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nemogcm.F90 in branches/2012/dev_MERGE_2012/NEMOGCM/NEMO/OPA_SRC – NEMO

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source: branches/2012/dev_MERGE_2012/NEMOGCM/NEMO/OPA_SRC/nemogcm.F90 @ 3701

Last change on this file since 3701 was 3701, checked in by smasson, 12 years ago
dev_MERGE_2012: add missing modifications for xios
Property svn:keywords set to `Id`
File size: 37.0 KB

Rev	Line
[2496]	1	MODULE nemogcm
[2442]	2	!!======================================================================
[2496]	3	!! * MODULE nemogcm *
	4	!! Ocean system : NEMO GCM (ocean dynamics, on-line tracers, biochemistry and sea-ice)
[2442]	5	!!======================================================================
[1593]	6	!! History : OPA ! 1990-10 (C. Levy, G. Madec) Original code
	7	!! 7.0 ! 1991-11 (M. Imbard, C. Levy, G. Madec)
	8	!! 7.1 ! 1993-03 (M. Imbard, C. Levy, G. Madec, O. Marti, M. Guyon, A. Lazar,
[2104]	9	!! P. Delecluse, C. Perigaud, G. Caniaux, B. Colot, C. Maes) release 7.1
[1593]	10	!! - ! 1992-06 (L.Terray) coupling implementation
	11	!! - ! 1993-11 (M.A. Filiberti) IGLOO sea-ice
	12	!! 8.0 ! 1996-03 (M. Imbard, C. Levy, G. Madec, O. Marti, M. Guyon, A. Lazar,
[2104]	13	!! P. Delecluse, L.Terray, M.A. Filiberti, J. Vialar, A.M. Treguier, M. Levy) release 8.0
[1593]	14	!! 8.1 ! 1997-06 (M. Imbard, G. Madec)
	15	!! 8.2 ! 1999-11 (M. Imbard, H. Goosse) LIM sea-ice model
	16	!! ! 1999-12 (V. Thierry, A-M. Treguier, M. Imbard, M-A. Foujols) OPEN-MP
	17	!! ! 2000-07 (J-M Molines, M. Imbard) Open Boundary Conditions (CLIPPER)
	18	!! NEMO 1.0 ! 2002-08 (G. Madec) F90: Free form and modules
	19	!! - ! 2004-06 (R. Redler, NEC CCRLE, Germany) add OASIS[3/4] coupled interfaces
	20	!! - ! 2004-08 (C. Talandier) New trends organization
	21	!! - ! 2005-06 (C. Ethe) Add the 1D configuration possibility
	22	!! - ! 2005-11 (V. Garnier) Surface pressure gradient organization
	23	!! - ! 2006-03 (L. Debreu, C. Mazauric) Agrif implementation
	24	!! - ! 2006-04 (G. Madec, R. Benshila) Step reorganization
	25	!! - ! 2007-07 (J. Chanut, A. Sellar) Unstructured open boundaries (BDY)
	26	!! 3.2 ! 2009-08 (S. Masson) open/write in the listing file in mpp
[2236]	27	!! 3.3 ! 2010-05 (K. Mogensen, A. Weaver, M. Martin, D. Lea) Assimilation interface
	28	!! - ! 2010-10 (C. Ethe, G. Madec) reorganisation of initialisation phase
[3294]	29	!! 3.3.1! 2011-01 (A. R. Porter, STFC Daresbury) dynamical allocation
	30	!! 3.4 ! 2011-11 (C. Harris) decomposition changes for running with CICE
[1593]	31	!!----------------------------------------------------------------------
[3]	32
	33	!!----------------------------------------------------------------------
[2496]	34	!! nemo_gcm : solve ocean dynamics, tracer, biogeochemistry and/or sea-ice
	35	!! nemo_init : initialization of the NEMO system
	36	!! nemo_ctl : initialisation of the contol print
	37	!! nemo_closefile : close remaining open files
[2715]	38	!! nemo_alloc : dynamical allocation
	39	!! nemo_partition : calculate MPP domain decomposition
	40	!! factorise : calculate the factors of the no. of MPI processes
[3]	41	!!----------------------------------------------------------------------
[2382]	42	USE step_oce ! module used in the ocean time stepping module
[888]	43	USE sbc_oce ! surface boundary condition: ocean
[2392]	44	USE cla ! cross land advection (tra_cla routine)
[3]	45	USE domcfg ! domain configuration (dom_cfg routine)
