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[svn-r22004] Reduced warnings and fixed conflicts resulting from including h5tools.h

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Tested: local linux
This commit is contained in:
Allen Byrne 2012-02-28 13:26:34 -05:00
parent 9423da6a4d
commit df6c92e506
33 changed files with 327 additions and 309 deletions

1
hl/tools/gif2h5/gif2hdf.c

@ -17,6 +17,7 @@
#include <stdlib.h>
#include "gif.h"
#include "h5tools.h"
#include "h5tools_utils.h"

2
hl/tools/gif2h5/gif2mem.c

@ -37,7 +37,7 @@
#include "gif.h"
#define VERSION "1.00"
#define GIF2VERSION "1.00"
GIFTOMEM
Gif2Mem(BYTE *MemGif)

1
hl/tools/gif2h5/hdf2gif.c

@ -17,6 +17,7 @@
#include <assert.h>
#include "gif.h"
#include "H5IMpublic.h"
#include "h5tools.h"
#include "h5tools_utils.h"

42
perform/pio_engine.c

@ -320,22 +320,22 @@ do_pio(parameters param)
/* Need barrier to make sure everyone starts at the same time */
MPI_Barrier(pio_comm_g);
set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, START);
set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTART);
hrc = do_fopen(&param, fname, &fd, PIO_CREATE | PIO_WRITE);
VRFY((hrc == SUCCESS), "do_fopen failed");
set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, START);
set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTART);
hrc = do_write(&res, &fd, &param, ndsets, nbytes, buf_size, buffer);
hrc == SUCCESS;
set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, STOP);
set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTOP);
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);
set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTOP);
VRFY((hrc == SUCCESS), "do_fclose failed");
if (!param.h5_write_only) {
@ -349,20 +349,20 @@ do_pio(parameters param)
MPI_Barrier(pio_comm_g);
/* Open file for read */
set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, START);
set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, TSTART);
hrc = do_fopen(&param, fname, &fd, PIO_READ);
VRFY((hrc == SUCCESS), "do_fopen failed");
set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, START);
set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, TSTART);
hrc = do_read(&res, &fd, &param, ndsets, nbytes, buf_size, buffer);
set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, STOP);
set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, TSTOP);
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);
set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, TSTOP);
VRFY((hrc == SUCCESS), "do_fclose failed");
}
@ -413,7 +413,7 @@ done:
static char *
pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size)
{
const char *prefix, *suffix="";
const char *prefix, *suffix = "";
char *ptr, last = '\0';
size_t i, j;
@ -968,7 +968,7 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
} /* end else */
/* Start "raw data" write timer */
set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, START);
set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTART);
while (nbytes_xfer < bytes_count){
/* Write */
@ -1399,7 +1399,7 @@ do_write(results *res, file_descr *fd, parameters *parms, long ndsets,
} /* end while */
/* Stop "raw data" write timer */
set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, STOP);
set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTOP);
/* Calculate write time */
@ -1899,7 +1899,7 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets,
} /* end else */
/* Start "raw data" read timer */
set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, START);
set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTART);
while (nbytes_xfer < bytes_count){
/* Read */
@ -2354,7 +2354,7 @@ do_read(results *res, file_descr *fd, parameters *parms, long ndsets,
} /* end while */
/* Stop "raw data" read timer */
set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, STOP);
set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTOP);
/* Calculate read time */
@ -3115,9 +3115,9 @@ 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);
set_time(timer_g, HDF5_MPI_READ, TSTART);
err=PMPI_File_read_at(fh, offset, buf, count, datatype, status);
set_time(timer_g, HDF5_MPI_READ, STOP);
set_time(timer_g, HDF5_MPI_READ, TSTOP);
return err;
}
@ -3126,9 +3126,9 @@ 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);
set_time(timer_g, HDF5_MPI_READ, TSTART);
err=PMPI_File_read_at_all(fh, offset, buf, count, datatype, status);
set_time(timer_g, HDF5_MPI_READ, STOP);
set_time(timer_g, HDF5_MPI_READ, TSTOP);
return err;
}
@ -3136,9 +3136,9 @@ 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);
set_time(timer_g, HDF5_MPI_WRITE, TSTART);
err=PMPI_File_write_at(fh, offset, buf, count, datatype, status);
set_time(timer_g, HDF5_MPI_WRITE, STOP);
set_time(timer_g, HDF5_MPI_WRITE, TSTOP);
return err;
}
@ -3146,9 +3146,9 @@ 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);
set_time(timer_g, HDF5_MPI_WRITE, TSTART);
err=PMPI_File_write_at_all(fh, offset, buf, count, datatype, status);
set_time(timer_g, HDF5_MPI_WRITE, STOP);
set_time(timer_g, HDF5_MPI_WRITE, TSTOP);
return err;
}

