Parallel Build, OpenMP Support with Fortran 90, and Improved Module Dependencies

15 files changed, 494 insertions, 257 deletions

diff --git a/Donjon/src/Makefile b/Donjon/src/Makefile
index f236c5e..b68f26a 100644
--- a/Donjon/src/Makefile
+++ b/Donjon/src/Makefile
@@ -1,7 +1,7 @@
 #---------------------------------------------------------------------------
 #
 #  Makefile for building the Donjon library and load module
-#  Author : A. Hebert (2018-5-10)
+#  Author : A. Hebert (2018-5-10) and C. Bienvenue (2025-11-04)
 #
 #---------------------------------------------------------------------------
 #
@@ -20,6 +20,8 @@ DIRNAME = $(shell uname -sm | sed 's/[ ]/_/')
 OS = $(shell uname -s | cut -d"_" -f1)
 opt = -O -g
 PREPRO = cpp
+DEFAULT_GOAL_PLACEHOLDER :=
+.DEFAULT_GOAL := all
 ifeq ($(openmp),1)
   COMP = -fopenmp
   PREPRO = cpp -D_OPENMP
@@ -46,12 +48,11 @@ else
 endif
 
 ifeq ($(OS),AIX)
-  python_version_major := 2
+  PY := python
 else
-  python_version_full := $(wordlist 2,4,$(subst ., ,$(shell python --version 2>&1)))
-  python_version_major := $(word 1,${python_version_full})
-  ifneq ($(python_version_major),2)
-    python_version_major := 3
+  PY := $(shell command -v python3 2>/dev/null)
+  ifeq ($(PY),)
+    PY := $(shell command -v python 2>/dev/null)
   endif
 endif
 
@@ -161,7 +162,9 @@ else
       lib_module = ../lib/$(DIRNAME)_llvm/modules
       INCLUDE = -I../../Ganlib/lib/$(DIRNAME)_llvm/modules/ -I../../Utilib/lib/$(DIRNAME)_llvm/modules/
       FFLAGS += -mmlir -fdynamic-heap-array
-      LFLAGS += -lclang_rt.osx
+      ifeq ($(OS),Darwin)
+        LFLAGS += -lclang_rt.osx
+      endif
     else
       lib = ../lib/$(DIRNAME)
       libUtl = ../../Utilib/lib/$(DIRNAME)
@@ -181,18 +184,32 @@ ifeq ($(hdf5),1)
   LFLAGS += -L${HDF5_API} -lhdf5
 endif
 
-SRCC = $(shell ls *.c)
-SRC77 = $(shell ls *.f)
-SRCF77 = $(shell ls *.F)
-ifeq ($(python_version_major),2)
-  SRC90 = $(shell python ../../script/make_depend.py *.f90)
+SRCC = $(shell ls *.c 2>/dev/null)
+SRC77 = $(shell ls *.f 2>/dev/null)
+SRCF77 = $(shell ls *.F 2>/dev/null)
+ifeq ($(PY),)
+  $(warning No Python interpreter found; Fortran dependency ordering may be suboptimal)
+  SRC90 = $(shell ls *.f90 2>/dev/null)
 else
-  SRC90 = $(shell python3 ../../script/make_depend_py3.py *.f90)
+  SRC90 = $(shell $(PY) ../../script/make_depend.py *.f90 *.F90)
+  
 endif
 OBJC = $(SRCC:.c=.o)
-OBJ90 = $(SRC90:.f90=.o)
+OBJ90 = $(patsubst %.f90,%.o,$(patsubst %.F90,%.o,$(SRC90)))
 OBJ77 = $(SRC77:.f=.o)
 OBJF77 = $(SRCF77:.F=.o)
+
+# Auto-generated dependency file capturing Fortran module and include deps
+DEPS_MK := .donjon_deps.mk
+-include $(DEPS_MK)
+$(DEPS_MK): $(SRC90) $(SRC77) $(SRCF77)
+ifeq ($(PY),)
+	@echo "# Dependencies not generated: no Python available" > $(DEPS_MK)
+else
+	@echo "# Generating Fortran dependencies into $(DEPS_MK)"; \
+	$(PY) ../../script/make_depend.py --make-deps $(SRC90) $(SRC77) $(SRCF77) > $(DEPS_MK) || { rm -f $(DEPS_MK); exit 1; }
+endif
+
 all : sub-make Donjon
 ifeq ($(openmp),1)
 	@echo 'Donjon: openmp is defined'
@@ -227,7 +244,7 @@ $(lib_module)/:
 $(lib)/: $(lib_module)/
 	mkdir -p $(lib)/
 libDonjon.a: $(OBJC) $(OBJ90) $(OBJ77) $(OBJF77) $(lib)/
-	ar r $@ $(OBJC) $(OBJ90) $(OBJ77) $(OBJF77)
+	ar rcs $@ $(OBJC) $(OBJ90) $(OBJ77) $(OBJF77)
 	cp $@ $(lib)/$@
 	cp *.mod $(lib_module)
 $(bin)/:
@@ -238,4 +255,4 @@ Donjon: libDonjon.a DONJON.o $(bin)/ sub-make
 	cp $@ $(bin)/$@
 clean:
 	$(MAKE) -C ../../Dragon/src clean
-	/bin/rm -f *.o *.mod *.a sub-make temp.* Donjon
+	/bin/rm -f *.o *.mod *.a sub-make temp.* Donjon $(DEPS_MK)
diff --git a/Dragon/data/TEST_GEO_hex_sect_tspc.access b/Dragon/data/TEST_GEO_hex_sect_tspc.access
index aebf920..6c57516 100755
--- a/Dragon/data/TEST_GEO_hex_sect_tspc.access
+++ b/Dragon/data/TEST_GEO_hex_sect_tspc.access
@@ -27,7 +27,9 @@ if [ -f "$pos"/draglibendfb7r1SHEM315_v5p1.gz ]
    then
     echo 'gunzipping DLIB_315'
     chmod 755 "$pos"
-    gunzip "$pos"/draglibendfb7r1SHEM315_v5p1.gz
+    if [ ! -f "$pos"/draglibendfb7r1SHEM315_v5p1 ]; then
+       gunzip "$pos"/draglibendfb7r1SHEM315_v5p1.gz
+    fi
 fi
 if [ -f "$pos"/draglibendfb7r1SHEM315_v5p1 ]
    then
diff --git a/Dragon/data/TEST_GEO_latt_tspc_S30.access b/Dragon/data/TEST_GEO_latt_tspc_S30.access
index bb190e8..10c3098 100755
--- a/Dragon/data/TEST_GEO_latt_tspc_S30.access
+++ b/Dragon/data/TEST_GEO_latt_tspc_S30.access
@@ -27,7 +27,9 @@ if [ -f "$pos"/draglibendfb7r1SHEM315_v5p1.gz ]
    then
     echo 'gunzipping draglibendfb7r1SHEM315_v5p1'
     chmod 755 "$pos"
-    gunzip "$pos"/draglibendfb7r1SHEM315_v5p1.gz
+    if [ ! -f "$pos"/draglibendfb7r1SHEM315_v5p1 ]; then
+       gunzip "$pos"/draglibendfb7r1SHEM315_v5p1.gz
+    fi
 fi
 if [ -f "$pos"/draglibendfb7r1SHEM315_v5p1 ]  
    then
diff --git a/Dragon/data/fbr_colorset.access b/Dragon/data/fbr_colorset.access
index 298d7b1..c25647b 100755
--- a/Dragon/data/fbr_colorset.access
+++ b/Dragon/data/fbr_colorset.access
@@ -27,7 +27,9 @@ if [ -f "$pos"/draglibendfb7r1SHEM315_v5p1.gz ]
    then
     echo 'gunzipping DLIB_315'
     chmod 755 "$pos"
-    gunzip "$pos"/draglibendfb7r1SHEM315_v5p1.gz
+    if [ ! -f "$pos"/draglibendfb7r1SHEM315_v5p1 ]; then
+       gunzip "$pos"/draglibendfb7r1SHEM315_v5p1.gz
+    fi
 fi
 if [ -f "$pos"/draglibendfb7r1SHEM315_v5p1 ]
    then
diff --git a/Dragon/data/fbr_tone.access b/Dragon/data/fbr_tone.access
index 396e3d6..fd8a33e 100755
--- a/Dragon/data/fbr_tone.access
+++ b/Dragon/data/fbr_tone.access
@@ -27,7 +27,9 @@ if [ -f "$pos"/draglibendfb7r1SHEM315_v5p1.gz ]
    then
     echo 'gunzipping DLIB_315'
     chmod 755 "$pos"
-    gunzip "$pos"/draglibendfb7r1SHEM315_v5p1.gz
+    if [ ! -f "$pos"/draglibendfb7r1SHEM315_v5p1 ]; then
+       gunzip "$pos"/draglibendfb7r1SHEM315_v5p1.gz
+    fi
 fi
 if [ -f "$pos"/draglibendfb7r1SHEM315_v5p1 ]
    then
diff --git a/Dragon/src/Makefile b/Dragon/src/Makefile
index c675c26..b423600 100644
--- a/Dragon/src/Makefile
+++ b/Dragon/src/Makefile
@@ -1,7 +1,7 @@
 #---------------------------------------------------------------------------
 #
 #  Makefile for building the Dragon library and load module
-#  Author : A. Hebert (2018-5-10)
+#  Author : A. Hebert (2018-5-10) and C. Bienvenue (2025-11-04)
 #
 #---------------------------------------------------------------------------
 #
@@ -20,6 +20,7 @@ DIRNAME = $(shell uname -sm | sed 's/[ ]/_/')
 OS = $(shell uname -s | cut -d"_" -f1)
 opt = -O -g
 PREPRO = cpp
+.DEFAULT_GOAL := all
 ifeq ($(openmp),1)
   COMP = -fopenmp
   PREPRO = cpp -D_OPENMP
@@ -46,12 +47,11 @@ else
 endif
 