	46	USE mppini ! shared/distributed memory setting (mpp_init routine)
	47	USE domain ! domain initialization (dom_init routine)
[3625]	48	#if defined key_nemocice_decomp
	49	USE ice_domain_size, only: nx_global, ny_global
	50	#endif
[3651]	51	USE tideini ! tidal components initialization (tide_ini routine)
[3]	52	USE obcini ! open boundary cond. initialization (obc_ini routine)
[3294]	53	USE bdyini ! open boundary cond. initialization (bdy_init routine)
	54	USE bdydta ! open boundary cond. initialization (bdy_dta_init routine)
[3651]	55	USE bdytides ! open boundary cond. initialization (bdytide_init routine)
[3]	56	USE istate ! initial state setting (istate_init routine)
	57	USE ldfdyn ! lateral viscosity setting (ldfdyn_init routine)
	58	USE ldftra ! lateral diffusivity setting (ldftra_init routine)
[2392]	59	USE zdfini ! vertical physics setting (zdf_init routine)
[3]	60	USE phycst ! physical constant (par_cst routine)
[2236]	61	USE trdmod ! momentum/tracers trends (trd_mod_init routine)
	62	USE asmtrj ! writing out state trajectory
	63	USE diaptr ! poleward transports (dia_ptr_init routine)
[3294]	64	USE diadct ! sections transports (dia_dct_init routine)
[2236]	65	USE diaobs ! Observation diagnostics (dia_obs_init routine)
[2496]	66	USE step ! NEMO time-stepping (stp routine)
[3609]	67	USE icbini ! handle bergs, initialisation
	68	USE icbstp ! handle bergs, calving, themodynamics and transport
[532]	69	#if defined key_oasis3
[1359]	70	USE cpl_oasis3 ! OASIS3 coupling
[599]	71	#elif defined key_oasis4
[1359]	72	USE cpl_oasis4 ! OASIS4 coupling (not working)
[532]	73	#endif
[900]	74	USE c1d ! 1D configuration
	75	USE step_c1d ! Time stepping loop for the 1D configuration
[1594]	76	#if defined key_top
[1593]	77	USE trcini ! passive tracer initialisation
[1594]	78	#endif
[1593]	79	USE lib_mpp ! distributed memory computing
[1412]	80	#if defined key_iomput
[3701]	81	USE xios
[1359]	82	#endif
[3651]	83	USE sbctide, ONLY: lk_tide
[268]	84
[3651]	85
[2715]	86	IMPLICIT NONE
[3]	87	PRIVATE
	88
[2496]	89	PUBLIC nemo_gcm ! called by model.F90
	90	PUBLIC nemo_init ! needed by AGRIF
[467]	91
[2498]	92	CHARACTER(lc) :: cform_aaa="( /, 'AAAAAAAA', / ) " ! flag for output listing
[1593]	93
[3]	94	!!----------------------------------------------------------------------
[2715]	95	!! NEMO/OPA 4.0 , NEMO Consortium (2011)
[2392]	96	!! $Id$
[2329]	97	!! Software governed by the CeCILL licence (NEMOGCM/NEMO_CeCILL.txt)
[3]	98	!!----------------------------------------------------------------------
	99	CONTAINS
	100
[2496]	101	SUBROUTINE nemo_gcm
[3]	102	!!----------------------------------------------------------------------
[2496]	103	!! * ROUTINE nemo_gcm *
[3]	104	!!
[2496]	105	!! ** Purpose : NEMO solves the primitive equations on an orthogonal
[1593]	106	!! curvilinear mesh on the sphere.
[3]	107	!!
	108	!! ** Method : - model general initialization
	109	!! - launch the time-stepping (stp routine)
[1593]	110	!! - finalize the run by closing files and communications
[3]	111	!!
[2715]	112	!! References : Madec, Delecluse, Imbard, and Levy, 1997: internal report, IPSL.
[1593]	113	!! Madec, 2008, internal report, IPSL.
[3]	114	!!----------------------------------------------------------------------
	115	INTEGER :: istp ! time step index
[389]	116	!!----------------------------------------------------------------------
[2382]	117	!
[392]	118	#if defined key_agrif
[1593]	119	CALL Agrif_Init_Grids() ! AGRIF: set the meshes
[389]	120	#endif
	121
[1593]	122	! !-----------------------!
