allow for the use of pure intel compiler and remove multiple definiti…

…ons as linker in Mac does not allow it

PDAFBuild/Makefile

@@ -0,0 +1,389 @@
+# $Id: Makefile 1856 2017-12-06 08:36:03Z lnerger $
+
+#######################################################
+# Generic Makefile for to build PDAF library          #
+# To choose the architecture set $PDAF_ARCH           #
+#######################################################
+
+.SUFFIXES: .F90 .f .o 
+
+######################################################
+
+# Include machine-specific definitions
+# For available include files see directory make.arch
+# To choose a file, set PDAF_ARCH either here or by an
+# environment variable.
+include ../make.arch/$(PDAF_ARCH).h
+
+
+######################################################
+# Define objects for PDAF library
+######################################################
+
+# Modules used in PDAF
+MOD_PDAF =    	PDAF_timer.o \
+		PDAF_memcount.o \
+		PDAF_mod_filtermpi.o \
+		PDAF_mod_filter.o
+
+# Module file with interface definitions
+# MOD_INTERFACE = PDAF_interfaces_module.o
+
+# Generic routines in PDAF
+OBJ_PDAF_GEN = 	PDAF_init.o \
+		PDAF_init_filters.o \
+		PDAF_alloc_filters.o \
+		PDAF_print_info.o \
+		PDAF_print_version.o \
+		PDAF_communicate_ens.o \
+		PDAF_set_comm_pdaf.o \
+		PDAF_options_filters.o \
+		PDAF_get_state.o \
+		PDAF_incremental.o \
+		PDAF_set_forget.o \
+		PDAF_set_forget_local.o \
+		PDAF_add_increment.o \
+		PDAF_generate_rndmat.o \
+		PDAF_local_weights.o \
+		PDAF_local_weight.o \
+		PDAF_force_analysis.o \
+		PDAF_set_memberid.o \
+		PDAF_get_memberid.o \
+		PDAF_get_obsmemberid.o \
+		PDAF_smoother_shift.o \
+		PDAF_smoother.o \
+		PDAF_smoother_local.o \
+		PDAF_set_smootherens.o \
+		PDAF_get_smootherens.o \
+		PDAF_set_ens_pointer.o \
+		PDAF_put_state_prepost.o \
+		PDAF_assimilate_prepost.o \
+		PDAF_prepost.o \
+		PDAF_inflate_ens.o \
+		PDAF_sampleens.o \
+		PDAF_mvnormalize.o \
+		PDAF_eofcovar.o \
+		PDAF_diag_histogram.o \
+		PDAF_diag_ensstats.o \
+		PDAF_diag_effsample.o \
+		PDAF_diag_crps.o \
+		PDAF_gather_dim_obs_f.o \
+		PDAF_gather_obs_f.o \
+		PDAF_gather_obs_f2.o \
+		PDAF_gather_obs_f_flex.o \
+		PDAF_gather_obs_f2_flex.o \
+		PDAF_allreduce.o \
+		PDAF_deallocate.o \
+		PDAF_get_assim_flag.o \
+		PDAF_get_localfilter.o \
+		PDAF_get_globalobs.o \
+		PDAF_inflate_weights.o \
+		PDAFomi_put_state_global.o \
+		PDAFomi_put_state_local.o \
+		PDAFomi_assimilate_global.o \
+		PDAFomi_assimilate_local.o \
+		PDAF_reset_forget.o \
+		PDAF_get_ensstats.o \
+		PDAF_set_debug_flag.o
+
+# Specific PDAF-routines for SEIK
+OBJ_SEIK =	PDAF_seik_init.o \
+		PDAF_seik_alloc.o \
+		PDAF_seik_options.o \
+		PDAF_seik_memtime.o \
+		PDAF_put_state_seik.o \
+		PDAF_assimilate_seik.o \
+		PDAF_seik_update.o \
+		PDAF_seik_analysis.o \
