fixed errors found by regression tests:

the H5Fed file data structure can't be created by >1 MPI task, so it is disabled in parallel mode (for now)
the H5Block3dSetHalo function was inverting the halo radii
the h5b_test wasn't writing the correct data in the halo case

src/C/H5Block.c

@@ -116,12 +116,12 @@ H5Block3dSetView (
 h5_err_t
 H5Block3dGetView (
 	h5_file_t *const f,	/*!< IN: File handle */
-	h5_size_t *i_start,	/*!< OUT: start index of \c i	*/ 
-	h5_size_t *i_end,	/*!< OUT: end index of \c i	*/  
-	h5_size_t *j_start,	/*!< OUT: start index of \c j	*/ 
-	h5_size_t *j_end,	/*!< OUT: end index of \c j	*/ 
-	h5_size_t *k_start,	/*!< OUT: start index of \c k	*/ 
-	h5_size_t *k_end	/*!< OUT: end index of \c k	*/ 
+	h5_int64_t *i_start,	/*!< OUT: start index of \c i	*/ 
+	h5_int64_t *i_end,	/*!< OUT: end index of \c i	*/  
+	h5_int64_t *j_start,	/*!< OUT: start index of \c j	*/ 
+	h5_int64_t *j_end,	/*!< OUT: end index of \c j	*/ 
+	h5_int64_t *k_start,	/*!< OUT: start index of \c k	*/ 
+	h5_int64_t *k_end	/*!< OUT: end index of \c k	*/ 
 	) {
 
 	SET_FNAME( f, __func__ );
@@ -139,12 +139,12 @@ H5Block3dGetView (
 h5_err_t
 H5Block3dGetReducedView (
 	h5_file_t *const f,	/*!< IN: File handle */
-	h5_size_t *i_start,	/*!< OUT: start index of \c i */ 
-	h5_size_t *i_end,	/*!< OUT: end index of \c i */  
-	h5_size_t *j_start,	/*!< OUT: start index of \c j */ 
-	h5_size_t *j_end,	/*!< OUT: end index of \c j */ 
-	h5_size_t *k_start,	/*!< OUT: start index of \c j */ 
-	h5_size_t *k_end	/*!< OUT: end index of \c j */ 
+	h5_int64_t *i_start,	/*!< OUT: start index of \c i */ 
+	h5_int64_t *i_end,	/*!< OUT: end index of \c i */  
+	h5_int64_t *j_start,	/*!< OUT: start index of \c j */ 
+	h5_int64_t *j_end,	/*!< OUT: end index of \c j */ 
+	h5_int64_t *k_start,	/*!< OUT: start index of \c j */ 
+	h5_int64_t *k_end	/*!< OUT: end index of \c j */ 
 	) {
 
 	SET_FNAME( f, __func__ );
@@ -184,12 +184,14 @@ h5_err_t
 H5Block3dGetChunk (
 	h5_file_t *const f,		/*!< IN: File handle */
 	const char *field_name, 	/*!< IN: name of dataset */
-	h5_size_t *dims			/*!< OUT: array containing the chunk dimensions */
+	h5_int64_t *i,			/*!< OUT: size of \c i */ 
+	h5_int64_t *j,			/*!< OUT: size of \c j */  
+	h5_int64_t *k			/*!< OUT: size of \c k */ 
 	) {
 
 	SET_FNAME( f, __func__ );
 
-	return h5b_3d_get_chunk(f, field_name, dims);
+	return h5b_3d_get_chunk(f, field_name, i, j, k);
 }
 
 /*!

src/C/Makefile.am

@@ -43,5 +43,5 @@ libH5hutC_a_SOURCES =				\
 	H5Fed_store.c				\
 	H5Fed_tags.c
 
-clean: cleam-am
+clean: clean-am
 

src/Fortran/H5Block_F.c

@@ -96,20 +96,12 @@ h5bl_3d_getview (
 
 	h5_file_t *filehandle = (h5_file_t*)(size_t)*f;
 	h5_set_funcname( filehandle, __func__ );
-        h5_size_t view[6];
 
 	h5_err_t herr = h5b_3d_get_view (
 		filehandle,
-                view+0, view+1, view+2, view+3, view+4, view+5 );
+		i_start, i_end, j_start, j_end, k_start, k_end );
 	if ( herr < 0 ) return herr;
 
