tested out packaging a tarball and compiling/install on Franklin

fixed several issues with the build system

configure.ac

@@ -1,6 +1,6 @@
 # Every configure script must call AC_INIT before doing anything else.
 # AC_INIT (package, version, [bug-report], [tarname])
-AC_INIT([H5hut], [1.99.0], [h5part@lists.psi.ch], H5Part)
+AC_INIT([H5hut], [1.99.0], [h5part@lists.psi.ch], H5hut)
 
 
 # Ensure that a recent enough version of Autoconf is being used. 
@@ -14,9 +14,7 @@ AC_PREREQ(2.59)
 # The AC_CONFIG_HEADERS macro selects this kind of output.
 AC_CONFIG_HEADER(config.h)
 
-
-BINDINGS=''
-BUILD_LIBS='libH5hut'
+BUILD_LIBS='libH5hut.a'
 USE_C='yes'
 
 ###############################################################################
@@ -53,12 +51,6 @@ AC_ARG_ENABLE(
 	[Compile the MPI/IO interface [default=no]])],
 	[USE_PARALLEL=$enableval])
 
-AC_ARG_ENABLE(
-	[tools],
-	[AC_HELP_STRING([--enable-tools],
-	[Compile h5part tools [default=no]])],
-	[USE_TOOLS=$enableval])
-
 AC_ARG_WITH(
 	[mpi],
 	[AC_HELP_STRING([--with-mpi],
@@ -83,12 +75,9 @@ AC_ARG_WITH(
 
 SAVE_CC=$CC
 SAVE_CXX=$CXX
-SAVE_FC=$FC
 SAVE_MPICC=$MPICC
 SAVE_MPICXX=$MPICXX
-SAVE_MPIFC=$MPIFC
 SAVE_CFLAGS=$CFLAGS
-SAVE_FFLAGS=$FFLAGS
 SAVE_INCLUDES=$INCLUDES
 SAVE_LDFLAGS=$LDFLAGS
 SAVE_LIBS=$LIBS
@@ -206,7 +195,10 @@ AC_MSG_CHECKING([if C interface enabled])
 if test "X$USE_C" = "Xyes"; then
 	AC_MSG_RESULT([yes])
 	BINDINGS="$BINDINGS C"
-        BUILD_LIBS="$BUILD_LIBS libH5hutC"
+	LIB_C="libH5hutC.a"
+	BUILD_LIBS="$BUILD_LIBS $LIB_C"
+	BUILD_TESTS="$BUILD_TESTS h5u_test h5b_test"
+	BUILD_TOOLS="$BUILD_TOOLS h5hutcc"
 fi
 
 ############################ fortran enabled ##################################
@@ -214,8 +206,8 @@ AC_MSG_CHECKING([if fortran interface enabled])
 if test "X$USE_FORTRAN" = "Xyes"; then
 	AC_MSG_RESULT([yes])
 	BINDINGS="$BINDINGS Fortran"
-        BUILD_LIBS="$BUILD_LIBS libH5hutF"
-
+	LIB_FORTRAN="libH5hutF.a"
+        BUILD_LIBS="$BUILD_LIBS $LIB_FORTRAN"
 
 	AC_PROG_FC(pgf90 ifort xlf_r pathf90 g95 g90 ftn gfortran)
 	if test -z "$FC" ; then
@@ -375,14 +367,6 @@ else  # --enable-parallel=no
 	fi
 fi
 
-AC_MSG_CHECKING([wheter tools are enabled])
-if test "X$USE_TOOLS" = "Xyes"; then
-	AC_MSG_RESULT([yes])
-	BUILD_TOOLS="h5pAttrib h5pToGNUplot # homdynToH5p"
-else
-	AC_MSG_RESULT([no])
-fi
-
 ###############################################################################
 ######################### PATH CHECKING & SETTING #############################
 ###############################################################################
@@ -443,8 +427,8 @@ if test -z "$LUSTREROOT"; then
 	AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
 else
         CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
-        INCLUDES="$INCLUDES -I$LUSTREROOT/include"
-        LDFLAGS="LDFLAGS -L$LUSTREROOT/lib"
+        INCLUDES="$INCLUDES -I$LUSTREROOT/usr/include"
+        LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
         LIBS="$LIBS -llustreapi"
 fi
 
@@ -532,25 +516,22 @@ AC_SUBST(FFLAGS)
 AC_SUBST(INCLUDES)
 AC_SUBST(LDFLAGS)
 AC_SUBST(LIBS)
-AC_SUBST(STDCXX)
 AC_SUBST(UNDERSCORE_H)
-AC_SUBST(BUILD_TOOLS)
-AC_SUBST(FORTRAN_LIB)
+AC_SUBST(LIB_C)
+AC_SUBST(LIB_FORTRAN)
 AC_SUBST(BINDINGS)
+AC_SUBST(BUILD_TESTS)
+AC_SUBST(BUILD_TOOLS)
 
