mirror of
https://github.com/HDFGroup/hdf5.git
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1e38c13785
----------------------
./RELEASE
Updated with important changes I made since the second beta.
./src/H5A.c
./src/H5D.c
./src/H5Dprivate.h
./src/H5G.c
./src/H5Gprivate.h
./src/H5R.c
./src/H5Rprivate.h
./src/H5T.c
./src/H5Tprivate.h
Any API function that used to take an `hid_t loc_id' followed
by a `const char *name' can now take any type of object for
the loc_id as long as the object is somehow associated with a
file. Internally, H5G_loc() was modified to return an
H5G_entry_t* instead of an H5G_t* so it's more general.
Among other things, this allows one to retrieve information
about an object like a named type or dataset without knowing
the name of the type or dataset:
int
get_nlinks (hid_t obj)
{
H5G_stat_t sb;
if (H5Gstat(obj, ".", TRUE, &sb)<0) return -1;
return sb.nlink;
}
./test/gheap.c
./test/istore.c
These files needed a couple of changes because they call some
of the internal functions whose H5G_t arguments changed to
H5G_entry_t.
./src/H5A.c
Got rid of all the switch statements for getting symbol table
entries for varous objects and replaced them with a call to
H5G_loc() allowing attributes to automatically apply to any
type of object that belongs to a file.
./test/Makefile.in
Moved the ragged array tests from the normal list of tests to
the `make timings' target.
./test/ragged.c
Added rewrite tests -- rewrite the rows of a dataset changing
the number of rows and the length of each row.
./test/mtime.c
Added a test that checks that H5Gstat() can be called with a
dataset as the first argument.
./src/H5S.c
Added #ifdef HAVE_PARALLEL around code to check for the
HDF5_MPI_OPT_TYPES environment variable because the global
variable that gets set is #ifdef'd.
./bin/release
bzip2 uses .bz2 as the file extension.
627 lines
17 KiB
C
627 lines
17 KiB
C
/*
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* Copyright © 1998 Spizella Software
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* All rights reserved.
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*
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* Programmer: Robb Matzke <robb@arborea.spizella.com>
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* Tuesday, August 25, 1998
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*/
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#include <assert.h>
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#include <hdf5.h>
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#include <signal.h>
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#include <stdlib.h>
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#include <H5private.h> /*for performance monitoring*/
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#define NOTIFY_INTERVAL 2 /*seconds*/
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#define TIME_LIMIT 60 /*seconds*/
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#define CH_SIZE 8192*8 /*approx chunk size in bytes*/
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#define MAX_NELMTS 3000000
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#define C_MTYPE unsigned int /*type in memory */
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#define H_MTYPE H5T_NATIVE_UINT /*type in memory */
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#define H_FTYPE H5T_NATIVE_UINT /*type in file */
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typedef struct {
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double percent;
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size_t lo, hi;
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size_t nhits;
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} quant_t;
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#if 1
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/* Typical VBT sizes */
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static quant_t quant_g[] = {
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{10.00, 1, 5},
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{89.00, 6, 20},
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{ 0.90, 21, 100},
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{ 0.09, 101, 1000},
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{ 0.01, 1001, 10000},
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};
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#elif 0
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/* Sizes for testing */
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static quant_t quant_g[] = {
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{10.0, 1, 5},
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{80.0, 6, 15},
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{10.0, 16, 20},
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};
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#elif 0
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/* Larger I/O */
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static quant_t quant_g[] = {
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{10.0, 1, 1000},
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{80.0, 1001, 5000},
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{10.0, 5001, 10000},
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};
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#else
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/* All same size */
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static quant_t quant_g[] = {
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{100.0, 1000, 1000}
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};
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#endif
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static volatile sig_atomic_t alarm_g = 0;
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static volatile sig_atomic_t timeout_g = 0;
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/*-------------------------------------------------------------------------
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* Function: catch_alarm
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*
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* Purpose: Increments the global `alarm_g' and resets the alarm for
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* another few seconds.
