--- cdat_lite-6.0rc2/libcdms/Makefile.in
+++ cdat_lite-6.0rc2/libcdms/Makefile.in
@@ -44,15 +44,15 @@
 PARMDIR=$(prefix)/lib/lats
 
 CC = @CC@
-CFLAGS = -I../../include @CFLAGS@ $(DEBUG) -Dgrads @GRIB2INC@ @GRIB2OPTS@
+CFLAGS = -fPIC -I../../include @CFLAGS@ -Dgrads @GRIB2INC@ @GRIB2OPTS@
 CPPFLAGS = @CPPFLAGS@
 DEBUG = -O
 DEFS = @DEFS@
 FC = @FC@
-FFLAGS = -I../../include @FFLAGS@ $(DEBUG)
+FFLAGS = -I../../include @FFLAGS@
 INSTALL = @INSTALL@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
-LDFLAGS = -L../../../lib -lcdms @NCOPTS@ @HDFOPTS@ @DRSOPTS@ @LIBS@ @GRIB2LIB@
+LDFLAGS += -L../../../lib -lcdms @NCOPTS@ @HDFOPTS@ @DRSOPTS@ @LIBS@ @GRIB2LIB@
 OS = @OS@
 RANLIB = @RANLIB@
 
--- cdat_lite-6.0rc2/libcdms/src/db_util/Makefile.in
+++ cdat_lite-6.0rc2/libcdms/src/db_util/Makefile.in
@@ -38,17 +38,18 @@
 PARMDIR=$(prefix)/lib/lats
 
 CC = @CC@
-CFLAGS = -I../../include @CFLAGS@ $(DEBUG) -Dgrads
+CFLAGS = -fPIC -I../../include @CFLAGS@ -Dgrads
 CPPFLAGS = @CPPFLAGS@
 DEBUG = -O
 DEFS = @DEFS@
 FC = @FC@
-FFLAGS = -I../../include @FFLAGS@ $(DEBUG)
+FFLAGS = -I../../include @FFLAGS@
 INSTALL = @INSTALL@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
-LDFLAGS = -L../../../lib -lcdms @NCOPTS@ @DRSOPTS@ @LIBS@
+LDFLAGS += -L../../../lib -lcdms @NCOPTS@ @DRSOPTS@ @LIBS@
 OS = @OS@
 RANLIB = @RANLIB@
+AR ?= ar
 
 # Shell to run make subcommands
 SHELL = /bin/sh
@@ -60,7 +61,7 @@
 		  cdUtil.o
 
 all:		$(OBJS) FORCE
-		ar rv $(LIBRARY) $(OBJS)
+		$(AR) rv $(LIBRARY) $(OBJS)
 		$(RANLIB) $(LIBRARY)
 
 cdTimeConv.o:	cdTimeConv.c ../../include/cdmsint.h ../../include/cdms.h ../../include/cdunif.h
--- cdat_lite-6.0rc2/libcdms/src/cdunif/Makefile.in
+++ cdat_lite-6.0rc2/libcdms/src/cdunif/Makefile.in
@@ -47,29 +47,29 @@
 PARMDIR=$(prefix)/lib/lats
 
 # Set the compiler flag for the 64-bit Opteron platform
+CC = @CC@
 ARCH=$(shell uname -m)
 ifeq ($(ARCH),x86_64)
-   CC = gcc -fPIC -D__x86_64__
-else
-   CC = @CC@
+   CC += -fPIC -D__x86_64__
 endif
 
 ifneq (@GRIB2INC@,)
-  CFLAGS = -I../../include -I"@NCINC@" -I@HDFINC@ -I@DRSINC@ @CFLAGS@ $(DEBUG) -Dgrads -I@GRIB2INC@ @GRIB2OPTS@
+  CFLAGS = -I../../include -I"@NCINC@" -I@HDFINC@ -I@DRSINC@ @CFLAGS@ -Dgrads -I@GRIB2INC@ @GRIB2OPTS@
 else
-  CFLAGS = -I../../include -I"@NCINC@" -I@HDFINC@ -I@DRSINC@ @CFLAGS@ $(DEBUG) -Dgrads
+  CFLAGS = -I../../include -I"@NCINC@" -I@HDFINC@ -I@DRSINC@ @CFLAGS@ -Dgrads
 endif
 