 # Make AC_OUTPUT create each `file' by copying an input file (by default `file.in'),
 # substituting the output variable values.
 AC_CONFIG_FILES([
 	Makefile
-	doc/Makefile
 	src/Makefile
 	src/C/Makefile
 	src/h5core/Makefile
         src/Fortran/Makefile
 	test/Makefile
-	test/H5Part/Makefile
-	test/H5Block/Makefile
-	test/H5Fed/Makefile
 	tools/Makefile
 	tools/h5hutcc
 ])

doc/Makefile.am

@@ -1,17 +1,10 @@
-DOXYGROUPS = \
-	h5part__attrib \
-	h5part__errhandle \
-	h5part__openclose \
-	h5part__read \
-	h5part__write \
-	h5block__c__api 
-
 EXTRA_DIST = \
-	Doxyfile doxyfooter
+	Doxyfile \
+        H5.dox
 
 all:
 
-doc:	doxydoc
+doc:
 
 doxydoc:
 	doxygen

src/C/H5Fed_retrieve.c

@@ -107,7 +107,7 @@ H5FedGetVertexCoordByID (
 	h5_float64_t P[3]
 	) {
 	SET_FNAME (f, __func__);
-	return h5t_get_vertrex_coords_by_id (f, vertex_id, P);
+	return h5t_get_vertex_coords_by_id (f, vertex_id, P);
 }
 
 h5_err_t

src/C/Makefile.am

@@ -6,7 +6,7 @@ LIBS = @LIBS@
 INCLUDES = -I../include @INCLUDES@
 
 # What to build... Will be determined by configure script.
-lib_LIBRARIES = libH5hutC.a
+lib_LIBRARIES = @LIB_C@
 
 # Listing of all possible targets that I may build.
 EXTRA_LIBRARIES = libH5hutC.a
@@ -20,6 +20,7 @@ include_HEADERS =				\
 	../include/H5Block.h			\
 	../include/H5Block_readwrite.h		\
 	../include/H5Fed.h			\
+	../include/H5Fed_adjacency.h		\
 	../include/H5Fed_inquiry.h		\
 	../include/H5Fed_retrieve.h		\
 	../include/H5Fed_store.h		\
@@ -42,8 +43,5 @@ libH5hutC_a_SOURCES =				\
 	H5Fed_store.c				\
 	H5Fed_tags.c
 
-all: ../lib/libH5hutC.a
-
-../lib/libH5hutC.a: libH5hutC.a
-	-cp $^ $@
+clean: cleam-am
 

src/Fortran/Makefile.am

@@ -23,7 +23,7 @@ EXTRA_DIST =		TestUnderscoreC.c \
 nodist_include_HEADERS = ../include/H5hutF.h
 
 # What to build... Will be determined by configure script.
-lib_LIBRARIES = @FORTRAN_LIB@
+lib_LIBRARIES = @LIB_FORTRAN@
 
 # Listing of all possible targets that I may build.
 EXTRA_LIBRARIES = libH5hutF.a
@@ -34,11 +34,11 @@ libH5hutF_a_SOURCES =	H5_F.c \
 			H5Block_F.c \
 			H5Block_readwrite_F.c
 
-all: ../include/H5hutF.h ../lib/libH5hutF.a
+libH5hutF_a_DEPENDENCIES = ../include/H5hutF.h
 
 ../include/H5hutF.h: $(F90_FILES)
 	awk '/INTEGER\*8 FUNCTION/{print "\t" $$1 " " $$3}' $^ >$@
 
-../lib/libH5hutF.a: libH5hutF.a
-	-cp $^ $@
+clean: clean-am
+	$(RM) ../include/H5hutF.h
 

