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|
/*
* h5ff_time_datasets.c: Do timings of various write / persist / prefetch / read operations for datasets
*
* /DL is dataset that is read back from transaction logs in BB
* /DP is dataset that is read back from prefetched replica in BB [optional, based on runtime param]
* /DS is dataset that is read back from stored data (DAOS) [optional, based on runtime param]
*/
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <string.h>
#include <sys/time.h>
#include "mpi.h"
#include "hdf5.h"
/* define filename for this app, and max size after username prepended */
#define FILENAME_APP "eff_time_datasets.h5"
#define FILENAME_SIZE 256
/* define default sizing parameters - can be changed via command line arguments */
#define DEFAULT_ROWS_PER_RANK 10
#define DEFAULT_COLS_PER_ROW 5
/* macros related to error reporting */
#define STATUS (ret >= 0) ? " " : " - FAILED"
#define ASSERT_RET assert( ret >= 0 )
/* option flags */
int cols_per_row = DEFAULT_COLS_PER_ROW;
int rows_per_rank = DEFAULT_ROWS_PER_RANK;
int prefetched_dset = 0; /* Create DP - defaults to no */
int stored_dset = 0; /* Create DS - defaults to no */
int num_iterations = 1; /* Number of times to perform the commit/persist/evict/prefetch/read/evict cycle */
int enable_checksums = 0; /* Enable checksums on raw data - defaults to no */
int verbose = 0; /* Verbose output - defaults to no */
/* global variables and macros used to make timing easier */
struct timeval tv_start;
struct timeval tv_end;
#define START_TIME gettimeofday( &tv_start, NULL )
#define END_TIME gettimeofday( &tv_end, NULL )
#define ELAPSED_TIME (ulong)( (tv_end.tv_usec + 1000000*tv_end.tv_sec) - (tv_start.tv_usec + 1000000*tv_start.tv_sec) )
/* function prototypes */
void print_container_contents( hid_t, hid_t, int );
int parse_options( int, char**, int, int );
void usage( const char* );
/**************************************************************************************************************/
int main( int argc, char **argv ) {
/* MPI */
int my_rank, comm_size;
int provided;
/* Container */
char *user_name; /* We'll prepend username to make filename unique */
char file_name[FILENAME_SIZE]; /* Actual filename to be opened will be user_name + FILENAME_APP */
hid_t fapl_id;
hid_t file_id;
/* Dataspaces */
hid_t space_l_id;
hid_t space_p_id;
hid_t space_s_id;
/* Datasets */
hid_t dset_l_id;
hid_t dset_p_id;
hid_t dset_s_id;
hsize_t dset_size[2];
hid_t space_id;
/* Data creation and transfer properties */
hid_t dcpl_id;
hid_t dxpl_l_id;
hid_t dxpl_p_id;
hid_t dxpl_s_id;
/* Replicas */
hrpl_t dset_p_replica;
/* Container Version & Read Contexts */
uint64_t version, versionH;
hid_t rc_id, rc_idH;
/* Transactions */
uint64_t tr_num;
hid_t tr_id;
hid_t trspl_id;
int num_tr_leaders;
/* Memory buffer - sized to hold complete DS or Map Values; sometimes partially used */
uint64_t *mbuf;
/* Sizing, dataspace, hyperslab parameters set per-rank */
hsize_t rank_mbuf_size[1];
hsize_t rank_offset[2], rank_count[2];
hid_t rank_space_id;
/* Variables used for reading data written by a neighbor rank */
int neighbor_rank;
hid_t neighbor_space_l_id;
hid_t neighbor_space_p_id;
hid_t neighbor_space_s_id;
hsize_t neighbor_offset[2], neighbor_count[2];
/* Misc */
herr_t ret;
uint64_t u, r, c;
