optional HDF5 compilation

via configure script and pre-processor macros

Makefile.am

@@ -36,10 +36,6 @@ ACLOCAL_AMFLAGS = -I m4
 CLEANFILES = trexio.mod
 BUILT_SOURCES = trexio.mod
 
-VERSION_MAJOR   = @VERSION_MAJOR@
-VERSION_MINOR   = @VERSION_MINOR@
-VERSION_PATCH   = @VERSION_PATCH@
-
 SUBDIRS = 
 
 pkgconfigdir = $(libdir)/pkgconfig
@@ -62,11 +58,16 @@ SOURCES = \
   src/trexio.c \
   src/trexio_private.h \
   src/trexio_s.h \
-  src/trexio_hdf5.c \
-  src/trexio_hdf5.h \
   src/trexio_text.c \
   src/trexio_text.h
 
+if DO_HDF5 
+
+SOURCES += src/trexio_hdf5.c \
+           src/trexio_hdf5.h 
+
+endif
+
 ORG_FILES = \
   src/templates_front/templator_front.org \
   src/templates_text/templator_text.org \
@@ -79,24 +80,30 @@ src_libtrexio_la_SOURCES = $(SOURCES)
 # =============== TESTS =============== #
 
 TESTS_C = \
-  tests/open_hdf5 \
   tests/open_text \
-  tests/io_num_hdf5 \
   tests/io_num_text \
-  tests/io_dset_float_hdf5 \
   tests/io_dset_float_text \
-  tests/io_dset_int_hdf5 \
   tests/io_dset_int_text \
-  tests/io_safe_dset_float_hdf5 \
   tests/io_safe_dset_float_text \
-  tests/io_str_hdf5 \
   tests/io_str_text \
-  tests/io_dset_str_hdf5 \
   tests/io_dset_str_text \
-  tests/overwrite_all_hdf5 \
   tests/overwrite_all_text \
   tests/io_all
 
+if DO_HDF5 
+
+TESTS_C += \
+  tests/open_hdf5 \
+  tests/io_num_hdf5 \
+  tests/io_dset_float_hdf5 \
+  tests/io_dset_int_hdf5 \
+  tests/io_safe_dset_float_hdf5 \
+  tests/io_str_hdf5 \
+  tests/io_dset_str_hdf5 \
+  tests/overwrite_all_hdf5 
+
+endif
+
 TESTS_F = \
   tests/test_f
 
@@ -108,24 +115,30 @@ LDADD = src/libtrexio.la
 
 # in principal, specifying -no-install (see below) is not mandatory
 # for the tests to compile and pass, but the produced test binaries differ 
-tests_open_hdf5_LDFLAGS = -no-install
 tests_open_text_LDFLAGS = -no-install
-tests_io_num_hdf5_LDFLAGS = -no-install
 tests_io_num_text_LDFLAGS = -no-install
-tests_io_dset_float_hdf5_LDFLAGS = -no-install
 tests_io_dset_float_text_LDFLAGS = -no-install
-tests_io_dset_int_hdf5_LDFLAGS = -no-install
 tests_io_dset_int_text_LDFLAGS = -no-install
-tests_io_safe_dset_float_hdf5_LDFLAGS = -no-install
 tests_io_safe_dset_float_text_LDFLAGS = -no-install
-tests_io_str_hdf5_LDFLAGS = -no-install
 tests_io_str_text_LDFLAGS = -no-install
-tests_io_dset_str_hdf5_LDFLAGS = -no-install
 tests_io_dset_str_text_LDFLAGS = -no-install
-tests_overwrite_all_hdf5_LDFLAGS = -no-install
 tests_overwrite_all_text_LDFLAGS = -no-install
 tests_io_all_LDFLAGS = -no-install
 
+if DO_HDF5 
+
+tests_open_hdf5_LDFLAGS = -no-install
+tests_io_num_hdf5_LDFLAGS = -no-install
+tests_io_dset_float_hdf5_LDFLAGS = -no-install
+tests_io_dset_int_hdf5_LDFLAGS = -no-install
+tests_io_safe_dset_float_hdf5_LDFLAGS = -no-install
+tests_io_str_hdf5_LDFLAGS = -no-install
+tests_io_dset_str_hdf5_LDFLAGS = -no-install
+tests_overwrite_all_hdf5_LDFLAGS = -no-install
+
+endif
+
+
 test_trexio_f = $(srcdir)/tests/trexio_f.f90
 