-	*i_start = view[0]+1;
-	*i_end   = view[1]+1;
-	*j_start = view[2]+1;
-	*j_end   = view[3]+1;
-	*k_start = view[4]+1;
-	*k_end   = view[5]+1;
-
 	return H5_SUCCESS;
 }
 
@@ -126,20 +118,12 @@ h5bl_3d_getreducedview (
 
 	h5_file_t *filehandle = (h5_file_t*)(size_t)*f;
 	h5_set_funcname( filehandle, __func__ );
-        h5_size_t view[6];
 
 	h5_err_t herr = h5b_3d_get_reduced_view (
 		filehandle,
-                view+0, view+1, view+2, view+3, view+4, view+5 );
+		i_start, i_end, j_start, j_end, k_start, k_end );
 	if ( herr < 0 ) return herr;
 
-	*i_start = view[0]+1;
-	*i_end   = view[1]+1;
-	*j_start = view[2]+1;
-	*j_end   = view[3]+1;
-	*k_start = view[4]+1;
-	*k_end   = view[5]+1;
-
 	return H5_SUCCESS;
 }
 

src/Fortran/H5_F.c

@@ -168,7 +168,7 @@ h5pt_opena_par_align (
        
 	h5_int32_t fbits = H5_O_APPEND | _flagsfor2c ( flags2 );
 
-	h5_file_t* f = H5OpenFile( file_name2, ccomm, fbits, __func__ );
+	h5_file_t* f = h5_open_file( file_name2, ccomm, fbits, __func__ );
 
 	free ( file_name2 );
 	free ( flags2 );

src/h5core/h5_openclose.c

@@ -24,7 +24,11 @@ h5_check_filehandle (
 	h5_file_t* const f	/*!< filehandle  to check validity of */
 	) {
 
-	if (f == NULL || f->file < 0 || f->u == NULL || f->b == NULL || f->t == NULL) {
+	if (f == NULL || f->file < 0 || f->u == NULL || f->b == NULL
+#ifndef PARALLEL_IO
+		|| f->t == NULL
+#endif
+		) {
 		return h5_error (
 			f,
 			H5_ERR_BADFD,
@@ -225,7 +229,9 @@ h5priv_open_file (
 
 	TRY( h5upriv_open_file (f) );
 	TRY( h5bpriv_open_file (f) );
+#ifndef PARALLEL_IO
 	TRY( h5tpriv_open_file (f) );
+#endif
 	return H5_SUCCESS;
 }
  
@@ -339,7 +345,9 @@ h5_close_file (
 	TRY( h5priv_close_step (f) );
 	TRY( h5upriv_close_file (f) );
 	TRY( h5bpriv_close_file (f) );
+#ifndef PARALLEL_IO
 	TRY( h5tpriv_close_file (f) );
+#endif
 	TRY( h5priv_close_hdf5_group (f, f->step_gid) );
 	TRY( h5priv_close_hdf5_property (f, f->xfer_prop) );
 	TRY( h5priv_close_hdf5_property (f, f->access_prop) );

src/h5core/h5b_model.c

@@ -523,12 +523,12 @@ h5b_3d_has_view (
 h5_err_t
 h5b_3d_set_view (
 	h5_file_t *const f,		/*!< IN: File handle		*/
-	const h5_size_t i_start,	/*!< IN: start index of \c i	*/ 
-	const h5_size_t i_end,		/*!< IN: end index of \c i	*/  
-	const h5_size_t j_start,	/*!< IN: start index of \c j	*/ 
-	const h5_size_t j_end,		/*!< IN: end index of \c j	*/ 
-	const h5_size_t k_start,	/*!< IN: start index of \c k	*/ 
-	const h5_size_t k_end		/*!< IN: end index of \c k	*/
+	const h5_int64_t i_start,	/*!< IN: start index of \c i	*/ 
+	const h5_int64_t i_end,		/*!< IN: end index of \c i	*/  
+	const h5_int64_t j_start,	/*!< IN: start index of \c j	*/ 
+	const h5_int64_t j_end,		/*!< IN: end index of \c j	*/ 
+	const h5_int64_t k_start,	/*!< IN: start index of \c k	*/ 
+	const h5_int64_t k_end		/*!< IN: end index of \c k	*/
 	) {
 