32
perform/pio_perf.c

@ -288,14 +288,14 @@ struct options {
unsigned interleaved; /* Interleaved vs. contiguous blocks */
unsigned collective; /* Collective vs. independent I/O */
unsigned dim2d; /* 1D vs. 2D geometry */
int print_times; /* print times as well as throughputs */
int print_raw; /* print raw data throughput info */
int print_times; /* print times as well as throughputs */
int print_raw; /* print raw data throughput info */
off_t h5_alignment; /* alignment in HDF5 file */
off_t h5_threshold; /* threshold for alignment in HDF5 file */
int h5_use_chunks; /* Make HDF5 dataset chunked */
int h5_write_only; /* Perform the write tests only */
int h5_use_chunks; /* Make HDF5 dataset chunked */
int h5_write_only; /* Perform the write tests only */
unsigned h5_use_mpi_posix; /* Use MPI-posix VFD for HDF5 I/O (instead of MPI-I/O VFD) */
int verify; /* Verify data correctness */
int verify; /* Verify data correctness */
};
typedef struct _minmax {
@ -683,7 +683,7 @@ run_test(iotype iot, parameters parms, struct options *opts)
/*
* Show various statistics
*/
/* Write statistics */
/* Write statistics */
/* Print the raw data throughput if desired */
if (opts->print_raw) {
/* accumulate and output the max, min, and average "raw write" times */
@ -749,7 +749,7 @@ run_test(iotype iot, parameters parms, struct options *opts)
}
if (!parms.h5_write_only) {
/* Read statistics */
/* Read statistics */
/* Print the raw data throughput if desired */
if (opts->print_raw) {
/* accumulate and output the max, min, and average "raw read" times */
@ -1103,10 +1103,10 @@ print_indent(register int indent)
MPI_Comm_rank(pio_comm_g, &myrank);
if (myrank == 0) {
indent *= TAB_SPACE;
indent *= TAB_SPACE;
for (; indent > 0; --indent)
fputc(' ', output);
for (; indent > 0; --indent)
fputc(' ', output);
}
}
@ -1131,11 +1131,11 @@ static void
print_io_api(long io_types)
{
if (io_types & PIO_POSIX)
HDfprintf(output, "posix ");
HDfprintf(output, "posix ");
if (io_types & PIO_MPI)
HDfprintf(output, "mpiio ");
HDfprintf(output, "mpiio ");
if (io_types & PIO_HDF5)
HDfprintf(output, "phdf5 ");
HDfprintf(output, "phdf5 ");
HDfprintf(output, "\n");
}
@ -1144,7 +1144,7 @@ report_parameters(struct options *opts)
{
int rank = comm_world_rank_g;
print_version("HDF5 Library"); /* print library version */
print_version("HDF5 Library"); /* print library version */
HDfprintf(output, "rank %d: ==== Parameters ====\n", rank);
HDfprintf(output, "rank %d: IO API=", rank);
@ -1565,7 +1565,7 @@ parse_size_directive(const char *size)
* Return: Nothing
* Programmer: Bill Wendling, 31. October 2001
* Modifications:
* Added 2D testing (Christian Chilan, 10. August 2005)
* Added 2D testing (Christian Chilan, 10. August 2005)
*/
static void
usage(const char *prog)
@ -1575,7 +1575,7 @@ usage(const char *prog)
MPI_Comm_rank(pio_comm_g, &myrank);
if (myrank == 0) {
print_version(prog);
print_version(prog);
printf("usage: %s [OPTIONS]\n", prog);
printf(" OPTIONS\n");
printf(" -h, --help Print a usage message and exit\n");

1
perform/pio_perf.h

@ -19,6 +19,7 @@
#ifndef STANDALONE
#include "H5private.h"
#include "h5test.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#else
#include "pio_standalone.h"

64
perform/pio_timer.c

@ -43,15 +43,15 @@ pio_time *timer_g; /* timer: global for stub functions */
* Function: sub_time
* Purpose: Struct two time values, and return the difference, in microseconds
*
* Note that the function assumes that a > b
* Note that the function assumes that a > b
* Programmer: Leon Arber, 1/27/06
*/
static double sub_time(struct timeval* a, struct timeval* b)
{
return (((double)a->tv_sec +
((double)a->tv_usec) / MICROSECOND) -
((double)b->tv_sec +
((double)b->tv_usec) / MICROSECOND));
((double)b->tv_sec +
((double)b->tv_usec) / MICROSECOND));
}
@ -89,7 +89,7 @@ pio_time_new(clock_type type)
void
pio_time_destroy(pio_time *pt)
{
free(pt);
HDfree(pt);
/* reset the global timer pointer too. */
timer_g = NULL;
}
@ -134,37 +134,37 @@ set_time(pio_time *pt, timer_type t, int start_stop)
{
if (pt) {
if (pt->type == MPI_TIMER) {
if (start_stop == START) {
if (start_stop == TSTART) {
pt->mpi_timer[t] = MPI_Wtime();
/* When we start the timer for HDF5_FINE_WRITE_FIXED_DIMS or HDF5_FINE_READ_FIXED_DIMS
* we compute the time it took to only open the file */
if(t == HDF5_FINE_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_OPEN] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_GROSS_WRITE_FIXED_DIMS];
else if(t == HDF5_FINE_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_OPEN] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_GROSS_READ_FIXED_DIMS];
/* When we start the timer for HDF5_FINE_WRITE_FIXED_DIMS or HDF5_FINE_READ_FIXED_DIMS
* we compute the time it took to only open the file */
if(t == HDF5_FINE_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_OPEN] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_GROSS_WRITE_FIXED_DIMS];
else if(t == HDF5_FINE_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_OPEN] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_GROSS_READ_FIXED_DIMS];
} else {
pt->total_time[t] += MPI_Wtime() - pt->mpi_timer[t];
pt->mpi_timer[t] = MPI_Wtime();
pt->mpi_timer[t] = MPI_Wtime();
/* When we stop the timer for HDF5_GROSS_WRITE_FIXED_DIMS or HDF5_GROSS_READ_FIXED_DIMS
* we compute the time it took to close the file after the last read/write finished */
if(t == HDF5_GROSS_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_CLOSE] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_FINE_WRITE_FIXED_DIMS];
else if(t == HDF5_GROSS_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_CLOSE] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_FINE_READ_FIXED_DIMS];
/* When we stop the timer for HDF5_GROSS_WRITE_FIXED_DIMS or HDF5_GROSS_READ_FIXED_DIMS
* we compute the time it took to close the file after the last read/write finished */
if(t == HDF5_GROSS_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_CLOSE] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_FINE_WRITE_FIXED_DIMS];
else if(t == HDF5_GROSS_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_CLOSE] += pt->mpi_timer[t] - pt->mpi_timer[HDF5_FINE_READ_FIXED_DIMS];
}
} else {
if (start_stop == START) {
if (start_stop == TSTART) {
HDgettimeofday(&pt->sys_timer[t], NULL);
/* When we start the timer for HDF5_FINE_WRITE_FIXED_DIMS or HDF5_FINE_READ_FIXED_DIMS
* we compute the time it took to only open the file */
if(t == HDF5_FINE_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_WRITE_FIXED_DIMS]));
else if(t == HDF5_FINE_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_READ_FIXED_DIMS]));
/* When we start the timer for HDF5_FINE_WRITE_FIXED_DIMS or HDF5_FINE_READ_FIXED_DIMS
* we compute the time it took to only open the file */
if(t == HDF5_FINE_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_WRITE_FIXED_DIMS]));
else if(t == HDF5_FINE_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_READ_FIXED_DIMS]));
} else {
@ -178,12 +178,12 @@ set_time(pio_time *pt, timer_type t, int start_stop)
((double)pt->sys_timer[t].tv_sec +
((double)pt->sys_timer[t].tv_usec) / MICROSECOND);*/
/* When we stop the timer for HDF5_GROSS_WRITE_FIXED_DIMS or HDF5_GROSS_READ_FIXED_DIMS
* we compute the time it took to close the file after the last read/write finished */
if(t == HDF5_GROSS_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_WRITE_FIXED_DIMS]));
else if(t == HDF5_GROSS_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_READ_FIXED_DIMS]));
/* When we stop the timer for HDF5_GROSS_WRITE_FIXED_DIMS or HDF5_GROSS_READ_FIXED_DIMS
* we compute the time it took to close the file after the last read/write finished */
if(t == HDF5_GROSS_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_WRITE_FIXED_DIMS]));
else if(t == HDF5_GROSS_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_READ_FIXED_DIMS]));
}
}
@ -231,7 +231,7 @@ set_time(pio_time *pt, timer_type t, int start_stop)
}
fprintf(output, " Proc %d: %s %s: %.2f\n", myrank, msg,
(start_stop == START ? "Start" : "Stop"),
(start_stop == TSTART ? "Start" : "Stop"),
pt->total_time[t]);
}
}

