[svn-r17616] Purpose:

    CFLAGS overhaul

Description:

    Modified the way configure handles CFLAGS.

    (note: all changes also apply to FCFLAGS, CXXFLAGS, CPPFLAGS, and LDFLAGS).

    1. The configure process will now always preserve a user's CFLAGS
    environment variable setup. Any additional flags necessary for compilation
    added at configure time will be passed into the Makefiles as AM_CFLAGS,
    which is an automake construct to be used in addition to CFLAGS.

    This will allow a user to have the final say, as CFLAGS will always appear
    later in the compile line than AM_CFLAGS. Additionally, setting CFLAGS
    during make will no longer completely erase all flags set by configure,
    since they're maintained in AM_CFLAGS.

    2. Additionally, where possible, flags previously being assigned directly
    into CFLAGS (and thus propagating into h5cc) have now been redirected into
    H5_CFLAGS, so they're used ONLY for compiling hdf5, and not embedded into
    the h5cc wrapper script as well.

    *Note that H5_CFLAGS ultimately is assigned into AM_CFLAGS for use in the
    Makefiles. Complete description of changes and build process will be
    included in a Configure Document that Elena and I are working on.

    3. Removed unsupported config files. This includes:

       config/dec-osf*
       config/hpux11.00
       config/irix5.x
       config/powerpc-ibm-aix4.x
       config/rs6000-ibm-aix5.x
       config/unicos*

     4. Modified configure summary to display additional values. Specifically,
     appropriate AM_* variables are being shown, as well as H5_FCFLAGS and
     H5_CXXFLAGS, which were for some reason not already present.

Tested:

    - H5committest
    - Tested on all THG / NCSA machines, using several combinations of the more
      prominent configure options (c++, fortran, szip, threadsafe, parallel,
      et cetera). (Thanks to Quincey for rysnc testing setup!)
    - With regards to new automated testing, anything *necessary* for
      compilation will be caught by the daily tests as it stands now. (i.e.,
      if LDFLAGS is not properly set when szip is used, linking will fail).
      Additionally, with regards to which flags get into h5cc, if any
      *necessary* flags have been improperly removed, then daily tests should
      fail during make installcheck. Additional machine-specific desired
      behaviors and/or checks may have to be set up separately within the
      daily tests, so this is something to work on.

21 files changed, 181 insertions, 104 deletions

diff --git a/tools/Makefile.in b/tools/Makefile.in
index 3675e3a..e482ea2 100644
--- a/tools/Makefile.in
+++ b/tools/Makefile.in
@@ -111,6 +111,16 @@ am__relativize = \
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -124,21 +134,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -161,7 +168,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
diff --git a/tools/h5copy/Makefile.am b/tools/h5copy/Makefile.am
index 1848972..dd0c5c3 100644
--- a/tools/h5copy/Makefile.am
+++ b/tools/h5copy/Makefile.am
@@ -34,7 +34,7 @@ bin_PROGRAMS=h5copy
 check_PROGRAMS=$(TEST_PROG)
 
 # Add h5copy specific linker flags here
-h5copy_LDFLAGS = $(LT_STATIC_EXEC)
+h5copy_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # source file for the test file generator
 h5copygentest_SOURCES=h5copygentest.c
diff --git a/tools/h5copy/Makefile.in b/tools/h5copy/Makefile.in
index b582057..d2a8e0d 100644
--- a/tools/h5copy/Makefile.in
+++ b/tools/h5copy/Makefile.in
@@ -103,6 +103,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -116,21 +126,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -153,7 +160,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -364,7 +371,7 @@ check_SCRIPTS = $(TEST_SCRIPT)
 SCRIPT_DEPEND = h5copy$(EXEEXT)
 
 # Add h5copy specific linker flags here
-h5copy_LDFLAGS = $(LT_STATIC_EXEC)
+h5copy_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # source file for the test file generator
 h5copygentest_SOURCES = h5copygentest.c
diff --git a/tools/h5diff/Makefile.am b/tools/h5diff/Makefile.am
index b56284b..0b8816f 100644
--- a/tools/h5diff/Makefile.am
+++ b/tools/h5diff/Makefile.am
@@ -34,7 +34,7 @@ endif
 bin_PROGRAMS=h5diff $(H5PDIFF)
 
 # Add h5diff specific linker flags here
-h5diff_LDFLAGS = $(LT_STATIC_EXEC)
+h5diff_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Test programs and scripts
 TEST_PROG=h5diffgentest
diff --git a/tools/h5diff/Makefile.in b/tools/h5diff/Makefile.in
index 91add70..04a64da 100644
--- a/tools/h5diff/Makefile.in
+++ b/tools/h5diff/Makefile.in
@@ -110,6 +110,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -123,21 +133,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -160,7 +167,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -371,7 +378,7 @@ INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 @BUILD_PARALLEL_CONDITIONAL_TRUE@TEST_SCRIPT_PARA = $(srcdir)/testph5diff.sh
 
