changesets 3713,3714,3725 merged from sandbox

.gitattributes

@@ -2,7 +2,6 @@
 /AUTHORS -text
 /COPYING -text
 /ChangeLog -text
-/GNUmakefile.orig -text
 /Makefile.am -text
 /NEWS -text
 /README -text

GNUmakefile.orig

@@ -1,133 +0,0 @@
-UNAME := $(shell uname | perl -pe 's/(sn\d\d\d\d|jsimpson)/UNICOS\/mk/')
-# for host specific options
-HOST := $(shell hostname)
-
-# for processor-specific options
-ifeq ($(UNAME), Linux)
-PROC := $(shell uname -p)
-endif
-
-CXX = c++
-CC = cc
-H5HOME = /usr/local/hdf5
-CFLAGS = -g -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
-
-# MacOS-X Serial
-ifeq ($(UNAME), Darwin)
-ifeq ($(PARALLEL), yes)
-CXX = g++
-CC = mpicc
-H5HOME = /usr/local
-CFLAGS = -O -g -I$(H5HOME)/include -DPARALLEL_IO
-LDFLAGS = -L$(H5HOME)/lib -lmpich -lpmpich -lhdf5 -lz -lm
-else
-CXX = c++
-CC = cc
-F90 = xlf
-H5HOME = /usr/local
-CFLAGS = -O -g -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
-endif
-endif
-
-# SGI MIPS/Irix
-ifeq ($(UNAME), IRIX64)
-CXX = CC
-CC = cc
-F90 = f90
-ifeq ($(PARALLEL), yes)
-H5HOME = $(HDF5_DIR)
-CFLAGS = -64 -O3 -I$(H5HOME)/include -DPARALLEL_IO
-LDFLAGS = -64 -O3 -L$(H5HOME)/lib -lhdf5 -lz -lmpi -lm
-else
-H5HOME = /usr/local
-CFLAGS = -O3 -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
-endif
-endif
-
-# AIX/SP-2 Parallel/serial : Seaborg
-ifeq ($(UNAME), AIX)
-ifeq ($(PARALLEL), yes) # parallel
-CXX = mpCC_r
-CC = mpxlc_r
-# H5HOME = /usr/common/usg/hdf5_64/1.4.5-post2/parallel
-H5HOME = /usr/common/usg/hdf5_64/1.6.1/parallel
-# /usr/common/usg/hdf5/1.4.4/parallel
-H4HOME = /usr/common/usg/hdf/default
-OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
-CFLAGS = -q64 -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lsz -lm
-else # serial
-CXX = xlC
-CC = xlc
-H5HOME = /usr/common/usg/hdf5/1.4.4/serial
-H4HOME = /usr/common/usg/hdf/default
-OPT = -qarch=auto -qtune=auto-qcache=auto -O3 -qhot
-CFLAGS = -g -bmaxdata:800000000  -bmaxstack:256000000 -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -L$(H4HOME)/lib -lz -lm
-endif
-endif
-
-# Linux
-ifeq ($(UNAME), Linux)
-# if this machine is NERSC/Davinci Altix system
-ifeq ($(PROC), ia64)
-CC = icc 
-CXX = icc
-
-ifeq ($(PARALLEL), yes)
-# IA64 Linux Parallel
-ifeq ($(HOST), davinci)
-H5HOME = $(HDF5_PAR)
-MPILIB = -lmpi
-else
-H5HOME = /usr/local
-HDF5_PAR_LIB = -L$(H5HOME)/lib -lhdf5 -lz -lm
-HDF5_PAR_INCLUDE = -I$(H5HOME)/include
-MPIHOME = /usr/local
-MPILIB = -lmpich
-endif # HOST
-CFLAGS = -O3 -DPARALLEL_IO -DH5_HAVE_PARALLEL $(HDF5_PAR_INCLUDE) 
-LDFLAGS = $(HDF5_PAR_LIB) $(MPILIB)
-else # IA64 Linux Serial
-CFLAGS = -O3 $(HDF5_INCLUDE)
-LDFLAGS = $(HDF5_LIB) -lm
-endif # PARALLEL
-
-# else this is standard IA32 linux
-else
-ifeq ($(PARALLEL), yes)
-# Linux Parallel
-CC = gcc
-CXX = g++
-H5HOME = /usr/local
-MPIHOME = /usr/local
-CFLAGS = -O -g -DPARALLEL_IO -DH5_HAVE_PARALLEL -I$(H5HOME)/include 
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lmpich -lrt -lz -lm
-else # Linux Serial
-CXX = g++
-CC = gcc
-CFLAGS = -O -g -I$(H5HOME)/include
-LDFLAGS = -L$(H5HOME)/lib -lhdf5 -lz -lm
-endif # !PARALLEL
-endif # PROC!ia64
-
-endif # !Linux
-
-ifeq ($(PARALLEL), yes) #parallel
-ifdef F90
-all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest H5PartF.o
-else
-all: H5PartTest H5PartTest.o H5Part.o H5PartTestParallel H5PartAndreasTest
-endif
-else
-ifdef F90
-all: H5PartTest H5PartTest.o H5Part.o H5PartF.o
-else
-all: H5PartTest H5PartTest.o H5Part.o
-endif
-endif
-
-include rules.make