 ifeq ($(OS),AIX)
-  python_version_major := 2
+  PY := python
 else
-  python_version_full := $(wordlist 2,4,$(subst ., ,$(shell python --version 2>&1)))
-  python_version_major := $(word 1,${python_version_full})
-  ifneq ($(python_version_major),2)
-    python_version_major := 3
+  PY := $(shell command -v python3 2>/dev/null)
+  ifeq ($(PY),)
+    PY := $(shell command -v python 2>/dev/null)
   endif
 endif
 
@@ -158,7 +158,9 @@ else
       lib_module = ../lib/$(DIRNAME)_llvm/modules
       INCLUDE = -I../../Ganlib/lib/$(DIRNAME)_llvm/modules/
       FFLAGS += -mmlir -fdynamic-heap-array
-      LFLAGS += -lclang_rt.osx
+      ifeq ($(OS),Darwin)
+        LFLAGS += -lclang_rt.osx
+      endif
     else
       lib = ../lib/$(DIRNAME)
       libUtl = ../../Utilib/lib/$(DIRNAME)
@@ -177,18 +179,35 @@ ifeq ($(hdf5),1)
   LFLAGS += -L${HDF5_API} -lhdf5
 endif
 
-SRCC = $(shell ls *.c)
-SRC77 = $(shell ls *.f)
-SRCF77 = $(shell ls *.F)
-ifeq ($(python_version_major),2)
-  SRC90 = $(shell python ../../script/make_depend.py *.f90)
+FFLAGS += -cpp
+
+SRCC = $(shell ls *.c 2>/dev/null)
+SRC77 = $(filter-out %.pp.f,$(shell ls *.f 2>/dev/null))
+SRCF77 = $(shell ls *.F 2>/dev/null)
+ifeq ($(PY),)
+  $(warning No Python interpreter found; Fortran dependency ordering may be suboptimal)
+  SRC90_RAW = $(shell ls *.f90 *.F90 2>/dev/null)
+  SRC90 = $(filter-out %.pp.f90,$(SRC90_RAW))
 else
-  SRC90 = $(shell python3 ../../script/make_depend_py3.py *.f90)
+  SRC90_RAW = $(shell $(PY) ../../script/make_depend.py *.f90 *.F90)
+  SRC90 = $(filter-out %.pp.f90,$(SRC90_RAW))
 endif
 OBJC = $(SRCC:.c=.o)
-OBJ90 = $(SRC90:.f90=.o)
+OBJ90 = $(patsubst %.f90,%.o,$(patsubst %.F90,%.o,$(SRC90)))
 OBJ77 = $(SRC77:.f=.o)
 OBJF77 = $(SRCF77:.F=.o)
+
+# Auto-generated dependency file capturing Fortran module and include deps
+DEPS_MK := .dragon_deps.mk
+-include $(DEPS_MK)
+$(DEPS_MK): $(SRC90) $(SRC77) $(SRCF77)
+ifeq ($(PY),)
+	@echo "# Dependencies not generated: no Python available" > $(DEPS_MK)
+else
+	@echo "# Generating Fortran dependencies into $(DEPS_MK)"; \
+	$(PY) ../../script/make_depend.py --make-deps $(SRC90) $(SRC77) $(SRCF77) > $(DEPS_MK) || { rm -f $(DEPS_MK); exit 1; }
+endif
+
 all : sub-make Dragon
 ifeq ($(openmp),1)
 	@echo 'Dragon: openmp is defined'
@@ -206,26 +225,29 @@ ifeq ($(hdf5),1)
 	@echo 'Dragon: hdf5 is defined'
 endif
 sub-make:
+	$(MAKE) openmp=$(openmp) intel=$(intel) nvidia=$(nvidia) llvm=$(llvm) hdf5=$(hdf5) -C ../../Utilib/src
+	$(MAKE) openmp=$(openmp) intel=$(intel) nvidia=$(nvidia) llvm=$(llvm) hdf5=$(hdf5) -C ../../Ganlib/src
 	$(MAKE) openmp=$(openmp) intel=$(intel) nvidia=$(nvidia) llvm=$(llvm) hdf5=$(hdf5) -C ../../Trivac/src
 %.o : %.c
 	$(C) $(CFLAGS) $(opt) $(COMP) -c $< -o $@
 %.o : %.f90
 	$(F90) $(FFLAGS) $(opt) $(COMP) $(INCLUDE) -c $< -o $@
+%.o : %.F90
+	# Use Fortran compiler's integrated preprocessor instead of cpp -traditional
+	$(F90) $(FFLAGS) $(opt) $(COMP) $(INCLUDE) $(FLAGS) -c $< -o $@
 %.o : %.f
-	@/bin/rm -f temp.f
 	$(F90) $(FFLAG77) $(opt) $(COMP) $(INCLUDE) -c $< -o $@
 %.o : %.F
-	$(PREPRO) -P -W -traditional  $(FLAGS) $< temp.f
-	$(F90) $(FFLAG77) $(opt) $(COMP) $(INCLUDE) -c temp.f -o $@
-	/bin/rm temp.f
+	# Use Fortran compiler's integrated preprocessor only for .F (not for .f)
+	$(F90) $(FFLAG77) -cpp $(opt) $(COMP) $(INCLUDE) $(FLAGS) -c $< -o $@
 $(lib_module)/:
 	mkdir -p $(lib_module)/
 $(lib)/: $(lib_module)/
 	mkdir -p $(lib)/
-libDragon.a: $(OBJC) $(OBJ90) $(OBJ77) $(OBJF77) $(lib)/
-	ar r $@ $(OBJC) $(OBJ90) $(OBJ77) $(OBJF77)
+libDragon.a: $(DEPS_MK) $(OBJC) $(OBJ90) $(OBJ77) $(OBJF77) $(lib)/
+	ar rcs $@ $(OBJC) $(OBJ90) $(OBJ77) $(OBJF77)
 	cp $@ $(lib)/$@
-	cp *.mod $(lib_module)
+	if ls *.mod 1> /dev/null 2>&1; then cp *.mod $(lib_module); fi
 $(bin)/:
 	mkdir -p $(bin)/
 Dragon: libDragon.a DRAGON.o $(bin)/ sub-make
@@ -234,4 +256,4 @@ Dragon: libDragon.a DRAGON.o $(bin)/ sub-make
 	cp $@ $(bin)/$@
 clean:
 	$(MAKE) -C ../../Trivac/src clean
-	/bin/rm -f *.o *.mod *.a sub-make temp.* Dragon
+	/bin/rm -f *.o *.mod *.a sub-make temp.* Dragon $(DEPS_MK) *.pp.f *.pp.f90
diff --git a/Ganlib/src/Makefile b/Ganlib/src/Makefile
index 0a4ad6f..4235f13 100644
--- a/Ganlib/src/Makefile
+++ b/Ganlib/src/Makefile
@@ -1,7 +1,7 @@
 #---------------------------------------------------------------------------
 #
 #  Makefile for building the Ganlib library and load module
-#  Author : A. Hebert (2018-5-10)
+#  Author : A. Hebert (2018-5-10) and C. Bienvenue (2025-11-04)
 #
 #---------------------------------------------------------------------------
 #
@@ -19,6 +19,7 @@ endif
 DIRNAME = $(shell uname -sm | sed 's/[ ]/_/')
 OS = $(shell uname -s | cut -d"_" -f1)
 opt = -O -g
+.DEFAULT_GOAL := all
 PREPRO = cpp
 ifeq ($(openmp),1)
   COMP = -fopenmp
@@ -54,12 +55,11 @@ else
 endif
 
