[svn-r11421] Purpose:

Feature

Description:
Added H5_CFLAGS, etc. to 1.7 branch.
Now compilation flags can be put in H5_*FLAGS and they'll be used when
building hdf5 but not in h5cc.


Platforms tested:
mir, sleipnir, modi4

Misc. update:

38 files changed, 440 insertions, 172 deletions

diff --git a/Makefile.in b/Makefile.in
index 93ac5b3..0e501b1 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -134,16 +134,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -166,11 +169,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/c++/Makefile.in b/c++/Makefile.in
index 5a67161..9dd9234 100644
--- a/c++/Makefile.in
+++ b/c++/Makefile.in
@@ -104,16 +104,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -136,11 +139,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/c++/examples/Makefile.in b/c++/examples/Makefile.in
index 0dfa1fb..362bde2 100644
--- a/c++/examples/Makefile.in
+++ b/c++/examples/Makefile.in
@@ -96,16 +96,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -128,11 +131,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/c++/src/Makefile.in b/c++/src/Makefile.in
index fdc5e87..342a82d 100644
--- a/c++/src/Makefile.in
+++ b/c++/src/Makefile.in
@@ -138,16 +138,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -170,11 +173,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/c++/test/Makefile.in b/c++/test/Makefile.in
index 6990f59..68d51b1 100644
--- a/c++/test/Makefile.in
+++ b/c++/test/Makefile.in
@@ -127,16 +127,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -159,11 +162,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/config/commence.am b/config/commence.am
index 84eb1ba..518aa13 100644
--- a/config/commence.am
+++ b/config/commence.am
@@ -42,6 +42,13 @@ H5CC_PP=$(bindir)/h5pcc
 H5FC=$(bindir)/h5fc
 H5FC_PP=$(bindir)/h5pfc
 
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS=@CFLAGS@ @H5_CFLAGS@
+CPPFLAGS=@CPPFLAGS@ @H5_CPPFLAGS@
+FFLAGS=@FFLAGS@ @H5_FFLAGS@
+CXXFLAGS=@CXXFLAGS@ @H5_CXXFLAGS@
+
 # Make sure that these variables are exported to the Makefiles
 F9XMODEXT=@F9XMODEXT@
 F9XMODFLAG=@F9XMODFLAG@
diff --git a/configure b/configure
index 6f910d1..2d97886 100755
--- a/configure
+++ b/configure
@@ -467,7 +467,7 @@ ac_includes_default="\
 # include <unistd.h>
 #endif"
 
-ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM mkdir_p AWK SET_MAKE am__leading_dot AMTAR am__tar am__untar MAINTAINER_MODE_TRUE MAINTAINER_MODE_FALSE MAINT build build_cpu build_vendor build_os host host_cpu host_vendor host_os CPPFLAGS HSIZET CC CFLAGS LDFLAGS ac_ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE HDF5_INTERFACES R_LARGE R_INTEGER HADDR_T HSIZE_T HSSIZE_T HID_T SIZE_T OBJECT_NAMELEN_DEFAULT_F F9XSUFFIXFLAG FSEARCH_DIRS FC FCFLAGS ac_ct_FC F9XMODFLAG F9XMODEXT FCLIBS CXX CXXFLAGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE CXXCPP LT_STATIC_EXEC PERL AR FORTRAN_SHARED_CONDITIONAL_TRUE FORTRAN_SHARED_CONDITIONAL_FALSE CXX_SHARED_CONDITIONAL_TRUE CXX_SHARED_CONDITIONAL_FALSE EGREP LN_S ECHO ac_ct_AR RANLIB ac_ct_RANLIB CPP F77 FFLAGS ac_ct_F77 LIBTOOL AM_MAKEFLAGS USE_FILTER_DEFLATE USE_FILTER_SZIP BUILD_PDB2HDF BUILD_PDB2HDF_CONDITIONAL_TRUE BUILD_PDB2HDF_CONDITIONAL_FALSE PTHREAD DEBUG_PKG TRACE_API INSTRUMENT_LIBRARY PARALLEL RUNSERIAL RUNPARALLEL TESTPARALLEL ADD_PARALLEL_FILES MPE FILTERS USE_FILTER_SHUFFLE USE_FILTER_FLETCHER32 USE_FILTER_NBIT USE_FILTER_SCALEOFFSET H5_VERSION CONFIG_DATE CONFIG_USER CONFIG_MODE BYTESEX STATIC_SHARED CC_VERSION ROOT DYNAMIC_DIRS HL HL_FOR BUILD_CXX_CONDITIONAL_TRUE BUILD_CXX_CONDITIONAL_FALSE BUILD_PABLO_CONDITIONAL_TRUE BUILD_PABLO_CONDITIONAL_FALSE BUILD_PARALLEL_CONDITIONAL_TRUE BUILD_PARALLEL_CONDITIONAL_FALSE BUILD_FORTRAN_CONDITIONAL_TRUE BUILD_FORTRAN_CONDITIONAL_FALSE BUILD_HDF5_HL_CONDITIONAL_TRUE BUILD_HDF5_HL_CONDITIONAL_FALSE SEARCH SETX LIBOBJS LTLIBOBJS'
+ac_subst_vars='SHELL PATH_SEPARATOR PACKAGE_NAME PACKAGE_TARNAME PACKAGE_VERSION PACKAGE_STRING PACKAGE_BUGREPORT exec_prefix prefix program_transform_name bindir sbindir libexecdir datadir sysconfdir sharedstatedir localstatedir libdir includedir oldincludedir infodir mandir build_alias host_alias target_alias DEFS ECHO_C ECHO_N ECHO_T LIBS INSTALL_PROGRAM INSTALL_SCRIPT INSTALL_DATA CYGPATH_W PACKAGE VERSION ACLOCAL AUTOCONF AUTOMAKE AUTOHEADER MAKEINFO install_sh STRIP ac_ct_STRIP INSTALL_STRIP_PROGRAM mkdir_p AWK SET_MAKE am__leading_dot AMTAR am__tar am__untar MAINTAINER_MODE_TRUE MAINTAINER_MODE_FALSE MAINT build build_cpu build_vendor build_os host host_cpu host_vendor host_os CPPFLAGS H5_CFLAGS H5_CPPFLAGS H5_FFLAGS H5_CXXFLAGS HSIZET CC CFLAGS LDFLAGS ac_ct_CC EXEEXT OBJEXT DEPDIR am__include am__quote AMDEP_TRUE AMDEP_FALSE AMDEPBACKSLASH CCDEPMODE am__fastdepCC_TRUE am__fastdepCC_FALSE HDF5_INTERFACES R_LARGE R_INTEGER HADDR_T HSIZE_T HSSIZE_T HID_T SIZE_T OBJECT_NAMELEN_DEFAULT_F F9XSUFFIXFLAG FSEARCH_DIRS FC FCFLAGS ac_ct_FC F9XMODFLAG F9XMODEXT FCLIBS CXX CXXFLAGS ac_ct_CXX CXXDEPMODE am__fastdepCXX_TRUE am__fastdepCXX_FALSE CXXCPP LT_STATIC_EXEC PERL AR FORTRAN_SHARED_CONDITIONAL_TRUE FORTRAN_SHARED_CONDITIONAL_FALSE CXX_SHARED_CONDITIONAL_TRUE CXX_SHARED_CONDITIONAL_FALSE EGREP LN_S ECHO ac_ct_AR RANLIB ac_ct_RANLIB CPP F77 FFLAGS ac_ct_F77 LIBTOOL AM_MAKEFLAGS USE_FILTER_DEFLATE USE_FILTER_SZIP BUILD_PDB2HDF BUILD_PDB2HDF_CONDITIONAL_TRUE BUILD_PDB2HDF_CONDITIONAL_FALSE PTHREAD DEBUG_PKG TRACE_API INSTRUMENT_LIBRARY PARALLEL RUNSERIAL RUNPARALLEL TESTPARALLEL ADD_PARALLEL_FILES MPE FILTERS USE_FILTER_SHUFFLE USE_FILTER_FLETCHER32 USE_FILTER_NBIT USE_FILTER_SCALEOFFSET H5_VERSION CONFIG_DATE CONFIG_USER CONFIG_MODE BYTESEX STATIC_SHARED CC_VERSION ROOT DYNAMIC_DIRS HL HL_FOR BUILD_CXX_CONDITIONAL_TRUE BUILD_CXX_CONDITIONAL_FALSE BUILD_PABLO_CONDITIONAL_TRUE BUILD_PABLO_CONDITIONAL_FALSE BUILD_PARALLEL_CONDITIONAL_TRUE BUILD_PARALLEL_CONDITIONAL_FALSE BUILD_FORTRAN_CONDITIONAL_TRUE BUILD_FORTRAN_CONDITIONAL_FALSE BUILD_HDF5_HL_CONDITIONAL_TRUE BUILD_HDF5_HL_CONDITIONAL_FALSE SEARCH SETX LIBOBJS LTLIBOBJS'
 ac_subst_files=''
 