4
perform/pio_timer.h

@ -53,8 +53,8 @@ typedef enum clock_type_ {
/* Miscellaneous identifiers */
enum {
START, /* Start a specified timer */
STOP /* Stop a specified timer */
TSTART, /* Start a specified timer */
TSTOP /* Stop a specified timer */
};
/* The performance time structure */

28
perform/sio_engine.c

@ -22,7 +22,7 @@
#include <stdlib.h>
#include <fcntl.h>
#ifdef H5_HAVE_UNISTD_H
# include <unistd.h>
# include <unistd.h>
#endif
#include <errno.h>
@ -233,18 +233,18 @@ do_sio(parameters param)
HDfprintf(output, "data filename=%s\n",
fname);
set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, START);
set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTART);
hrc = do_fopen(&param, fname, &fd, SIO_CREATE | SIO_WRITE);
VRFY((hrc == SUCCESS), "do_fopen failed");
set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, START);
set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTART);
hrc = do_write(&res, &fd, &param, buffer);
set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, STOP);
set_time(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTOP);
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);
set_time(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTOP);
VRFY((hrc == SUCCESS), "do_fclose failed");
if (!param.h5_write_only) {
@ -253,19 +253,19 @@ do_sio(parameters param)
*/
/* Open file for read */
set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, START);
set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, TSTART);
hrc = do_fopen(&param, fname, &fd, SIO_READ);
VRFY((hrc == SUCCESS), "do_fopen failed");
set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, START);
set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, TSTART);
hrc = do_read(&res, &fd, &param, buffer);
set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, STOP);
set_time(res.timers, HDF5_FINE_READ_FIXED_DIMS, TSTOP);
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);
set_time(res.timers, HDF5_GROSS_READ_FIXED_DIMS, TSTOP);
VRFY((hrc == SUCCESS), "do_fclose failed");
}
@ -551,7 +551,7 @@ do_write(results *res, file_descr *fd, parameters *parms, void *buffer)
}
/* Start "raw data" write timer */
set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, START);
set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTART);
/* Perform write */
hrc = dset_write(rank-1, fd, parms, buffer);
@ -563,7 +563,7 @@ do_write(results *res, file_descr *fd, parameters *parms, void *buffer)
/* Stop "raw data" write timer */
set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, STOP);
set_time(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTOP);
/* Calculate write time */
@ -628,7 +628,7 @@ static herr_t dset_write(int local_dim, file_descr *fd, parameters *parms, void
int cur_dim = order[local_dim]-1;
int ret_code = SUCCESS;
int k;
hsize_t dims[MAX_DIMS], maxdims[MAX_DIMS];
hsize_t dims[MAX_DIMS], maxdims[MAX_DIMS];
long i,j;
herr_t hrc;
@ -855,7 +855,7 @@ do_read(results *res, file_descr *fd, parameters *parms, void *buffer)
} /* end switch */
/* Start "raw data" read timer */
set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, START);
set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTART);
hrc = dset_read(rank-1, fd, parms, buffer, buffer2);
if (hrc < 0) {
@ -864,7 +864,7 @@ do_read(results *res, file_descr *fd, parameters *parms, void *buffer)
}
/* Stop "raw data" read timer */
set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, STOP);
set_time(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTOP);
/* Calculate read time */

30
perform/sio_perf.c

@ -295,15 +295,15 @@ struct options {
int buf_rank; /* Rank */
int order_rank; /* Rank */
int chk_rank; /* Rank */
int print_times; /* print times as well as throughputs */
int print_raw; /* print raw data throughput info */
int print_times; /* print times as well as throughputs */
int print_raw; /* print raw data throughput info */
off_t h5_alignment; /* alignment in HDF5 file */
off_t h5_threshold; /* threshold for alignment in HDF5 file */
int h5_use_chunks; /* Make HDF5 dataset chunked */
int h5_write_only; /* Perform the write tests only */
int h5_extendable; /* Perform the write tests only */
int h5_use_chunks; /* Make HDF5 dataset chunked */
int h5_write_only; /* Perform the write tests only */
int h5_extendable; /* Perform the write tests only */
unsigned h5_use_mpi_posix; /* Use MPI-posix VFD for HDF5 I/O (instead of MPI-I/O VFD) */
int verify; /* Verify data correctness */
int verify; /* Verify data correctness */
vfdtype vfd; /* File driver */
};
@ -558,7 +558,7 @@ run_test(iotype iot, parameters parms, struct options *opts)
/*
* Show various statistics
*/
/* Write statistics */
/* Write statistics */
/* Print the raw data throughput if desired */
if (opts->print_raw) {
/* accumulate and output the max, min, and average "raw write" times */
@ -604,7 +604,7 @@ run_test(iotype iot, parameters parms, struct options *opts)
output_results(opts,"Write Open-Close",write_gross_mm_table,parms.num_iters,raw_size);
if (!parms.h5_write_only) {
/* Read statistics */
/* Read statistics */
/* Print the raw data throughput if desired */
if (opts->print_raw) {
/* accumulate and output the max, min, and average "raw read" times */
@ -815,10 +815,10 @@ output_report(const char *fmt, ...)
static void
print_indent(register int indent)
{
indent *= TAB_SPACE;
indent *= TAB_SPACE;
for (; indent > 0; --indent)
fputc(' ', output);
for (; indent > 0; --indent)
fputc(' ', output);
}
static void
@ -842,9 +842,9 @@ static void
print_io_api(long io_types)
{
if (io_types & SIO_POSIX)
HDfprintf(output, "posix ");
HDfprintf(output, "posix ");
if (io_types & SIO_HDF5)
HDfprintf(output, "hdf5 ");
HDfprintf(output, "hdf5 ");
HDfprintf(output, "\n");
}
@ -854,7 +854,7 @@ report_parameters(struct options *opts)
int i, rank;
rank = opts->dset_rank;
print_version("HDF5 Library"); /* print library version */
print_version("HDF5 Library"); /* print library version */
HDfprintf(output, "==== Parameters ====\n");
HDfprintf(output, "IO API=");
@ -1348,7 +1348,7 @@ parse_size_directive(const char *size)
static void
usage(const char *prog)
{
print_version(prog);
print_version(prog);
printf("usage: %s [OPTIONS]\n", prog);
printf(" OPTIONS\n");
printf(" -h Print an usage message and exit\n");