 ifeq ($(OS),AIX)
-  python_version_major := 2
+  PY := python
 else
-  python_version_full := $(wordlist 2,4,$(subst ., ,$(shell python --version 2>&1)))
-  python_version_major := $(word 1,${python_version_full})
-  ifneq ($(python_version_major),2)
-    python_version_major := 3
+  PY := $(shell command -v python3 2>/dev/null)
+  ifeq ($(PY),)
+    PY := $(shell command -v python 2>/dev/null)
   endif
 endif
 
@@ -152,7 +152,9 @@ else
       bin = ../bin/$(DIRNAME)_llvm
       lib_module = ../lib/$(DIRNAME)_llvm/modules
       FFLAGS += -mmlir -fdynamic-heap-array
-      LFLAGS += -lclang_rt.osx
+      ifeq ($(OS),Darwin)
+        LFLAGS += -lclang_rt.osx
+      endif
     else
       lib = ../lib/$(DIRNAME)
       bin = ../bin/$(DIRNAME)
@@ -167,20 +169,34 @@ ifeq ($(hdf5),1)
   LFLAGS += -L${HDF5_API} -lhdf5
 endif
 
-SRCC = $(shell ls *.c)
-SRC77 = $(shell ls *.f)
-SRCF77 = $(shell ls *.F)
-ifeq ($(python_version_major),2)
-  SRC90 = $(shell python ../../script/make_depend.py *.f90)
+SRCC = $(shell ls *.c 2>/dev/null)
+SRC77 = $(shell ls *.f 2>/dev/null)
+SRCF77 = $(shell ls *.F 2>/dev/null)
+ifeq ($(PY),)
+  $(warning No Python interpreter found; Fortran dependency ordering may be suboptimal)
+  SRC90 = $(shell ls *.f90 2>/dev/null)
+  SRCF90 = $(shell ls *.F90 2>/dev/null)
 else
-  SRC90 = $(shell python3 ../../script/make_depend_py3.py *.f90)
+  SRC90 = $(shell $(PY) ../../script/make_depend.py *.f90 *.F90)
+  SRCF90 =
 endif
-SRCF90 = $(shell ls *.F90)
 OBJC = $(SRCC:.c=.o)
-OBJ90 = $(SRC90:.f90=.o)
+OBJ90 = $(patsubst %.f90,%.o,$(patsubst %.F90,%.o,$(SRC90)))
 OBJF90 = $(SRCF90:.F90=.o)
 OBJ77 = $(SRC77:.f=.o)
 OBJF77 = $(SRCF77:.F=.o)
+
+# Auto-generated dependency file capturing Fortran module and include deps
+DEPS_MK := .ganlib_deps.mk
+-include $(DEPS_MK)
+$(DEPS_MK): $(SRC90) $(SRC77) $(SRCF77)
+ifeq ($(PY),)
+	@echo "# Dependencies not generated: no Python available" > $(DEPS_MK)
+else
+	@echo "# Generating Fortran dependencies into $(DEPS_MK)"; \
+	$(PY) ../../script/make_depend.py --make-deps $(SRC90) $(SRC77) $(SRCF77) > $(DEPS_MK) || { rm -f $(DEPS_MK); exit 1; }
+endif
+
 all : sub-make Ganlib
 ifeq ($(mpi),1)
 	@echo 'Ganlib: mpi is defined'
@@ -200,27 +216,26 @@ endif
 ifeq ($(hdf5),1)
 	@echo 'Ganlib: hdf5 is defined'
 endif
-	@echo 'Ganlib: python version=' $(python_version_major)
+	@echo 'Ganlib: python=' $(PY)
 sub-make:
 %.o : %.c
 	$(C) $(CFLAGS) $(FLAGS) $(opt) $(COMP) -c $< -o $@
 %.o : %.f90
 	$(F90) $(FFLAGS) $(opt) $(COMP) -c $< -o $@
 %.o : %.F90
-	$(PREPRO) -P -W -traditional $(FLAGS) $< temp.f90
-	$(F90) $(FFLAGS) $(opt) $(COMP) -c temp.f90 -o $@
-	/bin/rm temp.f90
+	$(PREPRO) -P -W -traditional $(FLAGS) $< $(@:.o=.pp.f90)
+	$(F90) $(FFLAGS) $(opt) $(COMP) -c $(@:.o=.pp.f90) -o $@
+	/bin/rm -f $(@:.o=.pp.f90)
 %.o : %.f
-	@/bin/rm -f temp.f
 	$(F90) $(FFLAG77) $(opt) $(COMP) -c $< -o $@
 %.o : %.F
-	$(PREPRO) -P -W -traditional $(FLAGS) $(FMPI) $< temp.f
-	$(F90) $(FFLAG77) $(opt) $(COMP) -c temp.f -o $@
-	/bin/rm temp.f
+	$(PREPRO) -P -W -traditional $(FLAGS) $(FMPI) $< $(@:.o=.pp.f)
+	$(F90) $(FFLAG77) $(opt) $(COMP) -c $(@:.o=.pp.f) -o $@
+	/bin/rm -f $(@:.o=.pp.f)
 $(lib_module)/:
 	mkdir -p $(lib_module)/
-libGanlib.a: $(OBJC) $(OBJ90) $(OBJF90) $(OBJ77) $(OBJF77) $(lib_module)/
-	ar r $@ $(OBJC) $(OBJ90) $(OBJF90) $(OBJ77) $(OBJF77)
+libGanlib.a: $(DEPS_MK) $(OBJC) $(OBJ90) $(OBJF90) $(OBJ77) $(OBJF77) $(lib_module)/
+	ar rcs $@ $(OBJC) $(OBJ90) $(OBJF90) $(OBJ77) $(OBJF77)
 	cp $@ $(lib)/$@
 	cp *.mod $(lib_module)
 $(bin)/:
@@ -229,4 +244,4 @@ Ganlib: libGanlib.a GANMAIN.o $(bin)/
 	$(F90) $(opt) $(COMP) GANMAIN.o $(lib)/libGanlib.a $(LFLAGS) -o Ganlib
 	cp $@ $(bin)/$@
 clean:
-	/bin/rm -f *.o *.mod *.a sub-make temp.* Ganlib*
+	/bin/rm -f *.o *.mod *.a sub-make temp.* Ganlib* $(DEPS_MK) *.pp.f *.pp.f90
diff --git a/PyGan/src/Makefile b/PyGan/src/Makefile
index f48c98a..8520eef 100644
--- a/PyGan/src/Makefile
+++ b/PyGan/src/Makefile
@@ -16,6 +16,9 @@ PYTHONPATH = $(pylib)/python
 $(info set PYTHONPATH="$(PYTHONPATH)")
 export PYTHONPATH
 
