * 2];
async_statuses = new MPI_Status[nprocs * 2];
buffer = NULL;
c_1d_2d = 0;
o_1d = 0;
r_1d = 0;
w_1d = 0;
o_2d = 0;
r_2d = 0;
w_2d = 0;
o_f = 0;
close_in_dsets = 0;
close_out_dsets = 0;
num_allreduce = 0;
num_exscan = 0;
}
/*----< ~Concatenator() >----------------------------------------------------*/
Concatenator::~Concatenator()
{
size_t ii, jj;
for (ii=0; ii<num_groups; ii++) {
for (jj=0; jj<groups[ii].num_dsets; jj++) {
groups[ii].dsets[jj].in_dset_ids.clear();
groups[ii].dsets[jj].in_dim0.clear();
}
delete [] groups[ii].dsets;
}
delete [] groups;
delete [] lookup_table;
delete []async_reqs;
delete []async_statuses;
if (buffer != NULL)
delete []buffer;
}
/*----< set_rawdata_cache() >------------------------------------------------*/
/* This subroutine increases the raw data chunk cache size in hope to improve
* decompression time. However, experiments show it is not as effective as
* doing in-memory I/O. However, we observed no significant difference in
* performance for reading 2579 small-sized datasets.
*
* Note from HDF5 document for H5Pset_cache(), it says the followings.
* Raw dataset chunk caching is not currently supported when using the MPI I/O
* and MPI POSIX file drivers in read/write mode; see H5Pset_fapl_mpio and
* H5Pset_fapl_mpiposix, respectively. When using one of these file drivers,
* all calls to H5Dread and H5Dwrite will access the disk directly, and
* H5Pset_cache will have no effect on performance.
*/
static
int set_rawdata_cache(hid_t fapl_id,
size_t rdcc_nslots, /* Number of slots in hash table */
size_t rdcc_nbytes, /* Size of chunk cache in bytes */
double w0)
{
int err, err_exit=0;
/* set the raw data chunk cache to improve decompression time */
int mdc_nelmts; /* Dummy parameter in API, no longer used by HDF5 */
err = H5Pget_cache(fapl_id, &mdc_nelmts, &rdcc_nslots, &rdcc_nbytes, &w0);
if (err < 0) HANDLE_ERROR("H5Pget_cache")
/* increasing cache size for write seems no effect */
/* rdcc_nslots should be a prime number and approximately 100 times number
* of chunks that can fit in rdcc_nbytes. The default value used by HDF5 is
* 521. Others can be 10007, 67231. However, experiments show that
* increasing rdcc_nslots for this read operation actually performs worse.
*/
err = H5Pset_cache(fapl_id, mdc_nelmts, rdcc_nslots, rdcc_nbytes, w0);
if (err < 0) HANDLE_ERROR("H5Pset_cache")
fn_exit:
return err_exit;
}
/*----< op_func() >----------------------------------------------------------*/
/* Operator function to be called by H5Ovisit. */
static
herr_t op_func(hid_t obj, const char *name, const H5O_info_t *info, void *me)
{
return reinterpret_cast<Concatenator *>(me)->collect_metadata(obj, name, info);
}
/*----< construct_metadata() >-----------------------------------------------*/
/* Collect all metadata of groups and datasets from the assigned input files
* and call MPI functions to calculated the aggregated sizes.
*/
int Concatenator::construct_metadata(vector<string> const &inputs)
{
int err_exit=0;
herr_t err;
hid_t file_id, fapl_id;
/* Go through all assigned input files and collect all metadata. */
if (posix_open == true) {
/* use POSIX I/O mode to open and read each file */
if (in_memory_io == true) {
fapl_id = H5Pcreate(H5P_FILE_ACCESS);
if (fapl_id < 0) HANDLE_ERROR("H5Pcreate")
/* Enabling HDF5 in-memory I/O results in faster reads. When
* opening an existing file and in-memory-I/O is on, HDF5 reads the
* entire file into an internal buffer, no matter how big is the
* file. Thus, argument 'increment' of H5Pset_fapl_core take no
* effect on reading an existing file.
