Merge branch '21-hdf5-1-12-and-newer-support' into 'master'

Resolve "hdf5 1.12 and newer support"

Closes #21

See merge request H5hut/src!6

configure.ac

@@ -6,10 +6,11 @@
 #
 #  License: see file COPYING in top level of source distribution.
 #
-AC_INIT([H5hut], [2.0.0rc5], [h5part@lists.psi.ch], H5hut)
+AC_INIT([H5hut], [2.0.0rc7], [h5part@lists.psi.ch], H5hut)
 AC_PREREQ(2.60)
 AC_CONFIG_HEADERS(config.h)
 AC_CONFIG_MACRO_DIR([m4])
+LT_INIT
 AM_INIT_AUTOMAKE
 
 ENABLE_DEBUG='no'
@@ -138,7 +139,6 @@ 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($cxx_compilers)
@@ -147,7 +147,6 @@ if test "X$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 +158,6 @@ 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 +279,7 @@ 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 +426,10 @@ 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 +448,12 @@ 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 +474,6 @@ 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 +482,6 @@ 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/h5_file.c

@@ -92,7 +92,7 @@ mpi_init (
 		TRY (hdf5_set_fapl_mpiposix_property (f->props->access_prop,
                                                      f->props->comm, use_gpfs));
 
-        } else if ((f->props->flags & H5_VFD_CORE)) {
+        } else if ((f->props->flags & H5_VFD_CORE_IO)) {
 		h5_info("Selecting CORE VFD");
                 TRY (hdf5_set_fapl_core (f->props->access_prop,
                                          f->props->align, 1));
@@ -112,7 +112,7 @@ mpi_init (
 	}
 #else
 	// VFD_MPIO_POSIX has been removed in HDF5 1.8.13
-        if ((f->props->flags & H5_VFD_CORE)) {
+        if ((f->props->flags & H5_VFD_CORE_IO)) {
 		h5_info("Selecting CORE VFD");
                 TRY (hdf5_set_fapl_core (f->props->access_prop,
                                          f->props->align, 1));
@@ -197,7 +197,7 @@ h5_set_prop_file_mpio_collective (
 			(long long int)props->class);
         }
 #ifdef H5_HAVE_PARALLEL
-        props->flags &= ~(H5_VFD_MPIO_POSIX | H5_VFD_MPIO_INDEPENDENT | H5_VFD_CORE);
+        props->flags &= ~(H5_VFD_MPIO_POSIX | H5_VFD_MPIO_INDEPENDENT | H5_VFD_CORE_IO);
         props->flags |= H5_VFD_MPIO_COLLECTIVE;
         props->comm = *comm;
 	if (props->throttle > 0) {
@@ -225,7 +225,7 @@ h5_set_prop_file_mpio_independent (
 			(long long int)props->class);
         }
 #ifdef H5_HAVE_PARALLEL
-        props->flags &= ~(H5_VFD_MPIO_COLLECTIVE | H5_VFD_MPIO_POSIX | H5_VFD_CORE);
+        props->flags &= ~(H5_VFD_MPIO_COLLECTIVE | H5_VFD_MPIO_POSIX | H5_VFD_CORE_IO);
         props->flags |= H5_VFD_MPIO_INDEPENDENT;
         props->comm = *comm;
 #else
@@ -250,7 +250,7 @@ h5_set_prop_file_mpio_posix (
 			(long long int)props->class);
         }
 #ifdef H5_HAVE_PARALLEL
-        props->flags &= ~(H5_VFD_MPIO_COLLECTIVE | H5_VFD_MPIO_POSIX | H5_VFD_CORE);
+        props->flags &= ~(H5_VFD_MPIO_COLLECTIVE | H5_VFD_MPIO_POSIX | H5_VFD_CORE_IO);
         props->flags |= H5_VFD_MPIO_INDEPENDENT;
         props->comm = *comm;
 #else

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/h5core/private/h5_attribs.h