 $(test_trexio_f): $(trexio_f)

configure.ac

@@ -14,13 +14,9 @@ AC_CONFIG_MACRO_DIR([m4])
 VERSION_MAJOR=`echo ${PACKAGE_VERSION} | cut -d. -f1`
 VERSION_MINOR=`echo ${PACKAGE_VERSION} | cut -d. -f2`
 VERSION_PATCH=`echo ${PACKAGE_VERSION} | cut -d. -f3 | cut -d- -f1`
-AC_DEFINE_UNQUOTED(TREXIO_PACKAGE_VERSION, ["${PACKAGE_VERSION}"], [full version])
+AC_DEFINE_UNQUOTED(VERSION_MAJOR, [$VERSION_MAJOR], [major version])
-AC_DEFINE_UNQUOTED(TREXIO_VERSION_MAJOR, [$VERSION_MAJOR], [major version])
+AC_DEFINE_UNQUOTED(VERSION_MINOR, [$VERSION_MINOR], [minor version])
-AC_DEFINE_UNQUOTED(TREXIO_VERSION_MINOR, [$VERSION_MINOR], [minor version])
+AC_DEFINE_UNQUOTED(VERSION_PATCH, [$VERSION_PATCH], [patch version])
-AC_DEFINE_UNQUOTED(TREXIO_VERSION_PATCH, [$VERSION_PATCH], [patch version])
-AC_SUBST([VERSION_MAJOR])
-AC_SUBST([VERSION_MINOR])
-AC_SUBST([VERSION_PATCH])
 
 ## Save system information, e.g. user name
 
@@ -110,6 +106,8 @@ AC_SUBST([PKG_HDF5])
 AC_SUBST([PKG_CFLAGS])
 AC_SUBST([PKG_LIBS])
 
+AM_CONDITIONAL([DO_HDF5],[test "$with_hdf5" = "yes"])
+
 # The block below should only execute if the ax_lib_hdf5.m4 macro failed to find HDF5.
 # It is only needed to manually build Python API because setup.py depends on HDF5.
 
@@ -203,7 +201,7 @@ CC ............:  ${CC}
 CPPFLAGS ......:  ${CPPFLAGS}
 CFLAGS ........:  ${CFLAGS}
 FC ............:  ${FC}
-FCLAGS ........:  ${FCFLAGS}
+FCFLAGS .......:  ${FCFLAGS}
 LDFLAGS .......:  ${LDFLAGS}
 LIBS ..........:  ${LIBS}
 

src/templates_front/build.sh

@@ -4,20 +4,20 @@
 cat prefix_front.c   > trexio.c
 cat prefix_front.h   > trexio.h
 
+# parse the config-defined version attributes to pass them to Fortran module file
+VERSION_VAL=`grep "PACKAGE_VERSION" ../../include/config.h | cut -d " " -f 3`
+VERSION_MAJOR_VAL=`grep "VERSION_MAJOR" ../../include/config.h | cut -d " " -f 3`
+VERSION_MINOR_VAL=`grep "VERSION_MINOR" ../../include/config.h | cut -d " " -f 3`
+VERSION_PATCH_VAL=`grep "VERSION_PATCH" ../../include/config.h | cut -d " " -f 3`
+
 # grep some usefull constants from the config.h
 echo "" >> trexio.h
-grep "TREXIO_PACKAGE_VERSION" ../../include/config.h >> trexio.h
+echo "#define TREXIO_PACKAGE_VERSION ${VERSION_VAL}" >> trexio.h
-grep "TREXIO_VERSION_MAJOR" ../../include/config.h >> trexio.h
+echo "#define TREXIO_VERSION_MAJOR ${VERSION_MAJOR_VAL}" >> trexio.h
-grep "TREXIO_VERSION_MINOR" ../../include/config.h >> trexio.h
+echo "#define TREXIO_VERSION_MINOR ${VERSION_MINOR_VAL}" >> trexio.h
-grep "TREXIO_VERSION_PATCH" ../../include/config.h >> trexio.h
+echo "#define TREXIO_VERSION_PATCH ${VERSION_PATCH_VAL}" >> trexio.h
 echo "" >> trexio.h
 
-# parse the config-defined version attributes to pass them to Fortran module file
-VERSION_VAL=`grep "TREXIO_PACKAGE_VERSION" ../../include/config.h | cut -d " " -f 3`
-VERSION_MAJOR_VAL=`grep "TREXIO_VERSION_MAJOR" ../../include/config.h | cut -d " " -f 3`
-VERSION_MINOR_VAL=`grep "TREXIO_VERSION_MINOR" ../../include/config.h | cut -d " " -f 3`
-VERSION_PATCH_VAL=`grep "TREXIO_VERSION_PATCH" ../../include/config.h | cut -d " " -f 3`
-
 cat prefix_s_front.h > trexio_s.h
 cat prefix_fortran.f90   > trexio_f.f90
 cat prefix_python.py   > trexio.py

src/templates_front/templator_front.org

@@ -32,6 +32,11 @@ typedef int32_t trexio_exit_code;
 