29
perform/sio_perf.h

@ -19,6 +19,7 @@
#ifndef STANDALONE
#include "H5private.h"
#include "h5test.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#else
#include "sio_standalone.h"
@ -49,24 +50,24 @@ typedef enum vfdtype_ {
} vfdtype;
typedef struct parameters_ {
iotype io_type; /* The type of IO test to perform */
iotype io_type; /* The type of IO test to perform */
vfdtype vfd;
long num_files; /* Number of files to create */
long num_dsets; /* Number of datasets to create */
off_t num_bytes; /* Number of bytes in each dset */
long num_files; /* Number of files to create */
long num_dsets; /* Number of datasets to create */
off_t num_bytes; /* Number of bytes in each dset */
int num_iters; /* Number of times to loop doing the IO */
int rank; /* Rank of dataset */
off_t dset_size[MAX_DIMS]; /* Dataset size */
size_t buf_size[MAX_DIMS]; /* Buffer size */
size_t chk_size[MAX_DIMS]; /* Chunk size */
int order[MAX_DIMS]; /* Buffer size */
hsize_t h5_align; /* HDF5 object alignment */
hsize_t h5_thresh; /* HDF5 object alignment threshold */
int h5_use_chunks; /* Make HDF5 dataset chunked */
int h5_extendable; /* Make HDF5 dataset chunked */
int h5_write_only; /* Perform the write tests only */
off_t dset_size[MAX_DIMS]; /* Dataset size */
size_t buf_size[MAX_DIMS]; /* Buffer size */
size_t chk_size[MAX_DIMS]; /* Chunk size */
int order[MAX_DIMS]; /* Buffer size */
hsize_t h5_align; /* HDF5 object alignment */
hsize_t h5_thresh; /* HDF5 object alignment threshold */
int h5_use_chunks; /* Make HDF5 dataset chunked */
int h5_extendable; /* Make HDF5 dataset chunked */
int h5_write_only; /* Perform the write tests only */
unsigned h5_use_mpi_posix; /* VFD for HDF5 I/O */
int verify; /* Verify data correctness */
int verify; /* Verify data correctness */
} parameters;
typedef struct results_ {

36
perform/sio_timer.c

@ -39,15 +39,15 @@ sio_time *timer_g; /* timer: global for stub functions */
* Function: sub_time
* Purpose: Struct two time values, and return the difference, in microseconds
*
* Note that the function assumes that a > b
* Note that the function assumes that a > b
* Programmer: Leon Arber, 1/27/06
*/
static double sub_time(struct timeval* a, struct timeval* b)
{
return (((double)a->tv_sec +
((double)a->tv_usec) / MICROSECOND) -
((double)b->tv_sec +
((double)b->tv_usec) / MICROSECOND));
((double)b->tv_sec +
((double)b->tv_usec) / MICROSECOND));
}
@ -82,7 +82,7 @@ sio_time_new(void)
void
sio_time_destroy(sio_time *pt)
{
free(pt);
HDfree(pt);
/* reset the global timer pointer too. */
timer_g = NULL;
}
@ -100,15 +100,15 @@ sio_time *
set_time(sio_time *pt, timer_type t, int start_stop)
{
if (pt) {
if (start_stop == START) {
if (start_stop == TSTART) {
HDgettimeofday(&pt->sys_timer[t], NULL);
/* When we start the timer for HDF5_FINE_WRITE_FIXED_DIMS or HDF5_FINE_READ_FIXED_DIMS
* we compute the time it took to only open the file */
if(t == HDF5_FINE_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_WRITE_FIXED_DIMS]));
else if(t == HDF5_FINE_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_READ_FIXED_DIMS]));
/* When we start the timer for HDF5_FINE_WRITE_FIXED_DIMS or HDF5_FINE_READ_FIXED_DIMS
* we compute the time it took to only open the file */
if(t == HDF5_FINE_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_WRITE_FIXED_DIMS]));
else if(t == HDF5_FINE_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_OPEN] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_GROSS_READ_FIXED_DIMS]));
} else {
@ -122,12 +122,12 @@ set_time(sio_time *pt, timer_type t, int start_stop)
((double)pt->sys_timer[t].tv_sec +
((double)pt->sys_timer[t].tv_usec) / MICROSECOND);*/
/* When we stop the timer for HDF5_GROSS_WRITE_FIXED_DIMS or HDF5_GROSS_READ_FIXED_DIMS
* we compute the time it took to close the file after the last read/write finished */
if(t == HDF5_GROSS_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_WRITE_FIXED_DIMS]));
else if(t == HDF5_GROSS_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_READ_FIXED_DIMS]));
/* When we stop the timer for HDF5_GROSS_WRITE_FIXED_DIMS or HDF5_GROSS_READ_FIXED_DIMS
* we compute the time it took to close the file after the last read/write finished */
if(t == HDF5_GROSS_WRITE_FIXED_DIMS)
pt->total_time[HDF5_FILE_WRITE_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_WRITE_FIXED_DIMS]));
else if(t == HDF5_GROSS_READ_FIXED_DIMS)
pt->total_time[HDF5_FILE_READ_CLOSE] += sub_time(&(pt->sys_timer[t]), &(pt->sys_timer[HDF5_FINE_READ_FIXED_DIMS]));
}
@ -171,7 +171,7 @@ set_time(sio_time *pt, timer_type t, int start_stop)
}
fprintf(output, " %s %s: %.2f\n", msg,
(start_stop == START ? "Start" : "Stop"),
(start_stop == TSTART ? "Start" : "Stop"),
pt->total_time[t]);
}
}

6
perform/sio_timer.h

@ -27,7 +27,7 @@
#endif
#ifdef H5_HAVE_WINSOCK_H
# include <winsock2.h>
# include <winsock2.h>
#endif /* H5_HAVE_WINSOCK_H */
/* The different types of timers we can have */
@ -52,8 +52,8 @@ typedef enum timer_type_ {
/* Miscellaneous identifiers */
enum {
START, /* Start a specified timer */
STOP /* Stop a specified timer */
TSTART, /* Start a specified timer */
TSTOP /* Stop a specified timer */
};
/* The performance time structure */