 	h5b_partition_t *p = f->b->user_layout;
@@ -590,12 +590,12 @@ h5b_3d_set_view (
 h5_err_t
 h5b_3d_get_view (
 	h5_file_t *const f,	/*!< IN: File handle */
-	h5_size_t *i_start,	/*!< OUT: start index of \c i	*/ 
-	h5_size_t *i_end,	/*!< OUT: end index of \c i	*/  
-	h5_size_t *j_start,	/*!< OUT: start index of \c j	*/ 
-	h5_size_t *j_end,	/*!< OUT: end index of \c j	*/ 
-	h5_size_t *k_start,	/*!< OUT: start index of \c k	*/ 
-	h5_size_t *k_end	/*!< OUT: end index of \c k	*/ 
+	h5_int64_t *i_start,	/*!< OUT: start index of \c i	*/ 
+	h5_int64_t *i_end,	/*!< OUT: end index of \c i	*/  
+	h5_int64_t *j_start,	/*!< OUT: start index of \c j	*/ 
+	h5_int64_t *j_end,	/*!< OUT: end index of \c j	*/ 
+	h5_int64_t *k_start,	/*!< OUT: start index of \c k	*/ 
+	h5_int64_t *k_end	/*!< OUT: end index of \c k	*/ 
 	) {
 
 	h5b_partition_t *p = f->b->user_layout;
@@ -613,12 +613,12 @@ h5b_3d_get_view (
 h5_err_t
 h5b_3d_get_reduced_view (
 	h5_file_t *const f,	/*!< IN: File handle */
-	h5_size_t *i_start,	/*!< OUT: start index of \c i	*/ 
-	h5_size_t *i_end,	/*!< OUT: end index of \c i	*/  
-	h5_size_t *j_start,	/*!< OUT: start index of \c j	*/ 
-	h5_size_t *j_end,	/*!< OUT: end index of \c j	*/ 
-	h5_size_t *k_start,	/*!< OUT: start index of \c k	*/ 
-	h5_size_t *k_end	/*!< OUT: end index of \c k	*/ 
+	h5_int64_t *i_start,	/*!< OUT: start index of \c i	*/ 
+	h5_int64_t *i_end,	/*!< OUT: end index of \c i	*/  
+	h5_int64_t *j_start,	/*!< OUT: start index of \c j	*/ 
+	h5_int64_t *j_end,	/*!< OUT: end index of \c j	*/ 
+	h5_int64_t *k_start,	/*!< OUT: start index of \c k	*/ 
+	h5_int64_t *k_end	/*!< OUT: end index of \c k	*/ 
 	) {
 
 	h5b_partition_t *p = f->b->write_layout;
@@ -636,9 +636,9 @@ h5b_3d_get_reduced_view (
 h5_err_t
 h5b_3d_set_chunk (
 	h5_file_t *const f,		/*!< IN: File handle */
-	const h5_size_t i,		/*!< IN: size of \c i */ 
-	const h5_size_t j,		/*!< IN: size of \c j */  
-	const h5_size_t k		/*!< IN: size of \c k */ 
+	const h5_int64_t i,		/*!< IN: size of \c i */ 
+	const h5_int64_t j,		/*!< IN: size of \c j */  
+	const h5_int64_t k		/*!< IN: size of \c k */ 
 	) {
 
 	if ( i == 0 || j == 0 || k == 0 )
@@ -662,7 +662,9 @@ h5_err_t
 h5b_3d_get_chunk (
 	h5_file_t *const f,		/*!< IN: File handle */
 	const char *field_name, 	/*!< IN: name of dataset */
-	h5_size_t *dims			/*!< OUT: array containing the chunk dimensions */
+	h5_int64_t *i,			/*!< OUT: size of \c i */ 
+	h5_int64_t *j,			/*!< OUT: size of \c j */  
+	h5_int64_t *k			/*!< OUT: size of \c k */ 
 	) {
 