 # Add h5diff specific linker flags here
-h5diff_LDFLAGS = $(LT_STATIC_EXEC)
+h5diff_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Test programs and scripts
 TEST_PROG = h5diffgentest
diff --git a/tools/h5dump/Makefile.am b/tools/h5dump/Makefile.am
index 992586b..81e38d1 100644
--- a/tools/h5dump/Makefile.am
+++ b/tools/h5dump/Makefile.am
@@ -35,7 +35,7 @@ SCRIPT_DEPEND=h5dump$(EXEEXT)
 bin_PROGRAMS=h5dump
 
 # Add h5dump specific linker flags here
-h5dump_LDFLAGS = $(LT_STATIC_EXEC)
+h5dump_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # All the programs depend on the hdf5 and h5tools libraries
 LDADD=$(LIBH5TOOLS) $(LIBHDF5)
diff --git a/tools/h5dump/Makefile.in b/tools/h5dump/Makefile.in
index be8cf96..8ca6684 100644
--- a/tools/h5dump/Makefile.in
+++ b/tools/h5dump/Makefile.in
@@ -108,6 +108,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -121,21 +131,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -158,7 +165,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -369,7 +376,7 @@ check_SCRIPTS = $(TEST_SCRIPT)
 SCRIPT_DEPEND = h5dump$(EXEEXT)
 
 # Add h5dump specific linker flags here
-h5dump_LDFLAGS = $(LT_STATIC_EXEC)
+h5dump_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # All the programs depend on the hdf5 and h5tools libraries
 LDADD = $(LIBH5TOOLS) $(LIBHDF5)
diff --git a/tools/h5import/Makefile.am b/tools/h5import/Makefile.am
index 2202f5f..49f4f71 100644
--- a/tools/h5import/Makefile.am
+++ b/tools/h5import/Makefile.am
@@ -35,7 +35,7 @@ SCRIPT_DEPEND=h5import$(EXEEXT)
 bin_PROGRAMS=h5import
 
 # Add h5import specific linker flags here
-h5import_LDFLAGS = $(LT_STATIC_EXEC)
+h5import_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # All programs depend on the main hdf5 library and the tools library
 LDADD=$(LIBH5TOOLS) $(LIBHDF5)
diff --git a/tools/h5import/Makefile.in b/tools/h5import/Makefile.in
index f9e88ae..15fcf90 100755
--- a/tools/h5import/Makefile.in
+++ b/tools/h5import/Makefile.in
@@ -103,6 +103,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -116,21 +126,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -153,7 +160,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -361,7 +368,7 @@ check_SCRIPT = h5importtestutil.sh
 SCRIPT_DEPEND = h5import$(EXEEXT)
 
 # Add h5import specific linker flags here
-h5import_LDFLAGS = $(LT_STATIC_EXEC)
+h5import_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # All programs depend on the main hdf5 library and the tools library
 LDADD = $(LIBH5TOOLS) $(LIBHDF5)
diff --git a/tools/h5jam/Makefile.am b/tools/h5jam/Makefile.am
index d89a2d2..2f9bc00 100644
--- a/tools/h5jam/Makefile.am
+++ b/tools/h5jam/Makefile.am
@@ -28,8 +28,8 @@ check_PROGRAMS=tellub h5jamgentest getub
 TEST_SCRIPT=testh5jam.sh
 
 # Add h5jam and h5unjam specific linker flags here
-h5jam_LDFLAGS = $(LT_STATIC_EXEC)
-h5unjam_LDFLAGS = $(LT_STATIC_EXEC)
+h5jam_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5unjam_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 check_SCRIPTS=$(TEST_SCRIPT)
 SCRIPT_DEPEND=h5jam$(EXEEXT) h5unjam$(EXEEXT)
diff --git a/tools/h5jam/Makefile.in b/tools/h5jam/Makefile.in
index 12486a0..5509801 100644
--- a/tools/h5jam/Makefile.in
+++ b/tools/h5jam/Makefile.in
@@ -117,6 +117,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -130,21 +140,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -167,7 +174,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -373,8 +380,8 @@ INCLUDES = -I$(top_srcdir)/src -I$(top_srcdir)/tools/lib
 TEST_SCRIPT = testh5jam.sh
 
