updates configuration files to have similar setup as in 3D versions; …

…uses FLAGS_CHECK instead of DEF_FFLAGS to define user compilation flags

Makefile.in

@@ -48,17 +48,24 @@ FCFLAGS = @FCFLAGS@
 MPIFC = @MPIFC@
 MPILIBS = @MPILIBS@
 
-DEF_FFLAGS = @DEF_FFLAGS@ -I${SETUP}
+FLAGS_CHECK = @FLAGS_CHECK@
+
+FCFLAGS_f90 = @FCFLAGS_f90@ -I${SETUP}
+
+FC_MODEXT = @FC_MODEXT@
+FC_MODDIR = @FC_MODDIR@
+
+FCCOMPILE_CHECK =@FCENV@ ${FC} ${FCFLAGS} $(FLAGS_CHECK)
+
+MPIFCCOMPILE_CHECK =@FCENV@ ${MPIFC} ${FCFLAGS} $(FLAGS_CHECK)
 
 CC = @CC@
 CFLAGS = @CFLAGS@ $(CPPFLAGS) -I${SETUP}
 CPPFLAGS = @CPPFLAGS@ $(COND_MPI_CPPFLAGS)
 
-FC_MODEXT = @FC_MODEXT@
-FC_MODDIR = @FC_MODDIR@
+# all linker flags
+MPILIBS += @LDFLAGS@ @LIBS@
 
-LIB =
-LINK = $(F90)
 
 #######################################
 ####
@@ -67,8 +74,20 @@ LINK = $(F90)
 #######################################
 
 ## serial or parallel
-@COND_MPI_TRUE@F90 = $(MPIFC) $(FCFLAGS) @FC_DEFINE@USE_MPI @FC_DEFINE@USE_SCOTCH -I"@SCOTCH_INCLUDEDIR@" $(MPILIBS)
-@COND_MPI_FALSE@F90 = $(FC) $(FCFLAGS)
+@COND_MPI_TRUE@MPI = yes
+@COND_MPI_FALSE@MPI = no
+
+@COND_MPI_TRUE@FCLINK = $(MPIFCCOMPILE_CHECK)
+@COND_MPI_FALSE@FCLINK = $(FCCOMPILE_CHECK)
+
+@COND_MPI_TRUE@COND_MPI_CPPFLAGS = -DWITH_MPI
+@COND_MPI_FALSE@COND_MPI_CPPFLAGS =
+
+MPI_INCLUDES = @MPI_INCLUDES@
+
+# fortran compiler setting
+@COND_MPI_TRUE@F90 = $(MPIFCCOMPILE_CHECK) @FC_DEFINE@USE_MPI
+@COND_MPI_FALSE@F90 = $(FCCOMPILE_CHECK)
 
 #######################################
 ####
@@ -79,12 +98,17 @@ LINK = $(F90)
 USE_BUNDLED_SCOTCH = @USE_BUNDLED_SCOTCH@
 
 SCOTCH_DIR = @SCOTCH_DIR@
-SCOTCH_INCLUDEDIR = @SCOTCH_INCLUDEDIR@
+SCOTCH_INCDIR = @SCOTCH_INCLUDEDIR@
 SCOTCH_LIBDIR = @SCOTCH_LIBDIR@
 
+SCOTCH_INC = -I${SCOTCH_INCDIR}
+SCOTCH_LIBS = -L${SCOTCH_LIBDIR} -lscotch -lscotcherr
+
+@COND_MPI_TRUE@F90 += @FC_DEFINE@USE_SCOTCH $(SCOTCH_INC)
+
 ## scotch libraries
-@COND_MPI_TRUE@LIB += -L"@SCOTCH_LIBDIR@" -lscotch -lscotcherr
-@COND_MPI_FALSE@LIB +=
+@COND_MPI_TRUE@MPILIBS += ${SCOTCH_LIBS}
+@COND_MPI_FALSE@MPILIBS +=
 
 #######################################
 ####
@@ -103,12 +127,16 @@ SCOTCH_LIBDIR = @SCOTCH_LIBDIR@
 @COND_CUDA6_TRUE@CUDA6 = yes
 @COND_CUDA6_FALSE@CUDA6 = no
 
+# CUDA compilation with linking
+@COND_CUDA_PLUS_TRUE@CUDA_PLUS = yes
+@COND_CUDA_PLUS_FALSE@CUDA_PLUS = no
+
 # default cuda libraries
 # runtime library -lcudart -lcuda and -lcublas needed
 