uint64_t bytesPerCell, bytesPerRank, bytesPerDataset, bytesPerContainer;
int i;
int iteration;
/****
* Initialize and create container
****/
/* Confirm needed MPI functionality is available */
MPI_Init_thread( &argc, &argv, MPI_THREAD_MULTIPLE, &provided );
if ( MPI_THREAD_MULTIPLE != provided ) {
fprintf( stderr, "APP: ERROR: MPI does not have MPI_THREAD_MULTIPLE support\n" );
exit( 1 );
}
/* Find MPI rank & communicator size */
MPI_Comm_rank( MPI_COMM_WORLD, &my_rank );
MPI_Comm_size( MPI_COMM_WORLD, &comm_size );
if ( my_rank == 0 ) {
fprintf( stderr, "APP-r%d: Number of MPI processes = %d\n", my_rank, comm_size );
}
/* Parse command-line options controlling behavior */
if ( parse_options( argc, argv, my_rank, comm_size ) != 0 ) {
exit( 1 );
}
if ( my_rank == 0 ) {
fprintf( stderr, "APP-r0: Number of MPI processes = %d\n", comm_size );
fprintf( stderr, "APP-r0: Datasets will have %d rows (%d per rank).\n", (rows_per_rank*comm_size), rows_per_rank );
fprintf( stderr, "APP-r0: Datasets will have %d columns.\n", cols_per_row );
fprintf( stderr, "APP-r0: There will be %d iterations.\n", num_iterations );
if ( prefetched_dset ) {
fprintf( stderr, "APP-r0: /DP will be created\n" );
}
if ( stored_dset ) {
fprintf( stderr, "APP-r0: /DS will be created\n" );
}
}
/* Initialize the EFF stack, starting FS client, registering HDF5 VOL calls, requesting IOD init */
fprintf( stderr, "APP-r%d: Initialize EFF stack\n", my_rank );
EFF_init( MPI_COMM_WORLD, MPI_INFO_NULL );
/* Specify the IOD VOL plugin should be used and create H5File (EFF container), with user name prepended */
user_name = getenv( "USER" );
snprintf( file_name, FILENAME_SIZE, "%s_%s", user_name, FILENAME_APP );
fprintf( stderr, "APP-r%d: Create %s\n", my_rank, file_name );
fapl_id = H5Pcreate( H5P_FILE_ACCESS ); assert( fapl_id >= 0 );
ret = H5Pset_fapl_iod( fapl_id, MPI_COMM_WORLD, MPI_INFO_NULL ); ASSERT_RET;
file_id = H5Fcreate_ff( file_name, H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id, H5_EVENT_STACK_NULL ); assert( file_id >= 0 );
/* Create the memory buffer that will be used in many places - both for writing and reading */
bytesPerCell = sizeof( uint64_t );
bytesPerRank = bytesPerCell * rows_per_rank * cols_per_row; /* Bytes written by 1 rank to each dset */
bytesPerDataset = bytesPerRank * comm_size; /* Bytes written by all ranks to each dset */
bytesPerContainer = bytesPerDataset; /* Bytes written by all ranks to all dsets */
if ( prefetched_dset ) {
bytesPerContainer += bytesPerDataset;
}
if ( stored_dset ) {
bytesPerContainer += bytesPerDataset;
}
mbuf = (uint64_t *) calloc( (rows_per_rank * comm_size * cols_per_row), bytesPerCell );
/****
* Transaction 2: Rank 0 creates H5Objects in the container
****/
if ( my_rank == 0 ) {
/* Acquire read context for CV 1 */
version = 1;
rc_id = H5RCacquire( file_id, &version, H5P_DEFAULT, H5_EVENT_STACK_NULL ); assert( rc_id >= 0); assert( version == 1 );
fprintf( stderr, "APP-r%d: rc %lu - Acquired\n", my_rank, version );
/* Start a transaction with a single leader (the default) */
tr_num = 2;
fprintf( stderr, "APP-r%d: tr %lu - Start\n", my_rank, tr_num );
tr_id = H5TRcreate( file_id, rc_id, tr_num ); assert( tr_id >= 0 );
ret = H5TRstart( tr_id, H5P_DEFAULT, H5_EVENT_STACK_NULL ); ASSERT_RET;
/* Set Dataset Creation Property List to control use of checksums at IOD level */
