There was no ifndef CXXFLAGS, thus its value was not respected if set outside

Added some indentation to make the ifdef nesting a bit less cryptic

src/make.inc

 # FC defines the fortran compiler to use. If undefined, GNU Make tries to use `f77`
 ifndef FC
-override FC=gfortran
+  override FC=gfortran
 endif
 
 # FCFLAGS defines the compilation options for the fortran compiler
 ifndef FCFLAGS
-override FCFLAGS=-std=legacy -O3
+  override FCFLAGS=-std=legacy -O3
 endif
 
 # AR defines the command to create static library files
 ifndef AR
-override AR=ar
+  override AR=ar
 endif
 
 # ARFLAGS defines the flags for AR to create static library files
 ifndef ARFLAGS
-override ARFLAGS=-rs
+  override ARFLAGS=-rs
 endif
 
 # PICFLAGS defines the additional flags for the c++ compiler to create objects suitable for shared library creation
 ifndef PICFLAGS
-override PICFLAGS=-fPIC
+  override PICFLAGS=-fPIC
 endif
 
 # LDFLAGS defines the default linker flags
 ifndef LDFLAGS
-override LDFLAGS=
+  override LDFLAGS=
 endif
 
 # CXX defines the default C++ compiler to use. If undefined, GNU Make tries to use g++
 ifndef CXX
-ifdef USE_MPI
-override CXX=mpicxx
-else
-override CXX=g++
-endif
+  ifdef USE_MPI
+    override CXX=mpicxx
+  else
+    override CXX=g++
+  endif
 endif
 
 ifdef USE_MPI
-override MPI_CXXFLAGS+=-DUSE_MPI
+  override MPI_CXXFLAGS+=-DUSE_MPI
 endif
 
 # HDF5_INCLUDE defines the default path to the HDF5 include files to use
 ifndef HDF5_INCLUDE
-override HDF5_INCLUDE=/usr/include/hdf5/serial
+  override HDF5_INCLUDE=/usr/include/hdf5/serial
 endif
 
 # define (outside) USE_LAPACK for lapacke support, LAPACK_ILP64 for ilp64 interface, MKL_ILP64 the same if using MKL implementation
 ifdef USE_LAPACK
 # define (outside) USE_ILP64 for long long int support in lapack/mkl/magma interfaces
-ifdef USE_ILP64
-ifndef LAPACK_ILP64
-override LAPACK_ILP64=1
-endif #LAPACK_ILP64
-endif
+  ifdef USE_ILP64
+    ifndef LAPACK_ILP64
+      override LAPACK_ILP64=1
+    endif #LAPACK_ILP64
+  endif
 # define (outside) USE_MKL to use the MKL implementation of lapacke
-ifdef USE_MKL
+  ifdef USE_MKL
 # define (outside) USE_ILP64 for long long int support in lapack/mkl/magma interfaces
-ifdef USE_ILP64
-ifndef MKL_ILP64
-override MKL_ILP64=1
-endif #MKL_ILP64
-endif
-ifndef LAPACK_INCLUDE
+    ifdef USE_ILP64
+      ifndef MKL_ILP64
+        override MKL_ILP64=1
+      endif #MKL_ILP64
+    endif #USE_ILP64
+    ifndef LAPACK_INCLUDE
 # this is for the MKL implementation
-override LAPACK_INCLUDE=$(MKLROOT)/include
-endif #LAPACK_INCLUDE
-ifndef LAPACK_LDFLAGS
+      override LAPACK_INCLUDE=$(MKLROOT)/include
+    endif #LAPACK_INCLUDE
+    ifndef LAPACK_LDFLAGS
 # this is for the MKL implementation
 # define (outside) USE_ILP64 for long long int support in lapack/mkl/magma interfaces
-ifdef USE_ILP64
-override LAPACK_LDFLAGS=-L$(MKLROOT)/lib -Wl,--no-as-needed -lmkl_intel_ilp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl
+      ifdef USE_ILP64
+        override LAPACK_LDFLAGS=-L$(MKLROOT)/lib -Wl,--no-as-needed -lmkl_intel_ilp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl
 else
-override LAPACK_LDFLAGS=-L$(MKLROOT)/lib -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl
-endif
-endif #LAPACK_LDFLAGS
+        override LAPACK_LDFLAGS=-L$(MKLROOT)/lib -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl
+      endif #USE_ILP64
+    endif #LAPACK_LDFLAGS
 # the next else refers to USE_MKL
-else #this is for when USE_MKL is _not_ defined
-ifndef LAPACK_INCLUDE
+  else #this is for when USE_MKL is _not_ defined
+    ifndef LAPACK_INCLUDE
 # this is for standard "vanilla" lapacke64
-override LAPACK_INCLUDE=/usr/include
-endif # LAPACK_INCLUDE
-ifndef LAPACK_LDFLAGS
-ifdef USE_ILP64
+      override LAPACK_INCLUDE=/usr/include
+    endif # LAPACK_INCLUDE
+    ifndef LAPACK_LDFLAGS
+      ifdef USE_ILP64
 # this is for standard "vanilla" lapacke64
-override LAPACK_LDFLAGS=-llapacke64
-else
-override LAPACK_LDFLAGS=-llapacke
-endif
-endif #LAPACK_LDFLAGS
+        override LAPACK_LDFLAGS=-llapacke64
+      else
+        override LAPACK_LDFLAGS=-llapacke
+      endif #USE_ILP64
+    endif #LAPACK_LDFLAGS
 # the next endif is for USE_MKL
-endif
+  endif
 #the next endif is for USE_LAPACK
 endif
 