src/Makefile.am

@@ -1,3 +1,4 @@
 # test level Makefile.am
 
 SUBDIRS = h5core @BINDINGS@
+

src/h5core/Makefile.am

@@ -8,6 +8,7 @@ INCLUDES = -I../include @INCLUDES@
 EXTRA_HEADERS =					\
 	../include/h5core/h5_attribs.h		\
 	../include/h5core/h5_core.h		\
+	../include/h5core/h5_errno.h		\
 	../include/h5core/h5_errorhandling.h	\
 	../include/h5core/h5_hdf5.h		\
 	../include/h5core/h5_maps.h		\
@@ -20,6 +21,7 @@ EXTRA_HEADERS =					\
 	../include/h5core/h5b_model.h		\
 	../include/h5core/h5b_attribs.h		\
 	../include/h5core/h5t_adjacencies.h	\
+	../include/h5core/h5t_core.h		\
 	../include/h5core/h5t_inquiry.h		\
 	../include/h5core/h5t_map.h		\
 	../include/h5core/h5t_openclose.h	\
@@ -28,45 +30,46 @@ EXTRA_HEADERS =					\
 	../include/h5core/h5t_retrieve.h	\
 	../include/h5core/h5t_storemesh.h	\
 	../include/h5core/h5t_tags.h		\
+	h5b_errorhandling_private.h		\
+	h5b_model_private.h			\
+	h5b_types_private.h			\
+	h5_core_private.h			\
 	h5_errorhandling_private.h		\
 	h5_fcmp_private.h			\
 	h5_hdf5_private.h			\
 	h5_hsearch_private.h			\
+	h5_lustre_private.h			\
 	h5_mpi_private.h			\
 	h5_qsort_private.h			\
 	h5_readwrite_private.h			\
 	h5_syscall_private.h			\
-	h5_lustre_private.h			\
-	h5u_errorhandling_private.h             \
-	h5b_errorhandling_private.h		\
-        h5b_model_private.h			\
 	h5t_access_private.h			\
 	h5t_adjacencies_private.h		\
 	h5t_consts_private.h			\
+	h5t_core_private.h			\
 	h5t_errorhandling_private.h		\
 	h5t_hsearch_private.h			\
+	h5t_map_private.h			\
 	h5t_openclose_private.h			\
 	h5t_readwrite_private.h			\
 	h5t_retrieve_private.h			\
 	h5t_store_private.h			\
-	h5t_tags_private.h
+	h5t_store_trim_private.h		\
+	h5t_tags_private.h			\
+	h5t_types_private.h			\
+	h5_types_private.h			\
+	h5u_errorhandling_private.h		\
+	h5u_types_private.h
 
 # Extra files that I wish to include in the dist tar ball.
 EXTRA_DIST = $(EXTRA_HEADERS)
 
-# Files that I don't want to include in the dist tar ball
-nodist_include_HEADERS =
-
-#OBJEXT = o
 # What to build... Will be determined by configure script.
 lib_LIBRARIES = libH5hut.a
 
 # Listing of all possible targets that I may build.
 EXTRA_LIBRARIES = libH5hut.a
 
-# Header files that I wish to install in $(prefix)/include
-include_HEADERS =
-
 # Listing of sources
 libH5hut_a_SOURCES =				\
 	h5_attribs.c				\
@@ -112,10 +115,9 @@ libH5hut_a_SOURCES =				\
 
 libH5hut_a_DEPENDENCIES = $(EXTRA_HEADERS)
 
-all: ../lib/libH5hut.a
+install-exec-local:
+	@$(INSTALL) -d $(DESTDIR)$(includedir)/h5core
+	@$(INSTALL) -m644 ../include/h5core/*.h $(DESTDIR)$(includedir)/h5core/
 
-../lib/libH5hut.a: libH5hut.a
-	-cp $^ $@
-
-$(libH5hut_a_OBJECTS): $(libH5hut_a_DEPENDENCIES)
+clean: clean-am
 

src/h5core/h5_errorhandling.c

@@ -152,7 +152,11 @@ h5_abort_errorhandler (
 	if (h5priv_debug_level > 0) {
 		h5_verror (f, fmt, ap);
 	}
+#ifdef PARALLEL_IO
+        MPI_Abort(f->comm, -(int)f->__errno);
+#else
 	exit (-(int)f->__errno);
+#endif
 }
 
 static void

src/h5core/h5_lustre.c

@@ -28,7 +28,7 @@ _print_stripe_info(struct lov_user_md *lum)
 }
 
 static ssize_t
-_get_lustre_stripe_size ( const char *path )
+_get_lustre_stripe_size(h5_file_t *const f,  const char *path )
 {
 	size_t nbytes = sizeof(struct lov_user_md) +
 				INIT_ALLOC_NUM_OSTS * sizeof(struct lov_user_ost_data);
@@ -89,7 +89,7 @@ _get_lustre_stripe_size ( const char *path )
 	return stripe_size;
 }
 
-herr_t
+h5_err_t
 h5_optimize_for_lustre (
 	h5_file_t *const f,
 	const char *filename
@@ -114,17 +114,19 @@ h5_optimize_for_lustre (
 		}
 		else fclose(test);
 
-		stripe_size = _get_lustre_stripe_size(path);
+		stripe_size = _get_lustre_stripe_size(f, path);
 
 		free(path);
 	}
 
 	TRY( h5priv_mpi_bcast(f, &stripe_size, 1, MPI_LONG_LONG, 0, f->comm) );
-	h5_info(f, "Found lustre stripe size of %lld bytes", (long long)stripe_size);
+	h5_info(f, MSG_HEADER
+		"Found lustre stripe size of %lld bytes",
+		(long long)stripe_size);
 
 	hsize_t btree_ik = (stripe_size - 4096) / 96;
 	hsize_t btree_bytes = 64 + 96*btree_ik;
-	h5_info(f,
+	h5_info(f, MSG_HEADER
 		"Setting HDF5 btree ik to %lld (= %lld bytes at rank 3)",
 		(long long)btree_ik, (long long)btree_bytes);
 	TRY( h5priv_set_hdf5_btree_ik_property(f, f->create_prop, btree_ik) );
@@ -133,21 +135,19 @@ h5_optimize_for_lustre (
 	TRY( h5priv_set_hdf5_alignment_property(f,
 				f->access_prop, 0, stripe_size) );
 
