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|
/*
* Copyright (C) 2001, 2002
* National Center for Supercomputing Applications
* All rights reserved.
*
* Author: Albert Cheng of NCSA, Oct 24, 2001.
*/
#include <sys/types.h>
#include <sys/stat.h>
#include <stdio.h>
#include <stdlib.h>
#include <fcntl.h>
#include <unistd.h>
#include <errno.h>
#include "hdf5.h"
#ifdef H5_HAVE_PARALLEL
#include <mpi.h>
#ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */
# include <mpio.h>
#endif /* !MPI_FILE_NULL */
#include "pio_perf.h"
#include "pio_timer.h"
/* Macro definitions */
/* sizes of various items. these sizes won't change during program execution */
#define ELMT_SIZE ((int)sizeof(int)) /* we're doing ints */
#define GOTOERROR(errcode) { ret_code = errcode; goto done; }
#define GOTODONE { goto done; }
#define ERRMSG(mesg) { \
fprintf(stderr, "Proc %d: ", pio_mpi_rank_g); \
fprintf(stderr, "*** Assertion failed (%s) at line %4d in %s\n", \
mesg, (int)__LINE__, __FILE__); \
}
#define MSG(mesg) { \
fprintf(stderr, "Proc %d: ", pio_mpi_rank_g); \
fprintf(stderr, "(%s) at line %4d in %s\n", \
mesg, (int)__LINE__, __FILE__); \
}
/* verify: if val is false (0), print mesg. */
#define VRFY(val, mesg) do { \
if (!val) { \
ERRMSG(mesg); \
GOTOERROR(FAIL); \
} \
} while(0)
/* POSIX I/O macros */
#define POSIXCREATE(fn) HDopen(fn, O_CREAT|O_TRUNC|O_RDWR, 0600)
#define POSIXOPEN(fn, F) HDopen(fn, F, 0600)
#define POSIXCLOSE(F) HDclose(F)
#define POSIXSEEK(F,L) HDlseek(F, L, SEEK_SET)
#define POSIXWRITE(F,B,S) HDwrite(F,B,S)
#define POSIXREAD(F,B,S) HDread(F,B,S)
enum {
PIO_CREATE = 1,
PIO_WRITE = 2,
PIO_READ = 4
};
/* Global variables */
static int clean_file_g = -1; /*whether to cleanup temporary test */
/*files. -1 is not defined; */
/*0 is no cleanup; 1 is do cleanup */
/*
* In a parallel machine, the filesystem suitable for compiling is
* unlikely a parallel file system that is suitable for parallel I/O.
* There is no standard pathname for the parallel file system. /tmp
* is about the best guess.
*/
#ifndef HDF5_PARAPREFIX
# ifdef __PUMAGON__
/* For the PFS of TFLOPS */
# define HDF5_PARAPREFIX "pfs:/pfs_grande/multi/tmp_1"
# else
# define HDF5_PARAPREFIX "/tmp"
# endif /* __PUMAGON__ */
#endif /* !HDF5_PARAPREFIX */
#ifndef MIN
#define MIN(a,b) (a < b ? a : b)
#endif /* !MIN */
/* the different types of file descriptors we can expect */
typedef union _file_descr {
int posixfd; /* POSIX file handle*/
MPI_File mpifd; /* MPI file */
hid_t h5fd; /* HDF5 file */
} file_descr;
/* local functions */
static char *pio_create_filename(iotype iot, const char *base_name,
char *fullname, size_t size);
static herr_t do_write(results *res, file_descr *fd, parameters *parms,
long ndsets, off_t nelmts, size_t buf_size, void *buffer);
static herr_t do_read(results *res, file_descr *fd, parameters *parms,
long ndsets, off_t nelmts, size_t buf_size, void *buffer /*out*/);
static herr_t do_fopen(parameters *param, char *fname, file_descr *fd /*out*/,
int flags);
static herr_t do_fclose(iotype iot, file_descr *fd);
static void do_cleanupfile(iotype iot, char *fname);
/*
* Function: do_pio
* Purpose: PIO Engine where Parallel IO are executed.
