geodynamics · QuLogic · Oct 1, 2015 · Oct 1, 2015 · Oct 1, 2015 · Oct 6, 2015
diff --git a/.gitignore b/.gitignore
@@ -35,6 +35,8 @@ bin/CitcomSRegional
 bin/citcoms
 bin/mpipycitcoms
 bin/pycitcoms
+visual/h5tocap
+visual/h5tovelo
 visual/project_geoid
 Py2C/Py2C
 

diff --git a/bin/Makefile.am b/bin/Makefile.am
@@ -24,12 +24,7 @@
 # $Id$
 
 
-INCLUDES = -I$(top_srcdir)/lib
-
-AM_CPPFLAGS =
-if COND_HDF5
-    AM_CPPFLAGS += -DUSE_HDF5
-endif
+AM_CPPFLAGS = -I$(top_srcdir)/lib
 
 bin_PROGRAMS = CitcomSFull CitcomSRegional
 

diff --git a/configure.ac b/configure.ac
@@ -33,7 +33,6 @@ AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([foreign])
 
 # 'configure' options
-CIT_ARG_HDF5([auto])
 AC_ARG_VAR(HC_HOME, [home path to HC program, used by --with-ggrd])
 AC_ARG_WITH([ggrd],
     [AC_HELP_STRING([--with-ggrd],
@@ -63,21 +62,16 @@ AC_PROG_LIBTOOL
 AC_SEARCH_LIBS([MPI_Init], [mpi mpich], [], [AC_MSG_ERROR([MPI library not found])])
 
 
-CIT_CHECK_LIB_HDF5
-CIT_CHECK_LIB_HDF5_PARALLEL
-
 # Checks for header files.
 AC_CHECK_HEADER([mpi.h], [], [AC_MSG_ERROR([header 'mpi.h' not found])])
-CIT_CHECK_HEADER_HDF5
 
 # Checks for typedefs, structures, and compiler characteristics.
 
 # Checks for library functions.
 
-if test "$want_hdf5" != no; then
-    want_hdf5=yes
-fi
-AM_CONDITIONAL([COND_HDF5], [test "$want_hdf5" = yes])
+AX_LIB_HDF5([parallel])
+AM_CONDITIONAL([COND_HDF5], [test "$with_hdf5" = yes])
+
 AC_SEARCH_LIBS([gzopen], [z], [
 		CPPFLAGS="-DUSE_GZDIR $CPPFLAGS"
 		], [
@@ -153,7 +147,7 @@ echo -e "\t CFLAGS: " $CFLAGS
 echo -e "\t CPPFLAGS: " $CPPFLAGS
 echo -e "\t LDFLAGS: " $LDFLAGS
 echo -e "\t LIBS: " $LIBS
-echo -e "\t with-hdf5: " $want_hdf5
+echo -e "\t with-hdf5: " $with_hdf5
 echo -e "\t with-ggrd: " $want_ggrd
 echo
 

diff --git a/doc/citcoms-manual.tex b/doc/citcoms-manual.tex
@@ -1172,12 +1172,10 @@ \section{\label{sec:HDF5-Configuration}HDF5 Configuration (Optional)}
 \end{quote}
 By default, CitcomS will attempt to auto-detect your PHDF5 installation,
 and will disable HDF5 support if it is not found. You may specify
-the location of your PHDF5 installation by setting the PHDF5\_HOME
-environment variable to the appropriate installation prefix.
+the location of your PHDF5 installation by passing the \texttt{-{}-with-hdf5}
+argument with the appropriate installation prefix.
 \begin{lyxcode}
-\$~export~PHDF5\_HOME=/opt/phdf5/1.6.5
-
-\$~./configure~-{}-with-hdf5
+\$~./configure~-{}-with-hdf5=/opt/phdf5/1.6.5
 \end{lyxcode}
 
 \subsection{Additional Tools}

diff --git a/lib/Makefile.am b/lib/Makefile.am
@@ -31,9 +31,6 @@ lib_LTLIBRARIES =
 noinst_LIBRARIES += libCitcomS.a
 
 AM_CPPFLAGS =
-if COND_HDF5
-    AM_CPPFLAGS += -DUSE_HDF5
-endif
 
 CUDA_SOURCES =
 

diff --git a/lib/Output_h5.c b/lib/Output_h5.c
@@ -30,7 +30,7 @@
 #include "output_h5.h"
 
 
-#ifdef USE_HDF5
+#ifdef HAVE_HDF5
 
 /****************************************************************************
  * Structs for HDF5 output                                                  *
@@ -146,7 +146,7 @@ extern void compute_geoid(struct All_variables *);
 
 void h5output_allocate_memory(struct All_variables *E)
 {
-#ifdef USE_HDF5
+#ifdef HAVE_HDF5
     /*
      * Field variables
      */
@@ -220,7 +220,7 @@ void h5output_allocate_memory(struct All_variables *E)
 
 void h5output(struct All_variables *E, int cycles)
 {
-#ifndef USE_HDF5
+#ifndef HAVE_HDF5
     if(E->parallel.me == 0)
         fprintf(stderr, "h5output(): CitcomS was compiled without HDF5!\n");
     MPI_Finalize();
@@ -244,7 +244,7 @@ void h5output(struct All_variables *E, int cycles)
 
 void h5input_params(struct All_variables *E)
 {
-#ifdef USE_HDF5
+#ifdef HAVE_HDF5
 
     int m = E->parallel.me;
 