-	if (_verbose) {
-		fprintf(MSG_STREAM, MSG_HEADER "disabling metadata cache flushes.\n");
-	}
+	h5_info(f, MSG_HEADER "Disabling metadata cache flushes.");
 	/* disable metadata cache flushes */
 	/* defer metadata writes */
 	H5AC_cache_config_t config;
 	config.version = H5AC__CURR_CACHE_CONFIG_VERSION;
-	TRY( H5Pget_mdc_config( fapl_id, &config ) );
+	TRY( H5Pget_mdc_config( f->access_prop, &config ) );
 	config.set_initial_size = 1;
 	config.initial_size = 16 * 1024 * 1024;
 	config.evictions_enabled = 0;
 	config.incr_mode = H5C_incr__off;
 	config.decr_mode = H5C_decr__off;
 	config.flash_incr_mode = H5C_flash_incr__off;
-	TRY( H5Pset_mdc_config( fapl_id, &config ) );
+	TRY( H5Pset_mdc_config( f->access_prop, &config ) );
 
 	return H5_SUCCESS;
 }

src/h5core/h5_qsort.c

@@ -97,8 +97,6 @@ med3(char *a, char *b, char *c, cmp_t *cmp, void *thunk
 #ifndef I_AM_QSORT_R
 #if __GNUC__
 __attribute__((unused))
-#else
-__unused
 #endif
 #endif
 )

test/H5Fed/Makefile.am

@@ -2,9 +2,6 @@
 
 OBJEXT = o
 
-# PATH SETTING
-HDF5ROOT = @HDF5ROOT@
-
 # COMPILER SETTING
 CXX = @CXX@
 FC = @FC@
@@ -13,30 +10,14 @@ MPICXX = @MPICXX@
 MPICC = @MPICC@
 
 # COMPILER FLAG SETTING
-CFLAGS = @CFLAGS@
-FFLAGS = @FFLAGS@ @MPIINC@
+AM_CFLAGS = @CFLAGS@
+FFLAGS = @FFLAGS@
 
-# LIBRARIES
-SZLIB = @SZLIB@
-HDFLIB = -L$(HDF5ROOT)/lib -lhdf5 -lz $(SZLIB) @LDFLAGS@
-MPILIB = @MPILIB@
-H5LIB = -L${abs_top_builddir}/src/lib -lH5Core -lH5
+AM_LDFLAGS = -L../../src/lib @LDFLAGS@
+LIBS = -lH5hutC -lH5hut @LIBS@
+INCLUDES = -I../../src/include @INCLUDES@
 
-LIBS = ${H5LIB} $(HDFLIB) $(MPILIB) -lm @STDCXX@
-
-# H5Part compiled library location
-# H5PLIB = -L@prefix@/lib
-
-# INCLUDES
-HDFINC = -I$(HDF5ROOT)/include
-MPIINC = @MPIINC@
-H5INC = -I${abs_top_builddir}/src/include
-
-INC = $(HDFINC) $(MPIINC) $(H5INC)
-
-
-# What to build... make install will place these files in the $(prefix)/bin directory.
-bin_PROGRAMS =					\
+noinst_PROGRAMS =				\
 		tetmesh_write			\
 		tetmesh_write2			\
 		tetmesh_read			\
@@ -49,12 +30,6 @@ bin_PROGRAMS =					\
 #		map_tet2globalid \
 #		map_triangle2globalid
 
-# Some useful scripts that I wish to place in the $(prefix)/bin directory.
-bin_SCRIPTS =
-
-# Listing of all programs that maybe built. (Has to know statically...)
-EXTRA_PROGRAMS =
-
 # Extra files that I wish to include in the dist tar ball.
 EXTRA_DIST =					\
 		tetmesh_write.c			\
@@ -70,27 +45,8 @@ EXTRA_DIST =					\
 #		map_triangle2globalid.c \
 #		$(bin_SCRIPTS)
 
-all:	$(bin_PROGRAMS)
-
-###############################################################################
-% : %.o
-	$(CC) -o $@ $< $(H5LIB) $(LIBS)
-
-%.o : %.c
-	$(CC) $(CFLAGS) $(INC) -g -c $<
-
-%.o : %.f90
-	${FC} $(FFLAGS) -c $(H5INC) $<
-
-###############################################################################
-clean:
-	${RM} -f *~ *.o  ${bin_PROGRAMS}
-
-distclean: clean
-	${RM} -rf .deps
-	${RM} -rf .libs
-	${RM} -f parttest.h5
-	${RM} -rf config.status config.log config.h Makefile
-
+all:	$(noinst_PROGRAMS)
 
+clean: clean-am
+	rm -f *.h5
 

test/H5Fed/map_tet2globalid.c

@@ -1,8 +1,7 @@
 #include <stdio.h>
 #include <stdlib.h>
-#include <hdf5.h>
-#include "H5Part.h"
-#include "H5Fed.h"
+
+#include "H5hut.h"
 
