Merge branch '15-move-dissolving-ghost-zones-into-dedicated-function' into 'master'

Resolve "move dissolving ghost-zones into dedicated function"

Closes #15

See merge request !1

src/Fortran/H5Block_model.c

@@ -69,7 +69,8 @@ h5bl_3d_setview (
 		f,
 		*i_start-1, *i_end-1,
 		*j_start-1, *j_end-1,
-		*k_start-1, *k_end-1 ));
+		*k_start-1, *k_end-1,
+                0));
 }
 
 #define h5bl_3d_getview FC_MANGLING (					\

src/h5core/h5b_model.c

@@ -417,7 +417,6 @@ _dissolve_ghostzones (
 				p_el = p_save;
 			}
 		}
-
 	}
 	h5_free (p_begin);
 	H5_RETURN (H5_SUCCESS);
@@ -544,7 +543,8 @@ h5b_3d_set_view (
 	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_size_t k_end,		/*!< IN: end index of \c k	*/
+        const h5_int64_t dissolve_ghostzones /*!< IN: bool: dissolve ghost-zones */ 
 	) {
         h5_file_p f = (h5_file_p)fh;
 	H5_CORE_API_ENTER (h5_err_t,
@@ -571,7 +571,6 @@ h5b_3d_set_view (
 	h5b_partition_t *write_layout;
 
 	TRY (user_layout =  h5_calloc (f->nprocs, sizeof (*user_layout)));
-	TRY (write_layout = h5_calloc (f->nprocs, sizeof (*write_layout)));
 
         user_layout[f->myproc] = b->user_layout[0];
 
@@ -580,11 +579,7 @@ h5b_3d_set_view (
                      user_layout, 1, f->b->partition_mpi_t, f->props->comm));
 
 	_get_max_dimensions(f, user_layout);
-
-	TRY (_dissolve_ghostzones (f, user_layout, write_layout));
-	b->user_layout[0] = user_layout[f->myproc];
-	b->write_layout[0] = write_layout[f->myproc];
-
+	//b->user_layout[0] = user_layout[f->myproc];
 	h5_debug (
 		"User layout: %lld:%lld, %lld:%lld, %lld:%lld",
 		(long long)b->user_layout[0].i_start,
@@ -594,17 +589,25 @@ h5b_3d_set_view (
 		(long long)b->user_layout[0].k_start,
                 (long long)b->user_layout[0].k_end );
 
-	h5_debug (
-		"Ghost-zone layout: %lld:%lld, %lld:%lld, %lld:%lld",
-		(long long)b->write_layout[0].i_start,
-                (long long)b->write_layout[0].i_end,
-		(long long)b->write_layout[0].j_start,
-                (long long)b->write_layout[0].j_end,
-		(long long)b->write_layout[0].k_start,
-                (long long)b->write_layout[0].k_end );
+        if (dissolve_ghostzones) {
+                TRY (write_layout = h5_calloc (f->nprocs, sizeof (*write_layout)));
+                TRY (_dissolve_ghostzones (f, user_layout, write_layout));
+                b->write_layout[0] = write_layout[f->myproc];
+
+                h5_debug (
+                        "Ghost-zone layout: %lld:%lld, %lld:%lld, %lld:%lld",
+                        (long long)b->write_layout[0].i_start,
+                        (long long)b->write_layout[0].i_end,
+                        (long long)b->write_layout[0].j_start,
+                        (long long)b->write_layout[0].j_end,
+                        (long long)b->write_layout[0].k_start,
+                        (long long)b->write_layout[0].k_end );
+                h5_free(write_layout);
+        } else {
+                b->write_layout[0] = b->user_layout[0];
+        }
 
 	h5_free(user_layout);
-	h5_free(write_layout);
 #else
 	b->write_layout[0] = b->user_layout[0];
 	b->i_max = b->user_layout->i_end;

src/include/H5Block_model.h

@@ -220,7 +220,51 @@ H5Block3dSetView (
 		h5b_3d_set_view (f,
 				 i_start, i_end,
 				 j_start, j_end,
-				 k_start, k_end));
+				 k_start, k_end,
+                                 0
+                        ));
+}
+
+/**
+  Defines the partition of the field that this processor owns, using
+  Fortran ordering: the fastest moving index is \c i.
+
+  For writing ghost-zone are dissolved.
+
+  This routine uses an MPI_Allgather, so at large concurrency it should
+  be called as infrequently as possible. For instance, if several
+  steps/iteration use the same field dimensions, set the layout only
+  once.
+
+  \return \c H5_SUCCESS on success
+  \return \c H5_FAILURE on error
+*/
+static inline h5_err_t
+H5Block3dSetViewDissolveGhostZones (
+	const h5_file_t f,		///< [in]  File handle.
+	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_API_ENTER (h5_err_t,
+		      "f=%p, "
+		      "i_start=%lld, i_end=%lld, "
+		      "j_start=%lld, j_end=%lld, "
+		      "k_start=%lld, k_end=%lld",
+		      (h5_file_p)f,
+		      (long long)i_start, (long long)i_end,
+		      (long long)j_start, (long long)j_end,
+		      (long long)k_start, (long long)k_end);
+	H5_API_RETURN (
+		h5b_3d_set_view (f,
+				 i_start, i_end,
+				 j_start, j_end,
+				 k_start, k_end,
+                                 1
+                        ));
 }
 
 /**

src/include/h5core/h5b_model.h

@@ -51,7 +51,8 @@ h5b_3d_set_view (
         const h5_file_t,
         const h5_size_t, const h5_size_t,
         const h5_size_t, const h5_size_t,
-        const h5_size_t, const h5_size_t);
+        const h5_size_t, const h5_size_t,
+        const h5_int64_t);
 
 h5_err_t
 h5b_3d_get_view (