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*
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* Return: void
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*
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* Programmer: Robb Matzke
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* Wednesday, August 26, 1998
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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static void
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catch_alarm(int __unused__ signum)
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{
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static int ncalls=0;
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ncalls++;
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if (0==ncalls % NOTIFY_INTERVAL) {
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alarm_g++;
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}
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if (timeout_g>0) --timeout_g;
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alarm(1);
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}
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/*-------------------------------------------------------------------------
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* Function: display_error_cb
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*
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* Purpose: Displays the error stack after printing "*FAILED*".
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*
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* Return: Success: 0
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*
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* Failure: -1
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*
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* Programmer: Robb Matzke
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* Wednesday, March 4, 1998
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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static herr_t
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display_error_cb (void __unused__ *client_data)
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{
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putchar('\n');
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H5Eprint (stdout);
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return 0;
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}
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/*-------------------------------------------------------------------------
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* Function: rand_nelmts
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*
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* Purpose: Returns a the length of a 1-d array according to the
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* probabilities described above.
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*
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* Return: Success: Number of elements
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*
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* Failure: never fails
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*
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* Programmer: Robb Matzke
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* Thursday, August 20, 1998
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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static size_t
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rand_nelmts(int reset_counters)
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{
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double p = (rand() % 1000000)/1000000.0;
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double total = 0.0;
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size_t size=0, i;
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static size_t ncalls=0;
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if (reset_counters) {
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printf(" %9s %8s %8s\n", "Length", "Requsted", "Actual");
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printf(" --------------- -------- --------\n");
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for (i=0; i<NELMTS(quant_g); i++) {
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printf(" [%6lu,%6lu] %7.3f%% %7.3f%%\n",
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(unsigned long)(quant_g[i].lo),
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(unsigned long)(quant_g[i].hi),
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quant_g[i].percent,
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100.0*(double)(quant_g[i].nhits)/(double)ncalls);
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quant_g[i].nhits = 0;
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}
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printf(" --------------- -------- --------\n");
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ncalls = 0;
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size = 0;
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} else {
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for (i=0; i<NELMTS(quant_g); i++) {
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total += quant_g[i].percent/100.0;
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if (p<total) {
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size = rand()%(1+(quant_g[i].hi-quant_g[i].lo)) +
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quant_g[i].lo;
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quant_g[i].nhits++;
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break;
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}
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}
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assert(i<NELMTS(quant_g));
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ncalls++;
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}
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return size;
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}
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/*-------------------------------------------------------------------------
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* Function: ragged_write_all
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*
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* Purpose: Writes rows to the ragged array RA.
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*
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* Return: Success: 0
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*
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* Failure: -1
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*
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* Programmer: Robb Matzke
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* Thursday, August 27, 1998
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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static int
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ragged_write_all(hid_t ra, hsize_t rows_at_once)
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{
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int *dd, total_nelmts=0;
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hssize_t row; /*current row number */
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hsize_t i; /*counter */
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hsize_t max_width = quant_g[NELMTS(quant_g)-1].hi;
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hsize_t interval_nelmts; /*elmts/interval timer */
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hsize_t *size=NULL; /*size of each row */
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void **buf=NULL; /*buffer for each row */
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H5_timer_t timer, timer_total; /*performance timers */
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char s[64]; /*tempory string buffer */
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char testname[80];
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sprintf(testname, "Testing write all, units of %lu",
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(unsigned long)rows_at_once);
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printf("%s...\n", testname);
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fflush(stdout);
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timeout_g = 60;
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/* Create the ragged array row in memory */
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if (NULL==(dd = malloc(max_width*sizeof(C_MTYPE))) ||
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NULL==(size = malloc(rows_at_once*sizeof(*size))) ||
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NULL==(buf = malloc(rows_at_once*sizeof(*buf)))) {
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puts("Memory allocation failed");
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goto error;
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}
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for (i=0; i<max_width; i++) dd[i] = i+1;
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/*
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* Describe a few rows then add them to the ragged array. Print a status
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* report every once in a while too.