-CPPFLAGS = @CPPFLAGS@ -DSTNDALN=1 -DBYTEORDER=@GRADS_BYTEORDER@ -DGRADS_CRAY=@GRADS_CRAY@ @QLOPTS@ @PPOPTS@ @GRIB2OPTS@
+CPPFLAGS += @CPPFLAGS@ -DSTNDALN=1 -DBYTEORDER=@GRADS_BYTEORDER@ -DGRADS_CRAY=@GRADS_CRAY@ @QLOPTS@ @PPOPTS@ @GRIB2OPTS@
 DEBUG = -O
 DEFS = @DEFS@
 FC = @FC@
-FFLAGS = -I../../include @FFLAGS@ $(DEBUG)
+FFLAGS = -I../../include @FFLAGS@
 INSTALL = @INSTALL@
 INSTALL_PROGRAM = @INSTALL_PROGRAM@
-LDFLAGS = -L../../../lib -lcdms @NCOPTS@ @HDFOPTS@ @DRSOPTS@ @LIBS@ @GRIB2LIB@
+LDFLAGS += -L../../../lib -lcdms @NCOPTS@ @HDFOPTS@ @DRSOPTS@ @LIBS@ @GRIB2LIB@
 OS = @OS@
 RANLIB = @RANLIB@
+AR ?= ar
 
 # Shell to run make subcommands
 SHELL = /bin/sh
@@ -80,7 +80,7 @@
 OBJS		= cdunif.o cdunifint.o cdunifgen.o cdunifdrs.o cdunifgrads.o cdunifnc.o cdunifhdf.o cdunifslab.o cdunifstub.o cdunifra.o cdrra.o cdsort.o gamach.o gaio.o gaprnt.o gautil.o gaddes.o galloc.o gabufr.o gabufrtbl.o cdunifql.o @GRADS_IEEE2CRAY_OBJECT@
 
 all:		$(OBJS) FORCE
-		ar rv $(LIBRARY) $(OBJS)
+		$(AR) rv $(LIBRARY) $(OBJS)
 		cd cdunifpp; $(MAKE) DEBUG=$(DEBUG)
 		$(RANLIB) $(LIBRARY)
 
--- cdat_lite-6.0rc2/libcdms/src/cdunif/cdunifpp/Makefile.in
+++ cdat_lite-6.0rc2/libcdms/src/cdunif/cdunifpp/Makefile.in
@@ -37,12 +37,13 @@
 # set to blank if you don't want to rename symbols in unpacking routines
 
 CC = @CC@
-CFLAGS = -I../../../include/cdunifpp -I@NCINC@ @CFLAGS@ -I../../../include $(DEBUG)
+CFLAGS = -fPIC -I../../../include/cdunifpp -I@NCINC@ @CFLAGS@ -I../../../include
 CPPFLAGS = @CPPFLAGS@ @PPOPTS@ -Uhdf
 LIBRARY = ../../../lib/libcdms.a
+AR ?= ar
 
 all: $(OBJS)
-	ar rv $(LIBRARY) $(OBJS)
+	$(AR) rv $(LIBRARY) $(OBJS)
 # (ranlib called by higher-level makefile)
 
 %.o: %.c $(HEADERS)
--- cdat_lite-6.0rc2/setup_util.py
+++ cdat_lite-6.0rc2/setup_util.py
@@ -296,8 +296,6 @@
             nc4_defs = ''
 
         self._system('cd libcdms ; '
-                     'CFLAGS="-fPIC" '
-                     'CC=%(cc)s '
                      'sh ./configure --disable-drs --disable-hdf '
                      '--disable-ql --with-ncinc=%(ncinc)s --with-ncincf=%(ncinc)s --with-nclib=%(nclib)s %(nc4)s'
                      % dict(ncinc=netcdf_config.netcdf_incdir, nclib=netcdf_config.netcdf_libdir,