+# Build defaults and phony targets
+.DEFAULT_GOAL := all
+
 ifeq ($(intel),1)
   ifeq ($(INTELTOOLS),)
     $(error INTELTOOLS is not set)
@@ -50,11 +53,11 @@ else
   endif
 endif
 export COMPILER
+#	export FORTRANPATH
 
-all:
-	$(MAKE) donjon
+all: donjon
 checkPython: ; @which python3 > /dev/null
-ganlib: clean sub-make-ganlib pygan-ganlib
+ganlib: sub-make-ganlib pygan-ganlib
 ifeq ($(openmp),1)
 	@echo 'pygan_ganlib: openmp is defined'
 endif
@@ -70,7 +73,7 @@ endif
 ifeq ($(hdf5),1)
 	@echo 'pygan_ganlib: hdf5 is defined'
 endif
-trivac: clean sub-make-trivac pygan-trivac
+trivac: sub-make-trivac pygan-trivac
 ifeq ($(openmp),1)
 	@echo 'pygan_trivac: openmp is defined'
 endif
@@ -86,7 +89,7 @@ endif
 ifeq ($(hdf5),1)
 	@echo 'pygan_trivac: hdf5 is defined'
 endif
-dragon: clean sub-make-dragon pygan-dragon
+dragon: sub-make-dragon pygan-dragon
 ifeq ($(openmp),1)
 	@echo 'pygan_dragon: openmp is defined'
 endif
@@ -102,7 +105,7 @@ endif
 ifeq ($(hdf5),1)
 	@echo 'pygan_dragon: hdf5 is defined'
 endif
-donjon: clean sub-make-donjon pygan-donjon
+donjon: sub-make-donjon pygan-donjon
 ifeq ($(openmp),1)
 	@echo 'pygan_donjon: openmp is defined'
 endif
@@ -119,14 +122,14 @@ ifeq ($(hdf5),1)
 	@echo 'pygan_donjon: hdf5 is defined'
 endif
 sub-make-ganlib:
-	$(MAKE) openmp=$(openmp) hdf5=$(hdf5) -C ../../Ganlib/src
+	$(MAKE) openmp=$(openmp) intel=$(intel) nvidia=$(nvidia) llvm=$(llvm) hdf5=$(hdf5) -C ../../Ganlib/src
 sub-make-trivac: sub-make-ganlib
-	$(MAKE) openmp=$(openmp) -C ../../Utilib/src
-	$(MAKE) openmp=$(openmp) hdf5=$(hdf5) -C ../../Trivac/src
+	$(MAKE) openmp=$(openmp) intel=$(intel) nvidia=$(nvidia) llvm=$(llvm) -C ../../Utilib/src
+	$(MAKE) openmp=$(openmp) intel=$(intel) nvidia=$(nvidia) llvm=$(llvm) hdf5=$(hdf5) -C ../../Trivac/src
 sub-make-dragon: sub-make-trivac
-	$(MAKE) openmp=$(openmp) hdf5=$(hdf5) -C ../../Dragon/src
+	$(MAKE) openmp=$(openmp) intel=$(intel) nvidia=$(nvidia) llvm=$(llvm) hdf5=$(hdf5) -C ../../Dragon/src
 sub-make-donjon: sub-make-dragon
-	$(MAKE) openmp=$(openmp) hdf5=$(hdf5) -C ../../Donjon/src
+	$(MAKE) openmp=$(openmp) intel=$(intel) nvidia=$(nvidia) llvm=$(llvm) hdf5=$(hdf5) -C ../../Donjon/src
 libGanlib.a: $(lib)/ sub-make-ganlib
 	cp $(libGan)/libGanlib.a .
 	ar -d libGanlib.a xabort_c.o
@@ -144,8 +147,8 @@ ifeq ($(openmp),1)
 else
 	export CODE_EMBEDDED=GANLIB; cd $(DIRNAME); python3 setup_cle2000.py install --home=.
 endif
-	mv $(DIRNAME)/$(pylib)/* $(lib)/
-	/bin/rm -r $(DIRNAME)
+	cp -R $(DIRNAME)/$(pylib)/* $(lib)/
+	/bin/rm -rf $(DIRNAME)
 pygan-trivac: libGanlib.a sub-make-trivac checkPython
 	mkdir -p $(DIRNAME)
 	cp *.[ch] $(DIRNAME)
@@ -157,8 +160,8 @@ ifeq ($(openmp),1)
 else
 	export CODE_EMBEDDED=TRIVAC; cd $(DIRNAME); python3 setup_cle2000.py install --home=.
 endif
-	mv $(DIRNAME)/$(pylib)/* $(lib)/
-	/bin/rm -r $(DIRNAME)
+	cp -R $(DIRNAME)/$(pylib)/* $(lib)/
+	/bin/rm -rf $(DIRNAME)
 pygan-dragon: libGanlib.a sub-make-dragon checkPython
 	mkdir -p $(DIRNAME)
 	cp *.[ch] $(DIRNAME)
@@ -170,8 +173,8 @@ ifeq ($(openmp),1)
 else
 	export CODE_EMBEDDED=DRAGON; cd $(DIRNAME); python3 setup_cle2000.py install --home=.
 endif
-	mv $(DIRNAME)/$(pylib)/* $(lib)/
-	/bin/rm -r $(DIRNAME)
+	cp -R $(DIRNAME)/$(pylib)/* $(lib)/
+	/bin/rm -rf $(DIRNAME)
 pygan-donjon: libGanlib.a sub-make-donjon checkPython
 	mkdir -p $(DIRNAME)
 	cp *.[ch] $(DIRNAME)
@@ -183,8 +186,8 @@ ifeq ($(openmp),1)
 else
 	export CODE_EMBEDDED=DONJON; cd $(DIRNAME); python3 setup_cle2000.py install --home=.
 endif
-	mv $(DIRNAME)/$(pylib)/* $(lib)/
-	/bin/rm -r $(DIRNAME)
+	cp -R $(DIRNAME)/$(pylib)/* $(lib)/
+	/bin/rm -rf $(DIRNAME)
 	@echo 'makefile PYTHONPATH=' $(PYTHONPATH)
 clean:
 	@echo 'clean PyGan'
diff --git a/PyGan/src/setup_cle2000.py b/PyGan/src/setup_cle2000.py
index d416245..c712b26 100644
--- a/PyGan/src/setup_cle2000.py
+++ b/PyGan/src/setup_cle2000.py
@@ -10,14 +10,26 @@ else:
   from distutils.core import setup, Extension
 import sysconfig
 