+		PDAF_seik_resample.o \
+		PDAF_seik_analysis_newT.o \
+		PDAF_seik_resample_newT.o \
+		PDAF_seik_analysis_trans.o \
+		PDAF_seik_matrixT.o \
+		PDAF_seik_uinv.o \
+		PDAF_seik_omega.o \
+		PDAF_seik_TtimesA.o
+
+# Specific PDAF-routines for local SEIK
+OBJ_LSEIK =     PDAF_lseik_init.o \
+		PDAF_lseik_alloc.o \
+		PDAF_lseik_options.o \
+		PDAF_lseik_memtime.o \
+		PDAF_put_state_lseik.o \
+		PDAF_assimilate_lseik.o \
+		PDAF_lseik_update.o \
+		PDAF_lseik_analysis.o \
+		PDAF_lseik_resample.o \
+		PDAF_lseik_analysis_trans.o
+
+# Specific PDAF-routines for SEEK
+OBJ_SEEK =      PDAF_seek_init.o \
+		PDAF_seek_alloc.o \
+		PDAF_seek_options.o \
+		PDAF_seek_memtime.o \
+		PDAF_put_state_seek.o \
+		PDAF_assimilate_seek.o \
+		PDAF_seek_update.o \
+		PDAF_seek_analysis.o \
+		PDAF_seek_rediag.o
+
+# Specific PDAF-routines for EnKF
+OBJ_ENKF =	PDAF_enkf_init.o \
+		PDAF_enkf_alloc.o \
+		PDAF_enkf_options.o \
+		PDAF_enkf_memtime.o \
+		PDAF_put_state_enkf.o \
+		PDAF_assimilate_enkf.o \
+		PDAF_enkf_update.o \
+		PDAF_enkf_obs_ensemble.o \
+		PDAF_enkf_analysis_rlm.o \
+		PDAF_enkf_analysis_rsm.o \
+		PDAF_enkf_omega.o \
+		PDAF_enkf_Tleft.o \
+		PDAF_smoother_enkf.o
+
+# Specific PDAF-routines for ETKF
+OBJ_ETKF =	PDAF_etkf_init.o \
+		PDAF_etkf_alloc.o \
+		PDAF_etkf_options.o \
+		PDAF_etkf_memtime.o \
+		PDAF_put_state_etkf.o \
+		PDAF_assimilate_etkf.o \
+		PDAF_etkf_update.o \
+		PDAF_etkf_analysis.o \
+		PDAF_etkf_analysis_T.o \
+		PDAF_etkf_analysis_fixed.o \
+		PDAF_etkf_Tright.o \
+		PDAF_etkf_Tleft.o
+
+# Specific PDAF-routines for LETKF
+OBJ_LETKF =     PDAF_letkf_init.o \
+		PDAF_letkf_alloc.o \
+		PDAF_letkf_options.o \
+		PDAF_letkf_memtime.o \
+		PDAF_put_state_letkf.o \
+		PDAF_assimilate_letkf.o \
+		PDAF_letkf_update.o \
+		PDAF_letkf_analysis.o \
+		PDAF_letkf_analysis_T.o \
+		PDAF_letkf_analysis_fixed.o
+
+# Specific PDAF-routines for ESTKF
+OBJ_ESTKF =	PDAF_estkf_init.o \
+		PDAF_estkf_alloc.o \
+		PDAF_estkf_options.o \
+		PDAF_estkf_memtime.o \
+		PDAF_put_state_estkf.o \
+		PDAF_assimilate_estkf.o \
+		PDAF_estkf_update.o \
+		PDAF_estkf_analysis.o \
+		PDAF_estkf_analysis_fixed.o \
+		PDAF_estkf_AOmega.o \
+		PDAF_estkf_OmegaA.o
+
+# Specific PDAF-routines for LESTKF
+OBJ_LESTKF =	PDAF_lestkf_init.o \
+		PDAF_lestkf_alloc.o \
+		PDAF_lestkf_options.o \
+		PDAF_lestkf_memtime.o \
+		PDAF_put_state_lestkf.o \
+		PDAF_assimilate_lestkf.o \
+		PDAF_lestkf_update.o \
+		PDAF_lestkf_analysis.o \
+		PDAF_lestkf_analysis_fixed.o
+
+# Specific PDAF-routines for EnKF
+OBJ_LENKF =	PDAF_lenkf_init.o \
+		PDAF_lenkf_alloc.o \
+		PDAF_lenkf_options.o \
+		PDAF_lenkf_memtime.o \
+		PDAF_put_state_lenkf.o \
+		PDAFomi_put_state_lenkf.o \
+		PDAF_assimilate_lenkf.o \
+		PDAFomi_assimilate_lenkf.o \
+		PDAF_lenkf_update.o \
+		PDAF_enkf_gather_resid.o \
