test/H5BlockDissolveGhosts.c

- added

.gitattributes

@@ -95,6 +95,7 @@ src/TestUnderscoreC.c -text
 src/addToDoxygenMainPage.h -text
 test/Bench.c -text
 test/BlockTestSpecs.txt -text
+test/H5BlockDissolveGhosts.c -text
 test/H5BlockParTestScalarField.c -text
 test/H5BlockParTestScalarField.pbs -text
 test/H5BlockParallelTest1.c -text

test/H5BlockDissolveGhosts.c

@@ -0,0 +1,612 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <hdf5.h>
+#include "H5Part.h"
+#include "H5Block.h"
+#include "H5BlockTypes.h"
+
+static int _debug = 4;
+
+void
+_H5Part_vprint_error (
+	const char *fmt,
+	va_list ap
+	) {
+
+	if ( _debug < 1 ) return;
+	vfprintf ( stderr, fmt, ap );
+	fprintf ( stderr, "\n" );
+}
+
+void
+_H5Part_print_error (
+	const char *fmt,
+	...
+	) {
+
+	va_list ap;
+	va_start ( ap, fmt );
+	_H5Part_vprint_error ( fmt, ap );
+	va_end ( ap );
+}
+
+void
+_H5Part_vprint_warn (
+	const char *fmt,
+	va_list ap
+	) {
+
+	if ( _debug < 2 ) return;
+	vfprintf ( stderr, fmt, ap );
+	fprintf ( stderr, "\n" );
+}
+
+void
+_H5Part_print_warn (
+	const char *fmt,
+	...
+	) {
+
+	va_list ap;
+	va_start ( ap, fmt );
+	_H5Part_vprint_warn ( fmt, ap );
+	va_end ( ap );
+}
+
+void
+_H5Part_vprint_info (
+	const char *fmt,
+	va_list ap
+	) {
+
+	if ( _debug < 3 ) return;
+	vfprintf ( stdout, fmt, ap );
+	fprintf ( stdout, "\n" );
+}
+
+void
+_H5Part_print_info (
+	const char *fmt,
+	...
+	) {
+
+	va_list ap;
+	va_start ( ap, fmt );
+	_H5Part_vprint_info ( fmt, ap );
+	va_end ( ap );
+}
+
+void
+_H5Part_vprint_debug (
+	const char *fmt,
+	va_list ap
+	) {
+
+	if ( _debug < 4 ) return;
+	vfprintf ( stdout, fmt, ap );
+	fprintf ( stdout, "\n" );
+}
+
+void
+_H5Part_print_debug (
+	const char *fmt,
+	...
+	) {
+
+	va_list ap;
+	va_start ( ap, fmt );
+	_H5Part_vprint_debug ( fmt, ap );
+	va_end ( ap );
+}
+
+
+struct H5BlockPartition Layout1[1] = {
+	{ 0, 63, 0, 63, 0, 511 }
+};
+
+struct H5BlockPartition Layout8[8] = {
+		{  0,63,  0,63,   0, 63},
+		{  0,63,  0,63,  64,127},
+		{  0,63,  0,63, 128,191},
+		{  0,63,  0,63, 192,255},
+		{  0,63,  0,63, 256,319},
+		{  0,63,  0,63, 320,383},
+		{  0,63,  0,63, 384,447},
+		{  0,63,  0,63, 448,511}
+};
+
+struct H5BlockPartition Layout8G[8] = {
+		{  0,63,  0,63,   0, 64},
+		{  0,63,  0,63,  63,128},
+		{  0,63,  0,63, 127,192},
+		{  0,63,  0,63, 191,256},
+		{  0,63,  0,63, 255,320},
+		{  0,63,  0,63, 319,384},
+		{  0,63,  0,63, 383,448},
+		{  0,63,  0,63, 447,511}
+};
+
+struct H5BlockPartition Layout16[16] = {
+		{  0,63,  0,31,   0, 63},
+		{  0,63, 32,63,   0, 63},
+		{  0,63,  0,31,  64,127},
+		{  0,63, 32,63,  64,127},
+		{  0,63,  0,31, 128,191},
+		{  0,63, 32,63, 128,191},
+		{  0,63,  0,31, 192,255},
+		{  0,63, 32,63, 192,255},
+		{  0,63,  0,31, 256,319},