 # Add h5jam and h5unjam specific linker flags here
-h5jam_LDFLAGS = $(LT_STATIC_EXEC)
-h5unjam_LDFLAGS = $(LT_STATIC_EXEC)
+h5jam_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5unjam_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 check_SCRIPTS = $(TEST_SCRIPT)
 SCRIPT_DEPEND = h5jam$(EXEEXT) h5unjam$(EXEEXT)
 
diff --git a/tools/h5ls/Makefile.am b/tools/h5ls/Makefile.am
index 64e89f1..41e66f6 100644
--- a/tools/h5ls/Makefile.am
+++ b/tools/h5ls/Makefile.am
@@ -32,7 +32,7 @@ SCRIPT_DEPEND=h5ls$(EXEEXT)
 bin_PROGRAMS=h5ls
 
 # Add h5ls specific linker flags here
-h5ls_LDFLAGS = $(LT_STATIC_EXEC)
+h5ls_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # All programs depend on the hdf5 and h5tools libraries
 LDADD=$(LIBH5TOOLS) $(LIBHDF5)
diff --git a/tools/h5ls/Makefile.in b/tools/h5ls/Makefile.in
index bace577..c11dc43 100644
--- a/tools/h5ls/Makefile.in
+++ b/tools/h5ls/Makefile.in
@@ -97,6 +97,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -110,21 +120,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -147,7 +154,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -354,7 +361,7 @@ check_SCRIPTS = $(TEST_SCRIPT)
 SCRIPT_DEPEND = h5ls$(EXEEXT)
 
 # Add h5ls specific linker flags here
-h5ls_LDFLAGS = $(LT_STATIC_EXEC)
+h5ls_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # All programs depend on the hdf5 and h5tools libraries
 LDADD = $(LIBH5TOOLS) $(LIBHDF5)
diff --git a/tools/h5repack/Makefile.am b/tools/h5repack/Makefile.am
index 1f811f0..96f0082 100644
--- a/tools/h5repack/Makefile.am
+++ b/tools/h5repack/Makefile.am
@@ -37,7 +37,7 @@ SCRIPT_DEPEND=h5repack$(EXEEXT)
 bin_PROGRAMS=h5repack
 
 # Add h5repack specific linker flags here
-h5repack_LDFLAGS = $(LT_STATIC_EXEC)
+h5repack_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Depend on the hdf5 library, the tools library, the test library
 LDADD=$(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
diff --git a/tools/h5repack/Makefile.in b/tools/h5repack/Makefile.in
index 656cfa6..dd33879 100644
--- a/tools/h5repack/Makefile.in
+++ b/tools/h5repack/Makefile.in
@@ -117,6 +117,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -130,21 +140,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -167,7 +174,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -378,7 +385,7 @@ check_SCRIPTS = $(TEST_SCRIPT)
 SCRIPT_DEPEND = h5repack$(EXEEXT)
 
 # Add h5repack specific linker flags here
-h5repack_LDFLAGS = $(LT_STATIC_EXEC)
+h5repack_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Depend on the hdf5 library, the tools library, the test library
 LDADD = $(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
diff --git a/tools/h5stat/Makefile.am b/tools/h5stat/Makefile.am
index a14172d..13d9baf 100644
--- a/tools/h5stat/Makefile.am
+++ b/tools/h5stat/Makefile.am
@@ -36,7 +36,7 @@ bin_PROGRAMS=h5stat
 bin_SCRIPTS=
 
 # Add h5stat specific linker flags here
-h5stat_LDFLAGS = $(LT_STATIC_EXEC)
+h5stat_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Tell automake to clean h5redeploy script
 CLEANFILES=
diff --git a/tools/h5stat/Makefile.in b/tools/h5stat/Makefile.in
index 15b19ed..08de49b 100644
--- a/tools/h5stat/Makefile.in
+++ b/tools/h5stat/Makefile.in
@@ -126,6 +126,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -139,21 +149,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -176,7 +183,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -390,7 +397,7 @@ SCRIPT_DEPEND = h5stat$(EXEEXT)
 bin_SCRIPTS = 
 
 # Add h5stat specific linker flags here
-h5stat_LDFLAGS = $(LT_STATIC_EXEC)
+h5stat_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Tell automake to clean h5redeploy script
 CLEANFILES = 
diff --git a/tools/lib/Makefile.in b/tools/lib/Makefile.in
index 55785c7..2b269ca 100644
--- a/tools/lib/Makefile.in
+++ b/tools/lib/Makefile.in
@@ -96,6 +96,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -109,21 +119,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -146,7 +153,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
diff --git a/tools/misc/Makefile.am b/tools/misc/Makefile.am
index fe1acbd..11c86fa 100644
--- a/tools/misc/Makefile.am
+++ b/tools/misc/Makefile.am
@@ -36,9 +36,9 @@ bin_PROGRAMS=h5debug h5repart h5mkgrp
 bin_SCRIPTS=h5redeploy
 