+		PDAF_lenkf_analysis_rsm.o
+
+# Specific PDAF-routines for NETF
+OBJ_NETF =	PDAF_netf_init.o \
+		PDAF_netf_alloc.o \
+		PDAF_netf_options.o \
+		PDAF_netf_memtime.o \
+		PDAF_put_state_netf.o \
+		PDAF_assimilate_netf.o \
+		PDAF_netf_update.o \
+		PDAF_netf_smootherT.o \
+		PDAF_netf_analysis.o \
+		PDAF_smoother_netf.o
+
+# Specific PDAF-routines for LNETF
+OBJ_LNETF =	PDAF_lnetf_init.o \
+		PDAF_lnetf_alloc.o \
+		PDAF_lnetf_options.o \
+		PDAF_lnetf_memtime.o \
+		PDAF_put_state_lnetf.o \
+		PDAF_assimilate_lnetf.o \
+		PDAF_lnetf_update.o \
+		PDAF_lnetf_analysis.o \
+		PDAF_lnetf_smootherT.o \
+		PDAF_smoother_lnetf.o
+
+# Specific PDAF-routines for PF
+OBJ_PF =	PDAF_pf_init.o \
+		PDAF_pf_alloc.o \
+		PDAF_pf_options.o \
+		PDAF_pf_memtime.o \
+		PDAF_put_state_pf.o \
+		PDAF_assimilate_pf.o \
+		PDAF_pf_update.o \
+		PDAF_pf_analysis.o \
+		PDAF_pf_resampling.o \
+		PDAF_pf_add_noise.o
+
+# Specific PDAF-routines for LKNETF
+OBJ_LKNETF =	PDAF_lknetf_init.o \
+		PDAF_lknetf_alloc.o \
+		PDAF_lknetf_options.o \
+		PDAF_lknetf_memtime.o \
+		PDAF_put_state_lknetf.o \
+		PDAF_assimilate_lknetf.o \
+		PDAF_lknetf_update.o \
+		PDAF_lknetf_analysis_T.o \
+		PDAF_lknetf_step_update.o \
+		PDAF_lknetf_ana_lnetf.o \
+		PDAF_lknetf_ana_letkfT.o \
+		PDAF_lknetf_compute_gamma.o \
+		PDAF_lknetf_set_gamma.o \
+		PDAF_lknetf_alpha_neff.o \
+		PDAF_lknetf_reset_gamma.o
+
+# Specific PDAF-routines for generating observations
+OBJ_OBSGEN =	PDAF_genobs_init.o \
+		PDAF_genobs_alloc.o \
+		PDAF_genobs_options.o \
+		PDAF_put_state_generate_obs.o \
+		PDAFomi_put_state_generate_obs.o \
+		PDAF_generate_obs.o \
+		PDAFomi_generate_obs.o \
+		PDAF_gen_obs.o
+
+# Specific PDAF-routines for 3DVAR initialization part
+OBJ_3DVAR_INI =	PDAF_3dvar_init.o \
+		PDAF_3dvar_alloc.o \
+		PDAF_3dvar_options.o
+
+# Specific PDAF-routines for 3DVAR
+OBJ_3DVAR =	PDAF_3dvar_memtime.o \
+		PDAF_put_state_3dvar.o \
+		PDAF_assimilate_3dvar.o \
+		PDAF_3dvar_update.o \
+		PDAF_3dvar_analysis_cvt.o \
+		PDAF_3dvar_optim_lbfgs.o \
+		PDAF_3dvar_optim_cgplus.o \
+		PDAF_3dvar_costf_cvt.o \
+		PDAF_3dvar_costf_cg_cvt.o \
+		PDAF_3dvar_optim_cg.o \
+		PDAF_put_state_en3dvar_lestkf.o \
+		PDAF_assimilate_en3dvar_lestkf.o \
+		PDAF_en3dvar_update_lestkf.o \
+		PDAF_put_state_en3dvar_estkf.o \
+		PDAF_assimilate_en3dvar_estkf.o \
+		PDAF_en3dvar_update_estkf.o \
+		PDAF_en3dvar_analysis_cvt.o \
+		PDAF_en3dvar_optim_lbfgs.o \
+		PDAF_en3dvar_optim_cgplus.o \
+		PDAF_en3dvar_optim_cg.o \
+		PDAF_en3dvar_costf_cvt.o \
+		PDAF_en3dvar_costf_cg_cvt.o \
+		PDAF_put_state_hyb3dvar_lestkf.o \
+		PDAF_assimilate_hyb3dvar_lestkf.o \
+		PDAF_hyb3dvar_update_lestkf.o \
+		PDAF_hyb3dvar_analysis_cvt.o\
+		PDAF_put_state_hyb3dvar_estkf.o \
+		PDAF_assimilate_hyb3dvar_estkf.o \
+		PDAF_hyb3dvar_update_estkf.o \
+		PDAF_hyb3dvar_optim_lbfgs.o \