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*/
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printf(" %8s %8s %8s %10s\n",
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"Row", "Nelmts", "Complete", "Bandwidth");
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printf(" -------- -------- -------- ----------\n");
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H5_timer_reset(&timer_total);
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H5_timer_begin(&timer);
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interval_nelmts = 0;
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for (row=0; total_nelmts<MAX_NELMTS && timeout_g>0; row+=i) {
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for (i=0; i<rows_at_once && total_nelmts<MAX_NELMTS; i++) {
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size[i] = rand_nelmts(0);
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total_nelmts += size[i];
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buf[i] = dd;
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interval_nelmts += size[i];
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}
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if (H5Rwrite(ra, row, i, H_MTYPE, size, buf)<0) goto error;
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if (0==row || alarm_g) {
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alarm_g = 0;
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H5_timer_end(&timer_total, &timer);
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H5_bandwidth(s, (double)interval_nelmts*sizeof(C_MTYPE),
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timer.etime);
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printf(" %8lu %8lu %7.3f%% %10s%s\n",
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(unsigned long)(row+i), (unsigned long)total_nelmts,
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100.0*total_nelmts/MAX_NELMTS, s,
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0==timeout_g?" (aborting)":"");
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interval_nelmts = 0;
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H5_timer_begin(&timer);
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}
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}
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/* Conclusions */
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if (timeout_g) { /*a minor race condition, but who really cares?*/
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H5_timer_end(&timer_total, &timer);
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H5_bandwidth(s, (double)interval_nelmts*sizeof(C_MTYPE), timer.etime);
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printf(" %8lu %8lu %7.3f%% %10s\n",
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(unsigned long)row, (unsigned long)total_nelmts,
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100.0*total_nelmts/MAX_NELMTS, s);
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}
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printf(" -------- -------- -------- ----------\n");
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H5_bandwidth(s, (double)total_nelmts*sizeof(C_MTYPE), timer_total.etime);
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printf(" %27s%10s\n", "", s);
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/* Cleanup */
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free(dd);
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free(size);
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free(buf);
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printf("%-70s PASSED\n\n", testname);
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return 0;
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error:
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printf("%-70s*FAILED*\n\n", testname);
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return -1;
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}
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/*-------------------------------------------------------------------------
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* Function: ragged_read_all
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*
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* Purpose: Reads all rows of a ragged array in row order a few rows at a
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* time.
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*
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* Return: Success: 0
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*
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* Failure: -1
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*
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* Programmer: Robb Matzke
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* Thursday, August 27, 1998
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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static int
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ragged_read_all(hid_t ra, hsize_t rows_at_once)
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{
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int total_nelmts=0;
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hsize_t i, j; /*counters */
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hssize_t row; /*current row number */
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hsize_t interval_nelmts; /*elmts/interval timer */
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hsize_t *size=NULL; /*size of each row */
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C_MTYPE **buf=NULL; /*buffer for each row */
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H5_timer_t timer, timer_total; /*performance timers */
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char s[64]; /*tempory string buffer */
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char testname[80];
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sprintf(testname, "Testing read all, units of %lu",
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(unsigned long)rows_at_once);
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printf("%s...\n", testname);
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fflush(stdout);
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timeout_g = 60;
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/* Create the ragged array row in memory */
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if (NULL==(size = malloc(rows_at_once*sizeof(*size))) ||
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NULL==(buf = malloc(rows_at_once*sizeof(*buf)))) {
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puts("Memory allocation failed");
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goto error;
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}
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/*
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* Read a few rows at a time from the ragged array. Print a status report
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* every once in a while too.