+def _detect_gfortran_dir():
+  import subprocess, os
+  try:
+    out = subprocess.check_output(['gfortran', '-print-file-name=libgfortran.dylib'], text=True).strip()
+    if out and out != 'libgfortran.dylib':
+      d = os.path.dirname(out)
+      if os.path.isdir(d):
+        return d
+  except Exception:
+    pass
+  return None
+
 def main():
   import os
   from sysconfig import get_config_var
   mach = os.path.basename(os.getcwd())
   Code = os.environ.get("CODE_EMBEDDED", None) # Code selection
   Compiler = os.environ.get("COMPILER", None) # Compiler selection
-  FortranLib = os.environ.get(Compiler, None) # directory with libfortran.a
-  HDF5Lib = os.environ.get("HDF5_API", None) # directory with libhdf5.a
+  FortranLib = _detect_gfortran_dir() # directory with libfortran
+  HDF5Lib = os.environ.get("HDF5_API", None) # directory with libhdf5
   pylib = os.path.basename(get_config_var("LIBDIR")) # get lib or lib64
   print("install Cle2000 binding to", Code, "on directory",mach, "pylib=",pylib, "Compiler=",Compiler)
   if Compiler == "NVTOOLS":
@@ -49,6 +61,14 @@ def main():
     libDon="../../../Donjon/lib/"+mach
     extralink=["-lgfortran", ]
   print("debug Compiler=",Compiler,"libdir=",libdir,"Code=",Code)
+  if FortranLib:
+    print("debug FortranLib=", FortranLib)
+  if HDF5Lib:
+    print("debug HDF5Lib=", HDF5Lib)
+
+  # Build helper lists with None filtered out
+  def _dirs(*args):
+    return [d for d in args if d]
 
   if Code == "GANLIB":
     setup (name="Cle2000",
@@ -60,8 +80,8 @@ def main():
        ext_modules=[Extension('cle2000',sources=['cle2000module.c'],
                      extra_link_args = extralink,
                      include_dirs=["../../../Ganlib/src"],
-                     library_dirs=[libdir,FortranLib,HDF5Lib],
-                     runtime_library_dirs=[FortranLib,HDF5Lib],
+                     library_dirs=_dirs(libdir,FortranLib,HDF5Lib),
+                     runtime_library_dirs=_dirs(FortranLib,HDF5Lib),
                      libraries=["Ganlib","hdf5"] ) ])
   elif Code == "TRIVAC":
     setup (name="Cle2000",
@@ -74,8 +94,8 @@ def main():
                      define_macros=[('__trivac__', None)],
                      extra_link_args = extralink,
                      include_dirs=["../../../Ganlib/src"],
-                     library_dirs=[libdir,FortranLib,HDF5Lib,libUtl,libTri],
-                     runtime_library_dirs=[FortranLib,HDF5Lib],
+                     library_dirs=_dirs(libdir,FortranLib,HDF5Lib,libUtl,libTri),
+                     runtime_library_dirs=_dirs(FortranLib,HDF5Lib),
                      libraries=["Trivac","Utilib","Ganlib","hdf5"] ) ])
   elif Code == "DRAGON":
     setup (name="Cle2000",
@@ -88,8 +108,8 @@ def main():
                      define_macros=[('__dragon__', None)],
                      extra_link_args = extralink,
                      include_dirs=["../../../Ganlib/src"],
-                     library_dirs=[libdir,FortranLib,HDF5Lib,libUtl,libTri,libDra],
-                     runtime_library_dirs=[FortranLib,HDF5Lib],
+                     library_dirs=_dirs(libdir,FortranLib,HDF5Lib,libUtl,libTri,libDra),
+                     runtime_library_dirs=_dirs(FortranLib,HDF5Lib),
                      libraries=["Dragon","Trivac","Utilib","Ganlib","hdf5"] ) ])
   elif Code == "DONJON":
     setup (name="Cle2000",
@@ -102,8 +122,8 @@ def main():
                      define_macros=[('__donjon__', None)],
                      extra_link_args = extralink,
                      include_dirs=["../../../Ganlib/src"],
-                     library_dirs=[libdir,FortranLib,HDF5Lib,libUtl,libTri,libDra,libDon],
-                     runtime_library_dirs=[FortranLib,HDF5Lib],
+                     library_dirs=_dirs(libdir,FortranLib,HDF5Lib,libUtl,libTri,libDra,libDon),
+                     runtime_library_dirs=_dirs(FortranLib,HDF5Lib),
                      libraries=["Donjon","Dragon","Trivac","Utilib","Ganlib","hdf5"] ) ])
   elif Code == "GANLIB_OMP":
     setup (name="Cle2000",
@@ -115,8 +135,8 @@ def main():
        ext_modules=[Extension('cle2000',sources=['cle2000module.c'],
                      extra_link_args = ["-lgomp"]+extralink,
                      include_dirs=["../../../Ganlib/src"],
-                     library_dirs=[libdir,FortranLib,HDF5Lib],
-                     runtime_library_dirs=[FortranLib,HDF5Lib],
+                     library_dirs=_dirs(libdir,FortranLib,HDF5Lib),
+                     runtime_library_dirs=_dirs(FortranLib,HDF5Lib),
                      libraries=["Ganlib","hdf5"] ) ])
   elif Code == "TRIVAC_OMP":
     setup (name="Cle2000",
@@ -129,8 +149,8 @@ def main():
                      define_macros=[('__trivac__', None)],
                      extra_link_args = ["-lgomp"]+extralink,
                      include_dirs=["../../../Ganlib/src"],
-                     library_dirs=[libdir,FortranLib,HDF5Lib,libUtl,libTri],
-                     runtime_library_dirs=[FortranLib,HDF5Lib],
+                     library_dirs=_dirs(libdir,FortranLib,HDF5Lib,libUtl,libTri),
+                     runtime_library_dirs=_dirs(FortranLib,HDF5Lib),
                      libraries=["Trivac","Utilib","Ganlib","hdf5"] ) ])
   elif Code == "DRAGON_OMP":
     setup (name="Cle2000",
@@ -143,8 +163,8 @@ def main():
                      define_macros=[('__dragon__', None)],
                      extra_link_args = ["-lgomp"]+extralink,
                      include_dirs=["../../../Ganlib/src"],
-                     library_dirs=[libdir,FortranLib,HDF5Lib,libUtl,libTri,libDra],
-                     runtime_library_dirs=[FortranLib,HDF5Lib],
+                     library_dirs=_dirs(libdir,FortranLib,HDF5Lib,libUtl,libTri,libDra),
+                     runtime_library_dirs=_dirs(FortranLib,HDF5Lib),
                      libraries=["Dragon","Trivac","Utilib","Ganlib","hdf5"] ) ])
   elif Code == "DONJON_OMP":
     setup (name="Cle2000",
@@ -157,8 +177,8 @@ def main():
                      define_macros=[('__donjon__', None)],
                      extra_link_args = ["-lgomp"]+extralink,
                      include_dirs=["../../../Ganlib/src"],
-                     library_dirs=[libdir,FortranLib,HDF5Lib,libUtl,libTri,libDra,libDon],
-                     runtime_library_dirs=[FortranLib,HDF5Lib],
+                     library_dirs=_dirs(libdir,FortranLib,HDF5Lib,libUtl,libTri,libDra,libDon),
+                     runtime_library_dirs=_dirs(FortranLib,HDF5Lib),
                      libraries=["Donjon","Dragon","Trivac","Utilib","Ganlib","hdf5"] ) ])
   else:
     raise ValueError(Code+" is not implemented for setup.py bindings")
diff --git a/PyGan/src/setup_lcm.py b/PyGan/src/setup_lcm.py
index 79e7891..76829b4 100644
--- a/PyGan/src/setup_lcm.py
+++ b/PyGan/src/setup_lcm.py
@@ -22,16 +22,25 @@ def main():
     extralink=["-lnvc","-lnvcpumath"]
   elif Compiler == "LLVMTOOLS":
     libdir="../../lib/"+mach+"_llvm"
-    libNv=" "
+    libNv=None
     extralink=[ ]
   elif Compiler == "INTELTOOLS":
     libdir="../../lib/"+mach+"_intel"
-    libNv=" "
+    libNv=None
     extralink=[ ]
   else:
     libdir="../../lib/"+mach
-    libNv=" "
+    libNv=None
     extralink=[ ]
+  # Filter out missing/empty library dirs to avoid "-L " warnings
+  def _dirs(*paths):
+    out=[]
+    for p in paths:
+      if p and isinstance(p, str) and os.path.isdir(p):
+        out.append(p)
+    return out
+  lib_dirs = _dirs(libdir, libNv)
+  rpath_dirs = _dirs(libNv)
   setup(name="Lcm",
           version="5.0",
           description="Python interface for the lcm C library API",
@@ -41,8 +50,8 @@ def main():
           ext_modules=[Extension("lcm", ["lcmmodule.c"],
                       extra_link_args = extralink,
                       include_dirs=["../../../Ganlib/src",incdir],
-                      library_dirs=[libdir,libNv],
-                      runtime_library_dirs=[libNv],
+                      library_dirs=lib_dirs,
+                      runtime_library_dirs=rpath_dirs,
                       libraries=["Ganlib"] ) ])
 