dcpl_id = H5Pcreate( H5P_DATASET_CREATE );
if ( enable_checksums ) {
/* enabled by default */
} else {
H5Pset_ocpl_enable_checksum( dcpl_id, 0 );
}
/* Create Dataspace for Datasets */
dset_size[0] = rows_per_rank * comm_size;
dset_size[1] = cols_per_row;
space_id = H5Screate_simple( 2, dset_size, dset_size ); assert( space_id >= 0 );
/* Add updates to the transaction for Dataset creates */
fprintf( stderr, "APP-r%d: tr %d - Create Dataset(s)\n", my_rank, tr_num );
dset_l_id = H5Dcreate_ff( file_id, "DL", H5T_NATIVE_UINT64, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT, tr_id,
H5_EVENT_STACK_NULL ); assert( dset_l_id >= 0 );
if ( prefetched_dset ) {
dset_p_id = H5Dcreate_ff( file_id, "DP", H5T_NATIVE_UINT64, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT, tr_id,
H5_EVENT_STACK_NULL ); assert( dset_p_id >= 0 );
}
if ( stored_dset ) {
dset_s_id = H5Dcreate_ff( file_id, "DS", H5T_NATIVE_UINT64, space_id, H5P_DEFAULT, dcpl_id, H5P_DEFAULT, tr_id,
H5_EVENT_STACK_NULL ); assert( dset_s_id >= 0 );
}
ret = H5Sclose( space_id ); ASSERT_RET;
/* Finish and commit TR and get RC for it */
ret = H5TRfinish( tr_id, H5P_DEFAULT, &rc_idH, H5_EVENT_STACK_NULL ); ASSERT_RET;
ret = H5TRclose( tr_id ); ASSERT_RET;
fprintf( stderr, "APP-r%d: tr %lu - Finished\n", my_rank, tr_num );
assert( rc_idH >= 0 );
versionH = tr_num;
fprintf( stderr, "APP-r%d: rc %lu - Acquired\n", my_rank, versionH );
/* Release the read handle and close read context on earlier CV */
ret = H5RCrelease( rc_id, H5_EVENT_STACK_NULL); ASSERT_RET;
ret = H5RCclose( rc_id ); ASSERT_RET;
fprintf( stderr, "APP-r%d: rc %lu - Released and Closed\n", my_rank, version );
/* The just-acquired RC is now the primary rc_id we'll work with (for awhile) */
rc_id = rc_idH;
version = versionH;
}
/* Rank 0 notifies other ranks that transaction 2 committed and RC acquired */
MPI_Bcast( &version, 1, MPI_UINT64_T, 0, MPI_COMM_WORLD );
/****
* Read Context 2: Other ranks create RC and open HObjects created by rank 0.
****/
if ( my_rank != 0 ) {
rc_id = H5RCcreate( file_id, version );
assert( rc_id >= 0 ); assert ( version == 2 );
fprintf( stderr, "APP-r%d: rc %lu - Created for rank\n", my_rank, version );
dset_l_id = H5Dopen_ff( file_id, "DL", H5P_DEFAULT, rc_id, H5_EVENT_STACK_NULL ); assert( dset_l_id >= 0 );
if ( prefetched_dset ) {
dset_p_id = H5Dopen_ff( file_id, "DP", H5P_DEFAULT, rc_id, H5_EVENT_STACK_NULL ); assert( dset_p_id >= 0 );
}
if ( stored_dset ) {
dset_s_id = H5Dopen_ff( file_id, "DS", H5P_DEFAULT, rc_id, H5_EVENT_STACK_NULL ); assert( dset_s_id >= 0 );
}
} else {
if ( verbose ) print_container_contents( file_id, rc_id, my_rank );
}
/* Keep track of my_rank's neighbor */
neighbor_rank = my_rank + 1;
if ( neighbor_rank == comm_size ) {
neighbor_rank = 0;
}
/* Get the dataspaces for the three datasets and make a copy of each */
space_l_id = H5Dget_space( dset_l_id ); assert ( space_l_id >= 0 );
neighbor_space_l_id = H5Scopy( space_l_id );
if ( prefetched_dset ) {
space_p_id = H5Dget_space( dset_p_id ); assert ( space_p_id >= 0 );
neighbor_space_p_id = H5Scopy( space_p_id );
}
if ( stored_dset ) {
space_s_id = H5Dget_space( dset_s_id ); assert ( space_s_id >= 0 );
neighbor_space_s_id = H5Scopy( space_s_id );
}
/* Select the hyperslab that this rank will update and the hyperslab for reading neighbor's data */
rank_offset[0] = my_rank * rows_per_rank;