+		{  0,63, 32,63, 256,319},
+		{  0,63,  0,31, 320,383},
+		{  0,63, 32,63, 320,383},
+		{  0,63,  0,31, 384,447},
+		{  0,63, 32,63, 384,447},
+		{  0,63,  0,31, 448,511},
+		{  0,63, 32,63, 448,511}
+};
+
+struct H5BlockPartition Layout16G[16] = {
+		{  0,63,  0,32,   0, 64},
+		{  0,63, 31,63,   0, 64},
+		{  0,63,  0,32,  63,128},
+		{  0,63, 31,63,  63,128},
+		{  0,63,  0,32, 127,192},
+		{  0,63, 31,63, 127,192},
+		{  0,63,  0,32, 191,256},
+		{  0,63, 31,63, 191,256},
+		{  0,63,  0,32, 255,320},
+		{  0,63, 31,63, 255,320},
+		{  0,63,  0,32, 319,384},
+		{  0,63, 31,63, 319,384},
+		{  0,63,  0,32, 383,448},
+		{  0,63, 31,63, 383,448},
+		{  0,63,  0,32, 447,511},
+		{  0,63, 31,63, 447,511}
+};
+
+
+struct H5BlockPartition Layout32[32] = {
+		{  0,31,  0,31,   0, 63},
+		{  0,31, 32,63,   0, 63},
+		{ 32,63,  0,31,   0, 63},
+		{ 32,63, 32,63,   0, 63},
+		{  0,31,  0,31,  64,127},
+		{  0,31, 32,63,  64,127},
+		{ 32,63,  0,31,  64,127},
+		{ 32,63, 32,63,  64,127},
+		{  0,31,  0,31, 128,191},
+		{  0,31, 32,63, 128,191},
+		{ 32,63,  0,31, 128,191},
+		{ 32,63, 32,63, 128,191},
+		{  0,31,  0,31, 192,255},
+		{  0,31, 32,63, 192,255},
+		{ 32,63,  0,31, 192,255},
+		{ 32,63, 32,63, 192,255},
+		{  0,31,  0,31, 256,319},
+		{  0,31, 32,63, 256,319},
+		{ 32,63,  0,31, 256,319},
+		{ 32,63, 32,63, 256,319},
+		{  0,31,  0,31, 320,383},
+		{  0,31, 32,63, 320,383},
+		{ 32,63,  0,31, 320,383},
+		{ 32,63, 32,63, 320,383},
+		{  0,31,  0,31, 384,447},
+		{  0,31, 32,63, 384,447},
+		{ 32,63,  0,31, 384,447},
+		{ 32,63, 32,63, 384,447},
+		{  0,31,  0,31, 448,511},
+		{  0,31, 32,63, 448,511},
+		{ 32,63,  0,31, 448,511},
+		{ 32,63, 32,63, 448,511}
+};
+
+struct H5BlockPartition Layout32G[32] = {
+		{  0,32,  0,32,   0, 64},
+		{  0,32, 31,63,   0, 64},
+		{ 31,63,  0,32,   0, 64},
+		{ 31,63, 31,63,   0, 64},
+		{  0,32,  0,32,  63,128},
+		{  0,32, 31,63,  63,128},
+		{ 31,63,  0,32,  63,128},
+		{ 31,63, 31,63,  63,128},
+		{  0,32,  0,32, 127,192},
+		{  0,32, 31,63, 127,192},
+		{ 31,63,  0,32, 127,192},
+		{ 31,63, 31,63, 127,192},
+		{  0,32,  0,32, 191,256},
+		{  0,32, 31,63, 191,256},
+		{ 31,63,  0,32, 191,256},
+		{ 31,63, 31,63, 191,256},
+		{  0,32,  0,32, 255,320},
+		{  0,32, 31,63, 255,320},
+		{ 31,63,  0,32, 255,320},
+		{ 31,63, 31,63, 255,320},
+		{  0,32,  0,32, 319,384},
+		{  0,32, 31,63, 319,384},
+		{ 31,63,  0,32, 319,384},
+		{ 31,63, 31,63, 319,384},
+		{  0,31,  0,31, 383,448},
+		{  0,31, 31,63, 383,448},
+		{ 31,63,  0,31, 383,448},
+		{ 31,63, 31,63, 383,448},
+		{  0,32,  0,32, 447,511},
+		{  0,32, 31,63, 447,511},
+		{ 31,63,  0,32, 447,511},
+		{ 31,63, 31,63, 447,511}
+};
+
+
+
+#define _NO_GHOSTZONE(p,q) ( (p->i_end < q->i_start) \