 if __name__ == "__main__":
diff --git a/Trivac/src/Makefile b/Trivac/src/Makefile
index 6a70191..2ad728a 100644
--- a/Trivac/src/Makefile
+++ b/Trivac/src/Makefile
@@ -1,7 +1,7 @@
 #---------------------------------------------------------------------------
 #
 #  Makefile for building the Trivac library and load module
-#  Author : A. Hebert (2018-5-10)
+#  Author : A. Hebert (2018-5-10) and C. Bienvenue (2025-11-04)
 #
 #---------------------------------------------------------------------------
 #
@@ -19,6 +19,7 @@ endif
 DIRNAME = $(shell uname -sm | sed 's/[ ]/_/')
 OS = $(shell uname -s | cut -d"_" -f1)
 opt = -O -g
+.DEFAULT_GOAL := all
 ifeq ($(openmp),1)
   COMP = -fopenmp
 else
@@ -44,12 +45,11 @@ else
 endif
 
 ifeq ($(OS),AIX)
-  python_version_major := 2
+  PY := python
 else
-  python_version_full := $(wordlist 2,4,$(subst ., ,$(shell python --version 2>&1)))
-  python_version_major := $(word 1,${python_version_full})
-  ifneq ($(python_version_major),2)
-    python_version_major := 3
+  PY := $(shell command -v python3 2>/dev/null)
+  ifeq ($(PY),)
+    PY := $(shell command -v python 2>/dev/null)
   endif
 endif
 
@@ -134,7 +134,9 @@ else
       bin = ../bin/$(DIRNAME)_llvm
       INCLUDE = -I../../Ganlib/lib/$(DIRNAME)_llvm/modules/
       FFLAGS += -mmlir -fdynamic-heap-array
-      LFLAGS += -lclang_rt.osx
+      ifeq ($(OS),Darwin)
+        LFLAGS += -lclang_rt.osx
+      endif
     else
       lib = ../lib/$(DIRNAME)
       libUtl = ../../Utilib/lib/$(DIRNAME)
@@ -151,14 +153,27 @@ ifeq ($(hdf5),1)
   LFLAGS += -L${HDF5_API} -lhdf5
 endif
 
-SRC77 = $(shell ls *.f)
-ifeq ($(python_version_major),2)
-  SRC90 = $(shell python ../../script/make_depend.py *.f90)
+SRC77 = $(shell ls *.f 2>/dev/null)
+ifeq ($(PY),)
+  $(warning No Python interpreter found; Fortran dependency ordering may be suboptimal)
+  SRC90 = $(shell ls *.f90 2>/dev/null)
 else
-  SRC90 = $(shell python3 ../../script/make_depend_py3.py *.f90)
+  SRC90 = $(shell $(PY) ../../script/make_depend.py *.f90 *.F90)
 endif
-OBJ90 = $(SRC90:.f90=.o)
+OBJ90 = $(patsubst %.f90,%.o,$(patsubst %.F90,%.o,$(SRC90)))
 OBJ77 = $(SRC77:.f=.o)
+
+# Auto-generated dependency file capturing Fortran module and include deps
+DEPS_MK := .trivac_deps.mk
+-include $(DEPS_MK)
+$(DEPS_MK): $(SRC90) $(SRC77) $(SRCF77)
+ifeq ($(PY),)
+	@echo "# Dependencies not generated: no Python available" > $(DEPS_MK)
+else
+	@echo "# Generating Fortran dependencies into $(DEPS_MK)"; \
+	$(PY) ../../script/make_depend.py --make-deps $(SRC90) $(SRC77) $(SRCF77) > $(DEPS_MK) || { rm -f $(DEPS_MK); exit 1; }
+endif
+
 all : sub-make Trivac
 ifeq ($(openmp),1)
 	@echo 'Trivac: openmp is defined'
@@ -184,8 +199,8 @@ sub-make:
 	$(F90) $(FFLAG77) $(opt) $(COMP) $(INCLUDE) -c $< -o $@
 $(lib)/:
 	mkdir -p $(lib)/
-libTrivac.a: $(OBJ90) $(OBJ77) $(lib)/
-	ar r $@ $(OBJ90) $(OBJ77)
+libTrivac.a: $(DEPS_MK) $(OBJ90) $(OBJ77) $(lib)/
+	ar rcs $@ $(OBJ90) $(OBJ77)
 	cp $@ $(lib)/$@
 $(bin)/:
 	mkdir -p $(bin)/
@@ -196,4 +211,4 @@ Trivac: libTrivac.a TRIVAC.o $(bin)/ sub-make
 clean:
 	$(MAKE) -C ../../Utilib/src clean
 	$(MAKE) -C ../../Ganlib/src clean
-	/bin/rm -f *.o *.a sub-make temp.* Trivac
+	/bin/rm -f *.o *.a sub-make temp.* Trivac $(DEPS_MK)
diff --git a/Utilib/src/Makefile b/Utilib/src/Makefile
index 2bb6d73..e56d213 100644
--- a/Utilib/src/Makefile
+++ b/Utilib/src/Makefile
@@ -1,7 +1,7 @@
 #---------------------------------------------------------------------------
 #
 #  Makefile for building the Utilib library
-#  Author : A. Hebert (2018-5-10)
+#  Author : A. Hebert (2018-5-10) and C. Bienvenue (2025-11-04)
 #
 #---------------------------------------------------------------------------
 #
@@ -19,6 +19,7 @@ endif
 DIRNAME = $(shell uname -sm | sed 's/[ ]/_/')
 OS = $(shell uname -s | cut -d"_" -f1)
 opt = -O -g
+.DEFAULT_GOAL := all
 ifeq ($(openmp),1)
   COMP = -fopenmp
 else
@@ -44,12 +45,11 @@ else
 endif
 
 ifeq ($(OS),AIX)
-  python_version_major := 2
+  PY := python
 else
-  python_version_full := $(wordlist 2,4,$(subst ., ,$(shell python --version 2>&1)))
-  python_version_major := $(word 1,${python_version_full})
-  ifneq ($(python_version_major),2)
-    python_version_major := 3
+  PY := $(shell command -v python3 2>/dev/null)
+  ifeq ($(PY),)
+    PY := $(shell command -v python 2>/dev/null)
   endif
 endif
 