*/
err = H5Pset_fapl_core(fapl_id, 0, 0);
if (err < 0) HANDLE_ERROR("H5Pset_fapl_core")
if (chunk_caching) {
err = set_rawdata_cache(fapl_id, 521, raw_chunk_cache_size, 1.0);
if (err < 0) HANDLE_ERROR("set_rawdata_cache")
}
} else {
fapl_id = H5P_DEFAULT;
}
} else {
/* Use MPI-IO mode to open files. Note HDF5 in-memory I/O feature is
* not available when using MPI-IO driver
*/
fapl_id = H5Pcreate(H5P_FILE_ACCESS);
if (fapl_id < 0) HANDLE_ERROR("H5Pcreate")
/* use MPI_COMM_SELF to open files assigned */
err = H5Pset_fapl_mpio(fapl_id, MPI_COMM_SELF, info);
if (err < 0) HANDLE_ERROR("H5Pset_fapl_mpio")
/* Sets metadata I/O mode for read operations to independent */
err = H5Pset_all_coll_metadata_ops(fapl_id, false);
if (err < 0) HANDLE_ERROR("H5Pset_all_coll_metadata_ops")
}
/* iterate all input files assigned to this process */
for (auto it = inputs.begin(); it != inputs.end(); it++) {
/* open the assigned file in read-only mode */
file_id = H5Fopen(it->c_str(), H5F_ACC_RDONLY, fapl_id);
if (file_id < 0) HANDLE_ERROR(string("H5Fopen ") + *it)
/* iterate all data objects (groups and datasets in each group) to
* collect their metadata
*/
#if defined HAS_H5OVISIT3 && HAS_H5OVISIT3
err = H5Ovisit3(file_id, H5_INDEX_NAME, H5_ITER_NATIVE, op_func, this, H5O_INFO_ALL);
if (err < 0) HANDLE_ERROR(string("H5Ovisit3") + *it)
#else
err = H5Ovisit(file_id, H5_INDEX_NAME, H5_ITER_NATIVE, op_func, this);
if (err < 0) HANDLE_ERROR(string("H5Ovisit") + *it)
#endif
/* if partition key dataset is to be added and group /spill cannot be
* found, then error out.
*/
if (add_partition_key && spill_grp_no == -1) {
fprintf(stderr, "Error: group /spill cannot be found in file %s\n",
it->c_str());
err_exit = -1;
goto fn_exit;
}
/* Instead of closing the input files, we keep the file handles
* and re-use them later when concatenating datasets.
*/
input_files.insert(make_pair(*it, file_id));
}
if (fapl_id != H5P_DEFAULT) {
err = H5Pclose(fapl_id);
if (err < 0) HANDLE_ERROR("H5Pclose")
}
/* check if partitioning key base dataset in each group is found */
if (add_partition_key) {
for (size_t ii=0; ii<num_groups; ii++) {
if (groups[ii].key_base == NULL && rank == 0) {
printf("[%d] Warning: partition key base '%s' cannot be found in group '%s'\n",
rank, part_key_base.c_str(), groups[ii].name.c_str());
}
}
/* error out if the partition key base dataset is not found in group
* /spill
*/
if (groups[spill_grp_no].key_base == NULL) {
fprintf(stderr, "Error: partiition key base dataset '/spill/%s' cannot be found\n", part_key_base.c_str());
err_exit = -1;
goto fn_exit;
}
}
/* Sum the most significant dimension for all datasets. */
accumulate_dimensions();
/* Allocate I/O buffer space for read and write. */
if (io_buffer_size == 0) io_buffer_size = max_local_size_in_bytes;
buffer = new char[io_buffer_size];
fn_exit:
return err_exit;
}
/*----< set_metadata_cache() >-----------------------------------------------*/
static
int set_metadata_cache(hid_t file_id,
size_t cache_size,
double min_clean_fraction,
double dirty_bytes_threshold)
{
int err, err_exit=0;
H5AC_cache_config_t config;
/* Set the metadata cache size which may improve data object open time */
config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
err = H5Fget_mdc_config(file_id, &config);
if (err < 0) HANDLE_ERROR("H5Fget_mdc_config")
config.max_size = cache_size;
config.min_size = cache_size;
config.initial_size = cache_size;
config.min_clean_fraction = min_clean_fraction;
config.dirty_bytes_threshold = dirty_bytes_threshold * cache_size * min_clean_fraction;
config.decr_mode = H5C_decr__off;
err = H5Fset_mdc_config(file_id, &config);
if (err < 0) HANDLE_ERROR("H5Fset_mdc_config")
fn_exit:
return err_exit;
}
/*----< create_partition_key() >---------------------------------------------*/
/* Create a new partition key dataset in a group by inheriting most of the
* metadata of the base dataset.
