add needed rpath to executable

Makefile

@@ -6,6 +6,7 @@ SHELL = /bin/sh
 ############################################################################
 #
 #    Copyright 2006 Srdjan Dobricic, CMCC, Bologna
+#    Copyright 2025 Jacopo Nespolo, Matteo Poggi, eXact lab S.r.l, Trieste
 #
 #    This file is part of OceanVar.
 #
@@ -24,19 +25,6 @@ SHELL = /bin/sh
 #
 ############################################################################
 
-include compiler.inc
-
-ifndef NETCDF_INC
-        export NETCDF_INC=/usr/include
-endif
-
-ifndef NETCDF_LIB
-        export NETCDF_LIB=/usr/lib
-endif
-$(info $$NETCDF_INC  = ${NETCDF_INC})
-$(info $$NETCDF_LIB  = ${NETCDF_LIB})
-$(info $$LIBNCMEDLEV = ${LIBNCMEDLEV})
-
 EXEC = var_3d
 LIB  = libvar_3d.a
 
@@ -49,7 +37,7 @@ KNDSTR  =  \
 	set_knd.o
 OBJSTR  =  \
     filename_mod.o\
-		da_params.o\
+	da_params.o\
 	drv_str.o\
 	cns_str.o\
 	obs_str.o\
@@ -100,11 +88,15 @@ PHYSOBS  =  \
 
 OBJS    =  \
 	def_nml.o\
+	def_nml_multi.o\
 	def_grd.o\
 	sav_itr.o\
-	rdeofs.o\
-    rdrcorr.o\
-    mean_rdr.o\
+	rdeofs_chl.o\
+	rdeofs_n3n.o\
+	rdeofs_o2o.o\
+	rdeofs_multi.o\
+	rdrcorr.o\
+	mean_rdr.o\
 	netcdf_err.o\
 	get_obs.o\
 	get_obs_arg.o\
@@ -113,18 +105,23 @@ OBJS    =  \
 	obs_vec.o\
 	ini_cfn.o\
 	cnv_ctv.o\
-	ver_hor.o\
+	ver_hor_chl.o\
+	ver_hor_nut.o\
 	rcfl_x.o\
 	rcfl_y.o\
-	veof.o\
+	veof_chl.o\
+	veof_nut.o\
 	obsop.o\
 	obs_arg.o\
 	resid.o\
 	res_inc.o\
 	obsop_ad.o\
 	obs_arg_ad.o\
-	veof_ad.o\
-	ver_hor_ad.o\
+	veof_chl_ad.o\
+	veof_nut_ad.o\
+	veof_multiv_ad.o\
+	ver_hor_chl_ad.o\
+	ver_hor_nut_ad.o\
 	rcfl_x_ad.o\
 	rcfl_y_ad.o\
 	rcfl_y_ad_init.o\
@@ -137,8 +134,17 @@ OBJS    =  \
 	readAnisotropy.o\
 	bio_mod.o\
 	bio_mod_ad.o\
-	readBioStat.o\
-	wrt_bio_stat.o\
+	readChlStat.o\
+	readNutStat.o\
+	readNutCov.o\
+	readChlNutCov.o\
+	wrt_chl_stat.o\
+	wrt_upd_nut.o\
+	wrt_nut_stat.o\
+	wrt_o2o_stat.o\
+	cp_chl_stat.o\
+	cp_nut_stat.o\
+	cp_o2o_stat.o\
 	costf.o\
 	obs_sat.o\
 	bio_conv.o\
@@ -147,15 +153,41 @@ OBJS    =  \
 	readGrid.o\
 	def_cov.o\
 	tao_minimizer.o\
-    oceanvar.o
+  oceanvar.o
 
 MAINEXE = main.o
 
+# needed libraries
+depends = petsc netcdf netcdf-fortran pnetcdf
+
+# NOTE: It may happen that pkg-config returns a spurious `-I`. We pass the
+#       string through sed to sanitise.
+INCLUDE_FLAGS ?= \
+	$(shell pkg-config --cflags --keep-system-cflags $(depends) | sed -E 's/-I(\s+|$$)//g')
+
+# set rpath in the binary, required in order to find the correct libs at runtime.
+# Env modules nowadays do not pollute the env with LD_LIBRARY_PATH, for good reason.
+LDFLAGS ?= \
+	$(shell pkg-config --libs $(depends)) \
+	-Wl,-rpath -Wl,$(shell pkg-config --libs-only-L $(depends) |sed 's/-L//' |sed 's/-L/:/g' |sed 's/ //g')
+
+FFLAGS ?= -O2 -ffree-line-length-none -c
+FC ?= mpif90
+LD ?= mpif90
+
+$(info $$INCLUDE_FLAGS  = ${INCLUDE_FLAGS})
+$(info $$FFLAGS  = ${FFLAGS})
+$(info $$LDFLAGS  = ${LDFLAGS})
+$(info $$FC = ${FC})
+$(info $$LD = ${LD})
+
 .SUFFIXES: .f90
 
+.PHONY:all
 all:  $(EXEC) $(LIB)
 	@echo $(EXEC) is compiled
 
+.PHONY:install
 install:	$(EXEC)
 		cp -p $(EXEC) $(INSTDIR)
 