[2496]	123	CALL nemo_init !== Initialisations ==!
[1593]	124	! !-----------------------!
[2715]	125	#if defined key_agrif
[3680]	126	CALL Agrif_Declare_Var_dom ! AGRIF: set the meshes for DOM
	127	CALL Agrif_Declare_Var ! " " " " " DYN/TRA
[2715]	128	# if defined key_top
[3680]	129	CALL Agrif_Declare_Var_top ! " " " " " TOP
[2715]	130	# endif
[3680]	131	# if defined key_lim2
	132	CALL Agrif_Declare_Var_lim2 ! " " " " " LIM
	133	# endif
[2715]	134	#endif
[682]	135	! check that all process are still there... If some process have an error,
	136	! they will never enter in step and other processes will wait until the end of the cpu time!
[900]	137	IF( lk_mpp ) CALL mpp_max( nstop )
[682]	138
[1593]	139	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	140
	141	! !-----------------------!
	142	! !== time stepping ==!
	143	! !-----------------------!
[900]	144	istp = nit000
[2236]	145	#if defined key_c1d
[389]	146	DO WHILE ( istp <= nitend .AND. nstop == 0 )
[900]	147	CALL stp_c1d( istp )
[389]	148	istp = istp + 1
	149	END DO
[2236]	150	#else
	151	IF( lk_asminc ) THEN
	152	IF( ln_bkgwri ) CALL asm_bkg_wri( nit000 - 1 ) ! Output background fields
	153	IF( ln_trjwri ) CALL asm_trj_wri( nit000 - 1 ) ! Output trajectory fields
	154	IF( ln_asmdin ) THEN ! Direct initialization
	155	IF( ln_trainc ) CALL tra_asm_inc( nit000 - 1 ) ! Tracers
	156	IF( ln_dyninc ) THEN
	157	CALL dyn_asm_inc( nit000 - 1 ) ! Dynamics
	158	IF ( ln_asmdin ) CALL ssh_wzv ( nit000 - 1 ) ! update vertical velocity
	159	ENDIF
	160	IF( ln_sshinc ) CALL ssh_asm_inc( nit000 - 1 ) ! SSH
	161	ENDIF
	162	ENDIF
	163
[389]	164	DO WHILE ( istp <= nitend .AND. nstop == 0 )
[392]	165	#if defined key_agrif
[1593]	166	CALL Agrif_Step( stp ) ! AGRIF: time stepping
[389]	167	#else
[1593]	168	CALL stp( istp ) ! standard time stepping
[389]	169	#endif
	170	istp = istp + 1
[900]	171	IF( lk_mpp ) CALL mpp_max( nstop )
[389]	172	END DO
[2236]	173	#endif
	174
[3609]	175	IF( lk_diaobs ) CALL dia_obs_wri
	176	!
	177	IF( ln_icebergs ) CALL icb_end( nitend )
[1593]	178
	179	! !------------------------!
	180	! !== finalize the run ==!
	181	! !------------------------!
	182	IF(lwp) WRITE(numout,cform_aaa) ! Flag AAAAAAA
	183	!
	184	IF( nstop /= 0 .AND. lwp ) THEN ! error print
[682]	185	WRITE(numout,cform_err)
	186	WRITE(numout,*) nstop, ' error have been found'
[389]	187	ENDIF
[1593]	188	!
[3294]	189	#if defined key_agrif
	190	CALL Agrif_ParentGrid_To_ChildGrid()
	191	IF( lk_diaobs ) CALL dia_obs_wri
	192	IF( nn_timing == 1 ) CALL timing_finalize
	193	CALL Agrif_ChildGrid_To_ParentGrid()
	194	#endif
	195	IF( nn_timing == 1 ) CALL timing_finalize
	196	!
[2496]	197	CALL nemo_closefile
[532]	198	#if defined key_oasis3 \|\| defined key_oasis4
[1976]	199	CALL cpl_prism_finalize ! end coupling and mpp communications with OASIS
[532]	200	#else
[3701]	201	# if defined key_iomput
	202	IF( Agrif_Root() ) THEN
	203	CALL xios_finalize ! end mpp communications
	204	ENDIF
	205	# else
[1593]	206	IF( lk_mpp ) CALL mppstop ! end mpp communications
[3701]	207	# endif
[532]	208	#endif
[900]	209	!