 # Initialize some variables set by options.
@@ -2112,6 +2112,11 @@ host_os=`echo $ac_cv_host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'`
 
 
 
+
+
+
+
+
 DEFAULT_LIBS=""
 
 if test "x" = "x$FC"; then
@@ -3517,7 +3522,7 @@ fi
 
 
 # Provide some information about the compiler.
-echo "$as_me:3520:" \
+echo "$as_me:3525:" \
      "checking for Fortran compiler version" >&5
 ac_compiler=`set X $ac_compile; echo $2`
 { (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5
@@ -3812,7 +3817,7 @@ _ACEOF
 # flags.
 ac_save_FFLAGS=$FCFLAGS
 FCFLAGS="$FCFLAGS $ac_verb"
-(eval echo $as_me:3815: \"$ac_link\") >&5
+(eval echo $as_me:3820: \"$ac_link\") >&5
 ac_fc_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_fc_v_output" >&5
 FCFLAGS=$ac_save_FFLAGS
@@ -3890,7 +3895,7 @@ _ACEOF
 # flags.
 ac_save_FFLAGS=$FCFLAGS
 FCFLAGS="$FCFLAGS $ac_cv_prog_fc_v"
-(eval echo $as_me:3893: \"$ac_link\") >&5
+(eval echo $as_me:3898: \"$ac_link\") >&5
 ac_fc_v_output=`eval $ac_link 5>&1 2>&1 | grep -v 'Driving:'`
 echo "$ac_fc_v_output" >&5
 FCFLAGS=$ac_save_FFLAGS
@@ -6469,7 +6474,7 @@ ia64-*-hpux*)
   ;;
 *-*-irix6*)
   # Find out which ABI we are using.
-  echo '#line 6472 "configure"' > conftest.$ac_ext
+  echo '#line 6477 "configure"' > conftest.$ac_ext
   if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
   (eval $ac_compile) 2>&5
   ac_status=$?
@@ -7599,7 +7604,7 @@ fi
 
 
 # Provide some information about the compiler.
-echo "$as_me:7602:" \
+echo "$as_me:7607:" \
      "checking for Fortran 77 compiler version" >&5
 ac_compiler=`set X $ac_compile; echo $2`
 { (eval echo "$as_me:$LINENO: \"$ac_compiler --version </dev/null >&5\"") >&5
@@ -8668,11 +8673,11 @@ else
    -e 's:.*FLAGS}? :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:8671: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:8676: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:8675: \$? = $ac_status" >&5
+   echo "$as_me:8680: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings
@@ -8923,11 +8928,11 @@ else
    -e 's:.*FLAGS}? :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:8926: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:8931: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:8930: \$? = $ac_status" >&5
+   echo "$as_me:8935: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings
@@ -8983,11 +8988,11 @@ else
    -e 's:.*FLAGS}? :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:8986: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:8991: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:8990: \$? = $ac_status" >&5
+   echo "$as_me:8995: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -11255,7 +11260,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<EOF
-#line 11258 "configure"
+#line 11263 "configure"
 #include "confdefs.h"
 
 #if HAVE_DLFCN_H
@@ -11353,7 +11358,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<EOF
-#line 11356 "configure"
+#line 11361 "configure"
 #include "confdefs.h"
 
 #if HAVE_DLFCN_H
@@ -13589,11 +13594,11 @@ else
    -e 's:.*FLAGS}? :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:13592: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:13597: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:13596: \$? = $ac_status" >&5
+   echo "$as_me:13601: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings
@@ -13649,11 +13654,11 @@ else
    -e 's:.*FLAGS}? :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:13652: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:13657: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:13656: \$? = $ac_status" >&5
+   echo "$as_me:13661: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -15068,7 +15073,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<EOF
-#line 15071 "configure"
+#line 15076 "configure"
 #include "confdefs.h"
 
 #if HAVE_DLFCN_H
@@ -15166,7 +15171,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<EOF
-#line 15169 "configure"
+#line 15174 "configure"
 #include "confdefs.h"
 