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*/
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printf(" %8s %8s %8s %10s\n",
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"Row", "Nelmts", "Complete", "Bandwidth");
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printf(" -------- -------- -------- ----------\n");
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H5_timer_reset(&timer_total);
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H5_timer_begin(&timer);
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interval_nelmts = 0;
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for (row=0; total_nelmts<MAX_NELMTS && timeout_g>0; row+=i) {
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/* Clear data then read */
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HDmemset(size, 0, rows_at_once*sizeof(*size));
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HDmemset(buf, 0, rows_at_once*sizeof(*buf));
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if (H5Rread(ra, row, rows_at_once, H_MTYPE, size,
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(void**)buf)<0) {
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goto error;
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}
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/* Check values read */
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for (i=0; i<rows_at_once && size[i]; i++) {
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interval_nelmts += size[i];
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total_nelmts += size[i];
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for (j=0; j<size[i]; j++) {
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if (buf[i][j]!=j+1) {
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printf("Wrong value(s) read for row %ld.\n",
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(long)(row+i));
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for (j=0; j<size[i]; j++) {
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printf("%s%d", j?",":"", buf[i][j]);
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}
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putchar('\n');
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goto error;
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}
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}
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free(buf[i]);
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buf[i] = NULL;
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}
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/* Print statistics? */
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if (0==row || alarm_g) {
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alarm_g = 0;
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H5_timer_end(&timer_total, &timer);
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H5_bandwidth(s, (double)interval_nelmts*sizeof(C_MTYPE),
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timer.etime);
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printf(" %8lu %8lu %7.3f%% %10s%s\n",
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(unsigned long)(row+i), (unsigned long)total_nelmts,
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100.0*total_nelmts/MAX_NELMTS, s,
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0==timeout_g?" (aborting)":"");
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interval_nelmts = 0;
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H5_timer_begin(&timer);
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}
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if (0==size[rows_at_once-1]) {
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/* Reached the end of the array */
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assert(total_nelmts>=MAX_NELMTS);
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row += i;
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break;
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}
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}
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/* Conclusions */
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if (timeout_g) { /*a minor race condition, but who really cares?*/
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H5_timer_end(&timer_total, &timer);
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H5_bandwidth(s, (double)interval_nelmts*sizeof(C_MTYPE), timer.etime);
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printf(" %8lu %8lu %7.3f%% %10s\n",
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(unsigned long)row, (unsigned long)total_nelmts,
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100.0*total_nelmts/MAX_NELMTS, s);
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}
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printf(" -------- -------- -------- ----------\n");
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H5_bandwidth(s, (double)total_nelmts*sizeof(C_MTYPE), timer_total.etime);
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printf(" %27s%10s\n", "", s);
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/* Cleanup */
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free(size);
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free(buf);
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printf("%-70s PASSED\n\n", testname);
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return 0;
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error:
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printf("%-70s*FAILED*\n\n", testname);
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return -1;
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}
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/*-------------------------------------------------------------------------
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* Function: ragged_read_short
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*
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* Purpose: Reads all the data but only the part that is in the `raw'
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* dataset. We should see a nice speed increase because we
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* don't have to perform the little reads into the overflow
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* array.
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*
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* Return: Success: 0
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*
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* Failure: -1
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*
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* Programmer: Robb Matzke
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* Friday, August 28, 1998
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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static int
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ragged_read_short(hid_t ra, hsize_t rows_at_once, hsize_t width)
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{
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int total_nelmts=0;
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hsize_t i, j;
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hssize_t row; /*current row number */
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hsize_t interval_nelmts; /*elmts/interval timer */
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hsize_t *size=NULL; /*size of each row */
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C_MTYPE **buf=NULL; /*buffer for each row */
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H5_timer_t timer, timer_total; /*performance timers */
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char s[64]; /*tempory string buffer */
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char testname[80];
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sprintf(testname, "Testing read short, units of %lu",
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(unsigned long)rows_at_once);
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printf("%s...\n", testname);
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fflush(stdout);
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timeout_g = 60;
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/* Create the ragged array row in memory */
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if (NULL==(size = malloc(rows_at_once*sizeof(*size))) ||
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NULL==(buf = malloc(rows_at_once*sizeof(*buf)))) {
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puts("Memory allocation failed");
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goto error;
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}
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for (i=0; i<rows_at_once; i++) {
|
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if (NULL==(buf[i] = malloc(width*sizeof(C_MTYPE)))) {
|
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puts("Memory allocation failed");
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goto error;
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}
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}
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/*
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* Read a few rows at a time from the ragged array. Print a status report
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* every once in a while too.
