autotool fixes

configure.ac

@@ -259,13 +259,13 @@ fi
 AC_MSG_CHECKING([if parallel interface enabled])
 if test "X$ENABLE_PARALLEL" = "Xyes"; then
 	AC_MSG_RESULT([yes])
-	AM_CPPFLAGS="${AM_CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
+	CPPFLAGS="${CPPFLAGS} -DPARALLEL_IO -DMPICH_IGNORE_CXX_SEEK"
 
         if test "X$ENABLE_EXPERIMENTAL" = "Xyes"; then
         	AC_MSG_CHECKING([for ParMETIS])
                 if test "X$PARMETISPATH" != "X"; then
-                        AM_CPPFLAGS="$AM_CPPFLAGS -I$PARMETISPATH/include"
-	                AM_LDFLAGS="$AM_LDFLAGS -L$PARMETISPATH/lib"
+                        CPPFLAGS="$CPPFLAGS -I$PARMETISPATH/include"
+	                LDFLAGS="$LDFLAGS -L$PARMETISPATH/lib"
 	        fi
 
                 LIBS="$LIBS -lparmetis -lmetis"
@@ -285,11 +285,11 @@ fi
 ###############################################################################
 # LIBRARY PATHS
 if test -n "${HDF5_PREFIX}" ; then
-        AM_CPPFLAGS="$AM_CPPFLAGS -I$HDF5_PREFIX/include"
-        AM_LDFLAGS="$AM_LDFLAGS -L$HDF5_PREFIX/lib"
+        CPPFLAGS="$CPPFLAGS -I$HDF5_PREFIX/include"
+        LDFLAGS="$LDFLAGS -L$HDF5_PREFIX/lib"
 fi
 AC_CHECK_LIB([z], [compress2])
-AC_CHECK_LIB([hdf5], [H5open])
+AC_CHECK_LIB([hdf5], [H5open],,, [-lm])
 AS_IF([test "x$ac_cv_lib_hdf5_H5open" != xyes], 
         [AC_MSG_ERROR([Cannot compile and link a HDF5 program]); 
         exit 1])
@@ -317,8 +317,8 @@ if test -z "$LUSTREROOT"; then
 	AC_MSG_WARN([Couldn't locate the lustre API... building without support for lustre striping!])
 else
         CFLAGS="$CFLAGS -DH5_USE_LUSTRE"
-        AM_CPPFLAGS="$AM_CPPFLAGS -I$LUSTREROOT/usr/include"
-        AM_LDFLAGS="$AM_LDFLAGS -L$LUSTREROOT/usr/lib"
+        CPPFLAGS="$CPPFLAGS -I$LUSTREROOT/usr/include"
+        LDFLAGS="$LDFLAGS -L$LUSTREROOT/usr/lib"
         LIBS="$LIBS -llustreapi"
 fi
 
@@ -336,6 +336,9 @@ fi
 
 ###############################################################################
 # EXPORTING VARIABLES & CREATING OUTPUT FILES
+AM_CPPFLAGS=$CPP_FLAGS
+AM_LDFLAGS=$LD_FLAGS
+
 AC_SUBST(HDF5_PREFIX)
 AC_SUBST(CFLAGS)
 AC_SUBST(FFLAGS)

examples/H5/Makefile.am

@@ -1,6 +1,6 @@
-AM_CPPFLAGS += -I${abs_top_builddir}/src/include
+AM_CPPFLAGS += -I${abs_top_srcdir}/src/include
 FFLAGS += -cpp $(AM_CPPFLAGS)
-AM_LDFLAGS += -L${abs_top_builddir}/src/lib
+AM_LDFLAGS += -L${abs_top_builddir}/src/h5core/.libs
 
 LDADD = 
 

examples/H5Block/Makefile.am

@@ -1,6 +1,6 @@
-AM_CPPFLAGS += -I${abs_top_builddir}/src/include
+AM_CPPFLAGS += -I${abs_top_srcdir}/src/include
 FFLAGS += -cpp $(AM_CPPFLAGS)
-AM_LDFLAGS += -L${abs_top_builddir}/src/lib
+AM_LDFLAGS += -L${abs_top_builddir}/src/h5core/.libs
 
 LDADD = 
 

examples/H5Fed/Makefile.am

@@ -1,6 +1,6 @@
 AM_CPPFLAGS += -I${abs_top_builddir}/src/include
 FFLAGS += -cpp $(AM_CPPFLAGS)
-AM_LDFLAGS += -L${abs_top_builddir}/src/lib
+AM_LDFLAGS += -L${abs_top_builddir}/src/h5core/.libs
 
 LDADD =
 

examples/H5Part/Makefile.am

@@ -1,6 +1,6 @@
-AM_CPPFLAGS += -I${abs_top_builddir}/src/include
+AM_CPPFLAGS += -I${abs_top_srcdir}/src/include
 FFLAGS += -cpp $(AM_CPPFLAGS)
-AM_LDFLAGS += -L${abs_top_builddir}/src/lib
+AM_LDFLAGS += -L${abs_top_builddir}/src/h5core/.libs
 
 LDADD = 
 

src/h5core/Makefile.am

@@ -99,9 +99,9 @@ libH5hut_la_DEPENDENCIES = $(EXTRA_HEADERS)
 
 libH5hut_la_LDFLAGS = -version-info 2:0:0
 
-all-local:
-	$(INSTALL) -m0755 -d $(top_builddir)/src/lib
-	$(INSTALL) -m644 .libs/libH5hut.a $(top_builddir)/src/lib
+#all-local:
+#	$(INSTALL) -m0755 -d $(top_builddir)/src/lib
+#	$(INSTALL) -m644 .libs/libH5hut.a $(top_builddir)/src/lib
 
 install-exec-local:
 	@$(INSTALL) -d $(DESTDIR)$(includedir)/h5core

test/Makefile.am

@@ -1,5 +1,5 @@
 AM_CPPFLAGS += -I$(top_srcdir)/src/include
-AM_LDFLAGS += -L${abs_top_builddir}/src/lib
+AM_LDFLAGS += -L${abs_top_builddir}/src/h5core/.libs
 
 LDADD =
 LDADD += -lH5hut