 # define (outside) USE_MAGMA for magma support
 ifdef USE_MAGMA
-ifdef MAGMA_LIB
-override MAGMA_LDFLAGS= -L$(MAGMA_LIB)
-endif
-ifdef CUDA_HOME
-override MAGMA_LDFLAGS+= -L$(CUDA_HOME)/lib64
-endif
-override MAGMA_LDFLAGS+= -lmagma -lcudart
+  ifndef MAGMA_LDFLAGS
+    ifdef MAGMA_LIB
+      override MAGMA_LDFLAGS= -L$(MAGMA_LIB)
+    endif
+    ifdef CUDA_HOME
+      override MAGMA_LDFLAGS+= -L$(CUDA_HOME)/lib64
+    endif
+    override MAGMA_LDFLAGS+= -lmagma -lcudart
+#the next endif is for MAGMA_LDFLAGS
+  endif
 #the next endif is for USE_MAGMA
 endif
 
 # define (outside) USE_NVTX for NVIDIA profiling
 ifdef USE_NVTX
-override NVTX_FLAGS= -DUSE_NVTX
-ifdef CUDA_HOME
-override NVTX_FLAGS+= -I$(CUDA_HOME)/include
+  ifndef NVTX_CXXFLAGS
+    override NVTX_CXXFLAGS= -DUSE_NVTX
+    ifdef CUDA_HOME
+      override NVTX_CXXFLAGS+= -I$(CUDA_HOME)/include
 # closes CUDA_HOME
-endif
+    endif
+# closes NVTX_CXXFLAGS
+  endif
 # closes USE_NVTX
 endif
 