 #ifndef PARALLEL_IO
 #ifndef MPI_COMM_WORLD

test/H5Fed/map_triangle2globalid.c

@@ -1,8 +1,7 @@
 #include <stdio.h>
 #include <stdlib.h>
-#include <hdf5.h>
-#include "H5Part.h"
-#include "H5Fed.h"
+
+#include "H5hut.h"
 
 #ifndef PARALLEL_IO
 #ifndef MPI_COMM_WORLD

test/H5Fed/tetmesh_adjacencies.c

@@ -2,8 +2,7 @@
 #include <stdlib.h>
 #include <time.h>
 
-#include "H5Part.h"
-#include "H5Fed.h"
+#include "H5hut.h"
 
 #define PRINT_UPADJACENCIES 1
 #define PRINT_DOWNADJACENCIES 0

test/H5Fed/tetmesh_read.c

@@ -2,8 +2,7 @@
 #include <stdlib.h>
 #include <time.h>
 
-#include "H5Part.h"
-#include "H5Fed.h"
+#include "H5hut.h"
 
 const h5_oid_t MESH_TYPE = H5_TETRAHEDRAL_MESH;
 const char* FNAME = "simple_tet.h5";

test/H5Fed/tetmesh_read_tags.c

@@ -1,9 +1,8 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <time.h>
-#include <hdf5.h>
-#include "H5Part.h"
-#include "H5Fed.h"
+
+#include "H5hut.h"
 
 #ifndef PARALLEL_IO
 #ifndef MPI_COMM_WORLD

test/H5Fed/tetmesh_write.c

@@ -2,8 +2,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "H5Part.h"
-#include "H5Fed.h"
+#include "H5hut.h"
 
 #ifndef PARALLEL_IO
 #ifndef MPI_COMM_WORLD

test/H5Fed/tetmesh_write2.c

@@ -2,8 +2,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "H5Part.h"
-#include "H5Fed.h"
+#include "H5hut.h"
 
 const h5_oid_t MESH_TYPE = H5_TETRAHEDRAL_MESH;
 const char* FNAME = "simple_tet.h5";

test/H5Fed/tetmesh_write_tags.c

@@ -3,8 +3,7 @@
 #include <time.h>
 #include <string.h>
 
-#include "H5Part.h"
-#include "H5Fed.h"
+#include "H5hut.h"
 
 const h5_oid_t MESH_TYPE = H5_TETRAHEDRAL_MESH;
 const char* FNAME = "simple_tet.h5";

test/H5Fed/trimesh_read.c

@@ -1,8 +1,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 
-#include "H5Part.h"
-#include "H5Fed.h"
+#include "H5hut.h"
 
 const h5_oid_t MESH_TYPE = H5_TRIANGLE_MESH;
 const char* FNAME = "simple_triangle.h5";

test/H5Fed/trimesh_write.c

@@ -1,8 +1,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 
-#include "H5Part.h"
-#include "H5Fed.h"
+#include "H5hut.h"
 
 const h5_oid_t MESH_TYPE = H5_TRIANGLE_MESH;
 const char* FNAME = "simple_triangle.h5";

test/H5Fed/write_boundary.c

@@ -1,8 +1,7 @@
 #include <stdio.h>
 #include <stdlib.h>
-#include <hdf5.h>
-#include "H5Part.h"
-#include "H5Fed.h"
+
+#include "H5hut.h"
 
 #ifndef PARALLEL_IO
 #ifndef MPI_COMM_WORLD

test/Makefile.am

@@ -4,15 +4,15 @@
 
 OBJEXT=o
 
-LDFLAGS = -L../src/lib @LDFLAGS@
+AM_LDFLAGS = -L../src/h5core -L../src/C @LDFLAGS@
 LIBS = -lH5hutC -lH5hut @LIBS@
 
 INCLUDES = -I../src/include @INCLUDES@
 
-noinst_PROGRAMS = h5u_test h5b_test
+noinst_PROGRAMS = @BUILD_TESTS@
 
 TESTS_ENVIRONMENT = env LD_LIBRARY_PATH=@HDF5ROOT@/lib:$(LD_LIBRARY_PATH)
-TESTS = h5u_test h5b_test
+TESTS = @BUILD_TESTS@
 
 EXTRA_PROGRAMS = h5u_test h5b_test
 
@@ -25,8 +25,8 @@ h5u_test_SOURCES =	\
 		params.h
 
 h5u_test_DEPENDENCIES = \
-		../src/lib/libH5hut.a \
-		../src/lib/libH5hutC.a
+		../src/h5core/libH5hut.a \
+		../src/C/libH5hutC.a
 
 h5b_test_SOURCES =	\
 		h5b_test.c \
@@ -37,8 +37,8 @@ h5b_test_SOURCES =	\
 		params.h
 
 h5b_test_DEPENDENCIES = \
-		../src/lib/libH5hut.a \
-		../src/lib/libH5hutC.a
+		../src/h5core/libH5hut.a \
+		../src/C/libH5hutC.a
 
 clean: clean-am
 	rm -f *.h5

tools/Makefile.am

@@ -2,27 +2,26 @@
 
 OBJEXT=o
 
-LDFLAGS = -L../src/lib @LFLAGS@
+AM_LDFLAGS = -L../src/lib @LFLAGS@
 LIBS = -lH5hutC -lH5hut @LIBS@
 