 #if HAVE_DLFCN_H
@@ -16021,11 +16026,11 @@ else
    -e 's:.*FLAGS}? :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:16024: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:16029: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:16028: \$? = $ac_status" >&5
+   echo "$as_me:16033: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings
@@ -16081,11 +16086,11 @@ else
    -e 's:.*FLAGS}? :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:16084: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:16089: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:16088: \$? = $ac_status" >&5
+   echo "$as_me:16093: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -18137,11 +18142,11 @@ else
    -e 's:.*FLAGS}? :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:18140: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:18145: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:18144: \$? = $ac_status" >&5
+   echo "$as_me:18149: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings
@@ -18392,11 +18397,11 @@ else
    -e 's:.*FLAGS}? :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:18395: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:18400: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>conftest.err)
    ac_status=$?
    cat conftest.err >&5
-   echo "$as_me:18399: \$? = $ac_status" >&5
+   echo "$as_me:18404: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s "$ac_outfile"; then
      # The compiler can only warn and ignore the option if not recognized
      # So say no if there are warnings
@@ -18452,11 +18457,11 @@ else
    -e 's:.*FLAGS}? :&$lt_compiler_flag :; t' \
    -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
    -e 's:$: $lt_compiler_flag:'`
-   (eval echo "\"\$as_me:18455: $lt_compile\"" >&5)
+   (eval echo "\"\$as_me:18460: $lt_compile\"" >&5)
    (eval "$lt_compile" 2>out/conftest.err)
    ac_status=$?
    cat out/conftest.err >&5
-   echo "$as_me:18459: \$? = $ac_status" >&5
+   echo "$as_me:18464: \$? = $ac_status" >&5
    if (exit $ac_status) && test -s out/conftest2.$ac_objext
    then
      # The compiler can only warn and ignore the option if not recognized
@@ -20724,7 +20729,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<EOF
-#line 20727 "configure"
+#line 20732 "configure"
 #include "confdefs.h"
 
 #if HAVE_DLFCN_H
@@ -20822,7 +20827,7 @@ else
   lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
   lt_status=$lt_dlunknown
   cat > conftest.$ac_ext <<EOF
-#line 20825 "configure"
+#line 20830 "configure"
 #include "confdefs.h"
 
 #if HAVE_DLFCN_H
@@ -51939,6 +51944,10 @@ s,@host_cpu@,$host_cpu,;t t
 s,@host_vendor@,$host_vendor,;t t
 s,@host_os@,$host_os,;t t
 s,@CPPFLAGS@,$CPPFLAGS,;t t
+s,@H5_CFLAGS@,$H5_CFLAGS,;t t
+s,@H5_CPPFLAGS@,$H5_CPPFLAGS,;t t
+s,@H5_FFLAGS@,$H5_FFLAGS,;t t
+s,@H5_CXXFLAGS@,$H5_CXXFLAGS,;t t
 s,@HSIZET@,$HSIZET,;t t
 s,@CC@,$CC,;t t
 s,@CFLAGS@,$CFLAGS,;t t
diff --git a/configure.in b/configure.in
index a5ee50c..21efe50 100644
--- a/configure.in
+++ b/configure.in
@@ -74,6 +74,13 @@ esac
 AC_CANONICAL_HOST
 AC_SUBST([CPPFLAGS])
 