   #+begin_src c :tangle prefix_front.c :noweb yes
 <<header>>
+
+#ifdef HAVE_CONFIG_H
+  #include "config.h"
+#endif
+
 #include <pthread.h>
 #include <assert.h>
 #include <stdlib.h>
@@ -42,7 +47,9 @@ typedef int32_t trexio_exit_code;
 #include "trexio_private.h"
 #include "trexio_s.h"
 #include "trexio_text.h"
-#include "trexio_hdf5.h"
+#ifdef HAVE_HDF5 
+  #include "trexio_hdf5.h"
+#endif
 /*
 #include "trexio_json.h"
 ,*/
@@ -739,9 +746,11 @@ trexio_open(const char* file_name, const char mode,
     result_tmp = malloc(sizeof(trexio_text_t));
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     result_tmp = malloc(sizeof(trexio_hdf5_t));
     break;
+#endif
 /*
   case TREXIO_JSON:
     result = (trexio_t*) malloc (sizeof(trexio_json_t));
@@ -790,9 +799,11 @@ trexio_open(const char* file_name, const char mode,
     rc = trexio_text_init(result);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     rc = trexio_hdf5_init(result);
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc = trexio_json_init(result);
@@ -820,9 +831,11 @@ trexio_open(const char* file_name, const char mode,
       rc = trexio_text_write_metadata_package_version(result, TREXIO_PACKAGE_VERSION);
       break;
 
+#ifdef HAVE_HDF5 
     case TREXIO_HDF5:
       rc = trexio_hdf5_write_metadata_package_version(result, TREXIO_PACKAGE_VERSION);
       break;
+#endif 
 /*
     case TREXIO_JSON:
       rc = trexio_json_write_metadata_package_version(result, TREXIO_PACKAGE_VERSION);
@@ -848,9 +861,11 @@ trexio_open(const char* file_name, const char mode,
     rc = trexio_text_lock(result);
     break;
  /* HDF5 v.>=1.10 has file locking activated by default */
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     rc = TREXIO_SUCCESS;
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc = trexio_json_lock(result);
@@ -992,9 +1007,11 @@ trexio_close (trexio_t* file)
     rc = trexio_text_deinit(file);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     rc = trexio_hdf5_deinit(file);
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc = trexio_json_deinit(file);
@@ -1017,9 +1034,11 @@ trexio_close (trexio_t* file)
     rc = trexio_text_unlock(file);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     rc = TREXIO_SUCCESS;
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc = trexio_json_unlock(file);
@@ -1201,9 +1220,11 @@ trexio_read_$group_num$_64 (trexio_t* const file, $group_num_dtype_double$* cons
     return trexio_text_read_$group_num$(file, num);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     return trexio_hdf5_read_$group_num$(file, num);
     break;
+#endif
 /*
   case TREXIO_JSON:
     return trexio_json_read_$group_num$(file, num);
@@ -1229,9 +1250,11 @@ trexio_write_$group_num$_64 (trexio_t* const file, const $group_num_dtype_double
     return trexio_text_write_$group_num$(file, num);
     break;				       
 					       
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:			       
     return trexio_hdf5_write_$group_num$(file, num);
-    break;				       
+    break;
+#endif
 /*					       
   case TREXIO_JSON:			       
     return trexio_json_write_$group_num$(file, num);
@@ -1261,9 +1284,11 @@ trexio_read_$group_num$_32 (trexio_t* const file, $group_num_dtype_single$* cons
     rc = trexio_text_read_$group_num$(file, &num_64);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     rc = trexio_hdf5_read_$group_num$(file, &num_64);
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc =trexio_json_read_$group_num$(file, &num_64);
@@ -1293,9 +1318,11 @@ trexio_write_$group_num$_32 (trexio_t* const file, const $group_num_dtype_single
     return trexio_text_write_$group_num$(file, ($group_num_dtype_double$) num);
     break;					       
 						       