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*/
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printf(" %8s %8s %8s %10s\n",
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"Row", "Nelmts", "Complete", "Bandwidth");
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printf(" -------- -------- -------- ----------\n");
|
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H5_timer_reset(&timer_total);
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H5_timer_begin(&timer);
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interval_nelmts = 0;
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for (row=0; total_nelmts<MAX_NELMTS && timeout_g>0; row+=i) {
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/* Read data */
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for (i=0; i<rows_at_once; i++) size[i] = width;
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if (H5Rread(ra, row, rows_at_once, H_MTYPE, size,
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(void**)buf)<0) {
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goto error;
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}
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/* Check values read */
|
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for (i=0; i<rows_at_once && size[i]; i++) {
|
||
|
||
/*
|
||
* Number of useful elements actually read in this timing
|
||
* interval. This is used to calculate bandwidth.
|
||
*/
|
||
interval_nelmts += MIN(width, size[i]);
|
||
|
||
/*
|
||
* Total number of elements for all the rows read so far. This
|
||
* is used to calculate the percent done.
|
||
*/
|
||
total_nelmts += size[i];
|
||
|
||
/* Check the values */
|
||
for (j=0; j<MIN(width, size[i]); j++) {
|
||
if (buf[i][j]!=j+1) {
|
||
printf("Wrong value(s) read for row %ld.\n",
|
||
(long)(row+i));
|
||
for (j=0; j<MIN(width, size[i]); j++) {
|
||
printf("%s%d", j?",":"", buf[i][j]);
|
||
}
|
||
putchar('\n');
|
||
goto error;
|
||
}
|
||
}
|
||
}
|
||
|
||
/* Print statistics? */
|
||
if (0==row || alarm_g) {
|
||
alarm_g = 0;
|
||
H5_timer_end(&timer_total, &timer);
|
||
H5_bandwidth(s, (double)interval_nelmts*sizeof(C_MTYPE),
|
||
timer.etime);
|
||
printf(" %8lu %8lu %7.3f%% %10s%s\n",
|
||
(unsigned long)(row+i), (unsigned long)total_nelmts,
|
||
100.0*total_nelmts/MAX_NELMTS, s,
|
||
0==timeout_g?" (aborting)":"");
|
||
interval_nelmts = 0;
|
||
H5_timer_begin(&timer);
|
||
}
|
||
if (0==size[rows_at_once-1]) {
|
||
/* Reached the end of the array */
|
||
assert(total_nelmts>=MAX_NELMTS);
|
||
row += i;
|
||
break;
|
||
}
|
||
}
|
||
|
||
/* Conclusions */
|
||
if (timeout_g) { /*a minor race condition, but who really cares?*/
|
||
H5_timer_end(&timer_total, &timer);
|
||
H5_bandwidth(s, (double)interval_nelmts*sizeof(C_MTYPE), timer.etime);
|
||
printf(" %8lu %8lu %7.3f%% %10s\n",
|
||
(unsigned long)row, (unsigned long)total_nelmts,