[2496]	210	END SUBROUTINE nemo_gcm
[389]	211
	212
[2496]	213	SUBROUTINE nemo_init
[389]	214	!!----------------------------------------------------------------------
[2496]	215	!! * ROUTINE nemo_init *
[389]	216	!!
[2496]	217	!! ** Purpose : initialization of the NEMO GCM
[389]	218	!!----------------------------------------------------------------------
[2715]	219	INTEGER :: ji ! dummy loop indices
	220	INTEGER :: ilocal_comm ! local integer
	221	CHARACTER(len=80), DIMENSION(16) :: cltxt
[1593]	222	!!
[1601]	223	NAMELIST/namctl/ ln_ctl , nn_print, nn_ictls, nn_ictle, &
[3294]	224	& nn_isplt, nn_jsplt, nn_jctls, nn_jctle, &
	225	& nn_bench, nn_timing
[3]	226	!!----------------------------------------------------------------------
[1593]	227	!
[2496]	228	cltxt = ''
	229	!
[1593]	230	! ! open Namelist file
[1581]	231	CALL ctl_opn( numnam, 'namelist', 'OLD', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. )
[1593]	232	!
	233	READ( numnam, namctl ) ! Namelist namctl : Control prints & Benchmark
	234	!
	235	! !--------------------------------------------!
	236	! ! set communicator & select the local node !
	237	! !--------------------------------------------!
[1412]	238	#if defined key_iomput
[2200]	239	IF( Agrif_Root() ) THEN
[1412]	240	# if defined key_oasis3 \|\| defined key_oasis4
[3701]	241	CALL cpl_prism_init( ilocal_comm ) ! nemo local communicator given by oasis
	242	CALL xios_initialize( "oceanx",local_comm=ilocal_comm )
	243	# else
	244	CALL xios_initialize( "nemo",return_comm=ilocal_comm )
[1412]	245	# endif
[2200]	246	ENDIF
[2715]	247	narea = mynode( cltxt, numnam, nstop, ilocal_comm ) ! Nodes selection
[532]	248	#else
[1412]	249	# if defined key_oasis3 \|\| defined key_oasis4
[2236]	250	IF( Agrif_Root() ) THEN
[2715]	251	CALL cpl_prism_init( ilocal_comm ) ! nemo local communicator given by oasis
[2236]	252	ENDIF
[2715]	253	narea = mynode( cltxt, numnam, nstop, ilocal_comm ) ! Nodes selection (control print return in cltxt)
[1412]	254	# else
[2082]	255	ilocal_comm = 0
[2715]	256	narea = mynode( cltxt, numnam, nstop ) ! Nodes selection (control print return in cltxt)
[1412]	257	# endif
[532]	258	#endif
[2715]	259	narea = narea + 1 ! mynode return the rank of proc (0 --> jpnij -1 )
[3]	260
[2715]	261	lwp = (narea == 1) .OR. ln_ctl ! control of all listing output print
[1579]	262
[2715]	263	! If dimensions of processor grid weren't specified in the namelist file
	264	! then we calculate them here now that we have our communicator size
	265	IF( (jpni < 1) .OR. (jpnj < 1) )THEN
	266	#if defined key_mpp_mpi
	267	IF( Agrif_Root() ) CALL nemo_partition(mppsize)
	268	#else
	269	jpni = 1
	270	jpnj = 1
	271	jpnij = jpni*jpnj
	272	#endif
	273	END IF
	274
	275	! Calculate domain dimensions given calculated jpni and jpnj
	276	! This used to be done in par_oce.F90 when they were parameters rather
	277	! than variables
	278	IF( Agrif_Root() ) THEN
[3294]	279	#if defined key_nemocice_decomp
[3625]	280	jpi = ( nx_global+2-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
	281	jpj = ( ny_global+2-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
[3294]	282	#else
[3625]	283	jpi = ( jpiglo-2jpreci + (jpni-1) ) / jpni + 2jpreci ! first dim.
[2715]	284	jpj = ( jpjglo-2jprecj + (jpnj-1) ) / jpnj + 2jprecj ! second dim.
[3294]	285	#endif
[2715]	286	jpk = jpkdta ! third dim
	287	jpim1 = jpi-1 ! inner domain indices
	288	jpjm1 = jpj-1 ! " "
	289	jpkm1 = jpk-1 ! " "
	290	jpij = jpi*jpj ! jpi x j
	291	ENDIF
	292
[1593]	293	IF(lwp) THEN ! open listing units
	294	!