1
perform/zip_perf.c

@ -23,6 +23,7 @@
/* our header files */
#include "h5test.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#ifdef H5_HAVE_FILTER_DEFLATE

4
tools/h5copy/h5copy.c

@ -465,7 +465,7 @@ main (int argc, const char *argv[])
/* free link info path */
if (linkinfo.trg_path)
HDfree(linkinfo.trg_path);
HDfree((char*)linkinfo.trg_path);
/* close propertis */
if(H5Pclose(ocpl_id)<0)
@ -497,7 +497,7 @@ error:
/* free link info path */
if (linkinfo.trg_path)
HDfree(linkinfo.trg_path);
HDfree((char*)linkinfo.trg_path);
H5E_BEGIN_TRY {
H5Pclose(ocpl_id);

5
tools/h5diff/h5diff_common.c

@ -17,6 +17,7 @@
#include <string.h>
#include "h5diff.h"
#include "h5diff_common.h"
#include "h5tools.h"
#include "h5tools_utils.h"
static int check_n_input( const char* );
@ -53,7 +54,7 @@ static struct long_options l_opts[] = {
*
*-------------------------------------------------------------------------
*/
static check_options(diff_opt_t* options)
static void check_options(diff_opt_t* options)
{
/*--------------------------------------------------------------
* check for mutually exclusive options
@ -179,7 +180,7 @@ void parse_command_line(int argc,
}
/* init */
exclude_node->obj_path = opt_arg;
exclude_node->obj_path = (char*)opt_arg;
exclude_node->obj_type = H5TRAV_TYPE_UNKNOWN;
exclude_prev = exclude_head;

1
tools/h5diff/h5diff_main.c

@ -18,6 +18,7 @@
#include <memory.h>
#include "h5diff.h"
#include "h5diff_common.h"
#include "h5tools.h"
#include "h5tools_utils.h"

1
tools/h5diff/ph5diff_main.c

@ -19,6 +19,7 @@
#include <string.h>
#include <assert.h>
#include "h5diff_common.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/* Name of tool */

9
tools/h5import/h5import.c

@ -20,6 +20,7 @@
#include <string.h>
#include <ctype.h>
#include "h5import.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/* Name of tool */
@ -1361,7 +1362,7 @@ static int processConfigurationFile(char *infile, struct Input *in)
break;
case 12: /* EXTERNAL-STORAGE */
if (in->configOptionVector[EXTERNAL] == 1) {
if (in->configOptionVector[EXTERNALSTORE] == 1) {
(void) HDfprintf(stderr, err15a, infile);
HDfclose(strm);
return (-1);
@ -1372,7 +1373,7 @@ static int processConfigurationFile(char *infile, struct Input *in)
HDfclose(strm);
return (-1);
}
in->configOptionVector[EXTERNAL] = 1;
in->configOptionVector[EXTERNALSTORE] = 1;
break;
case 13: /* MAXIMUM-DIMENSIONS */
@ -1435,7 +1436,7 @@ static int validateConfigurationParameters(struct Input *in)
return (-1);
}
if (in->configOptionVector[EXTERNAL] == 1) {
if (in->configOptionVector[EXTERNALSTORE] == 1) {
if ((in->configOptionVector[COMPRESS] == 1) || (in->configOptionVector[CHUNK] == 1) || (in->configOptionVector[EXTEND] == 1)) {
(void) HDfprintf(stderr, "%s", err2);
return (-1);
@ -2360,7 +2361,7 @@ static int process(struct Options *opt)
H5Pset_deflate(proplist, (unsigned) in->compressionParam);
}
if (in->configOptionVector[EXTERNAL] == 1) {
if (in->configOptionVector[EXTERNALSTORE] == 1) {
/* creating the external file if it doesnt exist */
if ((extfile = HDfopen(in->externFilename, "ab")) == NULL) {
(void) HDfprintf(stderr, "%s", err4);

2
tools/h5import/h5import.h

@ -47,7 +47,7 @@
#define CHUNK 0
#define COMPRESS 1
#define EXTEND 2
#define EXTERNAL 3
#define EXTERNALSTORE 3
#define DIM 4
#define RANK 5
#define PATH 6

1
tools/h5jam/getub.c

@ -21,6 +21,7 @@
#endif
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
void parse_command_line (int argc, const char *argv[]);

1
tools/h5jam/h5jam.c

@ -15,6 +15,7 @@
#include "hdf5.h"
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/* Name of tool */

1
tools/h5jam/h5unjam.c

@ -15,6 +15,7 @@
#include "hdf5.h"
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/* Name of tool */

1
tools/h5jam/tellub.c

@ -21,6 +21,7 @@
#include "hdf5.h"
#include "H5private.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#define TRUE 1

4
tools/h5ls/h5ls.c

@ -3127,7 +3127,7 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter)
ret = H5tools_get_symlink_info(iter->fid, name, &lnk_info, follow_symlink_g);
/* lnk_info.trg_path is malloced in H5tools_get_symlink_info()
* so it will be freed via buf later */
buf = lnk_info.trg_path;
buf = (char*)lnk_info.trg_path;
/* error */
if (ret < 0)
goto done;
@ -3185,7 +3185,7 @@ list_lnk(const char *name, const H5L_info_t *linfo, void *_iter)
ret = H5tools_get_symlink_info(iter->fid, name, &lnk_info, follow_link);
/* lnk_info.trg_path is malloced in H5tools_get_symlink_info()
* so it will be freed via buf later */
buf = lnk_info.trg_path;
buf = (char*)lnk_info.trg_path;
/* error */
if (ret < 0)
goto done;

28
tools/h5repack/h5repack.c

@ -493,24 +493,24 @@ int copy_attr(hid_t loc_in,
type_class = H5Tget_class(wtype_id);
is_ref = (type_class == H5T_REFERENCE);
if (type_class == H5T_VLEN ||type_class == H5T_ARRAY ) {
hid_t base_type = -1;
base_type = H5Tget_super(ftype_id);
is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
H5Tclose(base_type);
hid_t base_type = -1;
base_type = H5Tget_super(ftype_id);
is_ref = (is_ref || (H5Tget_class(base_type)==H5T_REFERENCE));
H5Tclose(base_type);
}
if (type_class == H5T_COMPOUND) {
int nmembers = H5Tget_nmembers(wtype_id) ;
for (j=0; j<nmembers; j++) {
hid_t mtid = H5Tget_member_type( wtype_id, j );
H5T_class_t mtclass = H5Tget_class(mtid);
H5Tclose(mtid);
int nmembers = H5Tget_nmembers(wtype_id) ;
for (j=0; j<nmembers; j++) {
hid_t mtid = H5Tget_member_type( wtype_id, j );
H5T_class_t mtclass = H5Tget_class(mtid);
H5Tclose(mtid);
if (mtclass==H5T_REFERENCE) {
is_ref = 1;
break;
}
} /* for (j=0; i<nmembers; j++) */
if (mtclass==H5T_REFERENCE) {
is_ref = 1;
break;
}
} /* for (j=0; i<nmembers; j++) */
} /* if (type_class == H5T_COMPOUND) */
if(is_ref) {