 # CXXFLAGS defines the default compilation options for the C++ compiler
 ifndef CXXFLAGS
-override CXXFLAGS=-O3 -ggdb -pg -coverage -I$(HDF5_INCLUDE) $(MPI_CXXFLAGS) $(NVTX_FLAGS)
-ifdef USE_OPENMP
-override CXXFLAGS+= -fopenmp
+  override CXXFLAGS=-O3 -ggdb -pg -coverage -I$(HDF5_INCLUDE) $(MPI_CXXFLAGS) $(NVTX_CXXFLAGS)
+  ifdef USE_OPENMP
+    override CXXFLAGS+= -fopenmp
 # closes USE_OPENMP
-endif
-
-ifdef USE_ILP64
-override CXXFLAGS+= -DUSE_ILP64
-endif
-
-ifdef USE_LAPACK
-override CXXFLAGS+= -DUSE_LAPACK
-ifdef USE_ILP64
-override CXXFLAGS+= -DLAPACK_ILP64
-endif
+  endif
+  ifdef USE_ILP64
+    override CXXFLAGS+= -DUSE_ILP64
+  endif
+  ifdef USE_LAPACK
+    override CXXFLAGS+= -DUSE_LAPACK
+    ifdef USE_ILP64
+      override CXXFLAGS+= -DLAPACK_ILP64
+    endif
 # closes USE_LAPACK
-endif
-
-ifdef USE_MKL
-override CXXFLAGS+= -DUSE_MKL -I$(MKLROOT)/include
-ifdef USE_ILP64
-override CXXFLAGS+= -DMKL_ILP64
-endif
+  endif
+  ifdef USE_MKL
+    override CXXFLAGS+= -DUSE_MKL -I$(MKLROOT)/include
+    ifdef USE_ILP64
+      override CXXFLAGS+= -DMKL_ILP64
+    endif
 # closes USE_MKL
-endif
-
-ifdef USE_OPENMP
-override CXXFLAGS+= -fopenmp
+  endif
+  ifdef USE_OPENMP
+    override CXXFLAGS+= -fopenmp
 # closes USE_OPENMP
-endif
-
-ifdef USE_MAGMA
-override CXXFLAGS+= -DUSE_MAGMA
-ifdef CUDA_HOME
-override CXXFLAGS+= -I$(CUDA_HOME)/include
-endif
-ifdef MAGMA_INCLUDE
-override CXXFLAGS+= -I$(MAGMA_INCLUDE)
-endif
-ifdef USE_ILP64
-override CXXFLAGS+= -DMAGMA_ILP64
-endif
+  endif
+  ifdef USE_MAGMA
+    override CXXFLAGS+= -DUSE_MAGMA
+    ifdef CUDA_HOME
+      override CXXFLAGS+= -I$(CUDA_HOME)/include
+    endif
+    ifdef MAGMA_INCLUDE
+      override CXXFLAGS+= -I$(MAGMA_INCLUDE)
+    endif
+    ifdef USE_ILP64
+      override CXXFLAGS+= -DMAGMA_ILP64
+    endif
 # closes USE_MAGMA
+  endif
+#closes CXXFLAGS
 endif
 
-# closes CXXFLAGS
-endif
-
-
 # HDF5_LIB defines the default path to the HDF5 libraries to use
 # CXXLDFLAGS defines the default linker flags to use for C++ codes
 ifndef CXXLDFLAGS
-ifndef HDF5_LIB
-override HDF5_LIB=/usr/lib/x86_64-linux-gnu/hdf5/serial
-endif
-override CXXLDFLAGS=-L/usr/lib64 -L$(HDF5_LIB) -lhdf5 $(STATICFLAG)
-ifdef USE_LAPACK
-override CXXLDFLAGS+= $(LAPACK_LDFLAGS)
-endif
-ifdef USE_MAGMA
-override CXXLDFLAGS+= $(MAGMA_LDFLAGS)
-endif
-override CXXLDFLAGS+= $(LDFLAGS)
+  ifndef HDF5_LIB
+    override HDF5_LIB=/usr/lib/x86_64-linux-gnu/hdf5/serial
+  endif
+  override CXXLDFLAGS=-L/usr/lib64 -L$(HDF5_LIB) -lhdf5 $(STATICFLAG)
+  ifdef USE_LAPACK
+    override CXXLDFLAGS+= $(LAPACK_LDFLAGS)
+  endif
+  ifdef USE_MAGMA
+    override CXXLDFLAGS+= $(MAGMA_LDFLAGS)
+  endif
+  override CXXLDFLAGS+= $(LDFLAGS)
 endif
 
 #SOFLAGS defines the additional flags for the c++ compiler to create a shared object file
 ifndef SOFLAGS
-override SOFLAGS=-shared
+  override SOFLAGS=-shared
 endif
 
 %.o : %.f