 CUDA_FLAGS = @CUDA_FLAGS@ 
 CUDA_INC = @CUDA_CPPFLAGS@ -I${SETUP}
-CUDA_LINK = @CUDA_LDFLAGS@ @CUDA_LIBS@ -lcudart -lstdc++
+CUDA_LINK = @CUDA_LDFLAGS@ @CUDA_LIBS@
 
 @COND_CUDA_TRUE@NVCC = nvcc
 @COND_CUDA_FALSE@NVCC = @CC@
@@ -131,18 +159,18 @@ GENCODE_37 = -gencode=arch=compute_37,code=\"sm_37\"
 # CUDA version 5.x
 @COND_CUDA_TRUE@@COND_CUDA5_TRUE@GENCODE = $(GENCODE_35)
 # CUDA version 4.x
-@COND_CUDA_TRUE@@COND_CUDA5_FALSE@GENCODE = $(GENCODE_20)
+@COND_CUDA_TRUE@@COND_CUDA_PLUS_FALSE@GENCODE = $(GENCODE_20)
 
 # CUDA flags and linking
-@COND_CUDA_TRUE@NVCC_FLAGS_BASE = $(CUDA_FLAGS) $(CUDA_INC) $(COND_MPI_CPPFLAGS)
-@COND_CUDA_TRUE@@COND_CUDA5_TRUE@NVCC_FLAGS = $(NVCC_FLAGS_BASE) -DCUDA $(GENCODE) -ftz=true
-@COND_CUDA_TRUE@@COND_CUDA5_FALSE@NVCC_FLAGS = $(NVCC_FLAGS_BASE) -DCUDA -DUSE_OLDER_CUDA4_GPU $(GENCODE)
+@COND_CUDA_TRUE@NVCC_FLAGS_BASE = $(CUDA_FLAGS) $(CUDA_INC) $(MPI_INCLUDES) $(COND_MPI_CPPFLAGS)
+@COND_CUDA_TRUE@@COND_CUDA_PLUS_TRUE@NVCC_FLAGS = $(NVCC_FLAGS_BASE) -dc -DCUDA $(GENCODE) -ftz=true
+@COND_CUDA_TRUE@@COND_CUDA_PLUS_FALSE@NVCC_FLAGS = $(NVCC_FLAGS_BASE) -DCUDA -DUSE_OLDER_CUDA4_GPU $(GENCODE)
 
-@COND_CUDA_TRUE@@COND_CUDA5_TRUE@NVCCLINK_BASE = $(NVCC) $(CUDA_INC) $(COND_MPI_CPPFLAGS) -DCUDA
-@COND_CUDA_TRUE@@COND_CUDA5_TRUE@NVCCLINK = $(NVCCLINK_BASE) -dlink $(GENCODE)
-@COND_CUDA_TRUE@@COND_CUDA5_FALSE@NVCCLINK = $(NVCCLINK_BASE) -DUSE_OLDER_CUDA4_GPU $(GENCODE)
+@COND_CUDA_TRUE@@COND_CUDA_PLUS_TRUE@NVCCLINK_BASE = $(NVCC) $(CUDA_INC) $(MPI_INCLUDES) $(COND_MPI_CPPFLAGS) -DCUDA
+@COND_CUDA_TRUE@@COND_CUDA_PLUS_TRUE@NVCCLINK = $(NVCCLINK_BASE) -dlink $(GENCODE)
+@COND_CUDA_TRUE@@COND_CUDA_PLUS_FALSE@NVCCLINK = $(NVCCLINK_BASE) -DUSE_OLDER_CUDA4_GPU $(GENCODE)
 
-@COND_CUDA_FALSE@NVCC_FLAGS = $(COND_MPI_CPPFLAGS)
+@COND_CUDA_FALSE@NVCC_FLAGS = $(MPI_INCLUDES) $(COND_MPI_CPPFLAGS)
 @COND_CUDA_FALSE@NVCCLINK = $(NVCC) $(NVCC_FLAGS)
 
 
@@ -230,10 +258,15 @@ help:
 	@echo "    xmeshfem2D"
 	@echo ""
 	@echo "additional executables:"
+	@echo "- auxiliary executables: [make aux]"
 	@echo "    xadj_seismogram"
 	@echo "    xcheck_quality_external_mesh"
 	@echo "    xconvolve_source_timefunction"
 	@echo ""
+	@echo "- sensitivity kernel postprocessing tools: [make postprocess]"
+	@echo "    xcombine_sem"
+	@echo "    xsmooth_sem"
+	@echo ""
 
 
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