1
tools/h5repack/h5repack_main.c

@ -13,6 +13,7 @@
* access to either file, you may request a copy from help@hdfgroup.org. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5tools.h"
#include "h5tools_utils.h"
#include "h5repack.h"

1
tools/h5repack/h5repack_opttable.c

@ -14,6 +14,7 @@
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/*-------------------------------------------------------------------------

1
tools/h5repack/h5repack_parse.c

@ -14,6 +14,7 @@
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"
/*-------------------------------------------------------------------------

238
tools/h5repack/h5repack_refs.c

@ -28,7 +28,7 @@ static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options,
trav_table_t *travt, hid_t fidout);
static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
hid_t fid_out, void *ref_out, trav_table_t *travt);
hid_t fid_out, void *ref_out, trav_table_t *travt);
/*-------------------------------------------------------------------------
* Function: do_copy_refobjs
@ -432,13 +432,13 @@ error:
* Programmer: Pedro Vicente, pvn@ncsa.uiuc.edu
*
* Modifier: xcao@hdfgroup.org, 9/12/2011
* Update values of references(object and region) for the following types:
* Update values of references(object and region) for the following types:
* 1) References,
* 2) ARRAY of reference,
* 3) VLEN of references.
* 4) COMPOUND of references.
* This function does not handle references in other complicated structures,
* such as references in nested compound datatypes.
* such as references in nested compound datatypes.
*
* Date: October, 28, 2003
*
@ -479,7 +479,7 @@ static int copy_refs_attr(hid_t loc_in,
for(u = 0; u < (unsigned)oinfo.num_attrs; u++)
{
is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0;
is_ref = is_ref_vlen = is_ref_array = is_ref_comp = 0;
/* open attribute */
if((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t)u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
@ -500,39 +500,39 @@ static int copy_refs_attr(hid_t loc_in,
is_ref = (type_class == H5T_REFERENCE);
if (type_class == H5T_VLEN ) {
hid_t base_type = -1;
base_type = H5Tget_super(ftype_id);
is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
hid_t base_type = -1;
base_type = H5Tget_super(ftype_id);
is_ref_vlen = (H5Tget_class(base_type)==H5T_REFERENCE);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
}
if (type_class == H5T_ARRAY ) {
hid_t base_type = -1;
base_type = H5Tget_super(ftype_id);
is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
hid_t base_type = -1;
base_type = H5Tget_super(ftype_id);
is_ref_array = (H5Tget_class(base_type)==H5T_REFERENCE);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
}
if (type_class == H5T_COMPOUND) {
int nmembers = H5Tget_nmembers(ftype_id) ;
if (nmembers < 1)
goto error;
int nmembers = H5Tget_nmembers(ftype_id) ;
if (nmembers < 1)
goto error;
ref_comp_index = (int *)HDmalloc(nmembers*sizeof (int));
ref_comp_size = (size_t *)HDmalloc(nmembers*sizeof(ref_comp_size));
ref_comp_field_n = 0;
for (i=0; i<(unsigned)nmembers; i++) {
hid_t mtid = H5Tget_member_type( ftype_id, i );
if ((H5Tget_class(mtid)==H5T_REFERENCE)) {
ref_comp_index[ref_comp_field_n] = i;
ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid);
ref_comp_field_n++;
}
H5Tclose(mtid);
}
for (i=0; i<(unsigned)nmembers; i++) {
hid_t mtid = H5Tget_member_type( ftype_id, i );
if ((H5Tget_class(mtid)==H5T_REFERENCE)) {
ref_comp_index[ref_comp_field_n] = i;
ref_comp_size[ref_comp_field_n] = H5Tget_size(mtid);
ref_comp_field_n++;
}
H5Tclose(mtid);
}
/* if compound don't contain reference type member, free the above
* mallocs. Otherwise there can be memory leaks by the 'continue'
@ -541,14 +541,14 @@ static int copy_refs_attr(hid_t loc_in,
{
if (ref_comp_index)
{
HDfree(ref_comp_index);
ref_comp_index = NULL;
HDfree(ref_comp_index);
ref_comp_index = NULL;
}
if (ref_comp_size)
{
HDfree(ref_comp_size);
ref_comp_size = NULL;
HDfree(ref_comp_size);
ref_comp_size = NULL;
}
}
}
@ -556,10 +556,10 @@ static int copy_refs_attr(hid_t loc_in,
is_ref_comp = (ref_comp_field_n > 0);
if (!(is_ref || is_ref_vlen || is_ref_array || is_ref_comp)) {
H5Tclose(mtype_id);
H5Tclose(ftype_id);
H5Aclose(attr_id);
continue;
H5Tclose(mtype_id);
H5Tclose(ftype_id);
H5Aclose(attr_id);
continue;
}
/* get name */
@ -584,18 +584,18 @@ static int copy_refs_attr(hid_t loc_in,
nelmts *= dims[j];
if (is_ref_array) {
unsigned array_rank = 0;
hsize_t array_size = 1;
hsize_t array_dims[H5S_MAX_RANK];
hid_t base_type = -1;
base_type = H5Tget_super(ftype_id);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
unsigned array_rank = 0;
hsize_t array_size = 1;
hsize_t array_dims[H5S_MAX_RANK];
hid_t base_type = -1;
base_type = H5Tget_super(ftype_id);
msize = H5Tget_size(base_type);
H5Tclose(base_type);
array_rank = H5Tget_array_ndims(mtype_id);
H5Tget_array_dims2(mtype_id, array_dims);
array_rank = H5Tget_array_ndims(mtype_id);
H5Tget_array_dims2(mtype_id, array_dims);
for(j = 0; j <array_rank; j++)
array_size *= array_dims[j];
array_size *= array_dims[j];
nelmts *= array_size;
}
@ -626,7 +626,7 @@ static int copy_refs_attr(hid_t loc_in,
for(i = 0; i < (unsigned)nelmts; i++)
{
if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt)<0)
continue;
continue;
if(options->verbose)
printf("object <%s> reference created to <%s>\n", name, refname);
} /* k */
@ -657,13 +657,13 @@ static int copy_refs_attr(hid_t loc_in,
for(i = 0; i < (unsigned)nelmts; i++)
{
if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt)<0)
continue;
continue;
if(options->verbose)
printf("object <%s> region reference created to <%s>\n", name, refname);
}
} /* H5T_STD_REF_DSETREG */
else if (is_ref_vlen) {
/* handle VLEN of references */
/* handle VLEN of references */
buf = (hvl_t *)HDmalloc((unsigned)(nelmts * sizeof(hvl_t)));
refbuf = buf; /* reuse the read buffer for write */