@@ -99,7 +99,7 @@ h5priv_write_attrib (
 	                   attrib_name,
 	                   (long long int)attrib_type,
 	                   attrib_value,
-	                   attrib_nelem);
+	                   (long long unsigned)attrib_nelem);
 	hid_t space_id;
 	hid_t attrib_id;
 	hid_t hdf5_type;
@@ -147,7 +147,7 @@ h5priv_append_attrib (
 	                   attrib_name,
 	                   (long long int)attrib_type,
 	                   attrib_value,
-	                   attrib_nelem);
+	                   (long long unsigned)attrib_nelem);
 	h5_err_t exists;
 	TRY (exists = hdf5_attribute_exists (id, attrib_name));
 	if (exists) {

src/h5core/private/h5_file.h

@@ -9,7 +9,7 @@
 #define H5_VFD_MPIO_POSIX       0x00000010
 #define H5_VFD_MPIO_INDEPENDENT 0x00000020
 #define H5_VFD_MPIO_COLLECTIVE  0x00000040
-#define H5_VFD_CORE		0x00000080
+#define H5_VFD_CORE_IO		0x00000080
 
 #define H5_FLUSH_FILE		0x00001000
 #define H5_FLUSH_ITERATION	0x00002000

src/h5core/private/h5_hdf5.c

@@ -110,10 +110,18 @@ iter_op_get_obj_type (
 			        name);
 			return H5O_TYPE_UNKNOWN;
 		}
+#if H5_VERSION_GE(1,12,0)
+		herr = H5Oget_info(obj_id, &objinfo, H5O_INFO_ALL);
+#else
 		herr = H5Oget_info(obj_id, &objinfo);
+#endif
 	}
 	else { // H5L_TYPE_HARD
+#if H5_VERSION_GE(1,12,0)
+	  herr = H5Oget_info_by_name(g_id, name, &objinfo, H5O_INFO_BASIC, H5P_DEFAULT);
+#else
 		herr = H5Oget_info_by_name(g_id, name, &objinfo, H5P_DEFAULT);
+#endif
 	}
 
 	if (herr < 0) {
@@ -245,7 +253,8 @@ hdf5_get_name_of_group_by_idx (
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "loc_id=%lld (%s), idx=%llu, name=%p, len=%llu",
 	                    (long long int)loc_id, hdf5_get_objname (loc_id),
-	                    idx, name, (unsigned long long)len);
+	                    (long long unsigned)idx,
+			    name, (unsigned long long)len);
 	op_data_t op_data;
 	memset (&op_data, 0, sizeof (op_data));
 	op_data.type = H5O_TYPE_GROUP;
@@ -304,7 +313,8 @@ hdf5_get_name_of_dataset_by_idx (
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "loc_id=%lld (%s), idx=%llu, name=%p, len=%llu",
 	                    (long long int)loc_id, hdf5_get_objname (loc_id),
-	                    idx, name, (unsigned long long)len);
+	                    (long long unsigned)idx,
+			    name, (unsigned long long)len);
 	op_data_t op_data;
 	memset (&op_data, 0, sizeof (op_data));
 	op_data.type = H5O_TYPE_DATASET;