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:				       
     return trexio_hdf5_write_$group_num$(file, ($group_num_dtype_double$) num);
-    break;					       
+    break;
+#endif 
 /*						       
   case TREXIO_JSON:				       
     return trexio_json_write_$group_num$(file, ($group_num_dtype_double$) num);
@@ -1340,9 +1367,11 @@ trexio_has_$group_num$ (trexio_t* const file)
     return trexio_text_has_$group_num$(file);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     return trexio_hdf5_has_$group_num$(file);
     break;
+#endif
 /*
   case TREXIO_JSON:
     return trexio_json_has_$group_num$(file);
@@ -1583,9 +1612,11 @@ trexio_read_$group_dset$_64 (trexio_t* const file, $group_dset_dtype_double$* co
     rc = trexio_text_read_$group_dset$(file, $group_dset$, rank, dims);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     rc = trexio_hdf5_read_$group_dset$(file, $group_dset$, rank, dims);
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc = trexio_json_read_$group_dset$(file, $group_dset$, rank, dims);
@@ -1657,9 +1688,11 @@ trexio_write_$group_dset$_64 (trexio_t* const file, const $group_dset_dtype_doub
     rc = trexio_text_write_$group_dset$(file, $group_dset$_p, rank, dims);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     rc = trexio_hdf5_write_$group_dset$(file, $group_dset$_p, rank, dims);
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc = trexio_json_write_$group_dset$(file, $group_dset$_p, rank, dims);
@@ -1717,9 +1750,11 @@ trexio_read_$group_dset$_32 (trexio_t* const file, $group_dset_dtype_single$* co
     rc = trexio_text_read_$group_dset$(file, $group_dset$_64, rank, dims);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     rc = trexio_hdf5_read_$group_dset$(file, $group_dset$_64, rank, dims);
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc = trexio_json_read_$group_dset$(file, $group_dset$_64, rank, dims);
@@ -1796,9 +1831,11 @@ trexio_write_$group_dset$_32 (trexio_t* const file, const $group_dset_dtype_sing
     rc = trexio_text_write_$group_dset$(file, $group_dset$_64, rank, dims);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     rc = trexio_hdf5_write_$group_dset$(file, $group_dset$_64, rank, dims);
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc = trexio_json_write_$group_dset$(file, $group_dset$_64, rank, dims);
@@ -1960,9 +1997,11 @@ trexio_has_$group_dset$ (trexio_t* const file)
     return trexio_text_has_$group_dset$(file);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     return trexio_hdf5_has_$group_dset$(file);
     break;
+#endif
 /*
   case TREXIO_JSON:
     return trexio_json_has_$group_dset$(file);
@@ -2405,9 +2444,11 @@ trexio_read_$group_dset$_low (trexio_t* const file, char* dset_out, const int32_
     return trexio_text_read_$group_dset$(file, dset_out, rank, dims, (uint32_t) max_str_len);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     return trexio_hdf5_read_$group_dset$(file, dset_out, rank, dims, (uint32_t) max_str_len);
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc = trexio_json_read_$group_dset$(file, dset_out, rank, dims);
@@ -2529,9 +2570,11 @@ trexio_write_$group_dset$_low (trexio_t* const file, const char* dset_in, const
     rc = trexio_text_write_$group_dset$(file, (const char**) dset_str, rank, dims);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     rc = trexio_hdf5_write_$group_dset$(file, (const char**) dset_str, rank, dims);
     break;
+#endif
 /*
   case TREXIO_JSON:
     rc = trexio_json_write_$group_dset$(file, dset, rank, dims);
@@ -2597,9 +2640,11 @@ trexio_has_$group_dset$ (trexio_t* const file)
     return trexio_text_has_$group_dset$(file);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     return trexio_hdf5_has_$group_dset$(file);
     break;
+#endif
 /*
   case TREXIO_JSON:
     return trexio_json_has_$group_dset$(file);
@@ -2846,9 +2891,11 @@ trexio_read_$group_str$ (trexio_t* const file, char* const str_out, const int32_
     return trexio_text_read_$group_str$(file, str_out, (uint32_t) max_str_len);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     return trexio_hdf5_read_$group_str$(file, str_out, (uint32_t) max_str_len);
     break;
+#endif
 /*
   case TREXIO_JSON:
     return trexio_json_read_$group_str$(file, str);
@@ -2879,9 +2926,11 @@ trexio_write_$group_str$ (trexio_t* const file, const char* str, const int32_t m
     return trexio_text_write_$group_str$(file, str);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     return trexio_hdf5_write_$group_str$(file, str);
     break;
+#endif
 /*
   case TREXIO_JSON:
     return trexio_json_write_$group_str$(file, str);
@@ -2908,9 +2957,11 @@ trexio_has_$group_str$ (trexio_t* const file)
     return trexio_text_has_$group_str$(file);
     break;
 
+#ifdef HAVE_HDF5 
   case TREXIO_HDF5:
     return trexio_hdf5_has_$group_str$(file);
     break;
+#endif
 /*
   case TREXIO_JSON:
     return trexio_json_has_$group_str$(file);