@ -677,31 +677,31 @@ static int copy_refs_attr(hid_t loc_in,
if(H5Aread(attr_id, mtype_id, buf) < 0)
goto error;
if (H5R_OBJ_REF_BUF_SIZE==msize) {
hobj_ref_t ref_out;
for (i=0; i<(unsigned)nelmts; i++) {
hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p;
for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(&(ptr[j]), &ref_out, msize);
}
} /* for (i=0; i<nelems; i++) */
} else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
if (H5R_OBJ_REF_BUF_SIZE==msize) {
hobj_ref_t ref_out;
for (i=0; i<(unsigned)nelmts; i++) {
hobj_ref_t *ptr = (hobj_ref_t *)((hvl_t *)buf)[i].p;
for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
if (update_ref_value(attr_id, H5R_OBJECT, &(ptr[j]), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(&(ptr[j]), &ref_out, msize);
}
} /* for (i=0; i<nelems; i++) */
} else if (H5R_DSET_REG_REF_BUF_SIZE == msize) {
hdset_reg_ref_t ref_out;
for (i=0; i<(unsigned)nelmts; i++) {
hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p;
for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(&(ptr[j]), &ref_out, msize);
}
} /* for (i=0; i<nelems; i++) */
}
hdset_reg_ref_t ref_out;
for (i=0; i<(unsigned)nelmts; i++) {
hdset_reg_ref_t *ptr = (hdset_reg_ref_t *)((hvl_t *)buf)[i].p;
for (j=0; j<((hvl_t *)buf)[i].len; j++ ) {
if (update_ref_value(attr_id, H5R_DATASET_REGION, &(ptr[j]), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(&(ptr[j]), &ref_out, msize);
}
} /* for (i=0; i<nelems; i++) */
}
} /* else if (is_ref_vlen) */
else if (is_ref_comp) {
/* handle ref fields in a compound */
/* handle ref fields in a compound */
buf = HDmalloc((unsigned)(nelmts * msize));
refbuf = buf; /* reuse the read buffer for write */
@ -716,22 +716,22 @@ static int copy_refs_attr(hid_t loc_in,
goto error;
for (i=0; i<(unsigned)nelmts; i++) {
for (j=0; j<(unsigned)ref_comp_field_n; j++) {
if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) {
int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
hobj_ref_t ref_out;
if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
} /* if */
else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) {
int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
hdset_reg_ref_t ref_out;
if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
} /* else if */
} /* j */
for (j=0; j<(unsigned)ref_comp_field_n; j++) {
if (ref_comp_size[j] == H5R_OBJ_REF_BUF_SIZE) {
int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
hobj_ref_t ref_out;
if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
} /* if */
else if (ref_comp_size[j] == H5R_DSET_REG_REF_BUF_SIZE) {
int idx = i*msize+H5Tget_member_offset( mtype_id, (unsigned)ref_comp_index[j]);
hdset_reg_ref_t ref_out;
if (update_ref_value(attr_id, H5R_DATASET_REGION, (hdset_reg_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
continue;
HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
} /* else if */
} /* j */
} /* i */
} /* else if (is_ref_comp) */
@ -739,11 +739,11 @@ static int copy_refs_attr(hid_t loc_in,
goto error;
if (is_ref_vlen && buf)
H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf);
H5Dvlen_reclaim (mtype_id, space_id, H5P_DEFAULT, buf);
} /* if (nelmts) */
if (refbuf == buf)
refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */
refbuf = NULL; /* set it to NULL to avoid double free since buf and refbuf are the same. */
if(buf) {
HDfree(buf);
@ -756,13 +756,13 @@ static int copy_refs_attr(hid_t loc_in,
}
if (ref_comp_index) {
HDfree(ref_comp_index);
ref_comp_index = NULL;
HDfree(ref_comp_index);
ref_comp_index = NULL;
}
if (ref_comp_size) {
HDfree(ref_comp_size);
ref_comp_size = NULL;
HDfree(ref_comp_size);
ref_comp_size = NULL;
}
if(H5Aclose(attr_out) < 0)
@ -785,16 +785,16 @@ static int copy_refs_attr(hid_t loc_in,
return 0;
error:
if(refbuf)
HDfree(refbuf);
if(buf)
HDfree(buf);
if(refbuf)
HDfree(refbuf);
if(buf)
HDfree(buf);
if (ref_comp_index)
HDfree(ref_comp_index);
HDfree(ref_comp_index);
if (ref_comp_size)
HDfree(ref_comp_size);
HDfree(ref_comp_size);
H5E_BEGIN_TRY {
H5Tclose(ftype_id);
@ -808,9 +808,9 @@ error:
}
/*-------------------------------------------------------------------------
* Function: MapIdToName
* Function: MapIdToName
*
* Purpose: map a ID from a reference to a dataset name
* Purpose: map a ID from a reference to a dataset name
*
*-------------------------------------------------------------------------
*/
@ -843,41 +843,41 @@ out:
}
/*-------------------------------------------------------------------------
* Function: Update_Ref_value
* Function: Update_Ref_value
*
* Purpose: Update a reference value
* Purpose: Update a reference value
*
* Programmer: xcao@hdfgroup.org 9/12/2011
*
*-------------------------------------------------------------------------
*/
static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
hid_t fid_out, void *ref_out, trav_table_t *travt)
hid_t fid_out, void *ref_out, trav_table_t *travt)
{
herr_t ret = -1;
const char* ref_obj_name;
hid_t space_id=-1, ref_obj_id=-1;
herr_t ret = -1;
const char* ref_obj_name;
hid_t space_id=-1, ref_obj_id=-1;
ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in);
if (ref_obj_id<0)
goto done;
ref_obj_id = H5Rdereference2(obj_id, H5P_DEFAULT, ref_type, ref_in);
if (ref_obj_id<0)
goto done;
ref_obj_name = MapIdToName(ref_obj_id, travt);
if (ref_obj_name == NULL)
goto done;
ref_obj_name = MapIdToName(ref_obj_id, travt);
if (ref_obj_name == NULL)
goto done;
if (ref_type == H5R_DATASET_REGION) {
space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in);
if (space_id < 0)
goto done;
}
if (ref_type == H5R_DATASET_REGION) {
space_id = H5Rget_region(obj_id, H5R_DATASET_REGION, ref_in);
if (space_id < 0)
goto done;
}
ret = H5Rcreate(ref_out, fid_out, ref_obj_name, ref_type, space_id);
if (ret < 0)
goto done;
goto done;
ret = 0;
ret = 0;
done:
H5E_BEGIN_TRY {
@ -885,6 +885,6 @@ done:
H5Oclose(ref_obj_id);
} H5E_END_TRY;
return ret;
return ret;
}