+  		        ||   (p->j_end < q->j_start) \
+		        ||   (p->k_end < q->k_start) )
+
+/*
+#define _HAVE_GHOSTZONE(p,q) ( (p->i_end >= q->i_start) \
+  		          &&   (p->j_end >= q->j_start) \
+		          &&   (p->k_end >= q->k_start) \
+			  &&   (q->i_end >= p->i_start) \
+  		          &&   (q->j_end >= p->j_start) \
+		          &&   (q->k_end >= p->k_start) )
+*/
+
+static int
+_have_ghostzone (
+	const struct H5BlockPartition *p,
+	const struct H5BlockPartition *q
+	) {
+	return ( ! ( _NO_GHOSTZONE ( p, q ) || _NO_GHOSTZONE ( q, p ) ) );
+}
+
+static h5part_int64_t
+_volume_of_partition (
+	const struct H5BlockPartition *p
+	) {
+	return (p->i_end - p->i_start)
+		* (p->j_end - p->j_start)
+		* (p->k_end - p->k_start);
+}
+
+#define MIN( x, y ) ( (x) <= (y) ? (x) : (y) )  
+#define MAX( x, y ) ( (x) >= (y) ? (x) : (y) )  
+
+static h5part_int64_t
+_volume_of_ghostzone (
+	const struct H5BlockPartition *p,
+	const struct H5BlockPartition *q
+	) {
+
+	h5part_int64_t dx = MIN ( p->i_end, q->i_end )
+		- MAX ( p->i_start, q->i_start ) + 1;
+	h5part_int64_t dy = MIN ( p->j_end, q->j_end )
+		- MAX ( p->j_start, q->j_start ) + 1;
+	h5part_int64_t dz = MIN ( p->k_end, q->k_end )
+		- MAX ( p->k_start, q->k_start ) + 1;
+
+	return dx * dy * dz;
+}
+
+static h5part_int64_t
+_dissolve_X_ghostzone (
+	struct H5BlockPartition *p,
+	struct H5BlockPartition *q
+	) {
+
+	if ( p->i_start > q->i_start )
+		return _dissolve_X_ghostzone( q, p );
+
+	if ( q->i_end <= p->i_end )  /* no dissolving		*/
+		return -1;
+
+	p->i_end = ( p->i_end + q->i_start ) >> 1;
+	q->i_start = p->i_end + 1;
+	return 0;
+}
+
+static h5part_int64_t
+_dissolve_Y_ghostzone (
+	struct H5BlockPartition *p,
+	struct H5BlockPartition *q
+	) {
+
+	if ( p->j_start > q->j_start )
+		return _dissolve_Y_ghostzone( q, p );
+
+	if ( q->j_end <= p->j_end )    /* no dissolving		*/
+		return -1;
+
+	p->j_end = ( p->j_end + q->j_start ) >> 1;
+	q->j_start = p->j_end + 1;
+	return 0;
+}
+
+static h5part_int64_t
+_dissolve_Z_ghostzone (
+	struct H5BlockPartition *p,
+	struct H5BlockPartition *q
+	) {
+
+	if ( p->k_start > q->k_start )
+		return _dissolve_Z_ghostzone( q, p );
+
+	if ( q->k_end <= p->k_end )    /* no dissolving		*/
+		return -1;
+
+	p->k_end = ( p->k_end + q->k_start ) >> 1;
+	q->k_start = p->k_end + 1;
+	return 0;
+}
+
+#if 0
+static h5part_int64_t
+_dissolve_ghostzone_max_volume_of_dissolved_partitions (
+	struct H5BlockPartition *p,
+	struct H5BlockPartition *q
+	) {
+
+	struct H5BlockPartition p_;
+	struct H5BlockPartition q_;
+	struct H5BlockPartition p_best;
+	struct H5BlockPartition q_best;
+	h5part_int64_t vol;
+	h5part_int64_t max_vol = 0;
+
+	p_ = *p;
+	q_ = *q;
+	if ( _dissolve_X_ghostzone ( &p_, &q_ ) == 0 ) {