[1581]	295	CALL ctl_opn( numout, 'ocean.output', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE., narea )
[1593]	296	!
[1579]	297	WRITE(numout,*)
[3294]	298	WRITE(numout,*) ' CNRS - NERC - Met OFFICE - MERCATOR-ocean - INGV - CMCC'
[1593]	299	WRITE(numout,*) ' NEMO team'
[1579]	300	WRITE(numout,*) ' Ocean General Circulation Model'
[3294]	301	WRITE(numout,*) ' version 3.4 (2011) '
[1579]	302	WRITE(numout,*)
	303	WRITE(numout,*)
[1593]	304	DO ji = 1, SIZE(cltxt)
	305	IF( TRIM(cltxt(ji)) /= '' ) WRITE(numout,*) cltxt(ji) ! control print of mynode
[1579]	306	END DO
[1593]	307	WRITE(numout,cform_aaa) ! Flag AAAAAAA
	308	!
[473]	309	ENDIF
[2715]	310
	311	! Now we know the dimensions of the grid and numout has been set we can
	312	! allocate arrays
	313	CALL nemo_alloc()
	314
[2496]	315	! !-------------------------------!
	316	! ! NEMO general initialization !
	317	! !-------------------------------!
[473]	318
[2496]	319	CALL nemo_ctl ! Control prints & Benchmark
[531]	320
[2082]	321	! ! Domain decomposition
[1593]	322	IF( jpni*jpnj == jpnij ) THEN ; CALL mpp_init ! standard cutting out
	323	ELSE ; CALL mpp_init2 ! eliminate land processors
[3]	324	ENDIF
[2382]	325	!
[3294]	326	IF( nn_timing == 1 ) CALL timing_init
	327	!
[2082]	328	! ! General initialization
[2027]	329	CALL phy_cst ! Physical constants
	330	CALL eos_init ! Equation of state
	331	CALL dom_cfg ! Domain configuration
	332	CALL dom_init ! Domain
[413]	333
[3294]	334	IF( ln_nnogather ) CALL nemo_northcomms ! Initialise the northfold neighbour lists (must be done after the masks are defined)
	335
[2027]	336	IF( ln_ctl ) CALL prt_ctl_init ! Print control
	337
	338	IF( lk_obc ) CALL obc_init ! Open boundaries
[3651]	339
	340	CALL istate_init ! ocean initial state (Dynamics and tracers)
	341
	342	IF( lk_tide ) CALL tide_init( nit000 ) ! Initialisation of the tidal harmonics
	343
[3294]	344	IF( lk_bdy ) CALL bdy_init ! Open boundaries initialisation
	345	IF( lk_bdy ) CALL bdy_dta_init ! Open boundaries initialisation of external data arrays
[3651]	346	IF( lk_bdy ) CALL bdytide_init ! Open boundaries initialisation of tidal harmonic forcing
[2027]	347
[3294]	348	CALL dyn_nept_init ! simplified form of Neptune effect
	349
[3]	350	! ! Ocean physics
[2104]	351	CALL sbc_init ! Forcings : surface module
[2082]	352	! ! Vertical physics
	353	CALL zdf_init ! namelist read
	354	CALL zdf_bfr_init ! bottom friction
	355	IF( lk_zdfric ) CALL zdf_ric_init ! Richardson number dependent Kz
[2329]	356	IF( lk_zdftke ) CALL zdf_tke_init ! TKE closure scheme
	357	IF( lk_zdfgls ) CALL zdf_gls_init ! GLS closure scheme
	358	IF( lk_zdfkpp ) CALL zdf_kpp_init ! KPP closure scheme
[2082]	359	IF( lk_zdftmx ) CALL zdf_tmx_init ! tidal vertical mixing
[2027]	360	IF( lk_zdfddm .AND. .NOT. lk_zdfkpp ) &
[2082]	361	& CALL zdf_ddm_init ! double diffusive mixing
	362	! ! Lateral physics
	363	CALL ldf_tra_init ! Lateral ocean tracer physics
	364	CALL ldf_dyn_init ! Lateral ocean momentum physics
[2392]	365	IF( lk_ldfslp ) CALL ldf_slp_init ! slope of lateral mixing
[2082]	366
[2027]	367	! ! Active tracers
	368	CALL tra_qsr_init ! penetrative solar radiation qsr
[2325]	369	CALL tra_bbc_init ! bottom heat flux
[2027]	370	IF( lk_trabbl ) CALL tra_bbl_init ! advective (and/or diffusive) bottom boundary layer scheme