15
tools/h5repack/h5repack_verify.c

@ -14,16 +14,17 @@
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"
static int verify_layout(hid_t pid, pack_info_t *obj);
static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter);
/* number of members in an array */
#ifndef NELMTS
# define NELMTS(X) (sizeof(X)/sizeof(X[0]))
# define NELMTS(X) (sizeof(X)/sizeof(X[0]))
#endif
static int verify_layout(hid_t pid, pack_info_t *obj);
static int verify_filters(hid_t pid, hid_t tid, int nfilters, filter_info_t *filter);
/*-------------------------------------------------------------------------
* Function: h5repack_verify
@ -301,9 +302,9 @@ error:
*
* Purpose: verify which layout is present in the property list DCPL_ID
*
* H5D_COMPACT = 0
* H5D_CONTIGUOUS = 1
* H5D_CHUNKED = 2
* H5D_COMPACT = 0
* H5D_CONTIGUOUS = 1
* H5D_CHUNKED = 2
*
* Return: 1 has, 0 does not, -1 error
*

1
tools/h5repack/testh5repack_detect_szip.c

@ -16,6 +16,7 @@
#include <stdio.h>
#include "h5repack.h"
#include "h5tools.h"
#include "h5tools_utils.h"
#include "h5test.h"

44
tools/lib/h5diff.c

@ -614,7 +614,7 @@ static herr_t trav_grp_symlinks(const char *path, const H5L_info_t *linfo,
done:
if (lnk_info.trg_path)
HDfree(lnk_info.trg_path);
HDfree((char *)lnk_info.trg_path);
return 0;
}
@ -728,25 +728,25 @@ hsize_t h5diff(const char *fname1,
/* make the given object1 fullpath, start with "/" */
if (HDstrncmp(objname1, "/", 1))
{
HDstrcpy(obj1fullname, "/");
HDstrcat(obj1fullname, objname1);
HDstrcpy((char *)obj1fullname, "/");
HDstrcat((char *)obj1fullname, objname1);
}
else
HDstrcpy(obj1fullname, objname1);
HDstrcpy((char *)obj1fullname, objname1);
/* make the given object2 fullpath, start with "/" */
if (HDstrncmp(objname2, "/", 1))
{
HDstrcpy(obj2fullname, "/");
HDstrcat(obj2fullname, objname2);
HDstrcpy((char *)obj2fullname, "/");
HDstrcat((char *)obj2fullname, objname2);
}
else
HDstrcpy(obj2fullname, objname2);
HDstrcpy((char *)obj2fullname, objname2);
/*----------------------------------------------------------
* check if obj1 is root, group, single object or symlink
*/
if(!HDstrcmp(obj1fullname, "/"))
if(!HDstrcmp((char *)obj1fullname, "/"))
{
obj1type = H5TRAV_TYPE_GROUP;
}
@ -856,9 +856,9 @@ hsize_t h5diff(const char *fname1,
{
/* set root group */
obj1fullname = (char*)HDcalloc(2, sizeof(char));
HDstrcat(obj1fullname, "/");
HDstrcat((char *)obj1fullname, "/");
obj2fullname = (char*)HDcalloc(2, sizeof(char));
HDstrcat(obj2fullname, "/");
HDstrcat((char *)obj2fullname, "/");
}
@ -1045,15 +1045,15 @@ out:
/* free buffers */
if (obj1fullname)
HDfree(obj1fullname);
HDfree((char *)obj1fullname);
if (obj2fullname)
HDfree(obj2fullname);
HDfree((char *)obj2fullname);
/* free link info buffer */
if (trg_linfo1.trg_path)
HDfree(trg_linfo1.trg_path);
HDfree((char *)trg_linfo1.trg_path);
if (trg_linfo2.trg_path)
HDfree(trg_linfo2.trg_path);
HDfree((char *)trg_linfo2.trg_path);
/* close */
H5E_BEGIN_TRY
@ -1112,9 +1112,9 @@ hsize_t diff_match(hid_t file1_id, const char *grp1, trav_info_t *info1,
* make full path
*/
if (HDstrcmp (grp1, "/"))
grp1_path = grp1;
grp1_path = (char *)grp1;
if (HDstrcmp (grp2, "/"))
grp2_path = grp2;
grp2_path = (char *)grp2;
/*-------------------------------------------------------------------------
* regarding the return value of h5diff (0, no difference in files, 1 difference )
@ -1769,9 +1769,9 @@ out:
/* free link info buffer */
if (linkinfo1.trg_path)
HDfree(linkinfo1.trg_path);
HDfree((char *)linkinfo1.trg_path);
if (linkinfo2.trg_path)
HDfree(linkinfo2.trg_path);
HDfree((char *)linkinfo2.trg_path);
return nfound;
}
@ -2163,9 +2163,9 @@ hsize_t diff(hid_t file1_id,
/* free link info buffer */
if (linkinfo1.trg_path)
HDfree(linkinfo1.trg_path);
HDfree((char *)linkinfo1.trg_path);
if (linkinfo2.trg_path)
HDfree(linkinfo2.trg_path);
HDfree((char *)linkinfo2.trg_path);
return nfound;
@ -2206,9 +2206,9 @@ out2:
/* free link info buffer */
if (linkinfo1.trg_path)
HDfree(linkinfo1.trg_path);
HDfree((char *)linkinfo1.trg_path);
if (linkinfo2.trg_path)
HDfree(linkinfo2.trg_path);
HDfree((char *)linkinfo2.trg_path);
/* close */
/* disable error reporting */