rank_offset[1] = 0;
rank_count[0] = rows_per_rank;
rank_count[1] = cols_per_row;
neighbor_offset[0] = neighbor_rank * rows_per_rank;
neighbor_offset[1] = 0;
neighbor_count[0] = rows_per_rank;
neighbor_count[1] = cols_per_row;
ret = H5Sselect_hyperslab( space_l_id, H5S_SELECT_SET, rank_offset, NULL, rank_count, NULL ); ASSERT_RET;
ret = H5Sselect_hyperslab( neighbor_space_l_id, H5S_SELECT_SET, neighbor_offset, NULL, neighbor_count, NULL ); ASSERT_RET;
if ( prefetched_dset ) {
ret = H5Sselect_hyperslab( space_p_id, H5S_SELECT_SET, rank_offset, NULL, rank_count, NULL ); ASSERT_RET;
ret = H5Sselect_hyperslab( neighbor_space_p_id, H5S_SELECT_SET, neighbor_offset, NULL, neighbor_count, NULL ); ASSERT_RET;
}
if ( stored_dset ) {
ret = H5Sselect_hyperslab( space_s_id, H5S_SELECT_SET, rank_offset, NULL, rank_count, NULL ); ASSERT_RET;
ret = H5Sselect_hyperslab( neighbor_space_s_id, H5S_SELECT_SET, neighbor_offset, NULL, neighbor_count, NULL ); ASSERT_RET;
}
/* Create the memory dataspace for a rank - always first part of memory buffer */
rank_mbuf_size[0] = rows_per_rank * cols_per_row;
rank_space_id = H5Screate_simple( 1, rank_mbuf_size, rank_mbuf_size ); assert( rank_space_id >= 0 );
/* Create property lists that will be used */
dxpl_l_id = H5Pcreate( H5P_DATASET_XFER );
if ( enable_checksums ) {
ret = H5Pset_rawdata_integrity_scope( dxpl_l_id, H5_CHECKSUM_ALL ); ASSERT_RET;
} else {
ret = H5Pset_rawdata_integrity_scope( dxpl_l_id, H5_CHECKSUM_NONE ); ASSERT_RET;
}
if ( prefetched_dset ) {
dxpl_p_id = H5Pcreate( H5P_DATASET_XFER );
if ( enable_checksums ) {
ret = H5Pset_rawdata_integrity_scope( dxpl_p_id, H5_CHECKSUM_ALL ); ASSERT_RET;
} else {
ret = H5Pset_rawdata_integrity_scope( dxpl_p_id, H5_CHECKSUM_NONE ); ASSERT_RET;
}
}
if ( stored_dset ) {
dxpl_s_id = H5Pcreate( H5P_DATASET_XFER );
if ( enable_checksums ) {
ret = H5Pset_rawdata_integrity_scope( dxpl_s_id, H5_CHECKSUM_ALL ); ASSERT_RET;
} else {
ret = H5Pset_rawdata_integrity_scope( dxpl_s_id, H5_CHECKSUM_NONE ); ASSERT_RET;
}
}
for ( iteration = 0; iteration < num_iterations; iteration++ ) {
/****
* Cycle of:
* Tranasction N Start / Update / Commit: All ranks update Dataset(s) then commit
* CV N Persist: Rank 0
* Prefetch: Rank 0
* Read rank data: All Ranks
* Read neighbor rank data: All Ranks
* Read all data: All Ranks
****/
tr_num = tr_num + 1;
num_tr_leaders = comm_size;
/* Create a transaction and start it. */
fprintf( stderr, "APP-r%d: iter %05d tr %lu - Transaction Start with %d leaders\n",
my_rank, iteration, tr_num, num_tr_leaders );
tr_id = H5TRcreate( file_id, rc_id, tr_num ); assert( tr_id >= 0 );
trspl_id = H5Pcreate( H5P_TR_START ); assert( trspl_id >= 0 );
ret = H5Pset_trspl_num_peers( trspl_id, num_tr_leaders ); ASSERT_RET;
ret = H5TRstart( tr_id, trspl_id, H5_EVENT_STACK_NULL ); ASSERT_RET;
/* Set cell values (in memory) for this rank based on Row, Rank, Column, Transaction */
u = 0;
for ( r = 0; r < rows_per_rank; r++ ) {
for ( c = 0; c < cols_per_row; c++ ) {
mbuf[u] = (my_rank*rows_per_rank+r)*1000000 + c*100 + tr_num;
u++;
}
}
fprintf( stderr, "APP-r%d: iter %05d tr %lu - Add updates to transaction.\n", my_rank, iteration, tr_num );
/* Add dataset updates to transaction */
START_TIME;