src/h5core/h5_maps.c

@@ -105,18 +105,18 @@ h5priv_find_idlist (
 	if (!list) {
 		H5_PRIV_API_LEAVE (-1);
 	}
-	register h5_loc_idx_t low = 0;
-	register h5_loc_idx_t high = list->num_items - 1;
-	register h5_loc_id_t diff;
-	register h5_loc_id_t mid;
-	const h5_loc_id_t face_idx =  h5tpriv_get_face_idx(item);
-	const h5_loc_id_t elem_idx =  h5tpriv_get_elem_idx(item);
+	register size_t low = 0;
+	register size_t mid;
+	register size_t high = list->num_items - 1;
+	register h5_loc_idx_t diff;
+	const h5_loc_id_t face_id =  h5tpriv_get_face_id(item);
+	const h5_loc_idx_t elem_idx =  h5tpriv_get_elem_idx(item);
 	while (low <= high) {
 		mid = (low + high) / 2;
 		diff = h5tpriv_get_elem_idx(list->items[mid]) - elem_idx;
 		// if element indices are equal, we decide on the face indices
 		if (diff == 0) {
-			diff = h5tpriv_get_face_idx(list->items[mid]) - face_idx;
+			diff = h5tpriv_get_face_id (list->items[mid]) - face_id;
 		}
            	if ( diff > 0 )
                		high = mid - 1;

src/h5core/h5t_core_private.h

@@ -57,19 +57,22 @@
 #define H5T_FACE_MASK		(0x0f)
 #define H5T_TYPE_MASK		(0x70)
 
-#define h5tpriv_set_entity_type( type, elem_idx )	\
-	(((type) << (BITS_OF(elem_idx)-4)) | (elem_idx))
-				 
-#define h5tpriv_get_entity_type( entity_id )	\
-	((entity_id >> (BITS_OF(entity_id)-8)) & H5T_TYPE_MASK)
+#if 0
+enum elem_types {
+	vertex = 1,	// 1 vertex
+	edge,		// 2 vertices
+	triangle,	// 3 vertices
+	quadrangle,	// 4 vertices
+	tetrahedron,	// 4 vertices
+	pyramid,	// 5 vertices
+	prism,		// 6 vertices
+	hexahedron	// 8 vertices
+};
+#endif
 
 #define h5tpriv_build_entity_id( type, face_idx, elem_idx )	\
 	(((type) | (face_idx)) << (BITS_OF(elem_idx)-8) | (elem_idx))
 
-#define h5tpriv_build_entity_id2( face_id, elem_idx )		\
-	(((face_id) << (BITS_OF(elem_idx)-8)) |		\
-	 (elem_idx))
-
 #define h5tpriv_build_vertex_id( face_idx, elem_idx )			\
 	(h5tpriv_build_entity_id (H5T_TYPE_VERTEX, face_idx, elem_idx))
 
@@ -82,6 +85,9 @@
 #define h5tpriv_build_tet_id( face_idx, elem_idx )			\
 	(h5tpriv_build_entity_id (H5T_TYPE_TET, face_idx, elem_idx))
 
+#define h5tpriv_get_entity_type( entity_id )	\
+	((entity_id >> (BITS_OF(entity_id)-8)) & H5T_TYPE_MASK)
+
 #define h5tpriv_get_face_idx( entity_id )				\
 	(((entity_id) >> (BITS_OF(entity_id)-8)) & H5T_FACE_MASK)