 INCLUDES = -I../src/include @INCLUDES@
 
 # What to build... make install will place these files in the $(prefix)/bin directory.
-bin_PROGRAMS = @BUILD_TOOLS@
+bin_SCRIPTS = @BUILD_TOOLS@
 
 # Listing of all programs that maybe built. (Has to know statically...)
-EXTRA_PROGRAMS = h5pAttrib h5pToGNUplot # homdynToH5p
+EXTRA_SCRIPTS = h5hutcc
 
 # Extra files that I wish to include in the dist tar ball.
-EXTRA_DIST = h5pAttrib.cc h5pToGNUplot.cc## TO BE TAILORED LATER...
+#EXTRA_DIST = h5pAttrib.cc h5pToGNUplot.cc## TO BE TAILORED LATER...
 
 # Listing of sources
-h5pAttrib_SOURCES = h5pAttrib.cc
+#h5pAttrib_SOURCES = h5pAttrib.cc
 
-h5pToGNUplot_SOURCES = h5pToGNUplot.cc
+#h5pToGNUplot_SOURCES = h5pToGNUplot.cc
 
 #homdynToH5p_SOURCES = homdynToH5p.cc
 
-install-exec-local:
-	@$(INSTALL) h5hutcc $(DESTDIR)$(bindir)/h5hutcc
+clean: clean-am
 

tools/h5pAttrib.cc

@@ -8,8 +8,8 @@
 #include <stdlib.h>
 #include <cctype>
 #include <string.h>
-#include <hdf5.h>
-#include "H5Part.h"
+
+#include "H5hut.h"
 
 #define MAX_LEN 100
 
@@ -17,11 +17,11 @@
 int get_option(int argc, const char **argv, const char *opts, const struct long_options *l_opts);
 static void print_help();
 static void free_handler(struct arg_handler *hand, int len);
-static void print_all(H5PartFile* file);
-static void print_nstep(H5PartFile* file, char * garbage);
-static void print_file_attributes(H5PartFile* file, char * garbage);
-static void print_step_attributes(H5PartFile* file, char *attr);
-static void print_dataset(H5PartFile* file, char *attr);
+static void print_all(h5_file_t* file);
+static void print_nstep(h5_file_t* file, char * garbage);
+static void print_file_attributes(h5_file_t* file, char * garbage);
+static void print_step_attributes(h5_file_t* file, char *attr);
+static void print_dataset(h5_file_t* file, char *attr);
 static struct arg_handler* function_assign(int argc, const char *argv[]);
 
 /* Global variables */
@@ -66,7 +66,7 @@ static struct long_options l_opts[] =
 
 /* a structure for handling the order command-line parameters come in */
 struct arg_handler {
-    void (*func)(H5PartFile *, char *);
+    void (*func)(h5_file_t *, char *);
     char *obj;
 };
 
@@ -335,27 +335,27 @@ static void print_help()
 }
 
 /* For priting everything (default option when no flags provided.) */
-static void print_all(H5PartFile* file)
+static void print_all(h5_file_t* file)
 {
    int nt;
 
    char file_attrib[MAX_LEN];
-   h5part_int64_t type;
-   h5part_int64_t num_elem;
-   h5part_int64_t num_attrib;
+   h5_int64_t type;
+   h5_int64_t num_elem;
+   h5_int64_t num_attrib;
    char step_attrib[MAX_LEN];
-   h5part_int64_t i, j, k;
-   h5part_int64_t count;
+   h5_int64_t i, j, k;
+   h5_int64_t count;
    void* value = NULL;
-   h5part_int64_t timestep_ctr;
+   h5_int64_t timestep_ctr;
 
    char data_name[MAX_LEN];
-   h5part_int64_t num_dataset;
-   h5part_int64_t nparticles;
+   h5_int64_t num_dataset;
+   h5_int64_t nparticles;
 
    fprintf(stdout, "\n++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n");
    fprintf(stdout, "\n");
-   nt=H5PartGetNumSteps(file);
+   nt=H5GetNumSteps(file);
    fprintf(stdout, "There are total %d number of timesteps.\n",nt);
 
    fprintf(stdout, "\nDump result for \"%s\"...\n\n", global_fname);
@@ -364,25 +364,33 @@ static void print_all(H5PartFile* file)
 
    if(print_header)
    {
-      num_attrib = H5PartGetNumFileAttribs(file);
+      num_attrib = H5GetNumFileAttribs(file);
 
       for(i=0; i<num_attrib; i++)
       {
-         H5PartGetFileAttribInfo(file, i, file_attrib, MAX_LEN, &type, &num_elem);
+         H5GetFileAttribInfo(file, i, file_attrib, MAX_LEN, &type, &num_elem);
          fprintf(stdout, "\tAttribute #%lld = %s\n",(long long)i,file_attrib);
          fprintf(stdout, "\tThere are %lld elements in the attribute\n",(long long)num_elem);
 