[3294]	371	IF( ln_tradmp ) CALL tra_dmp_init ! internal damping trends
[2027]	372	CALL tra_adv_init ! horizontal & vertical advection
	373	CALL tra_ldf_init ! lateral mixing
	374	CALL tra_zdf_init ! vertical mixing and after tracer fields
	375
	376	! ! Dynamics
	377	CALL dyn_adv_init ! advection (vector or flux form)
[2104]	378	CALL dyn_vor_init ! vorticity term including Coriolis
[2027]	379	CALL dyn_ldf_init ! lateral mixing
[2104]	380	CALL dyn_hpg_init ! horizontal gradient of Hydrostatic pressure
[2027]	381	CALL dyn_zdf_init ! vertical diffusion
	382	CALL dyn_spg_init ! surface pressure gradient
[2392]	383
	384	! ! Misc. options
	385	IF( nn_cla == 1 ) CALL cla_init ! Cross Land Advection
[3609]	386	CALL icb_init( rdt, nit000) ! initialise icebergs instance
[2392]	387
[1594]	388	#if defined key_top
[2027]	389	! ! Passive tracers
[2082]	390	CALL trc_init
[1594]	391	#endif
[2382]	392	! ! Diagnostics
[3294]	393	IF( lk_floats ) CALL flo_init ! drifting Floats
[2027]	394	CALL iom_init ! iom_put initialization
[2392]	395	IF( lk_diaar5 ) CALL dia_ar5_init ! ar5 diag
[2027]	396	CALL dia_ptr_init ! Poleward TRansports initialization
[3294]	397	IF( lk_diadct ) CALL dia_dct_init ! Sections tranports
[2148]	398	CALL dia_hsb_init ! heat content, salt content and volume budgets
[2027]	399	CALL trd_mod_init ! Mixed-layer/Vorticity/Integral constraints trends
[2392]	400	IF( lk_diaobs ) THEN ! Observation & model comparison
[2382]	401	CALL dia_obs_init ! Initialize observational data
	402	CALL dia_obs( nit000 - 1 ) ! Observation operator for restart
[2236]	403	ENDIF
[2382]	404	! ! Assimilation increments
[2392]	405	IF( lk_asminc ) CALL asm_inc_init ! Initialize assimilation increments
[2382]	406	IF(lwp) WRITE(numout,*) 'Euler time step switch is ', neuler
[1593]	407	!
[2496]	408	END SUBROUTINE nemo_init
[467]	409
	410
[2496]	411	SUBROUTINE nemo_ctl
[467]	412	!!----------------------------------------------------------------------
[2496]	413	!! * ROUTINE nemo_ctl *
[467]	414	!!
[2442]	415	!! ** Purpose : control print setting
[467]	416	!!
[2442]	417	!! ** Method : - print namctl information and check some consistencies
[467]	418	!!----------------------------------------------------------------------
[2442]	419	!
[2496]	420	IF(lwp) THEN ! control print
[531]	421	WRITE(numout,*)
[2496]	422	WRITE(numout,*) 'nemo_ctl: Control prints & Benchmark'
[531]	423	WRITE(numout,*) '~~~~~~~ '
[1593]	424	WRITE(numout,*) ' Namelist namctl'
[1601]	425	WRITE(numout,*) ' run control (for debugging) ln_ctl = ', ln_ctl
	426	WRITE(numout,*) ' level of print nn_print = ', nn_print
	427	WRITE(numout,*) ' Start i indice for SUM control nn_ictls = ', nn_ictls
	428	WRITE(numout,*) ' End i indice for SUM control nn_ictle = ', nn_ictle
	429	WRITE(numout,*) ' Start j indice for SUM control nn_jctls = ', nn_jctls
	430	WRITE(numout,*) ' End j indice for SUM control nn_jctle = ', nn_jctle
	431	WRITE(numout,*) ' number of proc. following i nn_isplt = ', nn_isplt
	432	WRITE(numout,*) ' number of proc. following j nn_jsplt = ', nn_jsplt
	433	WRITE(numout,*) ' benchmark parameter (0/1) nn_bench = ', nn_bench
[3610]	434	WRITE(numout,*) ' timing activated (0/1) nn_timing = ', nn_timing
[531]	435	ENDIF
[2442]	436	!
