Merge branch '19-release-2-0-0rc6' into 'master'

Resolve "release 2.0.0rc6"

Closes #19

See merge request H5hut/src!4

configure.ac

@@ -6,7 +6,7 @@
 #
 #  License: see file COPYING in top level of source distribution.
 #
-AC_INIT([H5hut], [2.0.0rc5], [h5part@lists.psi.ch], H5hut)
+AC_INIT([H5hut], [2.0.0rc6], [h5part@lists.psi.ch], H5hut)
 AC_PREREQ(2.60)
 AC_CONFIG_HEADERS(config.h)
 AC_CONFIG_MACRO_DIR([m4])
@@ -138,7 +138,6 @@ fi
 AC_PROG_CC($c_compilers)
 if test "x$ac_cv_prog_cc_c89" = "xno"; then
 	AC_MSG_ERROR([C compiler not found!])
-	exit 1
 fi
 
 AC_PROG_CXX($cxx_compilers)
@@ -147,7 +146,6 @@ if test "X$ENABLE_FORTRAN" = "Xyes"; then
    	AC_PROG_FC($fc_compiler)
 	if test "x$FC" = "x"; then
 	   	AC_MSG_ERROR([Fortran compiler not found!])
-		exit 1
 	fi
 fi
 
@@ -159,7 +157,6 @@ AX_CXX_COMPILE_STDCXX_11
 AC_PROG_CC_C99
 if test "x$ac_cv_prog_cc_c99" = "xno"; then
 	AC_MSG_ERROR([Cannot set C compiler to use C99 standard!])
-	exit 1
 fi
 
 
@@ -281,8 +278,7 @@ if test -n "${HDF5_PREFIX}"; then
 fi
 AC_CHECK_LIB([hdf5], [H5open])
 AS_IF([test "x$ac_cv_lib_hdf5_H5open" != xyes], 
-        [AC_MSG_ERROR([Cannot compile and link a HDF5 program]); 
-        exit 1])
+        [AC_MSG_ERROR([Cannot compile and link a HDF5 program])])
 AC_MSG_CHECKING([checking whether hdf5 lib supports parallel IO])
 AC_COMPILE_IFELSE([AC_LANG_SOURCE([[
 #include "hdf5.h"
@@ -429,12 +425,10 @@ if test "X$ENABLE_PARALLEL" = "Xyes"; then
 	AC_MSG_RESULT([yes])
 
 	AS_IF([test "x$H5_HAVE_PARALLEL" = "xno"],
-	        [AC_MSG_ERROR([hdf5 does not support parallel IO!]);
-        	exit 1])
+	        [AC_MSG_ERROR([hdf5 does not support parallel IO!])])
 
 	if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
 	   	AC_MSG_ERROR([VTK to H5hut grid converter cannot be compiled parallel!])
-		exit 1
 	fi
 	CPPFLAGS="${CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
 
@@ -453,14 +447,12 @@ if test "X$ENABLE_PARALLEL" = "Xyes"; then
 
 	        if test "X$r" = "Xno"; then
 		        AC_MSG_ERROR([ParMETIS])
-		        exit 1
 	        fi
         fi
 else  # --enable-parallel=no
 	AC_MSG_RESULT([no])
 	AS_IF([test "x$H5_HAVE_PARALLEL" = "xyes"],
-	        [AC_MSG_ERROR([hdf5 with support for parallel IO cannot be used for non-parallel H5hut!]);
-        	exit 1])
+	        [AC_MSG_ERROR([hdf5 with support for parallel IO cannot be used for non-parallel H5hut!])])
 fi
 
 ###############################################################################
@@ -481,7 +473,6 @@ if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
 	if test "X$?" != "X0"; then
 		AC_MSG_RESULT([no])
 	        AC_MSG_ERROR([Cannot compile VTK to H5hut converter])
-        	exit 1
 	else
 		AC_MSG_RESULT([yes])
 	fi
@@ -490,7 +481,6 @@ if test "X$ENABLE_VTKCONVERTER" = "Xyes"; then
 	if test "X$?" != "X0"; then
 		AC_MSG_RESULT([no])
 	        AC_MSG_ERROR([Cannot compile VTK to H5hut converter]); 
-        	exit 1
 	else
 		AC_MSG_RESULT([yes])
 	fi

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/h5core/h5u_io.c

@@ -254,5 +254,6 @@ h5u_write_dataset (
 	hid_t dset_id;
 	TRY (dset_id = h5u_open_dataset (fh, name, type));
 	TRY (h5u_write (fh, dset_id, type, data));
+        TRY (hdf5_close_dataset(dset_id));
 	H5_RETURN (H5_SUCCESS);
 }

src/h5core/h5u_model.c

@@ -152,6 +152,8 @@ h5u_set_num_items (
 
 	TRY (hdf5_close_dataspace (u->shape));
 	u->shape = H5S_ALL;
+        TRY (hdf5_close_dataspace (u->memshape));
+        u->memshape = H5S_ALL;
 
 	u->nparticles = (hsize_t)nparticles;
 
@@ -212,7 +214,8 @@ h5u_set_num_items (
 	TRY( u->shape = hdf5_create_dataspace(1, &count, NULL) );
 
 	/* declare overall data size  but then will select a subset */
-	TRY( u->diskshape = hdf5_create_dataspace(1, &count, NULL) );
+        TRY (hdf5_close_dataspace (u->diskshape));
+        TRY (u->diskshape = hdf5_create_dataspace(1, &count, NULL));
 
 	count = nparticles;
 	if (count > 0) {

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 (