@@ -266,7 +266,7 @@ void h5input_params(struct All_variables *E)
 }
 
 
-#ifdef USE_HDF5
+#ifdef HAVE_HDF5
 
 static void h5output_const(struct All_variables *E)
 {
@@ -461,7 +461,7 @@ void h5output_coord(struct All_variables *E)
     h5create_field(E->hdf5.file_id, field, "coord", "coordinates of nodes");
 
     /* write to dataset */
-    dataset = H5Dopen(E->hdf5.file_id, "/coord");
+    dataset = H5Dopen(E->hdf5.file_id, "/coord", H5P_DEFAULT);
     status  = h5write_field(dataset, field, 1, 1);
 
     /* release resources */
@@ -2416,4 +2416,4 @@ herr_t set_attribute_double_vector(hid_t obj_id,
     return set_attribute_array(obj_id, attr_name, 1, &dim, H5T_NATIVE_DOUBLE, data);
 }
 
-#endif  /* #ifdef USE_HDF5 */
+#endif  /* #ifdef HAVE_HDF5 */
diff --git a/lib/global_defs.h b/lib/global_defs.h
@@ -47,7 +47,7 @@ to functions across the whole filespace of CITCOM.
 
 
 
-#ifdef USE_HDF5
+#ifdef HAVE_HDF5
 #include "hdf5.h"
 #endif
 
@@ -699,7 +699,7 @@ struct CITCOM_GNOMONIC {
 };
 
 
-#ifdef USE_HDF5
+#ifdef HAVE_HDF5
 #include "hdf5_related.h"
 #endif
 #include "tracer_defs.h"
@@ -715,7 +715,7 @@ struct All_variables {
     FILE *fptime;
     FILE *fp_out;
 
-#ifdef USE_HDF5
+#ifdef HAVE_HDF5
     struct HDF5_INFO hdf5;
 #endif
     struct HAVE Have;

diff --git a/m4 b/m4
diff --git a/visual/Makefile.am b/visual/Makefile.am
@@ -137,9 +137,18 @@ project_geoid_SOURCES = project_geoid.c
 
 if COND_HDF5
     bin_PROGRAMS += h5tocap h5tovelo
+
     h5tocap_SOURCES = h5tocap.c h5util.c h5util.h
+    h5tocap_CFLAGS = $(HDF5_CFLAGS)
+    h5tocap_CPPFLAGS = $(HDF5_CPPFLAGS)
+    h5tocap_LDFLAGS = $(HDF5_LDFLAGS)
+    h5tocap_LDADD = $(HDF5_LIBS)
+
     h5tovelo_SOURCES = h5tovelo.c h5util.c h5util.h
-    h5tovelo_LDADD = $(LIBHDF5)
+    h5tovelo_CFLAGS = $(HDF5_CFLAGS)
+    h5tovelo_CPPFLAGS = $(HDF5_CPPFLAGS)
+    h5tovelo_LDFLAGS = $(HDF5_LDFLAGS)
+    h5tovelo_LDADD = $(HDF5_LIBS)
 endif
 
 CLEANFILES = $(nodist_visual_DATA)

diff --git a/visual/h5tocap.c b/visual/h5tocap.c
@@ -119,7 +119,7 @@ int main(int argc, char *argv[])
      * Read model parameters from file
      */
 
-    input = H5Gopen(h5file, "input");
+    input = H5Gopen(h5file, "input", H5P_DEFAULT);
     if (input < 0)
     {
         fprintf(stderr, "Could not open /input group in \"%s\"\n", filename);

diff --git a/visual/h5tovelo.c b/visual/h5tovelo.c
@@ -104,7 +104,7 @@ int main(int argc, char *argv[])
      * Read model parameters from file1
      */
 
-    input = H5Gopen(h5file1, "input");
+    input = H5Gopen(h5file1, "input", H5P_DEFAULT);
     if (input < 0)
     {
         fprintf(stderr, "Could not open /input group in \"%s\"\n", filename1);
@@ -134,7 +134,7 @@ int main(int argc, char *argv[])
         return EXIT_FAILURE;
     }
 
-    input = H5Gopen(h5file2, "/");
+    input = H5Gopen(h5file2, "/", H5P_DEFAULT);
     status = get_attribute_float(input, "time", &time);
     status = H5Gclose(input);
 

diff --git a/visual/h5util.c b/visual/h5util.c
@@ -51,7 +51,7 @@ field_t *open_field(hid_t group, const char *name)
     field->maxdims = NULL;
     field->n = 0;
 
-    dataset = H5Dopen(group, name);
+    dataset = H5Dopen(group, name, H5P_DEFAULT);
     if(dataset < 0)
     {
         free(field);
@@ -122,7 +122,7 @@ herr_t read_field(hid_t group, field_t *field, int cap)
     if (group < 0 || field == NULL)
         return -1;
 
-    dataset = H5Dopen(group, field->name);
+    dataset = H5Dopen(group, field->name, H5P_DEFAULT);
 
     if (dataset < 0)
         return -1;