+		vol = _volume_of_partition ( &p_ ) + _volume_of_partition ( &q_ );
+		if ( vol > max_vol ) {
+			max_vol = vol;
+			p_best = p_;
+			q_best = q_;
+		}
+	}
+
+	p_ = *p;
+	q_ = *q;
+	if ( _dissolve_Y_ghostzone ( &p_, &q_ ) == 0 ) {
+		vol = _volume_of_partition ( &p_ ) + _volume_of_partition ( &q_ );
+		if ( vol > max_vol ) {
+			max_vol = vol;
+			p_best = p_;
+			q_best = q_;
+		}
+	}
+	p_ = *p;
+	q_ = *q;
+
+	if ( _dissolve_Z_ghostzone ( &p_, &q_ ) == 0 ) {
+		vol = _volume_of_partition ( &p_ ) + _volume_of_partition ( &q_ );
+		if ( vol > max_vol ) {
+			max_vol = vol;
+			p_best = p_;
+			q_best = q_;
+		}
+	}
+	if ( max_vol <= 0 ) {
+		return H5PART_ERR_LAYOUT;
+	}
+	*p = p_best;
+	*q = q_best;
+
+	return H5PART_SUCCESS;
+}
+
+
+static h5part_int64_t
+_dissolve_ghostzones_max_volume_of_dissolved_partitions (
+	H5PartFile *f
+	) {
+
+	h5part_int64_t herr;
+	struct H5BlockStruct *b = f->block;
+	struct H5BlockPartition *part1;
+	struct H5BlockPartition *part2;
+	int proc1, proc2;
+
+	memcpy ( b->write_layout, b->user_layout,
+		 f->nprocs * sizeof (*f->block->user_layout) );
+
+	for ( proc1 = 0, part1 = b->write_layout;
+	      proc1 < f->nprocs-1;
+	      proc1++, part1++ ) {
+		for ( proc2 = proc1+1, part2 = &b->write_layout[proc2];
+		      proc2 < f->nprocs;
+		      proc2++, part2++ ) {
+
+			if ( ! _have_ghostzone ( part1, part2 ) )
+				continue;
+
+			herr = _dissolve_ghostzone_max_volume_of_dissolved_partitions (
+				part1, part2 );
+			if ( herr < 0 ) return herr;
+		}
+	}
+	_H5Part_print_debug ("Layout after dissolving ghost-zones:");
+	for ( proc1 = 0, part1 = b->write_layout;
+	      proc1 < f->nprocs;
+	      proc1++, part1++ ) {
+		_H5Part_print_debug (
+			"PROC[%d]: proc[%d]: %lld:%lld, %lld:%lld, %lld:%lld  ",
+			f->myproc, proc1,
+			(long long)part1->i_start,
+			(long long)part1->i_end,
+			(long long)part1->j_start,
+			(long long)part1->j_end,
+			(long long)part1->k_start,
+			(long long)part1->k_end );
+	}
+	return H5PART_SUCCESS;
+}
+#endif
+
+static h5part_int64_t
+_dissolve_ghostzone (
+	struct H5BlockPartition *p,
+	struct H5BlockPartition *q
+	) {
+
+	struct H5BlockPartition p_;
+	struct H5BlockPartition q_;
+	struct H5BlockPartition p_best;
+	struct H5BlockPartition q_best;
+	h5part_int64_t vol;
+	h5part_int64_t max_vol = 0;
+
+	p_ = *p;
+	q_ = *q;
+	if ( _dissolve_X_ghostzone ( &p_, &q_ ) == 0 ) {
+		vol = _volume_of_partition ( &p_ ) + _volume_of_partition ( &q_ );
+		if ( vol > max_vol ) {
+			max_vol = vol;
+			p_best = p_;
+			q_best = q_;
+		}
+	}
+
+	p_ = *p;
+	q_ = *q;
+	if ( _dissolve_Y_ghostzone ( &p_, &q_ ) == 0 ) {
+		vol = _volume_of_partition ( &p_ ) + _volume_of_partition ( &q_ );
+		if ( vol > max_vol ) {
+			max_vol = vol;
+			p_best = p_;
+			q_best = q_;
+		}
+	}
+	p_ = *p;