* Return: results
* Programmer: Albert Cheng, Bill Wendling 2001/12/12
* Modifications:
*/
results
do_pio(parameters param)
{
/* return codes */
herr_t ret_code = 0; /*return code */
results res;
file_descr fd;
iotype iot;
char fname[FILENAME_MAX];
int maxprocs;
int nfiles, nf;
long ndsets;
off_t nelmts;
char *buffer = NULL; /*data buffer pointer */
size_t buf_size; /*data buffer size in bytes */
/* HDF5 variables */
herr_t hrc; /*HDF5 return code */
/* Sanity check parameters */
/* debug */
if (pio_debug_level>=4) {
h5_dump_info_object(pio_info_g);
}
/* IO type */
iot = param.io_type;
switch (iot) {
case MPIO:
fd.mpifd = MPI_FILE_NULL;
res.timers = pio_time_new(MPI_TIMER);
break;
case POSIXIO:
fd.posixfd = -1;
res.timers = pio_time_new(MPI_TIMER);
break;
case PHDF5:
fd.h5fd = -1;
res.timers = pio_time_new(MPI_TIMER);
break;
default:
/* unknown request */
fprintf(stderr, "Unknown IO type request (%d)\n", iot);
GOTOERROR(FAIL);
}
nfiles = param.num_files; /* number of files */
ndsets = param.num_dsets; /* number of datasets per file */
nelmts = param.num_elmts; /* number of elements per dataset */
maxprocs = param.num_procs; /* max number of mpi-processes to use */
buf_size = param.buf_size;
if (nfiles < 0 ) {
fprintf(stderr,
"number of files must be >= 0 (%d)\n",
nfiles);
GOTOERROR(FAIL);
}
if (ndsets < 0 ) {
fprintf(stderr,
"number of datasets per file must be >= 0 (%ld)\n",
ndsets);
GOTOERROR(FAIL);
}
if (maxprocs <= 0 ) {
fprintf(stderr,
"maximum number of process to use must be > 0 (%d)\n",
maxprocs);
GOTOERROR(FAIL);
}
#if akcdebug
/* debug*/
fprintf(stderr, "nfiles=%d\n", nfiles);
fprintf(stderr, "ndsets=%ld\n", ndsets);
fprintf(stderr, "nelmts=%ld\n", nelmts);
fprintf(stderr, "maxprocs=%d\n", maxprocs);
fprintf(stderr, "buffer size=%ld\n", buf_size);
fprintf(stderr, "total data size=%ld\n", ndsets*nelmts*sizeof(int));
nfiles=MIN(3, nfiles);
/*ndsets=MIN(5, ndsets);*/
/*nelmts=MIN(1000, nelmts);*/
buf_size=MIN(1024*1024, buf_size);
/* DEBUG END */
#endif
/* allocate data buffer */
if(buf_size>0) {
buffer = malloc(buf_size);
if (buffer == NULL){
fprintf(stderr, "malloc for data buffer size (%ld) failed\n",
buf_size);
GOTOERROR(FAIL);
}
}
if (pio_debug_level >= 4) {
int myrank;
MPI_Comm_rank(pio_comm_g, &myrank);
/* output all of the times for all iterations */
if (myrank == 0)
fprintf(output, "Timer details:\n");
}
for (nf = 1; nf <= nfiles; nf++) {
/*
* Write performance measurement
*/
/* Open file for write */
char base_name[256];
MPI_Barrier(pio_comm_g);
sprintf(base_name, "#pio_tmp_%u", nf);
pio_create_filename(iot, base_name, fname, sizeof(fname));
#if AKCDEBUG
fprintf(stderr, "filename=%s\n", fname);
#endif
set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, START);
hrc = do_fopen(¶m, fname, &fd, PIO_CREATE | PIO_WRITE);
VRFY((hrc == SUCCESS), "do_fopen failed");
set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, START);
hrc = do_write(&res, &fd, ¶m, ndsets, nelmts, buf_size, buffer);
set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, STOP);
VRFY((hrc == SUCCESS), "do_write failed");
/* Close file for write */
hrc = do_fclose(iot, &fd);
set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, STOP);
VRFY((hrc == SUCCESS), "do_fclose failed");
MPI_Barrier(pio_comm_g);
/*
* Read performance measurement
*/
/* Open file for read */
set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, START);
hrc = do_fopen(¶m, fname, &fd, PIO_READ);
VRFY((hrc == SUCCESS), "do_fopen failed");
set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, START);
hrc = do_read(&res, &fd, ¶m, ndsets, nelmts, buf_size, buffer);
set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, STOP);
VRFY((hrc == SUCCESS), "do_read failed");
/* Close file for read */
hrc = do_fclose(iot, &fd);
set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, STOP);
VRFY((hrc == SUCCESS), "do_fclose failed");
MPI_Barrier(pio_comm_g);
do_cleanupfile(iot, fname);
}
done:
/* clean up */
/* release HDF5 objects */
/* close any opened files */
/* no remove(fname) because that should have happened normally. */
switch (iot) {
case POSIXIO:
if (fd.posixfd != -1)
hrc = do_fclose(iot, &fd);
break;
case MPIO:
if (fd.mpifd != MPI_FILE_NULL)
hrc = do_fclose(iot, &fd);
break;
case PHDF5:
if (fd.h5fd != -1)
hrc = do_fclose(iot, &fd);
break;
}
/* release generic resources */
if(buffer)
free(buffer);
res.ret_code = ret_code;
return res;
}
/*
* Function: pio_create_filename
* Purpose: Create a new filename to write to. Determine the correct
* suffix to append to the filename by the type of I/O we're
* doing. Also, place in the /tmp/{$USER,$LOGIN} directory if
* USER or LOGIN are specified in the environment.
