diff --git a/src/MS/Makefile b/src/MS/Makefile
index 066a15e..7191c84 100644
--- a/src/MS/Makefile
+++ b/src/MS/Makefile
@@ -1,24 +1,26 @@
 OUTPUT=
 CXX=g++
-CXXFLAGS=-O3 -Wall -g #-pg #-fnostack-protector
+
+CXXFLAGS=-O3 -Wall -g -pg #-fnostack-protector
 # CASA_LIBDIR=-L/cm/shared/package/casacore/v2.1.0-gcc-4.9.3/lib -L/cm/shared/package/cfitsio/3380-gcc-4.9.3/lib -L/cm/shared/package/lapack/3.6.0-gcc-4.9.3/lib64
-CASA_LIBDIR=-L/cm/shared/package/casacore/v2.3.0-gcc-4.9.3/lib
-# CASA_INCDIR=-I/cm/shared/package/casacore/v2.3.0-g++-4.9.3/include -I/cm/shared/package/casacore/v2.3.0-g++-4.9.3/include/casacore
+CASA_LIBDIR=-L/cm/shared/package/casacore/v2.3.0-gcc-4.9.3/lib -L/cm/shared/package/cfitsio/3380-gcc-4.9.3/lib -L/cm/shared/package/lapack/3.6.0-gcc-4.9.3/lib64
+# CASA_INCDIR=-I/cm/shared/package/casacore/v2.1.0-g++-4.9.3/include -I/cm/shared/package/casacore/v2.1.0-g++-4.9.3/include/casacore
+
 CASA_INCDIR=-I/cm/shared/package/casacore/v2.3.0-gcc-4.9.3/include -I/cm/shared/package/casacore/v2.3.0-gcc-4.9.3/include/casacore
 CASA_LIBS=-lcasa_casa -lcasa_tables -lcasa_measures -lcasa_ms -lcfitsio
 #LAPACK=-llapack -lblas
 LAPACK=-lopenblas -lgfortran -lpthread
 # LAPACK_DIR=/cm/shared/apps/openblas/0.2.8/lib
+LAPACK_DIR=/cm/shared/package/openblas/0.2.17mt/lib
 #LAPACK_DIR=/usr/lib/atlas/sse/
 
-LDFLAGS=-Wl,--rpath-link,${CASA_LIBDIR}
-# LDFLAGS=-Wl,--rpath,/cm/shared/package/openblas/0.2.17mt/lib
+LDFLAGS=-Wl,--rpath,/cm/shared/package/openblas/0.2.17mt/lib/,${CASA_LIBDIR}
 #LDFLAGS=-Wl,-t,--rpath,/software/users/lofareor/SW/lib64
 # -Wl,--hash-style=both
 
-MY_LIBS=-lm -lsagecal
-INCLUDES=-I. -I./lib $(CASA_INCDIR) -I/usr/include
-LIBPATH=$(CASA_LIBDIR)  -L./lib -L/cm/shared/package/openblas/0.2.17mt/lib -L/cm/shared/package/cfitsio/3380-gcc-4.9.3/lib
+MY_LIBS=-lm -ldirac -lsagecal
+INCLUDES=-I. -I../lib/Dirac -I../lib/Radio $(CASA_INCDIR) -I/usr/include
+LIBPATH=-L$(LAPACK_DIR) $(CASA_LIBDIR)  -L../lib/Dirac -L../lib/Radio
 
