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

@@ -61,7 +61,7 @@ ifdef USE_ILP64
       ifndef MKL_ILP64
         override MKL_ILP64=1
       endif #MKL_ILP64
-endif
+    endif #USE_ILP64
     ifndef LAPACK_INCLUDE
 # this is for the MKL implementation
       override LAPACK_INCLUDE=$(MKLROOT)/include
@@ -73,7 +73,7 @@ ifdef USE_ILP64
         override LAPACK_LDFLAGS=-L$(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 #USE_ILP64
     endif #LAPACK_LDFLAGS
 # the next else refers to USE_MKL
   else #this is for when USE_MKL is _not_ defined
@@ -87,7 +87,7 @@ ifdef USE_ILP64
         override LAPACK_LDFLAGS=-llapacke64
       else
         override LAPACK_LDFLAGS=-llapacke
-endif
+      endif #USE_ILP64
     endif #LAPACK_LDFLAGS
 # the next endif is for USE_MKL
   endif
@@ -96,6 +96,7 @@ endif
 
 # define (outside) USE_MAGMA for magma support
 ifdef USE_MAGMA
+  ifndef MAGMA_LDFLAGS
     ifdef MAGMA_LIB
       override MAGMA_LDFLAGS= -L$(MAGMA_LIB)
     endif
@@ -103,31 +104,34 @@ ifdef CUDA_HOME
       override MAGMA_LDFLAGS+= -L$(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
+  ifndef NVTX_CXXFLAGS
+    override NVTX_CXXFLAGS= -DUSE_NVTX
     ifdef CUDA_HOME
-override NVTX_FLAGS+= -I$(CUDA_HOME)/include
+      override NVTX_CXXFLAGS+= -I$(CUDA_HOME)/include
 # closes CUDA_HOME
     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) $(NVTX_FLAGS)
+  override CXXFLAGS=-O3 -ggdb -pg -coverage -I$(HDF5_INCLUDE) $(MPI_CXXFLAGS) $(NVTX_CXXFLAGS)
   ifdef USE_OPENMP
     override CXXFLAGS+= -fopenmp
 # closes USE_OPENMP
   endif
-
   ifdef USE_ILP64
     override CXXFLAGS+= -DUSE_ILP64
   endif
-
   ifdef USE_LAPACK
     override CXXFLAGS+= -DUSE_LAPACK
     ifdef USE_ILP64
@@ -135,7 +139,6 @@ override CXXFLAGS+= -DLAPACK_ILP64
     endif
 # closes USE_LAPACK
   endif
-
   ifdef USE_MKL
     override CXXFLAGS+= -DUSE_MKL -I$(MKLROOT)/include
     ifdef USE_ILP64
@@ -143,12 +146,10 @@ override CXXFLAGS+= -DMKL_ILP64
     endif
 # closes USE_MKL
   endif
-
   ifdef USE_OPENMP
     override CXXFLAGS+= -fopenmp
 # closes USE_OPENMP
   endif
-
   ifdef USE_MAGMA
     override CXXFLAGS+= -DUSE_MAGMA
     ifdef CUDA_HOME
@@ -162,11 +163,9 @@ override CXXFLAGS+= -DMAGMA_ILP64
     endif
 # closes USE_MAGMA
   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