+	q_ = *q;
+
+	if ( _dissolve_Z_ghostzone ( &p_, &q_ ) == 0 ) {
+		vol = _volume_of_partition ( &p_ ) + _volume_of_partition ( &q_ );
+		if ( vol > max_vol ) {
+			max_vol = vol;
+			p_best = p_;
+			q_best = q_;
+		}
+	}
+	if ( max_vol <= 0 ) {
+		return H5PART_ERR_LAYOUT;
+	}
+	*p = p_best;
+	*q = q_best;
+
+	return H5PART_SUCCESS;
+}
+
+static h5part_int64_t
+_dissolve_ghostzones (
+	H5PartFile *f
+	) {
+
+	struct H5BlockStruct *b = f->block;
+	struct H5BlockPartition *p, *max_p;
+	struct H5BlockPartition *q, *max_q;
+	int proc_p, proc_q;
+	h5part_int64_t vol, max_vol;
+	int max_proc_p, max_proc_q;
+
+	memcpy ( b->write_layout, b->user_layout,
+		 f->nprocs * sizeof (*f->block->user_layout) );
+
+	while ( 1 ) {
+		max_vol = 0;
+		for ( proc_p = 0, p = b->write_layout;
+		      proc_p < f->nprocs-1;
+		      proc_p++, p++ ) {
+			for ( proc_q = proc_p+1, q = &b->write_layout[proc_q];
+			      proc_q < f->nprocs;
+			      proc_q++, q++ ) {
+
+				if ( ! _have_ghostzone ( p, q ) )
+					continue;
+				vol = _volume_of_ghostzone ( p, q );
+				if ( vol > max_vol ) {
+					max_vol = vol;
+					max_proc_p = proc_p;
+					max_proc_q = proc_q;
+					max_p = p;
+					max_q = q;
+				}
+			}
+		}
+		if ( max_vol == 0 )
+			break;
+
+		_dissolve_ghostzone ( max_p, max_q );
+	}
+
+	_H5Part_print_debug ("Layout after dissolving ghost-zones:");
+	for ( proc_p = 0, p = b->write_layout;
+	      proc_p < f->nprocs;
+	      proc_p++, p++ ) {
+		_H5Part_print_debug (
+			"PROC[%d]: proc[%d]: %lld:%lld, %lld:%lld, %lld:%lld  ",
+			f->myproc, proc_p,
+			(long long)p->i_start,
+			(long long)p->i_end,
+			(long long)p->j_start,
+			(long long)p->j_end,
+			(long long)p->k_start,
+			(long long)p->k_end );
+	}
+	return H5PART_SUCCESS;
+}
+
+static H5PartFile*
+_init (
+	void
+	) {
+
+	H5PartFile *f;
+	struct H5BlockStruct *b; 
+
+
+	f = (H5PartFile*) malloc( sizeof (H5PartFile) );
+	if( f == NULL ) {
+		return NULL;
+	}
+	memset (f, 0, sizeof (H5PartFile));
+	f->nprocs = 32;
+
+	f->block = malloc( sizeof (*f->block) );
+	if ( f->block == NULL ) {
+		return NULL;
+	}
+	b = f->block;
+	memset ( b, 0, sizeof (*b) );
+	b->user_layout = malloc ( f->nprocs * sizeof (b->user_layout[0]) );
+	if ( b->user_layout == NULL ) {
+		return NULL;
+	}
+	b->write_layout = malloc ( f->nprocs * sizeof (b->write_layout[0]) );
+	if ( b->write_layout == NULL ) {
+		return NULL;
+	}
+	b->timestep = -1;
+	b->blockgroup = -1;
+	b->shape = -1;
+	b->diskshape = -1;
+	b->memshape = -1;
+	b->field_group_id = -1;
+
+	return f;
+}
+
+
+
+int
+main (
+	int argc,
+	char *argv[]
+	) {
+
+	H5PartFile *f = _init ();
+
+	memcpy ( f->block->user_layout, Layout32G,
+		 f->nprocs * sizeof (*f->block->user_layout) );
+
+	_dissolve_ghostzones ( f );
+
+	return 0;
+}