*/
int Concatenator::create_partition_key(GrpInfo &grp)
{
DSInfo_t &seq = grp.dsets[grp.num_dsets++];
/* copy contents of base dataset over to key dataset, seq */
seq = *grp.key_base;
seq.is_key_base = false;
seq.is_key_seq = true;
seq.name = part_key_base + ".seq";
seq.type_id = H5T_STD_I64LE;
seq.type_size = H5Tget_size(H5T_STD_I64LE);
if (seq.global_dims[0] == 0)
seq.layout = H5D_COMPACT;
else
seq.layout = (enforce_contiguous == true) ? H5D_CONTIGUOUS : H5D_CHUNKED;
herr_t err = create_dataset(grp.id, seq, false);
if (err < 0) RETURN_ERROR("create_dataset", seq.name.c_str())
grp.seq_dset = &seq;
total_num_datasets++;
return 0;
}
/*----< file_create() >------------------------------------------------------*/
int Concatenator::file_create()
{
int err_exit=0, file_exist=1;
size_t ii, jj, kk;
herr_t err;
hid_t group_id=0, fapl_id;
#if defined PROFILE_HDF5_INTERNAL && PROFILE_HDF5_INTERNAL
MPI_Barrier(comm);
H5Vreset();
H5Venable();
#endif
/* Create the output file using MPI-IO driver */
fapl_id = H5Pcreate(H5P_FILE_ACCESS);
if (fapl_id < 0) HANDLE_ERROR("H5Pcreate")
err = H5Pset_fapl_mpio(fapl_id, comm, info);
if (err < 0) HANDLE_ERROR("H5Pset_fapl_mpio")
/* set collective mode for metadata reads and writes */
err = H5Pset_all_coll_metadata_ops(fapl_id, true);
if (err < 0) HANDLE_ERROR("H5Pset_all_coll_metadata_ops")
err = H5Pset_coll_metadata_write(fapl_id, true);
if (err < 0) HANDLE_ERROR("H5Pset_coll_metadata_write")
#ifdef HAVE_ACCESS
/* if access() is available, use it to check whether file already exists
* rank 0 calls access() and broadcasts file_exist */
if (rank == 0 && access(output_file_name.c_str(), F_OK) == -1)
file_exist = 0;
MPI_Bcast(&file_exist, 1, MPI_INT, 0, comm);
if (file_exist) {
cout<<output_file_name.c_str()<<" already exists." <<endl;
return -1;
}
#endif
if (one_process_create == true) {
/* Root process creates the file first, followed by all other processes
* open the file
*/
if (rank == 0) {
/* create a new file */
output_file_id = H5Fcreate(output_file_name.c_str(), H5F_ACC_EXCL,
H5P_DEFAULT, H5P_DEFAULT);
if (output_file_id < 0)
HANDLE_ERROR(string("H5Fcreate in exclusive mode ") + output_file_name.c_str())
/* rank 0 creates all the groups and datasets */
for (ii=0; ii<num_groups; ii++) {
/* create a new group */
group_id = H5Gcreate2(output_file_id, groups[ii].name.c_str(),
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (group_id < 0) HANDLE_ERROR("H5Gcreate2")
groups[ii].id = group_id;
for (jj=0; jj<groups[ii].num_dsets; jj++) {
/* Create a new dataset in the output file */
bool toFill = (groups[ii].dsets[jj].type_class == H5T_STRING);
err = create_dataset(group_id, groups[ii].dsets[jj], toFill);
if (err < 0) HANDLE_ERROR("create_dataset")
/* zero-sized datasets have been closed in create_dataset().
* Now, close non-zero sized datasets.