* Return: Pointer to filename or NULL
* Programmer: Bill Wendling, 21. November 2001
* Modifications:
*/
static char *
pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size)
{
const char *prefix, *suffix;
char *ptr, last = '\0';
size_t i, j;
if (!base_name || !fullname || size < 1)
return NULL;
memset(fullname, 0, size);
switch (iot) {
case POSIXIO:
suffix = ".posix";
break;
case MPIO:
suffix = ".mpio";
break;
case PHDF5:
suffix = ".h5";
break;
}
/* First use the environment variable and then try the constant */
prefix = getenv("HDF5_PARAPREFIX");
#ifdef HDF5_PARAPREFIX
if (!prefix)
prefix = HDF5_PARAPREFIX;
#endif /* HDF5_PARAPREFIX */
/* Prepend the prefix value to the base name */
if (prefix && *prefix) {
/* If the prefix specifies the HDF5_PARAPREFIX directory, then
* default to using the "/tmp/$USER" or "/tmp/$LOGIN"
* directory instead. */
register char *user, *login, *subdir;
user = getenv("USER");
login = getenv("LOGIN");
subdir = (user ? user : login);
if (subdir) {
for (i = 0; i < size && prefix[i]; i++)
fullname[i] = prefix[i];
fullname[i++] = '/';
for (j = 0; i < size && subdir[j]; i++, j++)
fullname[i] = subdir[j];
} else {
/* We didn't append the prefix yet */
strncpy(fullname, prefix, MIN(strlen(prefix), size));
}
if ((strlen(fullname) + strlen(base_name) + 1) < size) {
/* Append the base_name with a slash first. Multiple slashes are
* handled below. */
h5_stat_t buf;
if (HDstat(fullname, &buf) < 0)
/* The directory doesn't exist just yet */
if (mkdir(fullname, (mode_t)0755) < 0 && errno != EEXIST) {
/* We couldn't make the "/tmp/${USER,LOGIN}" subdirectory.
* Default to PREFIX's original prefix value. */
strcpy(fullname, prefix);
}
strcat(fullname, "/");
strcat(fullname, base_name);
} else {
/* Buffer is too small */
return NULL;
}
} else if (strlen(base_name) >= size) {
/* Buffer is too small */
return NULL;
} else {
strcpy(fullname, base_name);
}
/* Append a suffix */
if (suffix) {
if (strlen(fullname) + strlen(suffix) >= size)
return NULL;
strcat(fullname, suffix);
}
/* Remove any double slashes in the filename */
for (ptr = fullname, i = j = 0; ptr && i < size; i++, ptr++) {
if (*ptr != '/' || last != '/')
fullname[j++] = *ptr;
last = *ptr;
}
return fullname;
}
/*
* Function: do_write
* Purpose: Write the required amount of data to the file.
* Return: SUCCESS or FAIL
* Programmer: Albert Cheng, Bill Wendling, 2001/12/13
* Modifications:
*/
static herr_t
do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
off_t nelmts, size_t buf_size, void *buffer)
{
int ret_code = SUCCESS;
long rc; /*routine return code */
int mrc; /*MPI return code */
MPI_Offset mpi_offset;
MPI_Status mpi_status;
long ndset;
off_t nelmts_written;
size_t nelmts_towrite;
char dname[64];
off_t dset_offset; /*dataset offset in a file */
off_t file_offset; /*file offset of the next transfer */
off_t dset_size; /*one dataset size in bytes */
size_t nelmts_in_buf;
off_t elmts_begin; /*first elmt this process transfer */