src/h5core/private/h5_hdf5.h

@@ -718,7 +718,7 @@ hdf5_set_dataset_extent (
 	                    "dataset_id=%lld (%s), size=%llu",
 	                    (long long int)dataset_id,
 	                    hdf5_get_objname(dataset_id),
-	                    *size);
+	                    (long long unsigned int)*size);
 	if (H5Dset_extent(dataset_id, size) < 0) {
 		H5_RETURN_ERROR (
 			H5_ERR_HDF5,
@@ -873,7 +873,7 @@ static inline hid_t
 hdf5_create_string_type(
         const hsize_t len
         ) {
-	HDF5_WRAPPER_ENTER (hid_t, "len = %llu", len);
+  HDF5_WRAPPER_ENTER (hid_t, "len = %llu", (long long unsigned)len);
 	hid_t type_id = H5Tcopy (H5T_C_S1);
 	if (type_id < 0)
 		H5_RETURN_ERROR (
@@ -1003,7 +1003,7 @@ hdf5_set_chunk_property (
         ) {
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "plist=%lld, rank=%d, dims[0]=%llu ...",
-	                    (long long int)plist, rank, dims[0]);
+	                    (long long int)plist, rank, (long long unsigned)dims[0]);
 	if (H5Pset_chunk (plist, rank, dims) < 0)
 		H5_RETURN_ERROR (
 			H5_ERR_HDF5,
@@ -1146,7 +1146,8 @@ hdf5_set_btree_ik_property (
         ) {
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "fapl_id=%lld, btree_ik=%llu",
-	                    (long long int)fcpl_id, btree_ik);
+	                    (long long int)fcpl_id,
+			    (long long unsigned)btree_ik);
 	if (H5Pset_istore_k (fcpl_id, btree_ik) < 0)
 		H5_RETURN_ERROR (
 			H5_ERR_HDF5,
@@ -1164,13 +1165,16 @@ hdf5_set_alignment_property (
         ) {
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "plist=%lld, threshold=%llu, alignment=%llu",
-	                    (long long int)plist, threshold, alignment);
+	                    (long long int)plist, 
+			    (long long unsigned)threshold,
+			    (long long unsigned)alignment);
 	if (H5Pset_alignment (plist, threshold, alignment) < 0)
 		H5_RETURN_ERROR (
 			H5_ERR_HDF5,
 			"Cannot set alignment property to %llu "
 			"and threshold %llu",
-			alignment, threshold);
+			(long long unsigned)alignment,
+			(long long unsigned)threshold);
 	H5_RETURN (H5_SUCCESS);
 }
 
@@ -1181,12 +1185,13 @@ hdf5_set_meta_block_size (
         ) {
 	HDF5_WRAPPER_ENTER (h5_err_t,
 	                    "fapl_id=%lld, size=%llu",
-	                    (long long int)fapl_id, size);
+	                    (long long int)fapl_id,
+			    (long long unsigned)size);
 	if (H5Pset_meta_block_size (fapl_id, size) < 0)
 		H5_RETURN_ERROR (
 			H5_ERR_HDF5,
 			"Cannot set meta block size property to %llu",
-			size);
+			(long long unsigned)size);
 	H5_RETURN (H5_SUCCESS);
 }
 
@@ -1292,9 +1297,15 @@ hdf5_close_file (
 		for (ssize_t i = 0; i < max_objs; i++) {
 			hid_t object_id = obj_id_list [i];
 			h5_debug ("Open object: %lld", (long long)object_id);
+#if H5_VERSION_GE(1,12,0)
+			H5O_info_t object_info;
+			if (H5Oget_info (object_id, &object_info, H5O_INFO_ALL) < 0)
+				continue;
+#else
 			H5O_info_t object_info;
 			if (H5Oget_info (object_id, &object_info) < 0)
 				continue;
+#endif
 			switch (object_info.type) {
 			case H5O_TYPE_GROUP:
 			case H5O_TYPE_DATASET:

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/H5_const.f90

@@ -13,7 +13,8 @@
 
   INTEGER*8, PARAMETER :: H5_VFD_MPIPOSIX =        Z'00000010'
   INTEGER*8, PARAMETER :: H5_VFD_MPIIO_IND =       Z'00000020'
-  INTEGER*8, PARAMETER :: H5_VFD_CORE =            Z'00000040'
+  INTEGER*8, PARAMETER :: H5_VFD_MPIIO_COL =       Z'00000040'
+  INTEGER*8, PARAMETER :: H5_VFD_CORE_IO =         Z'00000080'
 
   INTEGER*8, PARAMETER :: H5_PROP_DEFAULT =        0
 

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 (

test/testframe.c

@@ -658,7 +658,11 @@ test_open_objects(h5_file_t file, int max_objects)
 		H5O_info_t info;
 		int i;
 		for (i=0; i<nopen; i++) {
-			H5Oget_info(list[i], &info);
+#if H5_VERSION_GE(1,12,0)
+		  H5Oget_info(list[i], &info, H5O_INFO_BASIC);
+#else
+		  H5Oget_info(list[i], &info);
+#endif
 			switch (info.type) {
 			case H5O_TYPE_GROUP:
 				TestErrPrintf("obj%d has type GROUP\n", i);