ret = H5Dwrite_ff( dset_l_id, H5T_NATIVE_UINT64, rank_space_id, space_l_id, dxpl_l_id, mbuf, tr_id, H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 01: Time to add Write updates for /DL (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerRank, ELAPSED_TIME );
if ( prefetched_dset ) {
START_TIME;
ret = H5Dwrite_ff( dset_p_id, H5T_NATIVE_UINT64, rank_space_id, space_p_id, dxpl_p_id, mbuf, tr_id,
H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 02: Time to add Write updates for /DP (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerRank, ELAPSED_TIME );
}
if ( stored_dset ) {
START_TIME;
ret = H5Dwrite_ff( dset_s_id, H5T_NATIVE_UINT64, rank_space_id, space_s_id, dxpl_s_id, mbuf, tr_id,
H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 03: Time to add Write updates for /DS (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerRank, ELAPSED_TIME );
}
/* Finish, (commit), and close transaction */
fprintf( stderr, "APP-r%d: iter %05d tr %lu - Finish and Commit\n", my_rank, iteration, tr_num );
ret = H5TRfinish( tr_id, H5P_DEFAULT, NULL, H5_EVENT_STACK_NULL ); ASSERT_RET;
ret = H5TRclose( tr_id ); ASSERT_RET;
ret = H5Pclose( trspl_id ); ASSERT_RET;
/* After commit completes on all ranks, acquire RC on rank 0 and create local handle for RC on other ranks */
MPI_Barrier( MPI_COMM_WORLD );
versionH = tr_num;
if ( my_rank == 0 ) {
rc_idH = H5RCacquire( file_id, &versionH, H5P_DEFAULT, H5_EVENT_STACK_NULL );
assert( rc_idH >= 0 ); assert ( versionH == tr_num );
fprintf( stderr, "APP-r%d: iter %05d rc %lu - Acquired\n", my_rank, iteration, versionH );
} else {
rc_idH = H5RCcreate( file_id, versionH );
assert( rc_idH >= 0 ); assert ( versionH == tr_num );
fprintf( stderr, "APP-r%d: iter %05d rc %lu - Created\n", my_rank, iteration, versionH );
}
MPI_Barrier( MPI_COMM_WORLD ); /* Wait to make sure rank 0 has acquired from IOD before proceeding */
/* Release previous Read Context */
if ( my_rank == 0 ) {
ret = H5RCrelease( rc_id, H5_EVENT_STACK_NULL); ASSERT_RET;
fprintf( stderr, "APP-r%d: iter %05d rc %lu - Released\n", my_rank, iteration, version );
}
ret = H5RCclose( rc_id ); ASSERT_RET;
fprintf( stderr, "APP-r%d: iter %05d rc %lu - Closed\n", my_rank, iteration, version );
/* The just-acquired RC is now the primary rc_id we'll work with (for awhile) */
rc_id = rc_idH;
version = versionH;
/* Rank 0:
- persists the container
- evicts DP & DS
- prefetches DP
*/
if ( my_rank == 0 ) {
if ( verbose ) print_container_contents( file_id, rc_id, my_rank );
START_TIME;
ret = H5RCpersist( rc_id, H5_EVENT_STACK_NULL ); ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 04: Time to Persist container (%lu bytes + KVs): %lu usec\n",
my_rank, iteration, bytesPerContainer, ELAPSED_TIME );
if ( prefetched_dset ) {
START_TIME;
ret = H5Devict_ff( dset_p_id, version, H5P_DEFAULT, H5_EVENT_STACK_NULL ); ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 05: Time to Evict /DP (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerDataset, ELAPSED_TIME );
}
if ( stored_dset ) {
START_TIME;
ret = H5Devict_ff( dset_s_id, version, H5P_DEFAULT, H5_EVENT_STACK_NULL ); ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 06: Time to Evict /DS (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerDataset, ELAPSED_TIME );
}
if ( prefetched_dset ) {
START_TIME;
ret = H5Dprefetch_ff( dset_p_id, rc_id, &dset_p_replica, H5P_DEFAULT, H5_EVENT_STACK_NULL ); ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 07: Time to Prefetch (%lu bytes) /DP: %lu usec\n",