+		PDAF_hyb3dvar_optim_cgplus.o \
+		PDAF_hyb3dvar_optim_cg.o \
+		PDAF_hyb3dvar_costf_cvt.o \
+		PDAF_hyb3dvar_costf_cg_cvt.o \
+		PDAFomi_assimilate_3dvar.o \
+		PDAFomi_assimilate_en3dvar_estkf.o \
+		PDAFomi_assimilate_en3dvar_lestkf.o \
+		PDAFomi_assimilate_hyb3dvar_estkf.o \
+		PDAFomi_assimilate_hyb3dvar_lestkf.o \
+		PDAFomi_put_state_3dvar.o \
+		PDAFomi_put_state_en3dvar_estkf.o \
+		PDAFomi_put_state_en3dvar_lestkf.o \
+		PDAFomi_put_state_hyb3dvar_estkf.o \
+		PDAFomi_put_state_hyb3dvar_lestkf.o
+
+# Routines for PDAF-OMI
+OBJ_PDAFOMI =	PDAFomi_obs_f.o \
+		PDAFomi_obs_l.o \
+		PDAFomi_obs_op.o \
+		PDAFomi.o \
+		PDAFomi_callback.o
+
+OBJ_PDAF =   $(OBJ_PDAFOMI) $(OBJ_PDAF_GEN) $(OBJ_SEIK) $(OBJ_LSEIK) $(OBJ_SEEK) \
+		$(OBJ_ENKF) $(OBJ_ETKF) $(OBJ_LETKF) \
+		$(OBJ_ESTKF) $(OBJ_LESTKF) $(OBJ_LENKF) $(OBJ_NETF) $(OBJ_LNETF) \
+		$(OBJ_LKNETF) $(OBJ_PF) $(OBJ_OBSGEN) $(OBJ_3DVAR_INI)
+
+OBJ_PDAF_VAR = $(OBJ_PDAF) $(OBJ_3DVAR) 
+
+# External optimizer libraries
+OBJ_OPTIM = ../external/CG+_mpi/cgfam.o ../external/CG+_mpi/cgsearch.o \
+	../external/CG+/cgfam.o ../external/CG+/cgsearch.o \
+	../external/LBFGS/lbfgsb.o ../external/LBFGS/linpack.o \
+	../external/LBFGS/timer.o
+
+######################################################
+
+../lib/libpdaf-d.a: 	$(MOD_PDAF) $(OBJ_PDAF)
+	@echo "++++++ Generate Filter library ++++++"
+	$(AR) -r $(AR_SPEC) $@ \
+	$(MOD_PDAF)  $(OBJ_PDAF)
+	$(RANLIB) ../lib/libpdaf-d.a
+	@cp *.mod ../include
+
+../lib/libpdaf-var.a: $(MOD_PDAF) $(OBJ_PDAF_VAR) $(OBJ_OPTIM)
+	@echo "++++++ Generate Filter library ++++++"
+	$(AR) -r $(AR_SPEC) $@ \
+	$(MOD_PDAF) $(OBJ_PDAF_VAR) $(OBJ_OPTIM)
+	$(RANLIB) ../lib/libpdaf-var.a
+	@cp *.mod ../include
+
+# Short alias for ../lib/libpdaf-var.a
+pdaf-var: ../lib/libpdaf-var.a
+
+
+.F90.o :
+	$(FC) $(OPT) $(MPI_INC) $(CPP_DEFS) -c $*.F90
+
+.f.o :
+	$(FC) -O3 -fPIC -o $*.o -c $*.f
+
+# For older compilers one might need to separate the
+# preprocessing from the compilation as defined below:
+#.F90.o :
+#	$(CPP) -P -C $(MPI_INC) $(CPP_DEFS) $*.F90 $*.f90
+#	$(FC) $(OPT) $(MPI_INC) -c $*.F90
+#	@rm -f  $*.f90
+
+######################################################
+# Cleans
+
+clean :
+	rm -f *.o *.mod ../lib/libpdaf-d.a ../lib/libpdaf-var.a ../include/*.mod
+	cd ../external/CG+; rm -f *.o; cd -
+	cd ../external/LBFGS; rm -f *.o; cd -
+
+######################################################
+# List arch files
+
+listarch:
+	@echo Available architecture-specific input files for PDAF_ARCH
+	@echo ---------------------------------------------------------
+	@ls -1 ../make.arch | cut -d"." -f1

pyPDAF/fortran/PDAF_c_binding.F90

@@ -1,6 +1,5 @@
 MODULE PDAF_c_binding
 use iso_c_binding, only: c_double, c_int, c_bool, c_ptr, c_loc
-use PDAF_interfaces_module
 use U_PDAF_interface_c_binding
 
 implicit none