@@ -165,31 +197,18 @@ $(EXEC) : $(LIBDEP)	$(KNDSTR) $(OBJSTR) $(OBJS) $(MAINEXE)
 $(LIB)  :       $(KNDSTR) $(OBJSTR) $(OBJS)
 	ar -r $(LIB) $(KNDSTR) $(OBJSTR) $(OBJS)
 
-tao_minimizer.o: tao_minimizer.f90
-	$(CPP) -I$(PETSC_INC) $*.f90 > cpp.$*.f90 ; $(F90) -I$(PETSC_INC) $(FFLAGS) cpp.$*.f90  ; $(MV) cpp.$*.o $*.o
-
-mpi_utils.o: mpi_utils.f90
-	$(CPP) -I$(PETSC_INC) $*.f90 > cpp.$*.f90 ; $(F90) -I$(PETSC_INC) $(FFLAGS) cpp.$*.f90  ; $(MV) cpp.$*.o $*.o
-
 .DEFAULTS:
 .f90.o :
-	$(CPP) $*.f90 > cpp.$*.f90 ; $(F90) $(FFLAGS) cpp.$*.f90  ; $(MV) cpp.$*.o $*.o
-
-.f.o :
-	$(CPP) $*.f > cpp.$*.f ; $(F77) $(FFLAGS) cpp.$*.f  ; $(MV) cpp.$*.o $*.o
-
-libf_exit.a :
-	cd $(LIBFEXIT) && $(MAKE)
+	$(FC) -cpp $(INCLUDE_FLAGS) $(FFLAGS) -o $@ $*.f90
 
-libnc-medlevel.a :
-		cd $(LIBNCMEDLEV) && $(MAKE)
+libnc-medlevel.a : nc-med-level-lib.o
+	$(AR) cr $@ $<
 
+.PHONY:clean
 clean:
-	$(RM) *.o *.mod cpp.* *.L
-	cd $(LIBNCMEDLEV) && $(MAKE) erase
-	cd ..
+	$(RM) *.o *.mod cpp.* *.L *.a
+	$(RM) libnc-medlevel/*.a libnc-medlevel/*.o
 
+.PHONY:erease
 erase:
 	$(RM) *.o *.mod cpp.* *.L $(EXEC)
-	cd $(LIBNCMEDLEV) && $(MAKE) erase
-	cd ..

bio_conv.f90

@@ -29,16 +29,22 @@ subroutine bio_conv
   !-----------------------------------------------------------------------
 
   use grd_str
+  use eof_str
   use bio_str
+  use drv_str
 
   implicit none
 
-  INTEGER(i4)   ::  i, j, k, l
+  INTEGER(i4)   ::  i, j, k, l, my_km
 
   grd%chl(:,:,:) = 0.0
 
+  my_km = grd%km
+  if(drv%multiv.eq.1) &
+    my_km = ros%kmchl
+
   do l = 1,bio%nphy
-    do k = 1,grd%km
+    do k = 1,my_km
       do j = 1,grd%jm
         do i = 1,grd%im
           grd%chl(i,j,k) = grd%chl(i,j,k) + bio%phy(i,j,k,l,1)

bio_conv_ad.f90

@@ -29,16 +29,22 @@ subroutine bio_conv_ad
   !-----------------------------------------------------------------------
 
   use grd_str
+  use eof_str
   use bio_str
+  use drv_str
 
   implicit none
 
-  INTEGER(i4)   ::  i, j, k, l
+  INTEGER(i4)   ::  i, j, k, l, my_km
 
   bio%phy_ad(:,:,:,:,:) = 0.0
 
+  my_km = grd%km
+  if(drv%multiv .eq. 1) &
+    my_km = ros%kmchl
+
   do l = 1,bio%nphy
-    do k = 1,grd%km
+    do k = 1,my_km
       do j = 1,grd%jm
         do i = 1,grd%im
           bio%phy_ad(i,j,k,l,1) = bio%phy_ad(i,j,k,l,1) + grd%chl_ad(i,j,k)

bio_mod.f90

@@ -31,16 +31,21 @@ subroutine bio_mod
   use grd_str
   use bio_str
   use eof_str
+  use drv_str
 
   IMPLICIT NONE
 
-  INTEGER(i4)     :: m, l, k,j ,i
+  INTEGER(i4)     :: m, l, k,j ,i, my_km
 
   bio%phy(:,:,:,:,:) = 0.0
 
+  my_km = grd%km
+  if(drv%multiv .eq. 1) &
+    my_km = ros%kmchl
+
   do m=1,bio%ncmp
     do l=1,bio%nphy
-      do k=1,grd%km
+      do k=1,my_km
         do j=1,grd%jm
           do i=1,grd%im
             bio%phy(i,j,k,l,m)=bio%cquot(i,j,k,l,m)*bio%pquot(i,j,k,l)*grd%chl(i,j,k)

bio_mod_ad.f90

@@ -31,16 +31,21 @@ subroutine bio_mod_ad
   use grd_str
   use bio_str
   use eof_str
+  use drv_str
 