*/
if (groups[ii].dsets[jj].global_dims[0] > 0) {
err = H5Dclose(groups[ii].dsets[jj].out_dset_id);
if (err < 0) HANDLE_ERROR("H5Dclose")
}
}
err = H5Gclose(group_id);
if (err < 0) HANDLE_ERROR("H5Gclose")
}
/* must flush as the file may still be cached locally */
err = H5Fflush(output_file_id, H5F_SCOPE_LOCAL);
if (err < 0) HANDLE_ERROR("H5Fflush")
err = H5Fclose(output_file_id);
if (err < 0) HANDLE_ERROR("H5Fclose")
}
/* all processes wait until root completes the file create */
MPI_Barrier(comm);
/* all ranks collectively open the newly created file */
output_file_id = H5Fopen(output_file_name.c_str(), H5F_ACC_RDWR,
fapl_id);
if (output_file_id < 0)
HANDLE_ERROR(string("H5Fopen ") + output_file_name)
err = set_metadata_cache(output_file_id, output_meta_cache_size,
0.3, 0.45);
if (err < 0) HANDLE_ERROR("set_metadata_cache")
/* all ranks collectively open all non-zero datasets */
for (ii=0; ii<num_groups; ii++) {
/* create a new group */
group_id = H5Gopen(output_file_id, groups[ii].name.c_str(),
H5P_DEFAULT);
if (group_id < 0) HANDLE_ERROR("H5Gopen")
groups[ii].id = group_id;
for (jj=0; jj<groups[ii].num_dsets; jj++) {
/* open only globally non-zero datasets */
if (groups[ii].dsets[jj].global_dims[0] > 0) {
hid_t id;
id = H5Dopen(group_id, groups[ii].dsets[jj].name.c_str(),
H5P_DEFAULT);
if (id < 0) HANDLE_ERROR(string("H5Dopen ")+groups[ii].dsets[jj].name)
groups[ii].dsets[jj].out_dset_id = id;
calculate_chunk_size(groups[ii].dsets[jj]);
}
}
/* After all the datasets have been created, create a new partition
* key dataset in each group. Note the partition key base dataset
* may be missing in a group. In this case, the key seq dataset
* will not be created for that group.
*/
if (add_partition_key && groups[ii].key_base != NULL) {
err = create_partition_key(groups[ii]);
if (err < 0) HANDLE_ERROR("create_partition_key")
}
err = H5Gclose(group_id);
if (err < 0) HANDLE_ERROR("H5Gclose")
}
}
else { /* all processes collectively create file and datasets */
if (chunk_caching) {
err = set_rawdata_cache(fapl_id, 67231, raw_chunk_cache_size, 1.0);
if (err < 0) HANDLE_ERROR("set_rawdata_cache")
}
/* collectively create a new output file */
output_file_id = H5Fcreate(output_file_name.c_str(), H5F_ACC_EXCL,
H5P_DEFAULT, fapl_id);
if (output_file_id < 0)
HANDLE_ERROR(string("H5Fcreate in exclusive mode ") + output_file_name.c_str())
err = set_metadata_cache(output_file_id, output_meta_cache_size,
0.3, 0.45);
if (err < 0) HANDLE_ERROR("set_metadata_cache")
/* Collectively create all the groups and datasets */
for (ii=0; ii<num_groups; ii++) {
group_id = H5Gcreate2(output_file_id, groups[ii].name.c_str(),
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (group_id < 0) HANDLE_ERROR("H5Gcreate2")
groups[ii].id = group_id;
for (jj=0; jj<groups[ii].num_dsets; jj++) {
/* Create a new dataset in the output file. Keep the handle
* opened so that it can be used later when concatenating
* datasets.
*/
bool toFill = (groups[ii].dsets[jj].type_class == H5T_STRING);
err = create_dataset(group_id, groups[ii].dsets[jj], toFill);
if (err < 0) HANDLE_ERROR("create_dataset")
}
/* After all the datasets have been created, create a new partition
* key dataset in each group. Note the partition key base dataset
* may be missing in a group. In this case, the key seq dataset
* will not be created for that group.