my_rank, iteration, bytesPerDataset, ELAPSED_TIME );
}
}
if ( prefetched_dset ) {
MPI_Bcast( &dset_p_replica, 1, MPI_UINT64_T, 0, MPI_COMM_WORLD );
ret = H5Pset_dxpl_replica( dxpl_p_id, dset_p_replica ); ASSERT_RET;
}
MPI_Barrier( MPI_COMM_WORLD ); /* Make sure all are here before continuing, (esp in case of no prefetch Bcast) */
/*
* All ranks read the same values they updated in last transaction
*/
/* Datasets */
START_TIME;
ret = H5Dread_ff( dset_l_id, H5T_NATIVE_UINT64, rank_space_id, space_l_id, dxpl_l_id, mbuf, rc_id, H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 08: Time to Read my rank entries for /DL (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerRank, ELAPSED_TIME );
if ( verbose ) {
fprintf( stderr, "APP-r%d: my first updated value in /DL: %09lu\n", my_rank, mbuf[0] );
}
if ( prefetched_dset ) {
START_TIME;
ret = H5Dread_ff( dset_p_id, H5T_NATIVE_UINT64, rank_space_id, space_p_id, dxpl_p_id, mbuf, rc_id, H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 09: Time to Read my rank entries for /DP (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerRank, ELAPSED_TIME );
if ( verbose ) {
fprintf( stderr, "APP-r%d: my first updated value in /DP: %09lu\n", my_rank, mbuf[0] );
}
}
if ( stored_dset ) {
START_TIME;
ret = H5Dread_ff( dset_s_id, H5T_NATIVE_UINT64, rank_space_id, space_s_id, dxpl_s_id, mbuf, rc_id, H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 10: Time to Read my rank entries for /DS (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerRank, ELAPSED_TIME );
if ( verbose ) {
fprintf( stderr, "APP-r%d: my first updated value in /DS: %09lu\n", my_rank, mbuf[0] );
}
}
/*
* All ranks read the values "next rank" neighbor updated in last transaction
*/
/* Datasets */
START_TIME;
ret = H5Dread_ff( dset_l_id, H5T_NATIVE_UINT64, rank_space_id, neighbor_space_l_id, dxpl_l_id, mbuf, rc_id,
H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 11: Time to Read neighbor's entries for /DL (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerRank, ELAPSED_TIME );
if ( verbose ) {
fprintf( stderr, "APP-r%d: neighbor's first updated value in /DL: %09lu\n", my_rank, mbuf[0] );
}
if ( prefetched_dset ) {
START_TIME;
ret = H5Dread_ff( dset_p_id, H5T_NATIVE_UINT64, rank_space_id, neighbor_space_p_id, dxpl_p_id, mbuf, rc_id,
H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 12: Time to Read neighbor's entries for /DP (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerRank, ELAPSED_TIME );
if ( verbose ) {
fprintf( stderr, "APP-r%d: neighbor's first updated value in /DP: %09lu\n", my_rank, mbuf[0]);
}
}
if ( stored_dset ) {
START_TIME;
ret = H5Dread_ff( dset_s_id, H5T_NATIVE_UINT64, rank_space_id, neighbor_space_s_id, dxpl_s_id, mbuf, rc_id,
H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 13: Time to Read neighbor's entries for /DS (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerRank, ELAPSED_TIME );
if ( verbose ) {
fprintf( stderr, "APP-r%d: neighbor's first updated value in /DS: %09lu\n", my_rank, mbuf[0] );
}
}
/*
* All ranks read all the values
*/
/* Datasets */
START_TIME;
ret = H5Dread_ff( dset_l_id, H5T_NATIVE_UINT64, H5S_ALL, H5S_ALL, dxpl_l_id, mbuf, rc_id, H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 14: Time to Read all entries for /DL (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerDataset, ELAPSED_TIME );