 # Add h5debug, h5repart, and h5mkgrp specific linker flags here
-h5debug_LDFLAGS = $(LT_STATIC_EXEC)
-h5repart_LDFLAGS = $(LT_STATIC_EXEC)
-h5mkgrp_LDFLAGS = $(LT_STATIC_EXEC)
+h5debug_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5repart_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5mkgrp_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Tell automake to clean h5redeploy script
 CLEANFILES=h5redeploy
diff --git a/tools/misc/Makefile.in b/tools/misc/Makefile.in
index 78a42b8..a3d3e23 100644
--- a/tools/misc/Makefile.in
+++ b/tools/misc/Makefile.in
@@ -151,6 +151,16 @@ DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = /home1/packages/automake/automake-1.9.6/bin/aclocal-1.9 -I /afs/ncsa/projects/hdf/packages/libtool_1.5.14/Linux_2.4/share/aclocal
 ADD_PARALLEL_FILES = @ADD_PARALLEL_FILES@
 AMTAR = @AMTAR@
+
+# H5_CFLAGS holds flags that should be used when building hdf5,
+# but which should not be exported to h5cc for building other programs.
+# AM_CFLAGS is an automake construct which should be used by Makefiles 
+# instead of CFLAGS, as CFLAGS is reserved solely for the user to define.
+AM_CFLAGS = @AM_CFLAGS@ @H5_CFLAGS@
+AM_CPPFLAGS = @AM_CPPFLAGS@ @H5_CPPFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@ @H5_CXXFLAGS@
+AM_FCFLAGS = @AM_FCFLAGS@ @H5_FCFLAGS@
+AM_LDFLAGS = @AM_LDFLAGS@
 AM_MAKEFLAGS = @AM_MAKEFLAGS@
 AR = @AR@
 
@@ -164,21 +174,18 @@ BYTESEX = @BYTESEX@
 CC = @CC@
 CCDEPMODE = @CCDEPMODE@
 CC_VERSION = @CC_VERSION@
-
-# 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@
+CFLAGS = @CFLAGS@
 CLEARFILEBUF = @CLEARFILEBUF@
 CODESTACK = @CODESTACK@
 CONFIG_DATE = @CONFIG_DATE@
 CONFIG_MODE = @CONFIG_MODE@
 CONFIG_USER = @CONFIG_USER@
 CPP = @CPP@
-CPPFLAGS = @CPPFLAGS@ @H5_CPPFLAGS@
+CPPFLAGS = @CPPFLAGS@
 CXX = @CXX@
 CXXCPP = @CXXCPP@
 CXXDEPMODE = @CXXDEPMODE@
-CXXFLAGS = @CXXFLAGS@ @H5_CXXFLAGS@
+CXXFLAGS = @CXXFLAGS@
 CYGPATH_W = @CYGPATH_W@
 DEBUG_PKG = @DEBUG_PKG@
 DEFAULT_API_VERSION = @DEFAULT_API_VERSION@
@@ -201,7 +208,7 @@ F9XMODEXT = @F9XMODEXT@
 F9XMODFLAG = @F9XMODFLAG@
 F9XSUFFIXFLAG = @F9XSUFFIXFLAG@
 FC = @FC@
-FCFLAGS = @FCFLAGS@ @H5_FCFLAGS@
+FCFLAGS = @FCFLAGS@
 FCFLAGS_f90 = @FCFLAGS_f90@
 FCLIBS = @FCLIBS@
 FGREP = @FGREP@
@@ -415,9 +422,9 @@ SCRIPT_DEPEND = h5repart$(EXEEXT) h5mkgrp$(EXEEXT)
 bin_SCRIPTS = h5redeploy
 
 # Add h5debug, h5repart, and h5mkgrp specific linker flags here
-h5debug_LDFLAGS = $(LT_STATIC_EXEC)
-h5repart_LDFLAGS = $(LT_STATIC_EXEC)
-h5mkgrp_LDFLAGS = $(LT_STATIC_EXEC)
+h5debug_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5repart_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5mkgrp_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
 
 # Tell automake to clean h5redeploy script
 CLEANFILES = h5redeploy
diff --git a/tools/misc/h5cc.in b/tools/misc/h5cc.in
index 1ead951..3422bdd 100755
--- a/tools/misc/h5cc.in
+++ b/tools/misc/h5cc.in
@@ -58,9 +58,9 @@ get_output_file="no"
 SHOW="eval"
 CCBASE="@CC@"
 CLINKERBASE="@CC@"
-CFLAGS="@CFLAGS@"
-CPPFLAGS="@CPPFLAGS@"
-LDFLAGS="@LDFLAGS@"
+CFLAGS="@AM_CFLAGS@ @CFLAGS@"
+CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@"
+LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
 LIBS="@LIBS@"
 
 CC="${HDF5_CC:-$CCBASE}"