*/
if (add_partition_key && groups[ii].key_base != NULL) {
err = create_partition_key(groups[ii]);
if (err < 0) HANDLE_ERROR("create_partition_key")
}
err = H5Gclose(group_id);
if (err < 0) HANDLE_ERROR("H5Gclose")
}
}
err = H5Pclose(fapl_id);
if (err < 0) HANDLE_ERROR("H5Pclose")
/* save the original total number of datasets */
original_total_num_datasets = total_num_datasets;
/* remove zero-sized datasets from each group from groups[].dsets[] */
for (ii=0; ii<num_groups; ii++) {
kk = -1;
for (jj=0; jj<groups[ii].num_dsets; jj++) {
if (groups[ii].dsets[jj].global_dims[0] == 0) {
groups[ii].dsets[jj].in_dset_ids.clear();
total_num_datasets--;
}
else if (++kk < jj) {
groups[ii].dsets[kk] = groups[ii].dsets[jj];
if (groups[ii].dsets[kk].is_key_base)
groups[ii].key_base = groups[ii].dsets + kk;
else if (groups[ii].dsets[kk].is_key_seq)
groups[ii].seq_dset = groups[ii].dsets + kk;
}
}
groups[ii].num_dsets = kk + 1;
}
/* remove empty groups from groups[] */
num_groups_have_key = 0;
kk = -1;
for (ii=0; ii<num_groups; ii++) {
if (groups[ii].num_dsets == 0) {
delete [] groups[ii].dsets;
continue;
}
else if (++kk < ii)
groups[kk] = groups[ii];
if (groups[kk].key_base != NULL)
num_groups_have_key++;
}
num_groups = kk + 1;
#if defined DEBUG && DEBUG
if (add_partition_key) {
for (ii=0; ii<num_groups; ii++) {
if (groups[ii].key_base != NULL) {
assert(groups[ii].seq_dset->is_key_seq);
}
}
}
#endif
/* Calculate the number of collective writes for each dataset based on the
* I/O buffer size.
*/
calculate_num_writes();
/* use MPI collective I/O */
dxpl_id = H5Pcreate(H5P_DATASET_XFER);
if (dxpl_id < 0) HANDLE_ERROR("H5Pcreate")
err = H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE);
if (err < 0) HANDLE_ERROR("H5Pset_dxpl_mpio")
#if defined PROFILE_HDF5_INTERNAL && PROFILE_HDF5_INTERNAL
MPI_Barrier(comm);
H5Vprint();
H5Vdisable();
#endif
fn_exit:
return err_exit;
}
/*----< file_open() >--------------------------------------------------------*/
int Concatenator::file_open()
{
int err_exit=0, file_exist=1;
size_t ii, jj, kk;
herr_t err;
hid_t group_id=0, fapl_id;
#if defined PROFILE_HDF5_INTERNAL && PROFILE_HDF5_INTERNAL
MPI_Barrier(comm);
H5Vreset();
H5Venable();
#endif
#ifdef HAVE_ACCESS
/* if access() is available, use it to check whether file already exists
* rank 0 calls access() and broadcasts file_exist */
if (rank == 0 && access(output_file_name.c_str(), F_OK) == -1)
file_exist = 0;
MPI_Bcast(&file_exist, 1, MPI_INT, 0, comm);
if (!file_exist) {
cout<<output_file_name.c_str()<<" does not exists." <<endl;
return -1;
}
#endif
original_total_num_datasets = 0;
total_num_datasets = 0;
/* remove zero-sized datasets from each group from groups[].dsets[] */
for (ii=0; ii<num_groups; ii++) {
/* save the original total number of datasets */
original_total_num_datasets += groups[ii].num_dsets;
kk = -1;
for (jj=0; jj<groups[ii].num_dsets; jj++) {
if (groups[ii].dsets[jj].global_dims[0] == 0) {
groups[ii].dsets[jj].in_dset_ids.clear();
}
else if (++kk < jj) {
groups[ii].dsets[kk] = groups[ii].dsets[jj];
if (groups[ii].dsets[kk].is_key_base)
groups[ii].key_base = groups[ii].dsets + kk;
else if (groups[ii].dsets[kk].is_key_seq)
groups[ii].seq_dset = groups[ii].dsets + kk;
}
}
groups[ii].num_dsets = kk + 1;
total_num_datasets += groups[ii].num_dsets;
}
/* remove empty groups from groups[] */
num_groups_have_key = 0;
kk = -1;
for (ii=0; ii<num_groups; ii++) {
if (groups[ii].num_dsets == 0) {
delete [] groups[ii].dsets;
continue;
}
else if (++kk < ii)
groups[kk] = groups[ii];
if (groups[kk].key_base != NULL)
num_groups_have_key++;
}
num_groups = kk + 1;
/* Open the output file using MPI-IO driver */
fapl_id = H5Pcreate(H5P_FILE_ACCESS);
if (fapl_id < 0) HANDLE_ERROR("H5Pcreate")
err = H5Pset_fapl_mpio(fapl_id, comm, info);
if (err < 0) HANDLE_ERROR("H5Pset_fapl_mpio")
/* set collective mode for metadata reads and writes */