if ( verbose ) {
fprintf( stderr, "APP-r%d: first value in /DL: %09lu\n", my_rank, mbuf[0] );
}
if ( prefetched_dset ) {
START_TIME;
ret = H5Dread_ff( dset_p_id, H5T_NATIVE_UINT64, H5S_ALL, H5S_ALL, dxpl_p_id, mbuf, rc_id, H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 15: Time to Read all entries for /DP (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerDataset, ELAPSED_TIME );
if ( verbose ) {
fprintf( stderr, "APP-r%d: first value in /DP: %09lu\n", my_rank, mbuf[0] );
}
}
if ( stored_dset ) {
START_TIME;
ret = H5Dread_ff( dset_s_id, H5T_NATIVE_UINT64, H5S_ALL, H5S_ALL, dxpl_s_id, mbuf, rc_id, H5_EVENT_STACK_NULL );
ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 16: Time to Read all entries for /DS (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerDataset, ELAPSED_TIME );
if ( verbose ) {
fprintf( stderr, "APP-r%d: first value in /DS: %09lu\n", my_rank, mbuf[0] );
}
}
/* Rank 0 evicts the replica */
MPI_Barrier( MPI_COMM_WORLD ); /* Make sure all ranks done reading the replica before evicting */
if ( my_rank == 0 ) {
if ( prefetched_dset ) {
START_TIME;
ret = H5Devict_ff( dset_p_id, version, dxpl_p_id, H5_EVENT_STACK_NULL ); ASSERT_RET;
END_TIME;
fprintf( stderr, "APP-r%d: iter %05d step 17: Time to Evict Replica of /DP (%lu bytes): %lu usec\n",
my_rank, iteration, bytesPerDataset, ELAPSED_TIME );
}
}
}
/*
* Wrap-up
*/
/* Print (if verbose) the final state */
if ( my_rank == 0 ) {
if ( verbose ) print_container_contents( file_id, rc_id, my_rank );
}
/* Close the dataset property lists */
if ( prefetched_dset ) {
ret = H5Pclose( dxpl_p_id ); ASSERT_RET;
}
/* Close the memory dataspace for the rank */
ret = H5Sclose( rank_space_id ); ASSERT_RET;
fprintf( stderr, "APP-r%d: Closing H5Objects\n", my_rank );
ret = H5Dclose_ff( dset_l_id, H5_EVENT_STACK_NULL ); ASSERT_RET;
ret = H5Sclose( space_l_id ); ASSERT_RET;
if ( prefetched_dset ) {
ret = H5Dclose_ff( dset_p_id, H5_EVENT_STACK_NULL ); ASSERT_RET;
ret = H5Sclose( space_p_id ); ASSERT_RET;
ret = H5Sclose( neighbor_space_p_id ); ASSERT_RET;
}
if ( stored_dset ) {
ret = H5Dclose_ff( dset_s_id, H5_EVENT_STACK_NULL ); ASSERT_RET;
ret = H5Sclose( space_s_id ); ASSERT_RET;
ret = H5Sclose( neighbor_space_s_id ); ASSERT_RET;
}
/* Release the read handle and close read context */
MPI_Barrier( MPI_COMM_WORLD ); /* Make sure all ranks done with RC */
if ( my_rank == 0 ) {
ret = H5RCrelease( rc_id, H5_EVENT_STACK_NULL); ASSERT_RET;
fprintf( stderr, "APP-r%d: rc %lu - Released\n", my_rank, version );
}
ret = H5RCclose( rc_id ); ASSERT_RET;
fprintf( stderr, "APP-r%d: rc %lu - Closed\n", my_rank, version );
/* Close H5 Objects that are still open */
fprintf( stderr, "APP-r%d: Closing %s\n", my_rank, file_name );
MPI_Barrier( MPI_COMM_WORLD );
ret = H5Fclose_ff( file_id, 1, H5_EVENT_STACK_NULL ); ASSERT_RET;
ret = H5Pclose( fapl_id ); ASSERT_RET;
/* Perform wrap-up operations */
fprintf( stderr, "APP-r%d: Finalize EFF stack\n", my_rank );
MPI_Barrier( MPI_COMM_WORLD );
EFF_finalize();
MPI_Finalize();
return 0;
}
/*
* Helper function used to recursively read and print container contents
* for container identified by "file_id"
* in read context identified by "rc_id"
* "my_rank" used to identify the process doing the reading / printing.