 	CHECK_TIMEGROUP ( f );
@@ -681,15 +683,15 @@ h5b_3d_get_chunk (
 	TRY( h5priv_close_hdf5_property(f, plist_id) );
 	TRY( h5priv_close_hdf5_dataset(f, dataset_id) );
 
-	dims[0] = hdims[2];
-	dims[1] = hdims[1];
-	dims[2] = hdims[0];
+	*i = hdims[2];
+	*j = hdims[1];
+	*k = hdims[0];
 
 	h5_info(f,
 		"Found chunk dimensions (%lld,%lld,%lld)",
-		(long long)dims[0],
-		(long long)dims[1],
-		(long long)dims[2] );
+		(long long)hdims[0],
+		(long long)hdims[1],
+		(long long)hdims[2] );
 
 	return H5_SUCCESS;
 }
@@ -818,20 +820,12 @@ h5b_3d_set_halo (
 
 	h5b_fdata_t *b = f->b;
 
-	b->user_layout->i_start	-= k;
-	b->user_layout->i_end	+= k;
+	b->user_layout->i_start	-= i;
+	b->user_layout->i_end	+= i;
 	b->user_layout->j_start	-= j;
 	b->user_layout->j_end	+= j;
-	b->user_layout->k_start	-= i;
-	b->user_layout->k_end	+= i;
-
-	b->user_layout->i_start = MAX(0, b->user_layout->i_start);
-	b->user_layout->j_start = MAX(0, b->user_layout->j_start);
-	b->user_layout->k_start = MAX(0, b->user_layout->k_start);
-
-	b->user_layout->i_end = MIN(b->i_max, b->user_layout->i_end);
-	b->user_layout->j_end = MIN(b->j_max, b->user_layout->j_end);
-	b->user_layout->k_end = MIN(b->k_max, b->user_layout->k_end);
+	b->user_layout->k_start	-= k;
+	b->user_layout->k_end	+= k;
 
 	return H5_SUCCESS;
 }

src/h5core/h5b_types_private.h

@@ -2,12 +2,12 @@
 #define __H5B_TYPES_PRIVATE_H
 
 struct h5b_partition {
-	h5_size_t	i_start;
-	h5_size_t	i_end;
-	h5_size_t	j_start;
-	h5_size_t	j_end;
-	h5_size_t	k_start;
-	h5_size_t	k_end;
+	h5_int64_t	i_start;
+	h5_int64_t	i_end;
+	h5_int64_t	j_start;
+	h5_int64_t	j_end;
+	h5_int64_t	k_start;
+	h5_int64_t	k_end;
 };
 
 struct h5b_fdata {

src/include/h5core/h5b_model.h

@@ -37,49 +37,51 @@ h5b_3d_has_view (
 h5_err_t
 h5b_3d_set_view (
 	h5_file_t *const f,		/*!< IN: File handle		*/
-	const h5_size_t i_start,	/*!< IN: start index of \c i	*/ 
-	const h5_size_t i_end,		/*!< IN: end index of \c i	*/  
-	const h5_size_t j_start,	/*!< IN: start index of \c j	*/ 
-	const h5_size_t j_end,		/*!< IN: end index of \c j	*/ 
-	const h5_size_t k_start,	/*!< IN: start index of \c k	*/ 
-	const h5_size_t k_end		/*!< IN: end index of \c k	*/
+	const h5_int64_t i_start,	/*!< IN: start index of \c i	*/ 
+	const h5_int64_t i_end,		/*!< IN: end index of \c i	*/  
+	const h5_int64_t j_start,	/*!< IN: start index of \c j	*/ 
+	const h5_int64_t j_end,		/*!< IN: end index of \c j	*/ 
+	const h5_int64_t k_start,	/*!< IN: start index of \c k	*/ 
+	const h5_int64_t k_end		/*!< IN: end index of \c k	*/
 	);
 