+dnl H5_CFLAGS (and company) are for CFLAGS that should be used on HDF5, but
+dnl not exported to h5cc (or h5fc, etc.)
+AC_SUBST([H5_CFLAGS])
+AC_SUBST([H5_CPPFLAGS])
+AC_SUBST([H5_FFLAGS])
+AC_SUBST([H5_CXXFLAGS])
+
 dnl Different compilers may need default libraries. They are specified in
 dnl the config/* files, so we put this statement here so that it'll be
 dnl set by the code which follows...
diff --git a/examples/Makefile.in b/examples/Makefile.in
index a28ccee..6d54b76 100644
--- a/examples/Makefile.in
+++ b/examples/Makefile.in
@@ -96,16 +96,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -128,11 +131,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/fortran/Makefile.in b/fortran/Makefile.in
index 5cb7977..095f95e 100644
--- a/fortran/Makefile.in
+++ b/fortran/Makefile.in
@@ -108,16 +108,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -140,11 +143,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/fortran/examples/Makefile.in b/fortran/examples/Makefile.in
index 2ba8e5e..9187a7d 100644
--- a/fortran/examples/Makefile.in
+++ b/fortran/examples/Makefile.in
@@ -96,16 +96,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -128,11 +131,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/fortran/src/Makefile.in b/fortran/src/Makefile.in
index 4f0d976..abf9514 100644
--- a/fortran/src/Makefile.in
+++ b/fortran/src/Makefile.in
@@ -163,16 +163,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -195,11 +198,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/fortran/test/Makefile.in b/fortran/test/Makefile.in
index 5745a6a..8857376 100644
--- a/fortran/test/Makefile.in
+++ b/fortran/test/Makefile.in
@@ -157,16 +157,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -189,11 +192,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/fortran/testpar/Makefile.in b/fortran/testpar/Makefile.in
index a08a5fd..03ebef7 100644
--- a/fortran/testpar/Makefile.in
+++ b/fortran/testpar/Makefile.in
@@ -120,16 +120,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -152,11 +155,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/hl/Makefile.in b/hl/Makefile.in
index 9282106..f208c50 100755
--- a/hl/Makefile.in
+++ b/hl/Makefile.in
@@ -100,16 +100,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -132,11 +135,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/hl/c++/Makefile.in b/hl/c++/Makefile.in
index 9da9c36..cf1403f 100644
--- a/hl/c++/Makefile.in
+++ b/hl/c++/Makefile.in
@@ -105,16 +105,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -137,11 +140,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/hl/c++/src/Makefile.in b/hl/c++/src/Makefile.in
index 3026d44..d71319c 100644
--- a/hl/c++/src/Makefile.in
+++ b/hl/c++/src/Makefile.in
@@ -127,16 +127,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -159,11 +162,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/hl/c++/test/Makefile.in b/hl/c++/test/Makefile.in
index 1029002..088823f 100644
--- a/hl/c++/test/Makefile.in
+++ b/hl/c++/test/Makefile.in
@@ -121,16 +121,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -153,11 +156,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/hl/fortran/Makefile.in b/hl/fortran/Makefile.in
index fe12efb..906885d 100644
--- a/hl/fortran/Makefile.in
+++ b/hl/fortran/Makefile.in
@@ -100,16 +100,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -132,11 +135,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/hl/fortran/src/Makefile.in b/hl/fortran/src/Makefile.in
index 97b516b..a92512e 100644
--- a/hl/fortran/src/Makefile.in
+++ b/hl/fortran/src/Makefile.in
@@ -121,16 +121,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -153,11 +156,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/hl/fortran/test/Makefile.in b/hl/fortran/test/Makefile.in
index 828c15d..a27b557 100644
--- a/hl/fortran/test/Makefile.in
+++ b/hl/fortran/test/Makefile.in
@@ -120,16 +120,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -152,11 +155,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/hl/src/Makefile.in b/hl/src/Makefile.in
index 1e38ccb..33015e3 100644
--- a/hl/src/Makefile.in
+++ b/hl/src/Makefile.in
@@ -118,16 +118,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -150,11 +153,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/hl/test/Makefile.in b/hl/test/Makefile.in
index 9a3d8aa..61b49cf 100644
--- a/hl/test/Makefile.in
+++ b/hl/test/Makefile.in
@@ -130,16 +130,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -162,11 +165,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/hl/tools/gif2h5/Makefile.in b/hl/tools/gif2h5/Makefile.in
index d48d0ad..2aff089 100644
--- a/hl/tools/gif2h5/Makefile.in
+++ b/hl/tools/gif2h5/Makefile.in