   IMPLICIT NONE
 
-  INTEGER(i4)     :: m, l, k, j, i
+  INTEGER(i4)     :: m, l, k, j, i, my_km
 
   grd%chl_ad(:,:,:) = 0.0
 
+  my_km = grd%km
+  if(drv%multiv .eq. 1) &
+    my_km = ros%kmchl
+
   do m=1,bio%ncmp
     do l=1,bio%nphy
-      do k=1,grd%km
+      do k=1,my_km
         do j=1,grd%jm
           do i=1,grd%im
             grd%chl_ad(i,j,k) = grd%chl_ad(i,j,k) + bio%cquot(i,j,k,l,m) * bio%pquot(i,j,k,l) * bio%phy_ad(i,j,k,l,m)

bio_str.f90

@@ -40,13 +40,21 @@ MODULE bio_str
         REAL(r8),    POINTER  ::  pquot(:,:,:,:)       ! Phytoplankton component quotas
         REAL(r8),    POINTER  ::  phy(:,:,:,:,:)       ! biogeochemical variables 
         REAL(r8),    POINTER  ::  phy_ad(:,:,:,:,:)    ! biogeochemical adjoint variables
-        REAL(r8),    POINTER  ::  InitialChl(:,:,:)     ! initial amount of chlorophyll
+        REAL(r8),    POINTER  ::  InitialChl(:,:,:)    ! initial amount of chlorophyll
+        REAL(r8),    POINTER  ::  InitialNut(:,:,:,:)  ! initial amount of nutrients
+        REAL(r8),    POINTER  ::  covn3n_n1p(:,:,:)    ! covariance n3n n1p
+        REAL(r8),    POINTER  ::  covn3n_chl(:,:,:)    ! covariance n3n chl
+        REAL(r8),    POINTER  ::  covn1p_chl(:,:,:)    ! covariance n3n chl
 
         INTEGER               ::  nphy                 ! number of phytoplankton types
         INTEGER               ::  ncmp                 ! No. of phytoplankton components
 
-        LOGICAL               ::  ApplyConditions       ! Apply conditions in snutell operations
-
+        LOGICAL               ::  ApplyConditions      ! Apply conditions in snutell operations
+
+        INTEGER(i4)           ::  N3n                  ! N3n assimilation
+        INTEGER(i4)           ::  updateN1p            ! N1p update based on N3n assimilation
+        INTEGER(i4)           ::  O2o                  ! O2o assimilation
+
    END TYPE bio_t
 
    TYPE (bio_t)                 :: bio

clean_mem.f90

@@ -51,6 +51,7 @@ subroutine clean_mem
      DEALLOCATE ( arg%ib, arg%jb, arg%kb)
      DEALLOCATE ( arg%pq1, arg%pq2, arg%pq3, arg%pq4)
      DEALLOCATE ( arg%pq5, arg%pq6, arg%pq7, arg%pq8)
+     DEALLOCATE ( arg%par)
      DEALLOCATE (grd%lon, grd%lat)
   endif
 
@@ -72,11 +73,16 @@ subroutine clean_mem
   DEALLOCATE ( rcf%sc)
 
   DEALLOCATE(SendCountX3D, SendDisplX3D)
+  DEALLOCATE(SendCountX3D_chl, SendDisplX3D_chl)
   DEALLOCATE(RecCountX3D, RecDisplX3D)
+  DEALLOCATE(RecCountX3D_chl, RecDisplX3D_chl)
 
   DEALLOCATE(ChlExtended)
+  DEALLOCATE(ChlExtended_3d,N3nExtended_3d,O2oExtended_3d)
   DEALLOCATE(SendBottom, RecTop)
   DEALLOCATE(SendTop, RecBottom)
+  DEALLOCATE(SendTop_2d, RecBottom_2d)
+  DEALLOCATE(SendBottom_2d, RecTop_2d)
 
   if(MyId .eq. 0) then
     write(*,*) ' ALL MEMORY CLEAN'

cnv_inn.f90

@@ -35,13 +35,36 @@ subroutine cnv_inn
   use eof_str
   use ctl_str
   use drv_str
+  use bio_str
 
   implicit none
 
   ! --------
   ! Convert the control vector to v
   call cnv_ctv
-
-  call ver_hor
 
+  if (drv%multiv .eq. 0) then
+    if(drv%chl_assim .eq. 1) then
+      call ver_hor_chl
+    endif
+    if(drv%nut .eq. 1) then
+      if(bio%N3n .eq. 1) then
+        call ver_hor_nut(grd%n3n, grd%n3n_ad,'N')
+      endif
+      if(bio%O2o .eq. 1) then
+        call ver_hor_nut(grd%o2o, grd%o2o_ad,'O')
+      endif
+    endif
+  endif
+
+  if (drv%multiv .eq. 1) then
+    call ver_hor_chl
+    call ver_hor_nut(grd%n3n, grd%n3n_ad,'N')
+  endif
+
+  ! ---
+  ! Apply biological repartition of the chlorophyll
+  if((drv%chl_assim .eq. 1) .or. (drv%multiv .eq. 1)) &
+    call bio_mod
+
 end subroutine cnv_inn