 h5_err_t
 h5b_3d_get_view (
 	h5_file_t *const f,	/*!< IN: File handle */
-	h5_size_t *i_start,	/*!< OUT: start index of \c i	*/ 
-	h5_size_t *i_end,	/*!< OUT: end index of \c i	*/  
-	h5_size_t *j_start,	/*!< OUT: start index of \c j	*/ 
-	h5_size_t *j_end,	/*!< OUT: end index of \c j	*/ 
-	h5_size_t *k_start,	/*!< OUT: start index of \c k	*/ 
-	h5_size_t *k_end	/*!< OUT: end index of \c k	*/ 
+	h5_int64_t *i_start,	/*!< OUT: start index of \c i	*/ 
+	h5_int64_t *i_end,	/*!< OUT: end index of \c i	*/  
+	h5_int64_t *j_start,	/*!< OUT: start index of \c j	*/ 
+	h5_int64_t *j_end,	/*!< OUT: end index of \c j	*/ 
+	h5_int64_t *k_start,	/*!< OUT: start index of \c k	*/ 
+	h5_int64_t *k_end	/*!< OUT: end index of \c k	*/ 
 	);
 
 h5_err_t
 h5b_3d_get_reduced_view (
 	h5_file_t *const f,	/*!< IN: File handle */
-	h5_size_t *i_start,	/*!< OUT: start index of \c i	*/ 
-	h5_size_t *i_end,	/*!< OUT: end index of \c i	*/  
-	h5_size_t *j_start,	/*!< OUT: start index of \c j	*/ 
-	h5_size_t *j_end,	/*!< OUT: end index of \c j	*/ 
-	h5_size_t *k_start,	/*!< OUT: start index of \c k	*/ 
-	h5_size_t *k_end	/*!< OUT: end index of \c k	*/ 
+	h5_int64_t *i_start,	/*!< OUT: start index of \c i	*/ 
+	h5_int64_t *i_end,	/*!< OUT: end index of \c i	*/  
+	h5_int64_t *j_start,	/*!< OUT: start index of \c j	*/ 
+	h5_int64_t *j_end,	/*!< OUT: end index of \c j	*/ 
+	h5_int64_t *k_start,	/*!< OUT: start index of \c k	*/ 
+	h5_int64_t *k_end	/*!< OUT: end index of \c k	*/ 
 	);
 
 h5_err_t
 h5b_3d_set_chunk (
 	h5_file_t *const f,		/*!< IN: File handle */
-	const h5_size_t i,		/*!< IN: size of \c i */ 
-	const h5_size_t j,		/*!< IN: size of \c j */  
-	const h5_size_t k		/*!< IN: size of \c k */ 
+	const h5_int64_t i,		/*!< IN: size of \c i */ 
+	const h5_int64_t j,		/*!< IN: size of \c j */  
+	const h5_int64_t k		/*!< IN: size of \c k */ 
 	);
 
 h5_err_t
 h5b_3d_get_chunk (
 	h5_file_t *const f,		/*!< IN: File handle */
 	const char *field_name, 	/*!< IN: name of dataset */
-	h5_size_t *dims			/*!< OUT: array containing the chunk dimensions */
+	h5_int64_t *i,			/*!< OUT: size of \c i */ 
+	h5_int64_t *j,			/*!< OUT: size of \c j */  
+	h5_int64_t *k			/*!< OUT: size of \c k */ 
 	);
 
 h5_err_t

test/h5b_read.c

@@ -56,6 +56,7 @@ test_read_field_attribs(
 static void
 test_read_data64(h5_file_t *file, int step)
 {
+	extern h5_size_t grid[3];
 	extern h5_size_t layout[6];
 
 	int i,t;
@@ -114,9 +115,9 @@ test_read_data64(h5_file_t *file, int step)
 		IVALUE(type[0], type[1], "field type");
 