err = H5Pset_all_coll_metadata_ops(fapl_id, true);
if (err < 0) HANDLE_ERROR("H5Pset_all_coll_metadata_ops")
err = H5Pset_coll_metadata_write(fapl_id, true);
if (err < 0) HANDLE_ERROR("H5Pset_coll_metadata_write")
if (chunk_caching) {
err = set_rawdata_cache(fapl_id, 67231, raw_chunk_cache_size, 1.0);
if (err < 0) HANDLE_ERROR("set_rawdata_cache")
}
/* collectively open the output file */
output_file_id = H5Fopen(output_file_name.c_str(), H5F_ACC_RDWR, fapl_id);
if (output_file_id < 0)
HANDLE_ERROR(string("H5Fopen ") + output_file_name)
err = set_metadata_cache(output_file_id, output_meta_cache_size, 0.3, 0.45);
if (err < 0) HANDLE_ERROR("set_metadata_cache")
/* Collectively open all the groups and datasets */
for (ii=0; ii<num_groups; ii++) {
group_id = H5Gopen(output_file_id, groups[ii].name.c_str(), H5P_DEFAULT);
if (group_id < 0) HANDLE_ERROR("H5Gopen")
groups[ii].id = group_id;
for (jj=0; jj<groups[ii].num_dsets; jj++) {
/* Open dataset jj in group ii. Keep the dataset opened, so that it
* can be used later when appending.
*/
err = open_dataset(group_id, groups[ii].dsets[jj]);
if (err < 0) HANDLE_ERROR("open_dataset")
}
/* check if this group contains a key dataset */
if (add_partition_key && groups[ii].key_base != NULL) {
/* key dataset is the last one in dsets[] */
DSInfo_t &seq = groups[ii].dsets[groups[ii].num_dsets];
/* copy contents of key base dataset over to key dataset seq */
seq = *groups[ii].key_base;
seq.name = part_key_base + ".seq";
/* zero-sized dataset has been removed earlier */
assert(seq.global_dims[0] > 0);
/* Open key dataset. In append mode, the partition key dataset must
* have already existed
*/
seq.out_dset_id = H5Dopen(group_id, seq.name.c_str(), H5P_DEFAULT);
if (seq.out_dset_id < 0)
HANDLE_ERROR(string("H5Dopen on partition key dataset ")+seq.name)
/* seq.global_dims has been increased in key_base.global_dims */
err = H5Dset_extent(seq.out_dset_id, seq.global_dims);
if (err < 0) RETURN_ERROR("H5Dset_extent",seq.name.c_str())
seq.is_key_base = false;
seq.is_key_seq = true;
seq.type_id = H5T_STD_I64LE;
seq.type_size = H5Tget_size(H5T_STD_I64LE);
groups[ii].seq_dset = &seq;
groups[ii].num_dsets++;
total_num_datasets++;
}
err = H5Gclose(group_id);
if (err < 0) HANDLE_ERROR("H5Gclose")
}
err = H5Pclose(fapl_id);
if (err < 0) HANDLE_ERROR("H5Pclose")
/* Calculate the number of collective writes for each dataset based on the
* I/O buffer size.
*/
calculate_num_writes();
/* use MPI collective I/O */
dxpl_id = H5Pcreate(H5P_DATASET_XFER);
if (dxpl_id < 0) HANDLE_ERROR("H5Pcreate")
err = H5Pset_dxpl_mpio(dxpl_id, H5FD_MPIO_COLLECTIVE);
if (err < 0) HANDLE_ERROR("H5Pset_dxpl_mpio")
#if defined PROFILE_HDF5_INTERNAL && PROFILE_HDF5_INTERNAL
MPI_Barrier(comm);
H5Vprint();
H5Vdisable();
#endif
fn_exit:
return err_exit;
}
/*----< collect_metadata() >-------------------------------------------------*/
int Concatenator::collect_metadata(hid_t obj_id,
char const *name,
H5O_info_t const *obj_info)
{
static int grp_no=-1, file_no=-1;
herr_t err;
unordered_map<string, DSInfo_t> grp;
if (obj_info->type == H5O_TYPE_GROUP) {
/* This object is a group. Retrieve metadata about this group */
H5G_info_t grp_info;
err = H5Gget_info_by_name(obj_id, name, &grp_info, H5P_DEFAULT);
if (err < 0) RETURN_ERROR("H5Gget_info_by_name", name)
/* Root group is '.' also first object read by a new input file */
if (!strcmp(name, ".")) {
if (file_no == -1) { /* set only when reading the 1st file */
num_groups = grp_info.nlinks;
original_num_groups = num_groups;
groups = new GrpInfo[num_groups];
}
file_no++; /* number of input file */
grp_no = -1; /* restart from -1 for a new input file */
return 0;
}
else grp_no++;
if (file_no == 0) { /* set only when reading the 1st file */
groups[grp_no].name.assign(name);
/* allocate space for dataset metadata in this group.