off_t elmts_count; /*number of elmts this process transfer */
hid_t dcpl = -1; /* Dataset creation property list */
/* HDF5 variables */
herr_t hrc; /*HDF5 return code */
hsize_t h5dims[1]; /*dataset dim sizes */
hid_t h5dset_space_id = -1; /*dataset space ID */
hid_t h5mem_space_id = -1; /*memory dataspace ID */
hid_t h5ds_id = -1; /*dataset handle */
#if AKCDEBUG
fprintf(stderr, "In do_write\n");
fprintf(stderr, "ndsets=%ld\n", ndsets);
fprintf(stderr, "nelmts=%ld\n", nelmts);
fprintf(stderr, "buffer size=%ld\n", buf_size);
#endif
/* calculate dataset parameters. data type is always native C int */
dset_size = nelmts * ELMT_SIZE;
nelmts_in_buf = buf_size/ELMT_SIZE;
/* hdf5 data space setup */
if (parms->io_type == PHDF5){
if(nelmts>0) {
/* define a contiquous dataset of nelmts native ints */
h5dims[0] = nelmts;
h5dset_space_id = H5Screate_simple(1, h5dims, NULL);
VRFY((h5dset_space_id >= 0), "H5Screate_simple");
} /* end if */
else {
h5dset_space_id = H5Screate(H5S_SCALAR);
VRFY((h5dset_space_id >= 0), "H5Screate");
} /* end else */
/* create the memory dataspace that corresponds to the xfer buffer */
if(nelmts_in_buf>0) {
h5dims[0] = nelmts_in_buf;
h5mem_space_id = H5Screate_simple(1, h5dims, NULL);
VRFY((h5mem_space_id >= 0), "H5Screate_simple");
} /* end if */
else {
h5mem_space_id = H5Screate(H5S_SCALAR);
VRFY((h5mem_space_id >= 0), "H5Screate");
} /* end else */
}
for (ndset = 1; ndset <= ndsets; ++ndset) {
/* Calculate dataset offset within a file */
/* create dataset */
switch (parms->io_type) {
case POSIXIO:
case MPIO:
/* both posix and mpi io just need dataset offset in file*/
dset_offset = (ndset - 1) * dset_size;
break;
case PHDF5:
dcpl = H5Pcreate(H5P_DATASET_CREATE);
if (dcpl < 0) {
fprintf(stderr, "HDF5 Property List Create failed\n");
GOTOERROR(FAIL);
}
/* Make the dataset chunked if asked */
if(parms->h5_use_chunks) {
/* Set the chunk size to be the same as the buffer size */
h5dims[0] = nelmts_in_buf;
hrc = H5Pset_chunk(dcpl, 1, h5dims);
if (hrc < 0) {
fprintf(stderr, "HDF5 Property List Set failed\n");
GOTOERROR(FAIL);
} /* end if */
} /* end if */
#if H5_VERS_MAJOR > 1 || H5_VERS_MINOR > 4
/* Disable writing fill values if asked */
if(parms->h5_no_fill) {
hrc = H5Pset_fill_time(dcpl, H5D_FILL_TIME_NEVER);
if (hrc < 0) {
fprintf(stderr, "HDF5 Property List Set failed\n");
GOTOERROR(FAIL);
} /* end if */
} /* end if */
#endif
sprintf(dname, "Dataset_%ld", ndset);
h5ds_id = H5Dcreate(fd->h5fd, dname, H5T_NATIVE_INT,
h5dset_space_id, dcpl);
if (h5ds_id < 0) {
fprintf(stderr, "HDF5 Dataset Create failed\n");
GOTOERROR(FAIL);
}
hrc = H5Pclose(dcpl);
/* verifying the close of the dcpl */
if (hrc < 0) {
fprintf(stderr, "HDF5 Property List Close failed\n");
GOTOERROR(FAIL);
}
break;
}
/* Calculate the first element and how many elements this process
* transfer. First calculate the beginning element of this process
* and the next process. Count of elements is the difference between
* these two beginnings. This way, it avoids any rounding errors.