@@ -128,7 +128,9 @@ else
       lib = ../lib/$(DIRNAME)_llvm
       lib_module = ../lib/$(DIRNAME)_llvm/modules
       FFLAGS += -mmlir -fdynamic-heap-array
-      LFLAGS += -lclang_rt.osx
+      ifeq ($(OS),Darwin)
+        LFLAGS += -lclang_rt.osx
+      endif
     else
       lib = ../lib/$(DIRNAME)
       lib_module = ../lib/$(DIRNAME)/modules
@@ -136,16 +138,29 @@ else
   endif
 endif
 
-SRCC = $(shell ls *.c)
-SRC77 = $(shell ls *.f)
-ifeq ($(python_version_major),2)
-  SRC90 = $(shell python ../../script/make_depend.py *.f90)
+SRCC = $(shell ls *.c 2>/dev/null)
+SRC77 = $(shell ls *.f 2>/dev/null)
+ifeq ($(PY),)
+  $(warning No Python interpreter found; Fortran dependency ordering may be suboptimal)
+  SRC90 = $(shell ls *.f90 2>/dev/null)
 else
-  SRC90 = $(shell python3 ../../script/make_depend_py3.py *.f90)
+  SRC90 = $(shell $(PY) ../../script/make_depend.py *.f90 *.F90)
 endif
 OBJC = $(SRCC:.c=.o)
-OBJ90 = $(SRC90:.f90=.o)
+OBJ90 = $(patsubst %.f90,%.o,$(patsubst %.F90,%.o,$(SRC90)))
 OBJ77 = $(SRC77:.f=.o)
+
+ # Auto-generated dependency file capturing Fortran module and include deps
+DEPS_MK := .utilib_deps.mk
+-include $(DEPS_MK)
+$(DEPS_MK): $(SRC90) $(SRC77) $(SRCF77)
+ifeq ($(PY),)
+	@echo "# Dependencies not generated: no Python available" > $(DEPS_MK)
+else
+	@echo "# Generating Fortran dependencies into $(DEPS_MK)"; \
+	$(PY) ../../script/make_depend.py --make-deps $(SRC90) $(SRC77) $(SRCF77) > $(DEPS_MK) || { rm -f $(DEPS_MK); exit 1; }
+endif
+
 all : libUtilib.a
 	@echo 'Utilib: fflags=' $(FFLAGS)
 ifeq ($(openmp),1)
@@ -158,9 +173,9 @@ ifeq ($(nvidia),1)
 	@echo 'Utilib: nvidia is defined'
 endif
 ifeq ($(llvm),1)
-]	@echo 'Utilib: llvm is defined'
+	@echo 'Utilib: llvm is defined'
 endif
-	@echo "Utilib: python version=" ${python_version_major}
+	@echo "Utilib: python=" $(PY)
 %.o : %.c
 	$(C) $(CFLAGS) $(opt) $(COMP) -c $< -o $@
 %.o : %.f90
@@ -173,8 +188,8 @@ $(lib_module)/:
 $(lib)/: $(lib_module)/
 	mkdir -p $(lib)/
 libUtilib.a: $(OBJC) $(OBJ90) $(OBJ77) $(lib)/
-	ar r $@ $(OBJC) $(OBJ90) $(OBJ77)
+	ar rcs $@ $(OBJC) $(OBJ90) $(OBJ77)
 	cp $@ $(lib)/$@
 	cp *.mod $(lib_module)
 clean:
-	/bin/rm -f *.o *.mod *.a
+	/bin/rm -f *.o *.mod *.a $(DEPS_MK)
diff --git a/doc/IGE335/Section6.00.tex b/doc/IGE335/Section6.00.tex
index f49f89b..c26d277 100644
--- a/doc/IGE335/Section6.00.tex
+++ b/doc/IGE335/Section6.00.tex
@@ -42,6 +42,12 @@ make
 make clean
 \end{verbatim}
 