* +1 is for an additional partitioning key dataset */
groups[grp_no].dsets = new DSInfo_t[grp_info.nlinks + 1];
groups[grp_no].key_base = NULL;
groups[grp_no].seq_dset = NULL;
/* save the groups[] array index of group /spill */
if (!strcmp(name, "spill")) spill_grp_no = grp_no;
}
groups[grp_no].num_dsets = 0; /* to be increased in later visit */
}
else if (obj_info->type == H5O_TYPE_DATASET) {
/* This object is a dataset */
DSInfo_t &dset = groups[grp_no].dsets[groups[grp_no].num_dsets];
groups[grp_no].num_dsets++;
hid_t dset_id;
/* retrieve group name and dataset name */
char *name_copy = strdup(name);
char *group_name = strtok(name_copy, "/");
char *dataset_name = strtok(NULL, "/");
/* group should have already been registered, because groups are
* visited first */
if (groups[grp_no].name.compare(group_name)) {
printf("Expecting group name %s of dataset %s but got %s\n",
groups[grp_no].name.c_str(), dataset_name, group_name);
return -1;
}
/* Open the dataset. Note that obj_id is not the dataset/group ID. */
dset_id = H5Dopen(obj_id, name, H5P_DEFAULT);
if (dset_id < 0) RETURN_ERROR("H5Dopen",name)
/* obtain dataset's dimension sizes into dset_dims[] */
hid_t space_id = H5Dget_space(dset_id);
if (space_id < 0) RETURN_ERROR("H5Dget_space",name)
hsize_t dset_dims[2];
int ndims = H5Sget_simple_extent_dims(space_id, dset_dims, NULL);
if (ndims < 0) RETURN_ERROR("H5Sget_simple_extent_dims",name)
err = H5Sclose(space_id);
if (err < 0) RETURN_ERROR("H5Sclose",name)
if (file_no == 0) { /* This is the first input file */
dset.name.assign(dataset_name);
dset.local_dims[0] = dset_dims[0];
dset.local_dims[1] = dset_dims[1];
dset.type_id = H5Dget_type(dset_id);
if (dset.type_id < 0) RETURN_ERROR("H5Dget_type",name)
dset.type_class = H5Tget_class(dset.type_id);
if (dset.type_class < 0) RETURN_ERROR("H5Tget_class", name);
if (dset.type_class == H5T_STRING) {
/* special treatment for string datasets of variable length */
dset.type_id = H5Tcopy(H5T_C_S1);
if (dset.type_id < 0) RETURN_ERROR("H5Tcopy",name)
err = H5Tset_size(dset.type_id, MAX_STR_LEN);
if (err < 0) RETURN_ERROR("H5Tset_size",name)
dset.type_size = MAX_STR_LEN;
}
else {
dset.type_size = H5Tget_size(dset.type_id);
if (dset.type_size < 0) RETURN_ERROR("H5Tget_size",name)
}
dset.layout = (enforce_contiguous == true) ? H5D_CONTIGUOUS
: H5D_CHUNKED;
dset.is_key_seq = false;
dset.is_key_base = false;
if (add_partition_key) {
string key_name = part_key_base + ".seq";
/* check if key dataset 'seq' has already existed */
if (key_name.compare(dataset_name) == 0) {
printf("Error: dataset '%s' already existed in group %s\n",
dataset_name,group_name);
return -1;
}
/* check if this is the partition key base dataset */
if (part_key_base.compare(dataset_name) == 0) {
assert(groups[grp_no].key_base == NULL);
dset.is_key_base = true;
groups[grp_no].key_base = &dset;
}
}
total_num_datasets++;
}
else {
/* accumulate this dataset's dimension sizes across all assigned
* input files */
dset.local_dims[0] += dset_dims[0];
assert(dset_dims[1] == dset.local_dims[1]);
assert(dset.name.compare(dataset_name) == 0);
}
/* Note all datasets in the same group share the size of dimension 0 */
groups[grp_no].shared_dim0 = dset.local_dims[0];
/* a dataset may be of zero size */
if (dset_dims[0] > 0) {
dset.in_dset_ids.push_back(dset_id); /* save dataset ID */
dset.in_dim0.push_back(dset_dims[0]); /* save dataset dim0 size */
hsize_t dset_size = dset_dims[0] * dset_dims[1] * dset.type_size;
/* find the max size among all datasets */
if (max_local_size_in_bytes < dset_size)
max_local_size_in_bytes = dset_size;
}
else {
/* This dataset is of zero size in this input file. Keep the vector
* size the same as num_input_files, in case this dataset is of
* size zero but non-zero sized in another file.