*/
elmts_begin = (long)(((double)nelmts)/pio_mpi_nprocs_g*pio_mpi_rank_g);
if (pio_mpi_rank_g < (pio_mpi_nprocs_g - 1))
elmts_count = (long)((((double)nelmts) / pio_mpi_nprocs_g * (pio_mpi_rank_g + 1))
- (double)elmts_begin);
else
/* last process. Take whatever are left */
elmts_count = nelmts - elmts_begin;
#if AKCDEBUG
fprintf(stderr, "proc %d: elmts_begin=%ld, elmts_count=%ld\n",
pio_mpi_rank_g, elmts_begin, elmts_count);
#endif
nelmts_written = 0 ;
/* Start "raw data" write timer */
set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, START);
while (nelmts_written < elmts_count){
nelmts_towrite = elmts_count - nelmts_written;
if ((elmts_count - nelmts_written) >= nelmts_in_buf) {
nelmts_towrite = nelmts_in_buf;
} else {
/* last write of a partial buffer */
nelmts_towrite = elmts_count - nelmts_written;
}
#if AKCDEBUG
/*Prepare write data*/
{
int *intptr = (int *)buffer;
register int i;
for (i = 0; i < nelmts_towrite; ++i)
*intptr++ = nelmts_towrite + i;
}
#endif
/* Write */
/* Calculate offset of write within a dataset/file */
switch (parms->io_type) {
case POSIXIO:
/* need to (off_t) the elmnts_begin expression because they */
/* may be of smaller sized integer types */
file_offset = dset_offset + (off_t)(elmts_begin + nelmts_written)*ELMT_SIZE;
#if AKCDEBUG
fprintf(stderr, "proc %d: writes %ld bytes at file-offset %ld\n",
pio_mpi_rank_g, nelmts_towrite*ELMT_SIZE, file_offset);
#endif
rc = POSIXSEEK(fd->posixfd, file_offset);
VRFY((rc>=0), "POSIXSEEK");
rc = POSIXWRITE(fd->posixfd, buffer, (size_t)(nelmts_towrite * ELMT_SIZE));
VRFY((rc == (nelmts_towrite*ELMT_SIZE)), "POSIXWRITE");
break;
case MPIO:
mpi_offset = dset_offset + (elmts_begin + nelmts_written)*ELMT_SIZE;
#if AKCDEBUG
fprintf(stderr, "proc %d: writes %ld bytes at mpi-offset %ld\n",
pio_mpi_rank_g, nelmts_towrite*ELMT_SIZE, mpi_offset);
#endif
mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buffer,
(int)(nelmts_towrite*ELMT_SIZE), MPI_CHAR,
&mpi_status);
VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE");
break;
case PHDF5:
/*set up the dset space id to select the segment to process */
{
hsize_t block[1], stride[1], count[1];
hssize_t start[1];
start[0] = elmts_begin + nelmts_written;
stride[0] = block[0] = nelmts_towrite;
count[0] = 1;
hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET,
start, stride, count, block);
VRFY((hrc >= 0), "H5Sset_hyperslab");
/*setup the memory space id too. Only start is different */
start[0] = 0;
hrc = H5Sselect_hyperslab(h5mem_space_id, H5S_SELECT_SET,
start, stride, count, block);
VRFY((hrc >= 0), "H5Sset_hyperslab");
}
/* set write time here */
hrc = H5Dwrite(h5ds_id, H5T_NATIVE_INT, h5mem_space_id,
h5dset_space_id, H5P_DEFAULT, buffer);
VRFY((hrc >= 0), "H5Dwrite");
break;
}
nelmts_written += nelmts_towrite;
}
/* Stop "raw data" write timer */
set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, STOP);
/* Calculate write time */
/* Close dataset. Only HDF5 needs to do an explicit close. */
if (parms->io_type == PHDF5){
hrc = H5Dclose(h5ds_id);
if (hrc < 0) {
fprintf(stderr, "HDF5 Dataset Close failed\n");
GOTOERROR(FAIL);
}
h5ds_id = -1;
}
}
done:
/* release HDF5 objects */
if (h5dset_space_id != -1) {
hrc = H5Sclose(h5dset_space_id);
if (hrc < 0){
fprintf(stderr, "HDF5 Dataset Space Close failed\n");
ret_code = FAIL;
} else {
h5dset_space_id = -1;
}
}
if (h5mem_space_id != -1) {
hrc = H5Sclose(h5mem_space_id);
if (hrc < 0) {
fprintf(stderr, "HDF5 Memory Space Close failed\n");
ret_code = FAIL;
} else {
h5mem_space_id = -1;
}
}
return ret_code;
}
/*
* Function: do_read
* Purpose: read the required amount of data from the file.