+To speed up the build, run make with multiple jobs using the \texttt{-jN} option.  For example, to run 8 parallel jobs:
+\begin{verbatim}
+make -j8
+make clean
+\end{verbatim}
+
 \noindent To build an OpenMP-enabled version, simply write
 \begin{verbatim}
 make openmp=1
diff --git a/script/make_depend.py b/script/make_depend.py
index 15c656e..ce8f688 100755
--- a/script/make_depend.py
+++ b/script/make_depend.py
@@ -1,57 +1,222 @@
-#!/bin/env python
-""" generation of module dependances for a xxx.f90 or xxx.F90 file """
-
-import string,sys
-from subprocess import Popen, PIPE
-
-def noComment(mot):
-    """ remove comment characters in a word """
-    ind= string.find(mot,'!')
-    if ind != -1:
-        mot= mot[:ind]
-    return mot
-
-class md9:
-    """ a file, its module and its dependances """
-    def __init__(self,fic):
-        self.name= fic
-        self.used= []
-        #find all module dependances
-        listeLignes= open(self.name,'r').readlines()
-        self.module= "dummy"
-        for ligne in listeLignes:
-            ligne= string.lower(ligne)
-            if string.count(ligne,'use'):
-                ligne= string.replace(ligne,',',' ')
-                listeMots= string.split(ligne)
-                if listeMots[0] == 'use':
-                    mod= noComment(listeMots[1])
-                    if mod not in self.used and mod != 'intrinsic':
-                        self.used.append(mod)
-            elif string.count(ligne,'module'):
-                listeMots= string.split(ligne)
-                if listeMots[0] == 'module' and \
-                   noComment(listeMots[1]) != 'procedure':
-                    self.module= listeMots[1]
-    def utilise(self,other):
-        return (other.module in self.used)
-
-listeClasse= list()
-for x in sys.argv[1:]:
-    if x.endswith('.f90') or x.endswith('.F90') : listeClasse.append(md9(x))
-#sort the file list
-listeRes= []
-while listeClasse:
-    lgav= len(listeClasse)
-    for fic in listeClasse:
-        if len(filter(lambda x,y=fic:y.utilise(x),listeClasse)) == 0:
-            listeRes.append(fic)
-            listeClasse.remove(fic)
-    lgap= len(listeClasse)
-    if lgav == lgap and lgap != 0:
-        raise RuntimeError("make_depend: cross-references found")
-#result output
-resstr=''
-for fic in listeRes:
-    resstr=resstr+fic.name+' '
-print resstr
+#!/usr/bin/env python
+"""
+Generate Fortran dependencies from sources (*.f90, *.F90).
+
+Usage:
+    - Default: prints a dependency-ordered list of source files.
+    - --make-deps: prints Makefile-style dependency rules.
+"""
+
+from __future__ import print_function
+import sys
+import os
+import io
+import re
+import glob
+
+def strip_comment(line):
+    idx = line.find('!')
+    return line if idx == -1 else line[:idx]
+
+class FortranUnit(object):
+    USE_RE = re.compile(r"^\s*use\s+([a-z0-9_]+)", re.IGNORECASE)
+    MODULE_RE = re.compile(r"^\s*module\s+([a-z0-9_]+)", re.IGNORECASE)
+    MODULE_PROC_RE = re.compile(r"^\s*module\s+procedure\b", re.IGNORECASE)
+    END_MODULE_RE = re.compile(r"^\s*end\s*module\b", re.IGNORECASE)
+    CONTAINS_RE = re.compile(r"^\s*contains\b", re.IGNORECASE)
+    INCLUDE_RE = re.compile(r"^\s*include\s*[\'\"]([^\'\"]+)[\'\"]", re.IGNORECASE)
+
+    def __init__(self, path):
+        self.name = path
+        self.base = os.path.basename(path)
+        self.base_lc = self.base.lower()
+        self.module = None
+        self.uses = []
+        self.includes_in_contains = []
+        self._parse()
+
+    def _parse(self):
+        in_module = False
+        in_contains = False
+        try:
+            with io.open(self.name, 'r') as f:
+                lines = f.readlines()
+        except IOError:
+            return
+        for raw in lines:
+            line = strip_comment(raw).strip('\n')
+            if not line:
+                continue
+            low = line.lower()
+            if self.MODULE_RE.match(low) and not self.MODULE_PROC_RE.match(low):
+                m = self.MODULE_RE.match(low)
+                if m:
+                    self.module = m.group(1)
+                    in_module = True
+                    in_contains = False
+                continue
+            if in_module and self.CONTAINS_RE.match(low):
+                in_contains = True
+                continue
+            if in_module and self.END_MODULE_RE.match(low):
+                in_module = False
+                in_contains = False
+                continue
+            m_use = self.USE_RE.match(low)
+            if m_use:
+                mod = m_use.group(1)
+                if mod != 'intrinsic' and mod not in self.uses:
+                    self.uses.append(mod)
+                continue
+            if in_module and in_contains:
+                m_inc = self.INCLUDE_RE.match(low)
+                if m_inc:
+                    inc = m_inc.group(1).strip()
+                    self.includes_in_contains.append(os.path.basename(inc))
+
+def build_units(paths):
+    exts = (".f90", ".F90", ".f", ".F")
+    return [FortranUnit(p) for p in paths if p.lower().endswith(exts)]
+
+def build_dependency_order(paths):
+    units = build_units(paths)
+    by_base_lc = dict((u.base_lc, u) for u in units)
+    module_to_unit = dict((u.module, u) for u in units if u.module)
+    included_to_container = {}
+    for u in units:
+        if u.module and u.includes_in_contains:
+            for inc in u.includes_in_contains:
+                included_to_container.setdefault(inc.lower(), set()).add(u)
+
+    edges = dict((u, set()) for u in units)
+    indeg = dict((u, 0) for u in units)
+
+    def add_edge(src, dst):
+        if src is dst:
+            return
+        if dst not in edges[src]:
+            edges[src].add(dst)
+            indeg[dst] += 1
+
+    for u in units:
+        for mod in u.uses:
+            v = module_to_unit.get(mod)
+            if not v:
+                continue
+            included_containers = included_to_container.get(u.base_lc, set())
+            if v in included_containers:
+                continue
+            add_edge(v, u)
+
+    for container in units:
+        if container.module and container.includes_in_contains:
+            for inc in container.includes_in_contains:
+                inc_u = by_base_lc.get(inc.lower())
+                if inc_u:
+                    add_edge(inc_u, container)
+
+    ordered = []
+    zero = [u for u in units if indeg[u] == 0]
+    zero.sort(key=lambda x: x.base_lc)
+    while zero:
+        n = zero.pop(0)
+        ordered.append(n)
+        for m in list(edges[n]):
+            edges[n].remove(m)
+            indeg[m] -= 1
+            if indeg[m] == 0:
+                zero.append(m)
+        zero.sort(key=lambda x: x.base_lc)
+
+    remaining = [u for u in units if u not in ordered]
+    if remaining:
+        remaining.sort(key=lambda x: (0 if not x.module else 1, x.base_lc))
+        ordered.extend(remaining)
+
+    excluded_bases = set()
+    for u in units:
+        if u.module and u.includes_in_contains:
+            for inc in u.includes_in_contains:
+                excluded_bases.add(inc.lower())
+
+    return [u.name for u in ordered if u.base_lc not in excluded_bases]
+
+def make_obj_name(path):
+    base, ext = os.path.splitext(path)
+    return base + ".o"
+
+def generate_make_deps(paths):
+    units = build_units(paths)
+    if not units:
+        return ""
+    by_base_lc = dict((u.base_lc, u) for u in units)
+    module_to_unit = dict((u.module, u) for u in units if u.module)
+    included_to_container = {}
+    for u in units:
+        if u.module and u.includes_in_contains:
+            for inc in u.includes_in_contains:
+                included_to_container.setdefault(inc.lower(), set()).add(u)
+
+    lines = []
+    for u in units:
+        deps_objs = set()
+        deps_files = set()
+
+        for mod in u.uses:
+            v = module_to_unit.get(mod)
+            if not v:
+                continue
+            included_containers = included_to_container.get(u.base_lc, set())
+            if v in included_containers:
+                continue
+            if v is not u:
+                deps_objs.add(make_obj_name(v.name))
+
+        if u.includes_in_contains:
+            for inc in u.includes_in_contains:
+                inc_u = by_base_lc.get(os.path.basename(inc).lower())
+                if inc_u:
+                    deps_files.add(inc_u.name)
+                else:
+                    deps_files.add(inc)
+
+        if deps_objs or deps_files:
+            target = make_obj_name(u.name)
+            deps = sorted(deps_objs) + sorted(deps_files)
+            lines.append("{}: {}".format(target, ' '.join(deps)))
+
+    return "\n".join(lines) + ("\n" if lines else "")
+
+def main():
+    argv = sys.argv[1:]
+    if not argv:
+        print("")
+        return
+
+    make_deps = False
+    if "--make-deps" in argv:
+        make_deps = True
+        argv = [a for a in argv if a != "--make-deps"]
+
+    paths = []
+    for a in argv:
+        if any(ch in a for ch in ['*', '?', '[']):
+            paths.extend(glob.glob(a))
+        else:
+            paths.append(a)
+
+    seen = set()
+    unique_paths = []
+    for p in paths:
+        if p not in seen:
+            seen.add(p)
+            unique_paths.append(p)
+
+    if make_deps:
+        sys.stdout.write(generate_make_deps(unique_paths))
+    else:
+        result = build_dependency_order(unique_paths)
+        sys.stdout.write("%s\n" % (" ".join(result)))
+
+if __name__ == '__main__':
+    main()
diff --git a/script/make_depend_py3.py b/script/make_depend_py3.py
deleted file mode 100755
index a47d7fb..0000000
--- a/script/make_depend_py3.py
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/bin/env python3
-""" generation of module dependances for a xxx.f90 or xxx.F90 file """
-
-import string,sys
-from subprocess import Popen, PIPE
-
-def noComment(mot):
-    """ remove comment characters in a word """
-    ind= mot.find('!')
-    if ind != -1:
-        mot= mot[:ind]
-    return mot
-
-class md9:
-    """ a file, its module and its dependances """
-    def __init__(self,fic):
-        self.name= fic
-        self.used= []
-        #find all module dependances
-        listeLignes= open(self.name,'r',encoding='utf8',errors='ignore').readlines()
-        self.module= "dummy"
-        for ligne in listeLignes:
-            ligne= ligne.lower()
-            if ligne.count('use'):
-                ligne= ligne.replace(',',' ')
-                listeMots= ligne.split()
-                if listeMots[0] == 'use':
-                    mod= noComment(listeMots[1])
-                    if mod not in self.used and mod != 'intrinsic':
-                        self.used.append(mod)
-            elif ligne.count('module'):
-                listeMots= ligne.split()
-                if listeMots[0] == 'module' and \
-                   noComment(listeMots[1]) != 'procedure':
-                    self.module= listeMots[1]
-    def utilise(self,other):
-        return (other.module in self.used)
-
-#list the file names
-listeClasse= list()
-for x in sys.argv[1:]:
-    if x.endswith('.f90') or x.endswith('.F90'): listeClasse.append(md9(x))
-#sort the file list
-listeRes= []
-while listeClasse:
-    lgav= len(listeClasse)
-    for fic in listeClasse:
-        if len(list(filter(lambda x,y=fic:y.utilise(x),listeClasse))) == 0:
-            listeRes.append(fic)
-            listeClasse.remove(fic)
-    lgap= len(listeClasse)
-    if lgav == lgap and lgap != 0:
-        raise RuntimeError("make_depend: cross-references found")
-#result output
-resstr=''
-for fic in listeRes:
-    resstr=resstr+fic.name+' '
-print(resstr)