@@ -128,16 +128,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -160,11 +163,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/perform/Makefile.in b/perform/Makefile.in
index 32bf2ba..a96d9c1 100644
--- a/perform/Makefile.in
+++ b/perform/Makefile.in
@@ -151,16 +151,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -183,11 +186,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/src/Makefile.in b/src/Makefile.in
index f628d84..7ecf6b7 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -164,16 +164,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -196,11 +199,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/test/Makefile.in b/test/Makefile.in
index 665201b..26f435f 100644
--- a/test/Makefile.in
+++ b/test/Makefile.in
@@ -318,16 +318,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -350,11 +353,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/testpar/Makefile.in b/testpar/Makefile.in
index f168fce..bd9c4cd 100644
--- a/testpar/Makefile.in
+++ b/testpar/Makefile.in
@@ -130,16 +130,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -162,11 +165,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/tools/Makefile.in b/tools/Makefile.in
index f3f8d45..d7467c9 100644
--- a/tools/Makefile.in
+++ b/tools/Makefile.in
@@ -105,16 +105,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -137,11 +140,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/tools/gifconv/Makefile.in b/tools/gifconv/Makefile.in
index d48d0ad..2aff089 100644
--- a/tools/gifconv/Makefile.in
+++ b/tools/gifconv/Makefile.in
@@ -128,16 +128,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -160,11 +163,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/tools/h5diff/Makefile.in b/tools/h5diff/Makefile.in
index b7c8755..f4fe95e 100644
--- a/tools/h5diff/Makefile.in
+++ b/tools/h5diff/Makefile.in
@@ -136,16 +136,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -168,11 +171,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/tools/h5dump/Makefile.in b/tools/h5dump/Makefile.in
index b113164..9e67b56 100644
--- a/tools/h5dump/Makefile.in
+++ b/tools/h5dump/Makefile.in
@@ -129,16 +129,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -161,11 +164,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/tools/h5import/Makefile.in b/tools/h5import/Makefile.in
index faadde3..fc60334 100755
--- a/tools/h5import/Makefile.in
+++ b/tools/h5import/Makefile.in
@@ -129,16 +129,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -161,11 +164,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/tools/h5jam/Makefile.in b/tools/h5jam/Makefile.in
index e37ace5..92fe854 100644
--- a/tools/h5jam/Makefile.in
+++ b/tools/h5jam/Makefile.in
@@ -124,16 +124,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -156,11 +159,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/tools/h5ls/Makefile.in b/tools/h5ls/Makefile.in
index 805146c..65b6aeb 100644
--- a/tools/h5ls/Makefile.in
+++ b/tools/h5ls/Makefile.in
@@ -122,16 +122,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -154,11 +157,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/tools/h5repack/Makefile.in b/tools/h5repack/Makefile.in
index 2d8564e..a9eed90 100644
--- a/tools/h5repack/Makefile.in
+++ b/tools/h5repack/Makefile.in
@@ -144,16 +144,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -176,11 +179,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/tools/lib/Makefile.in b/tools/lib/Makefile.in
index 70e6fd8..09832e1 100644
--- a/tools/lib/Makefile.in
+++ b/tools/lib/Makefile.in
@@ -126,16 +126,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -158,11 +161,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@
diff --git a/tools/misc/Makefile.in b/tools/misc/Makefile.in
index 032ab6a..8387ee6 100644
--- a/tools/misc/Makefile.in
+++ b/tools/misc/Makefile.in
@@ -148,16 +148,19 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-CFLAGS = @CFLAGS@
+
+# H5_CFLAGS holds flags that should be used as CFLAGS when building hdf5,
+# but which shouldn't be exported to h5cc for building other programs.
+CFLAGS = @CFLAGS@ @H5_CFLAGS@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
 CXX_SHARED_CONDITIONAL_FALSE = @CXX_SHARED_CONDITIONAL_FALSE@
 CXX_SHARED_CONDITIONAL_TRUE = @CXX_SHARED_CONDITIONAL_TRUE@
 CYGPATH_W = @CYGPATH_W@
@@ -180,11 +183,15 @@ F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
 FCFLAGS = @FCFLAGS@
 FCLIBS = @FCLIBS@
-FFLAGS = @FFLAGS@
+FFLAGS = @FFLAGS@ @H5_FFLAGS@
 FILTERS = @FILTERS@
 FORTRAN_SHARED_CONDITIONAL_FALSE = @FORTRAN_SHARED_CONDITIONAL_FALSE@
 FORTRAN_SHARED_CONDITIONAL_TRUE = @FORTRAN_SHARED_CONDITIONAL_TRUE@
 FSEARCH_DIRS = @FSEARCH_DIRS@
+H5_CFLAGS = @H5_CFLAGS@
+H5_CPPFLAGS = @H5_CPPFLAGS@
+H5_CXXFLAGS = @H5_CXXFLAGS@
+H5_FFLAGS = @H5_FFLAGS@
 H5_VERSION = @H5_VERSION@
 HADDR_T = @HADDR_T@
 HDF5_INTERFACES = @HDF5_INTERFACES@