* Return: SUCCESS or FAIL
* Programmer: Albert Cheng 2001/12/13
* Modifications:
*/
static herr_t
do_read(results *res, file_descr *fd, parameters *parms, long ndsets,
off_t nelmts, size_t buf_size, void *buffer /*out*/)
{
int ret_code = SUCCESS;
long rc; /*routine return code */
int mrc; /*MPI return code */
MPI_Offset mpi_offset;
MPI_Status mpi_status;
long ndset;
size_t nelmts_toread;
off_t nelmts_read;
char dname[64];
off_t dset_offset; /*dataset offset in a file */
off_t file_offset; /*file offset of the next transfer */
off_t dset_size; /*one dataset size in bytes */
size_t nelmts_in_buf;
off_t elmts_begin; /*first elmt this process transfer */
off_t elmts_count; /*number of elmts this process transfer */
/* HDF5 variables */
herr_t hrc; /*HDF5 return code */
hsize_t h5dims[1]; /*dataset dim sizes */
hid_t h5dset_space_id = -1; /*dataset space ID */
hid_t h5mem_space_id = -1; /*memory dataspace ID */
hid_t h5ds_id = -1; /*dataset handle */
#if AKCDEBUG
fprintf(stderr, "In do_read\n");
fprintf(stderr, "ndsets=%ld\n", ndsets);
fprintf(stderr, "nelmts=%ld\n", nelmts);
fprintf(stderr, "buffer size=%ld\n", buf_size);
#endif
/* calculate dataset parameters. data type is always native C int */
dset_size = nelmts * ELMT_SIZE;
nelmts_in_buf = buf_size/ELMT_SIZE;
/* hdf5 data space setup */
if (parms->io_type == PHDF5){
if(nelmts>0) {
/* define a contiquous dataset of nelmts native ints */
h5dims[0] = nelmts;
h5dset_space_id = H5Screate_simple(1, h5dims, NULL);
VRFY((h5dset_space_id >= 0), "H5Screate_simple");
} /* end if */
else {
h5dset_space_id = H5Screate(H5S_SCALAR);
VRFY((h5dset_space_id >= 0), "H5Screate");
} /* end else */
/* create the memory dataspace that corresponds to the xfer buffer */
if(nelmts_in_buf>0) {
h5dims[0] = nelmts_in_buf;
h5mem_space_id = H5Screate_simple(1, h5dims, NULL);
VRFY((h5mem_space_id >= 0), "H5Screate_simple");
} /* end if */
else {
h5mem_space_id = H5Screate(H5S_SCALAR);
VRFY((h5mem_space_id >= 0), "H5Screate");
} /* end else */
}
for (ndset = 1; ndset <= ndsets; ++ndset) {
/* Calculate dataset offset within a file */
/* create dataset */
switch (parms->io_type) {
case POSIXIO:
case MPIO:
/* both posix and mpi io just need dataset offset in file*/
dset_offset = (ndset - 1) * dset_size;
break;
case PHDF5:
sprintf(dname, "Dataset_%ld", ndset);
h5ds_id = H5Dopen(fd->h5fd, dname);
if (h5ds_id < 0) {
fprintf(stderr, "HDF5 Dataset open failed\n");
GOTOERROR(FAIL);
}
break;
}
/*
* Calculate the first element and how many elements this process
* transfer. First calculate the beginning element of this process
* and the next process. Count of elements is the difference between
* these two beginnings. This way, it avoids any rounding errors.
*/
elmts_begin = (long)(((double)nelmts)/pio_mpi_nprocs_g*pio_mpi_rank_g);
if (pio_mpi_rank_g < (pio_mpi_nprocs_g - 1))
elmts_count = (long)((((double)nelmts) / pio_mpi_nprocs_g * (pio_mpi_rank_g + 1)) -
(double)elmts_begin);
else
/* last process. Take whatever are left */
elmts_count = nelmts - elmts_begin;
#if AKCDEBUG
fprintf(stderr, "proc %d: elmts_begin=%ld, elmts_count=%ld\n",
pio_mpi_rank_g, elmts_begin, elmts_count);
#endif
nelmts_read = 0 ;
/* Start "raw data" read timer */
set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, START);
while (nelmts_read < elmts_count){
nelmts_toread = elmts_count - nelmts_read;
if ((elmts_count - nelmts_read) >= nelmts_in_buf)
nelmts_toread = nelmts_in_buf;
else
/* last read of a partial buffer */
nelmts_toread = elmts_count - nelmts_read;
/* read */
/* Calculate offset of read within a dataset/file */
switch (parms->io_type){
case POSIXIO:
/* need to (off_t) the elmnts_begin expression because they */
/* may be of smaller sized integer types */
file_offset = dset_offset + (off_t)(elmts_begin + nelmts_read)*ELMT_SIZE;
#if AKCDEBUG
fprintf(stderr, "proc %d: read %ld bytes at file-offset %ld\n",
pio_mpi_rank_g, nelmts_toread*ELMT_SIZE, file_offset);
#endif
rc = POSIXSEEK(fd->posixfd, file_offset);
VRFY((rc>=0), "POSIXSEEK");
rc = POSIXREAD(fd->posixfd, buffer, (size_t)(nelmts_toread*ELMT_SIZE));
VRFY((rc==(nelmts_toread*ELMT_SIZE)), "POSIXREAD");
break;
case MPIO:
mpi_offset = dset_offset + (elmts_begin + nelmts_read)*ELMT_SIZE;
#if AKCDEBUG
fprintf(stderr, "proc %d: read %ld bytes at mpi-offset %ld\n",
pio_mpi_rank_g, nelmts_toread*ELMT_SIZE, mpi_offset);
#endif
mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buffer,
(int)(nelmts_toread*ELMT_SIZE), MPI_CHAR,
&mpi_status);