 		IVALUE(field_rank[0], 3, "field rank");
-		IVALUE(field_dims[0], NBLOCKX, "field dims x");
-		IVALUE(field_dims[1], NBLOCKY, "field dims y");
-		IVALUE(field_dims[2], NBLOCKZ, "field dims z");
+		IVALUE(field_dims[0], grid[0]*NBLOCKX, "field dims x");
+		IVALUE(field_dims[1], grid[1]*NBLOCKY, "field dims y");
+		IVALUE(field_dims[2], grid[2]*NBLOCKZ, "field dims z");
 		if (i==1) {
 			CVALUE(name[0], 'e', "field name");
 			IVALUE(elem_rank[0], 1, "elem rank");
@@ -231,10 +232,10 @@ test_read_data32(h5_file_t *file, int step)
 		int i;
 		for (i=0; i<nelems; i++)
 		{
-			FVALUE(e[i] , 0.0 + (float)(i+nelems*t), " e data");
-			FVALUE(ex[i], 0.1 + (float)(i+nelems*t), " ex data");
-			FVALUE(ey[i], 0.2 + (float)(i+nelems*t), " ey data");
-			FVALUE(ez[i], 0.3 + (float)(i+nelems*t), " ez data");
+			FVALUE(e[i] , 0.0f + (float)(i+nelems*t), " e data");
+			FVALUE(ex[i], 0.1f + (float)(i+nelems*t), " ex data");
+			FVALUE(ey[i], 0.2f + (float)(i+nelems*t), " ey data");
+			FVALUE(ez[i], 0.3f + (float)(i+nelems*t), " ez data");
 			IVALUE(id[i],              (i+nelems*t), " id data");
 		}
 	}

test/h5b_test.c

@@ -8,6 +8,7 @@
 /* global */
 h5_size_t grid[3];
 h5_size_t layout[6];
+h5_size_t fields_dims[3];
 
 /* from write.c */
 void h5b_test_write1(void);

test/h5b_write.c

@@ -116,14 +116,14 @@ test_write_data32(h5_file_t *file, int step)
 {
 	extern h5_size_t grid[3];
 
-	int i,t;
+	int i,j,k,t;
 	h5_int64_t status, val;
 
 	float *e;
 	float *ex,*ey,*ez;
 	int *id;
 
-	const size_t nelems = NBLOCKX * (NBLOCKY+2) * (NBLOCKZ+4);
+	size_t nelems = NBLOCKX * (NBLOCKY+2) * (NBLOCKZ+4);
 
 	e=(float*)malloc(nelems*sizeof(double));
 	ex=(float*)malloc(nelems*sizeof(double));
@@ -131,17 +131,23 @@ test_write_data32(h5_file_t *file, int step)
 	ez=(float*)malloc(nelems*sizeof(double));
 	id=(int*)malloc(nelems*sizeof(int));
 
+	nelems = NBLOCKX * NBLOCKY * NBLOCKZ;
+
 	TEST("Writing 32-bit data");
 
 	for (t=step; t<step+NTIMESTEPS; t++)
 	{
-		for (i=0; i<nelems; i++)
+		for (k=0; k<NBLOCKZ+4; k++)
+		for (j=0; j<NBLOCKY+2; j++)
+		for (i=0; i<NBLOCKX; i++)
 		{
-			e[i]   = 0.0 + (float)(i+nelems*t);
-			ex[i]  = 0.1 + (float)(i+nelems*t);
-			ey[i]  = 0.2 + (float)(i+nelems*t);
-			ez[i]  = 0.3 + (float)(i+nelems*t);
-			id[i] = i + nelems*t;
+			int idx = i + j*NBLOCKX + k*NBLOCKX*(NBLOCKY+2);
+			int n = i + (j-1)*NBLOCKX + (k-2)*NBLOCKX*NBLOCKY;
+			e[idx]   = 0.0f + (float)(n+nelems*t);
+			ex[idx]  = 0.1f + (float)(n+nelems*t);
+			ey[idx]  = 0.2f + (float)(n+nelems*t);
+			ez[idx]  = 0.3f + (float)(n+nelems*t);
+			id[idx] = n + nelems*t;
 		}
 
 		val = H5HasStep(file, t);