 #### glib
 GLIBI=-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/x86_64-linux-gnu/glib-2.0/include/ -I/usr/lib64/glib-2.0/include
@@ -31,7 +33,8 @@ main.o:main.cpp
 	$(CXX) $(CXXFLAGS) $(INCLUDES) $(GLIBI) -c $<
 data.o:data.cpp data.h
 	$(CXX) $(CXXFLAGS) $(INCLUDES) $(GLIBI) -c $<
-sagecal:$(OBJECTS) ./lib/libsagecal.a
-	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(INCLUDES) $(GLIBI) $(LIBPATH)  -o $@  $(OBJECTS) $(MY_LIBS) $(LAPACK) $(CASA_LIBS) $(GLIBL)
+sagecal:$(OBJECTS) ../lib/Radio/libsagecal.a ../lib/Dirac/libdirac.a 
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(INCLUDES) $(GLIBI) $(LIBPATH)  -o $@  $(OBJECTS) $(MY_LIBS) $(LAPACK) $(CASA_LIBS)  $(GLIBL)
 clean:
-	rm *.o
+	rm *.o *.tmp *.fits *.swp *.swo *.o *.output
+
diff --git a/src/MS/Makefile.gpu b/src/MS/Makefile.gpu
index 6f503f1..0f3875b 100644
--- a/src/MS/Makefile.gpu
+++ b/src/MS/Makefile.gpu
@@ -1,33 +1,31 @@
 OUTPUT=
 CXX=g++
-CXXFLAGS=-O3 -Wall -g -DHAVE_CUDA
-CASA_LIBDIR=/cm/shared/package/casacore/v2.3.0-gcc-4.9.3/lib
-CASA_INCDIR=/cm/shared/package/casacore/v2.3.0-gcc-4.9.3/include -I/cm/shared/package/casacore/v2.3.0-gcc-4.9.3/include/casacore
+CXXFLAGS=-O3 -Wall -g -DHAVE_CUDA -pg -std=c++11
+CASA_LIBDIR=-L/cm/shared/package/casacore/v2.3.0-gcc-4.9.3/lib -L/cm/shared/package/cfitsio/3380-gcc-4.9.3/lib -L/cm/shared/package/lapack/3.6.0-gcc-4.9.3/lib64
+CASA_INCDIR=-I/cm/shared/package/casacore/v2.3.0-gcc-4.9.3/include -I/cm/shared/package/casacore/v2.3.0-gcc-4.9.3/include/casacore
 CASA_LIBS=-lcasa_casa -lcasa_tables -lcasa_measures -lcasa_ms -lcfitsio
-#LAPACK=-llapack -lblas
+# LAPACK=-llapack -lblas
 LAPACK=-lopenblas -lgfortran -lpthread
-#LAPACK_DIR=/usr/local/OpenBLAS/lib/
+LAPACK_DIR=/cm/shared/package/openblas/0.2.17mt/lib
 #LAPACK_DIR=/usr/lib/atlas/sse/
 
-# CUDAINC=-I/usr/local/cuda/include
-# CUDALIB=-L/usr/local/cuda/lib64 -lcuda -lcudart
 CUDAINC=-I/cm/shared/apps/cuda80/toolkit/8.0.44/include/
-CUDALIB=-lcuda -lcudart -lcublas -lcusolver -lcudadevrt
+CUDALIB=-L/cm/shared/apps/cuda80/toolkit/8.0.44/lib64/ -lcuda -lcudart
+
+CULALIB=-lcublas -lcusolver -lcudadevrt
 # NVML
 NVML_INC=/usr/include/nvidia/gdk/
 NVML_LIB=-lnvidia-ml -L/usr/lib64/nvidia/
 
-# I should be able to compile with cuda90, but it cannot find -lnvidia-ml.
-# However, that management library is in a system path, so it should be able to find it.
-# Possibly the rpath below makes it impossible to find it, even when a cuda90 path is used.
-LDFLAGS=-Wl,--rpath,$(CASA_LIBDIR),--rpath,/cm/shared/apps/cuda80/toolkit/8.0.44/lib64/
+
+LDFLAGS=-Wl,--rpath,/cm/shared/package/openblas/0.2.17mt/lib,${CASA_LIBDIR}
 #LDFLAGS=-Wl,-t,--rpath,/software/users/lofareor/SW/lib64
 # -Wl,--hash-style=both
 
 # with multithread FFTW
-MY_LIBS=-lm -lsagecal
-INCLUDES=-I. -I./lib -I$(CASA_INCDIR) -I/usr/include $(CUDAINC) -I$(NVML_INC)
-LIBPATH=-L$(CASA_LIBDIR)  -L./lib -L/cm/shared/package/openblas/0.2.17mt/lib -L/cm/shared/package/cfitsio/3380-gcc-4.9.3/lib
+MY_LIBS=-lm -lsagecal -ldirac 
+INCLUDES=-I. -I../lib/Dirac/ -I../lib/Radio/ $(CASA_INCDIR) -I/usr/include $(CUDAINC) -I$(NVML_INC)
+LIBPATH=-L$(LAPACK_DIR) -L$(CASA_LIBDIR) -L../lib/Dirac/ -L../lib/Radio/
 
 #### glib
 GLIBI=-I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/lib/x86_64-linux-gnu/glib-2.0/include/ -I/usr/lib64/glib-2.0/include
@@ -40,7 +38,7 @@ main.o:main.cpp
 	$(CXX) $(CXXFLAGS) $(INCLUDES) $(GLIBI) -c $<
 data.o:data.cpp data.h
 	$(CXX) $(CXXFLAGS) $(INCLUDES) $(GLIBI) -c $<
-sagecal:$(OBJECTS) ./lib/libsagecal.a
+sagecal:$(OBJECTS) ../lib/Radio/libsagecal.a ../lib/Dirac/libdirac.a 
 	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(INCLUDES) $(GLIBI) $(LIBPATH)  -o $@  $(OBJECTS) $(MY_LIBS) $(CASA_LIBS)  $(GLIBL) $(LAPACK)  $(CUDALIB) $(CULALIB) $(NVML_LIB)
 clean:
 	rm *.o *.tmp *.fits