VRFY((mrc==MPI_SUCCESS), "MPIO_read");
break;
case PHDF5:
/*set up the dset space id to select the segment to process */
{
hsize_t block[1], stride[1], count[1];
hssize_t start[1];
start[0] = elmts_begin + nelmts_read;
stride[0] = block[0] = nelmts_toread;
count[0] = 1;
hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET,
start, stride, count, block);
VRFY((hrc >= 0), "H5Sset_hyperslab");
/*setup the memory space id too. Only start is different */
start[0] = 0;
hrc = H5Sselect_hyperslab(h5mem_space_id, H5S_SELECT_SET,
start, stride, count, block);
VRFY((hrc >= 0), "H5Sset_hyperslab");
}
/* set read time here */
hrc = H5Dread(h5ds_id, H5T_NATIVE_INT, h5mem_space_id,
h5dset_space_id, H5P_DEFAULT, buffer);
VRFY((hrc >= 0), "H5Dread");
break;
}
#if AKCDEBUG & 0
/*verify read data*/
{
int *intptr = (int *)buffer;
register int i;
for (i = 0; i < nelmts_towrite; ++i)
/* TO BE IMPLEMENTED */
;
}
#endif
nelmts_read += nelmts_toread;
}
/* Stop "raw data" read timer */
set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, STOP);
/* Calculate read time */
/* Close dataset. Only HDF5 needs to do an explicit close. */
if (parms->io_type == PHDF5){
hrc = H5Dclose(h5ds_id);
if (hrc < 0) {
fprintf(stderr, "HDF5 Dataset Close failed\n");
GOTOERROR(FAIL);
}
h5ds_id = -1;
}
}
done:
/* release HDF5 objects */
if (h5dset_space_id != -1) {
hrc = H5Sclose(h5dset_space_id);
if (hrc < 0){
fprintf(stderr, "HDF5 Dataset Space Close failed\n");
ret_code = FAIL;
} else {
h5dset_space_id = -1;
}
}
if (h5mem_space_id != -1) {
hrc = H5Sclose(h5mem_space_id);
if (hrc < 0) {
fprintf(stderr, "HDF5 Memory Space Close failed\n");
ret_code = FAIL;
} else {
h5mem_space_id = -1;
}
}
return ret_code;
}
/*
* Function: do_fopen
* Purpose: Open the specified file.
* Return: SUCCESS or FAIL
* Programmer: Albert Cheng, Bill Wendling, 2001/12/13
* Modifications:
*/
static herr_t
do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags)
{
int ret_code = SUCCESS, mrc;
herr_t hrc;
hid_t acc_tpl = -1; /* file access templates */
switch (param->io_type) {
case POSIXIO:
if (flags & (PIO_CREATE | PIO_WRITE))
fd->posixfd = POSIXCREATE(fname);
else
fd->posixfd = POSIXOPEN(fname, O_RDONLY);
if (fd->posixfd < 0 ) {
fprintf(stderr, "POSIX File Open failed(%s)\n", fname);
GOTOERROR(FAIL);
}
/* The perils of POSIX I/O in a parallel environment. The problem is:
*
* - Process n opens a file with truncation and then starts
* writing to the file.
* - Process m also opens the file with truncation, but after
* process n has already started to write to the file. Thus,
* all of the stuff process n wrote is now lost.
*/
MPI_Barrier(pio_comm_g);
break;
case MPIO:
if (flags & (PIO_CREATE | PIO_WRITE)) {
MPI_File_delete(fname, pio_info_g);
mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_CREATE | MPI_MODE_RDWR,
pio_info_g, &fd->mpifd);
if (mrc != MPI_SUCCESS) {
fprintf(stderr, "MPI File Open failed(%s)\n", fname);
GOTOERROR(FAIL);
}
/*since MPI_File_open with MPI_MODE_CREATE does not truncate */
/*filesize , set size to 0 explicitedly. */
mrc = MPI_File_set_size(fd->mpifd, (MPI_Offset)0);
if (mrc != MPI_SUCCESS) {
fprintf(stderr, "MPI_File_set_size failed\n");
GOTOERROR(FAIL);
}
} else {
mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_RDONLY,
pio_info_g, &fd->mpifd);
if (mrc != MPI_SUCCESS) {
fprintf(stderr, "MPI File Open failed(%s)\n", fname);
GOTOERROR(FAIL);
}
}
break;
case PHDF5:
acc_tpl = H5Pcreate(H5P_FILE_ACCESS);
if (acc_tpl < 0) {
fprintf(stderr, "HDF5 Property List Create failed\n");
GOTOERROR(FAIL);
}
/* Set the file driver to the MPI-I/O driver */
hrc = H5Pset_fapl_mpio(acc_tpl, pio_comm_g, pio_info_g);
if (hrc < 0) {
fprintf(stderr, "HDF5 Property List Set failed\n");
GOTOERROR(FAIL);
}
/* Set the alignment of objects in HDF5 file */
hrc = H5Pset_alignment(acc_tpl, param->h5_thresh, param->h5_align);
if (hrc < 0) {
fprintf(stderr, "HDF5 Property List Set failed\n");
GOTOERROR(FAIL);
}
/* create the parallel file */
if (flags & (PIO_CREATE | PIO_WRITE)) {
fd->h5fd = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
} else {
fd->h5fd = H5Fopen(fname, H5P_DEFAULT, acc_tpl);
}
hrc = H5Pclose(acc_tpl);
if (fd->h5fd < 0) {
fprintf(stderr, "HDF5 File Create failed(%s)\n", fname);
GOTOERROR(FAIL);
}
/* verifying the close of the acc_tpl */
if (hrc < 0) {
fprintf(stderr, "HDF5 Property List Close failed\n");
GOTOERROR(FAIL);
}
break;
}
done:
return ret_code;
}
/*
* Function: do_fclose
* Purpose: Close the specified file descriptor.