-         if (type == H5T_NATIVE_INT64)
+         if (type == H5_INT64_T)
          {
-            fprintf(stdout, "\tAttribute Type: H5T_NATIVE_INT64\n");
+            fprintf(stdout, "\tAttribute Type: H5_INT64_T\n");
          }
-         else if (type == H5T_NATIVE_CHAR)
+         else if (type == H5_INT32_T)
          {
-            fprintf(stdout, "\tAttribute Type: H5T_NATIVE_CHAR\n");
+            fprintf(stdout, "\tAttribute Type: H5_INT32_T\n");
          }
-         else if (type == H5T_NATIVE_DOUBLE)
+         else if (type == H5_FLOAT64_T)
          {
-            fprintf(stdout, "\tAttribute Type: H5T_NATIVE_DOUBLE\n");
+            fprintf(stdout, "\tAttribute Type: H5_FLOAT64_T\n");
+         }
+         else if (type == H5_FLOAT32_T)
+         {
+            fprintf(stdout, "\tAttribute Type: H5_FLOAT32_T\n");
+         }
+         else if (type == H5_STRING_T)
+         {
+            fprintf(stdout, "\tAttribute Type: H5_STRING_T\n");
          }
          else
          {
@@ -396,18 +404,18 @@ static void print_all(H5PartFile* file)
    }
    else
    {
-      num_attrib = H5PartGetNumFileAttribs(file);
+      num_attrib = H5GetNumFileAttribs(file);
 
       for(i=0; i<num_attrib; i++)
       {
-         H5PartGetFileAttribInfo(file, i, file_attrib, MAX_LEN, &type, &num_elem);
+         H5GetFileAttribInfo(file, i, file_attrib, MAX_LEN, &type, &num_elem);
          fprintf(stdout, "\tAttribute #%lld = %s\n",(long long)i,file_attrib);
          fprintf(stdout, "\tThere are %lld elements in the attribute\n",(long long)num_elem);
 
          if (type == H5T_NATIVE_INT64)
          {
-            value = (h5part_int64_t*)malloc(sizeof(h5part_int64_t)*num_elem);
-            H5PartReadFileAttrib(file, file_attrib, (h5part_int64_t*)value);
+            value = (h5_int64_t*)malloc(sizeof(h5_int64_t)*num_elem);
+            H5PartReadFileAttrib(file, file_attrib, (h5_int64_t*)value);
 
             fprintf(stdout, "\tAttribute Type: H5T_NATIVE_INT64\n");
 
@@ -546,8 +554,8 @@ static void print_all(H5PartFile* file)
 
              if (type == H5T_NATIVE_INT64)
              {
-                value = (long long int*)malloc(sizeof(h5part_int64_t)*num_elem);
-                H5PartReadStepAttrib(file, step_attrib, (h5part_int64_t*)value);
+                value = (long long int*)malloc(sizeof(h5_int64_t)*num_elem);
+                H5PartReadStepAttrib(file, step_attrib, (h5_int64_t*)value);
 
                 fprintf(stdout, "\tAttribute Type: H5T_NATIVE_INT64\n");
 
@@ -675,8 +683,8 @@ static void print_all(H5PartFile* file)
 
             if (type == H5T_NATIVE_INT64)
             {
-               value = (h5part_int64_t*)malloc(sizeof(h5part_int64_t)*nparticles);
-               H5PartReadDataInt64(file, data_name, (h5part_int64_t*)value);
+               value = (h5_int64_t*)malloc(sizeof(h5_int64_t)*nparticles);
+               H5PartReadDataInt64(file, data_name, (h5_int64_t*)value);
                fprintf(stdout, "\tDataset Type: H5T_NATIVE_INT64\n");
                fprintf(stdout, "\tPrinting %lld element value(s):\n", (long long)nparticles);
 
@@ -745,7 +753,7 @@ static void print_all(H5PartFile* file)
 }
 
 /* For printing number of timesteps in the file */
-static void print_nstep(H5PartFile* file, char * garbage)
+static void print_nstep(h5_file_t* file, char * garbage)
 {
     int nt;
 
@@ -758,14 +766,14 @@ static void print_nstep(H5PartFile* file, char * garbage)
 }
 