*/
dset.in_dset_ids.push_back(-1);
dset.in_dim0.push_back(0);
/* No need to keep zero-size dataset open */
err = H5Dclose(dset_id);
if (err < 0) RETURN_ERROR("H5Dclose",name)
}
free(name_copy);
}
return 0;
}
/*----< calculate_num_writes() >---------------------------------------------*/
void Concatenator::calculate_num_writes()
{
size_t ii, jj, kk;
size_t *numWrites;
numWrites = new size_t[total_num_datasets];
/* calculate number of rounds of collective writes per dataset, given the
* I/O buffer size
*/
kk = 0;
for (ii=0; ii<num_groups; ii++) {
for (jj=0; jj<groups[ii].num_dsets; jj++) {
DSInfo_t &dset = groups[ii].dsets[jj];
assert(dset.global_dims[0] > 0);
size_t nrows_in_buffer = io_buffer_size
/ (dset.local_dims[1] * dset.type_size);
numWrites[kk++] = (dset.local_dims[0] % nrows_in_buffer == 0) ?
(dset.local_dims[0] / nrows_in_buffer) :
(dset.local_dims[0] / nrows_in_buffer) + 1;
}
}
assert(kk == total_num_datasets);
/* find the maximumsr among all processes */
MPI_Allreduce(MPI_IN_PLACE, numWrites, total_num_datasets, MPI_SIZE_T,
MPI_MAX, comm);
num_allreduce++;
/* copy to local objects */
kk = 0;
for (ii=0; ii<num_groups; ii++)
for (jj=0; jj<groups[ii].num_dsets; jj++)
groups[ii].dsets[jj].num_writes = numWrites[kk++];
delete []numWrites;
}
#if defined DEBUG && DEBUG
/*----< check_h5_objects() >-------------------------------------------------*/
static
int check_h5_objects(const char *filename, hid_t fid)
{
ssize_t num_objs;
size_t ii, howmany;
H5I_type_t ot;
hid_t *objs;
char obj_name[1024];
num_objs = H5Fget_obj_count(fid, H5F_OBJ_ALL);
if (num_objs <= 0) return num_objs;
/* ignore FILE object */
if (num_objs > 1) printf("%zd object(s) open\n", num_objs);
objs = (hid_t*) malloc(num_objs * sizeof(hid_t));
howmany = H5Fget_obj_ids(fid, H5F_OBJ_ALL, num_objs, objs);
if (howmany > 1) printf("open objects:\n");
for (ii=0; ii<howmany; ii++) {
string type_name="";
ot = H5Iget_type(objs[ii]);
if (ot == H5I_FILE) continue; /* type_name = "H5I_FILE"; */
else if (ot == H5I_GROUP) type_name = "H5I_GROUP";
else if (ot == H5I_DATATYPE) type_name = "H5I_DATATYPE";
else if (ot == H5I_DATASPACE) type_name = "H5I_DATASPACE";
else if (ot == H5I_DATASET) type_name = "H5I_DATASET";
else if (ot == H5I_ATTR) type_name = "H5I_ATTR";
H5Iget_name(objs[ii], obj_name, 1024);
printf("Still opened in file %s %4zd: type %s, name %s\n",
filename, ii, type_name.c_str(), obj_name);
}
free(objs);
return howmany;
}
#endif
/*----< close_output_file() >------------------------------------------------*/
int Concatenator::close_output_file()