* Return: SUCCESS or FAIL
* Programmer: Albert Cheng, Bill Wendling, 2001/12/13
* Modifications:
*/
static herr_t
do_fclose(iotype iot, file_descr *fd /*out*/)
{
herr_t ret_code = SUCCESS, hrc;
int mrc = 0, rc = 0;
switch (iot) {
case POSIXIO:
rc = POSIXCLOSE(fd->posixfd);
if (rc != 0){
fprintf(stderr, "POSIX File Close failed\n");
GOTOERROR(FAIL);
}
fd->posixfd = -1;
break;
case MPIO:
mrc = MPI_File_close(&fd->mpifd);
if (mrc != MPI_SUCCESS){
fprintf(stderr, "MPI File close failed\n");
GOTOERROR(FAIL);
}
fd->mpifd = MPI_FILE_NULL;
break;
case PHDF5:
hrc = H5Fclose(fd->h5fd);
if (hrc < 0) {
fprintf(stderr, "HDF5 File Close failed\n");
GOTOERROR(FAIL);
}
fd->h5fd = -1;
break;
}
done:
return ret_code;
}
/*
* Function: do_fclose
* Purpose: Cleanup temporary file unless HDF5_NOCLEANUP is set.
* Only Proc 0 of the PIO communicator will do the cleanup.
* Other processes just return.
* Return: void
* Programmer: Albert Cheng 2001/12/12
* Modifications:
*/
static void
do_cleanupfile(iotype iot, char *fname)
{
if (pio_mpi_rank_g != 0)
return;
if (clean_file_g == -1)
clean_file_g = (getenv("HDF5_NOCLEANUP")==NULL) ? 1 : 0;
if (clean_file_g){
switch (iot){
case POSIXIO:
remove(fname);
break;
case MPIO:
case PHDF5:
MPI_File_delete(fname, pio_info_g);
break;
}
}
}
#ifndef TIME_MPI
#define TIME_MPI
#endif
#ifdef TIME_MPI
/* instrument the MPI_File_wrirte_xxx and read_xxx calls to measure
* pure time spent in MPI_File code.
*/
int MPI_File_read_at(MPI_File fh, MPI_Offset offset, void *buf,
int count, MPI_Datatype datatype, MPI_Status *status)
{
int err;
set_time(timer_g, HDF5_MPI_READ, START);
err=PMPI_File_read_at(fh, offset, buf, count, datatype, status);
set_time(timer_g, HDF5_MPI_READ, STOP);
return err;
}
int MPI_File_read_at_all(MPI_File fh, MPI_Offset offset, void *buf,
int count, MPI_Datatype datatype, MPI_Status *status)
{
int err;
set_time(timer_g, HDF5_MPI_READ, START);
err=PMPI_File_read_at_all(fh, offset, buf, count, datatype, status);
set_time(timer_g, HDF5_MPI_READ, STOP);
return err;
}
int MPI_File_write_at(MPI_File fh, MPI_Offset offset, void *buf,
int count, MPI_Datatype datatype, MPI_Status *status)
{
int err;
set_time(timer_g, HDF5_MPI_WRITE, START);
err=PMPI_File_write_at(fh, offset, buf, count, datatype, status);
set_time(timer_g, HDF5_MPI_WRITE, STOP);
return err;
}
int MPI_File_write_at_all(MPI_File fh, MPI_Offset offset, void *buf,
int count, MPI_Datatype datatype, MPI_Status *status)
{
int err;
set_time(timer_g, HDF5_MPI_WRITE, START);
err=PMPI_File_write_at_all(fh, offset, buf, count, datatype, status);
set_time(timer_g, HDF5_MPI_WRITE, STOP);
return err;
}
#endif /* TIME_MPI */
#endif /* H5_HAVE_PARALLEL */
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