 /* For printing file attributes */
-static void print_file_attributes(H5PartFile* file, char * garbage)
+static void print_file_attributes(h5_file_t* file, char * garbage)
 {
     char file_attrib[MAX_LEN];
-    h5part_int64_t type;
-    h5part_int64_t num_elem;
-    h5part_int64_t num_attrib;
-    h5part_int64_t i, j, k;
-    h5part_int64_t count;
+    h5_int64_t type;
+    h5_int64_t num_elem;
+    h5_int64_t num_attrib;
+    h5_int64_t i, j, k;
+    h5_int64_t count;
     void* value = NULL;
 
     if(print_header)
@@ -820,8 +828,8 @@ static void print_file_attributes(H5PartFile* file, char * garbage)
 
           if (type == H5T_NATIVE_INT64)
           {
-             value = (h5part_int64_t*)malloc(sizeof(h5part_int64_t)*num_elem);
-             H5PartReadFileAttrib(file, file_attrib, (h5part_int64_t*)value);
+             value = (h5_int64_t*)malloc(sizeof(h5_int64_t)*num_elem);
+             H5PartReadFileAttrib(file, file_attrib, (h5_int64_t*)value);
 
              fprintf(stdout, "Attribute Type: H5T_NATIVE_INT64\n");
 
@@ -914,14 +922,14 @@ static void print_file_attributes(H5PartFile* file, char * garbage)
 }
 
 /* For printing step attribute names [& values] */
-static void print_step_attributes(H5PartFile* file, char *attr)
+static void print_step_attributes(h5_file_t* file, char *attr)
 {
     char step_attrib[MAX_LEN];
-    h5part_int64_t type;
-    h5part_int64_t num_elem;
-    h5part_int64_t num_attrib;
-    h5part_int64_t i, j, k;
-    h5part_int64_t count;
+    h5_int64_t type;
+    h5_int64_t num_elem;
+    h5_int64_t num_attrib;
+    h5_int64_t i, j, k;
+    h5_int64_t count;
     void* value = NULL;
 
     if(print_header)
@@ -960,8 +968,8 @@ static void print_step_attributes(H5PartFile* file, char *attr)
 
           if (type == H5T_NATIVE_INT64)
           {
-             value = (h5part_int64_t*)malloc(sizeof(h5part_int64_t)*num_elem);
-             H5PartReadStepAttrib(file, step_attrib, (h5part_int64_t*)value);
+             value = (h5_int64_t*)malloc(sizeof(h5_int64_t)*num_elem);
+             H5PartReadStepAttrib(file, step_attrib, (h5_int64_t*)value);
 
              fprintf(stdout, "Attribute Type is H5T_NATIVE_INT64\n");
 
@@ -1054,14 +1062,14 @@ static void print_step_attributes(H5PartFile* file, char *attr)
 }
 
 /* For printing dataset names [& values] */
-static void print_dataset(H5PartFile* file, char *attr)
+static void print_dataset(h5_file_t* file, char *attr)
 {
     char data_name[MAX_LEN];
     int i, j, k;
     long count;
-    h5part_int64_t type;
+    h5_int64_t type;
     int num_dataset;
-    h5part_int64_t nparticles;
+    h5_int64_t nparticles;
     void* value = NULL;
 
 
@@ -1108,7 +1116,7 @@ static void print_dataset(H5PartFile* file, char *attr)
        fprintf(stdout, "\n++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n");
        fprintf(stdout, "\nPrinting names of datasets for: %s ...\n", global_fname);
        fprintf(stdout, "\n");
-       H5PartSetStep(file,atoi(attr));
+       H5SetStep(file,atoi(attr));
        num_dataset = H5PartGetNumDatasets(file);
        fprintf(stdout, "The number of datasets for timestep #%d is %d ...\n\n", atoi(attr), num_dataset);
 
@@ -1119,8 +1127,8 @@ static void print_dataset(H5PartFile* file, char *attr)
 
           if (type == H5T_NATIVE_INT64)
           {
-             value = (h5part_int64_t*)malloc(sizeof(h5part_int64_t)*nparticles);
-             H5PartReadDataInt64(file, data_name, (h5part_int64_t*)value);
+             value = (h5_int64_t*)malloc(sizeof(h5_int64_t)*nparticles);
+             H5PartReadDataInt64(file, data_name, (h5_int64_t*)value);
              fprintf(stdout, "Dataset Type is H5T_NATIVE_INT64\n");
              fprintf(stdout, "Printing %lld element value(s):\n", (long long)nparticles);
 
@@ -1206,7 +1214,7 @@ int main(int argc, const char *argv[])
    /* Numerous variables */
    struct arg_handler   *hand = NULL;
    int                   i;
-   H5PartFile           *h5file = NULL;
+   h5_file_t           *h5file = NULL;
    const char         *fname = NULL;
 
    //h5pAttrib_function_table = &major_function_table;
@@ -1228,7 +1236,7 @@ int main(int argc, const char *argv[])
    /* Process accordingly */
    fname = argv[opt_ind];
    global_fname = fname; // To use in funtions
-   h5file = H5PartOpenFile(fname,H5PART_READ);
+   h5file = H5OpenFile(fname,H5_O_RDONLY,0);
 
    if ( h5file == NULL )
    {
@@ -1253,7 +1261,7 @@ int main(int argc, const char *argv[])
    }
 
    free_handler(hand, argc);
-   H5PartCloseFile(h5file);
+   H5CloseFile(h5file);
    fprintf(stdout,"done\n");
    return 0;
 }