*/
void
print_container_contents( hid_t file_id, hid_t rc_id, int my_rank )
{
herr_t ret;
uint64_t cv;
hbool_t exists;
char path_to_object[1024];
char name[30];
int i, d;
char preface[128];
/* Get the container version for the read context */
ret = H5RCget_version( rc_id, &cv ); ASSERT_RET;
/* Set up the preface and adding version number */
sprintf( preface, "APP-r%d: cv %d: ", my_rank, (int)cv );
/* Start the printing */
fprintf( stderr, "%s ----- Container Contents ------------\n", preface );
for ( d = 0; d < 3; d++ ) {
if ( d == 0 ) {
sprintf( path_to_object, "%s", "/DL" );
} else if ( d == 1 ) {
sprintf( path_to_object, "%s", "/DP" );
} else if ( d == 2 ) {
sprintf( path_to_object, "%s", "/DS" );
}
ret = H5Lexists_ff( file_id, path_to_object, H5P_DEFAULT, &exists, rc_id, H5_EVENT_STACK_NULL );
if ( exists ) {
hid_t dset_id;
hid_t space_id;
int nDims;
hsize_t current_size[2];
hsize_t max_size[2];
hsize_t totalSize;
hid_t dxpl_id;
uint64_t *data;
uint64_t u, e;
dset_id = H5Dopen_ff( file_id, path_to_object, H5P_DEFAULT, rc_id, H5_EVENT_STACK_NULL );
assert( dset_id >= 0 );
space_id = H5Dget_space( dset_id ); assert ( space_id >= 0 );
nDims = H5Sget_simple_extent_dims( space_id, current_size, max_size );
assert( nDims == 2 );
totalSize = current_size[0] * current_size[1];
data = (uint64_t *)calloc( totalSize, sizeof(uint64_t) );
dxpl_id = H5Pcreate( H5P_DATASET_XFER );
if ( enable_checksums ) {
ret = H5Pset_rawdata_integrity_scope( dxpl_id, H5_CHECKSUM_ALL ); ASSERT_RET;
} else {
ret = H5Pset_rawdata_integrity_scope( dxpl_id, H5_CHECKSUM_NONE ); ASSERT_RET;
}
ret = H5Dread_ff( dset_id, H5T_NATIVE_UINT64, space_id, space_id, dxpl_id, data, rc_id, H5_EVENT_STACK_NULL );
ASSERT_RET;
/* note that by printing piece-by-piece, other output may be interspersed. trade-off since won't know line size */
fprintf( stderr, "%s %s data:\n", preface, path_to_object );
e = 0;
for ( i = 0; i < totalSize; i++ ) {
if ( e == 0 ) fprintf( stderr, "%s\t", preface );
fprintf( stderr, "%09lu ", data[i] );
if ( ++e == cols_per_row ) {
fprintf( stderr, "\n" );
e = 0;
}
}
free( data );
sleep( 1 ); /* give output a chance to be printed before diag messages from lower layers on close */
ret = H5Dclose_ff( dset_id, H5_EVENT_STACK_NULL ); ASSERT_RET;
ret = H5Sclose( space_id ); ASSERT_RET;
}
}
/* End printing */
fprintf( stderr, "%s -----------------\n", preface );
return;
}
/*
* parse_options - parse command line options
*/
int
parse_options( int argc, char** argv, int my_rank, int comm_size ) {
int i, n;
char* app = argv[0];
while ( --argc ) {
if ( **(++argv) != '-' ) {
break;
} else {
switch( *(*argv+1) ) {
case 'c':
if ( ( --argc == 0 ) || ( **(argv+1) == '-' ) ) {
if ( my_rank == 0 ) {
printf( "Error: No number specified after -c option.\n" );
usage( app );
}
return( 1 );
} else {
++argv;
cols_per_row = atoi( *argv );
}
break;
case 'r':
if ( ( --argc == 0 ) || ( **(argv+1) == '-' ) ) {
if ( my_rank == 0 ) {
printf( "Error: No number specified after -r option.\n" );
usage( app );
}
return( 1 );
} else {
++argv;
rows_per_rank = atoi( *argv );
}
break;
case 'i':
if ( ( --argc == 0 ) || ( **(argv+1) == '-' ) ) {
if ( my_rank == 0 ) {
printf( "APP-r0: Error: No number specified after -i option.\n" );
usage( app );
}
return( 1 );
} else {
++argv;
num_iterations = atoi( *argv );
}
break;
case 'e':
enable_checksums = 1;
break;
case 'p':
prefetched_dset = 1;
break;
case 's':
stored_dset = 1;
break;
case 'v':
verbose = 1;
break;
default:
if ( my_rank == 0 ) {
usage( app );
}
return( 1 );
}
}
}
return( 0 );
}
/*
* usage - display usage message
*/
void
usage( const char* app ) {
printf( "Usage: %s [-r rows_per_rank] [-c cols_per_row] [-i num_iterations] [-e] [-p] [-s] [-v] \n", app );
printf( "\tr: number of rows each rank writes in created H5Datasets (total rows = this * # of ranks)\n" );
printf( "\tc: number of columns in each row of created H5Datasets\n" );
printf( "\ti: number of iterations to do update/commit/persist/evict/prefetch/read/evict\n" );
printf( "\te: enable checksums on raw data in H5Datasets\n" );
printf( "\tp: create /DP dataset - data will be evicted, replica prefetched, reads from replica\n" );
printf( "\ts: create /DS dataset - data will be evicted, reads from storage (DAOS)\n" );
printf( "\tv: verbose output\n" );
}
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