|
||
100.0*total_nelmts/MAX_NELMTS, s);
|
||
}
|
||
printf(" -------- -------- -------- ----------\n");
|
||
H5_bandwidth(s, (double)total_nelmts*sizeof(C_MTYPE), timer_total.etime);
|
||
printf(" %27s%10s\n", "", s);
|
||
|
||
/* Cleanup */
|
||
for (i=0; i<rows_at_once; i++) free(buf[i]);
|
||
free(size);
|
||
free(buf);
|
||
printf("%-70s PASSED\n\n", testname);
|
||
return 0;
|
||
|
||
error:
|
||
printf("%-70s*FAILED*\n\n", testname);
|
||
return -1;
|
||
}
|
||
|
||
|
||
/*-------------------------------------------------------------------------
|
||
* Function: main
|
||
*
|
||
* Purpose:
|
||
*
|
||
* Return: Success:
|
||
*
|
||
* Failure:
|
||
*
|
||
* Programmer: Robb Matzke
|
||
* Friday, August 21, 1998
|
||
*
|
||
* Modifications:
|
||
*
|
||
*-------------------------------------------------------------------------
|
||
*/
|
||
int
|
||
main(int argc, char *argv[])
|
||
{
|
||
hid_t file, dcpl, ra;
|
||
hsize_t ch_size[2]; /*chunk size */
|
||
struct sigaction act; /*alarm signal handler */
|
||
hsize_t rows_at_once=100; /*row aggregation */
|
||
int argno=1;
|
||
|
||
/* Parse command line options */
|
||
if (argno<argc) {
|
||
rows_at_once = strtol(argv[argno++], NULL, 0);
|
||
}
|
||
|
||
/* Display HDF5 API errors in a special way */
|
||
H5Eset_auto(display_error_cb, NULL);
|
||
|
||
/* Get a SIGALRM every few seconds */
|
||
act.sa_handler = catch_alarm;
|
||
sigemptyset(&(act.sa_mask));
|
||
act.sa_flags = 0;
|
||
sigaction(SIGALRM, &act, NULL);
|
||
alarm(1);
|
||
|
||
/* Create the file and ragged array */
|
||
if ((file=H5Fcreate("ragged.h5", H5F_ACC_TRUNC, H5P_DEFAULT,
|
||
H5P_DEFAULT))<0) goto error;
|
||
if ((dcpl=H5Pcreate(H5P_DATASET_CREATE))<0) goto error;
|
||
ch_size[1] = 20;
|
||
ch_size[0] = MAX(1, CH_SIZE/(ch_size[1]*sizeof(C_MTYPE))); /*length*/
|
||
printf("Chunk size is %lu by %lu\n",
|
||
(unsigned long)(ch_size[0]), (unsigned long)(ch_size[1]));
|
||
if (H5Pset_chunk(dcpl, 2, ch_size)<0) goto error;
|
||
if ((ra=H5Rcreate(file, "ra", H_FTYPE, dcpl))<0) goto error;
|
||
if (H5Pclose(dcpl)<0) goto error;
|
||
|
||
/* The tests */
|
||
if (ragged_write_all(ra, rows_at_once)<0) goto error;
|
||
if (ragged_read_all(ra, rows_at_once)<0) goto error;
|
||
if (ragged_read_short(ra, rows_at_once, ch_size[1])<0) goto error;
|
||
|
||
/* The tests again */
|
||
if (ragged_write_all(ra, rows_at_once)<0) goto error;
|
||
if (ragged_read_all(ra, rows_at_once)<0) goto error;
|
||
if (ragged_read_short(ra, rows_at_once, ch_size[1])<0) goto error;
|
||
|
||
/* Conclusions */
|
||
printf("\n\nDistribution of row lengths:\n");
|
||
rand_nelmts(1);
|
||
|
||
/* Cleanup */
|
||
if (H5Rclose(ra)<0) goto error;
|
||
if (H5Fclose(file)<0) goto error;
|
||
|
||
puts("All ragged array tests passed.");
|
||
return 0;
|
||
|
||
error:
|
||
puts("*** RAGGED ARRAY TEST(S) FAILED ***");
|
||
return -1;
|
||
}
|