[1601]	437	nprint = nn_print ! convert DOCTOR namelist names into OLD names
	438	nictls = nn_ictls
	439	nictle = nn_ictle
	440	njctls = nn_jctls
	441	njctle = nn_jctle
	442	isplt = nn_isplt
	443	jsplt = nn_jsplt
	444	nbench = nn_bench
[2442]	445	! ! Parameter control
[1593]	446	!
	447	IF( ln_ctl ) THEN ! sub-domain area indices for the control prints
[3294]	448	IF( lk_mpp .AND. jpnij > 1 ) THEN
[2496]	449	isplt = jpni ; jsplt = jpnj ; ijsplt = jpni*jpnj ! the domain is forced to the real split domain
[531]	450	ELSE
	451	IF( isplt == 1 .AND. jsplt == 1 ) THEN
[1593]	452	CALL ctl_warn( ' - isplt & jsplt are equal to 1', &
	453	& ' - the print control will be done over the whole domain' )
[531]	454	ENDIF
[1593]	455	ijsplt = isplt * jsplt ! total number of processors ijsplt
[531]	456	ENDIF
	457	IF(lwp) WRITE(numout,*)' - The total number of processors over which the'
	458	IF(lwp) WRITE(numout,*)' print control will be done is ijsplt : ', ijsplt
[1593]	459	!
	460	! ! indices used for the SUM control
	461	IF( nictls+nictle+njctls+njctle == 0 ) THEN ! print control done over the default area
	462	lsp_area = .FALSE.
	463	ELSE ! print control done over a specific area
[531]	464	lsp_area = .TRUE.
	465	IF( nictls < 1 .OR. nictls > jpiglo ) THEN
	466	CALL ctl_warn( ' - nictls must be 1<=nictls>=jpiglo, it is forced to 1' )
	467	nictls = 1
	468	ENDIF
	469	IF( nictle < 1 .OR. nictle > jpiglo ) THEN
	470	CALL ctl_warn( ' - nictle must be 1<=nictle>=jpiglo, it is forced to jpiglo' )
	471	nictle = jpiglo
	472	ENDIF
	473	IF( njctls < 1 .OR. njctls > jpjglo ) THEN
	474	CALL ctl_warn( ' - njctls must be 1<=njctls>=jpjglo, it is forced to 1' )
	475	njctls = 1
	476	ENDIF
	477	IF( njctle < 1 .OR. njctle > jpjglo ) THEN
	478	CALL ctl_warn( ' - njctle must be 1<=njctle>=jpjglo, it is forced to jpjglo' )
	479	njctle = jpjglo
	480	ENDIF
[1593]	481	ENDIF
	482	ENDIF
[2442]	483	!
	484	IF( nbench == 1 ) THEN ! Benchmark
[531]	485	SELECT CASE ( cp_cfg )
[1593]	486	CASE ( 'gyre' ) ; CALL ctl_warn( ' The Benchmark is activated ' )
	487	CASE DEFAULT ; CALL ctl_stop( ' The Benchmark is based on the GYRE configuration:', &
	488	& ' key_gyre must be used or set nbench = 0' )
[531]	489	END SELECT
	490	ENDIF
[1593]	491	!
[2496]	492	IF( lk_c1d .AND. .NOT.lk_iomput ) CALL ctl_stop( 'nemo_ctl: The 1D configuration must be used ', &
	493	& 'with the IOM Input/Output manager. ' , &
[2442]	494	& 'Compile with key_iomput enabled' )
[2409]	495	!
[2496]	496	END SUBROUTINE nemo_ctl
[467]	497
	498
[2496]	499	SUBROUTINE nemo_closefile
[467]	500	!!----------------------------------------------------------------------
[2496]	501	!! * ROUTINE nemo_closefile *
[467]	502	!!
	503	!! ** Purpose : Close the files
	504	!!----------------------------------------------------------------------
[1593]	505	!
	506	IF( lk_mpp ) CALL mppsync
	507	!
[1685]	508	CALL iom_close ! close all input/output files managed by iom_*
[1593]	509	!
[3294]	510	IF( numstp /= -1 ) CLOSE( numstp ) ! time-step file
	511	IF( numsol /= -1 ) CLOSE( numsol ) ! solver file
	512	IF( numnam /= -1 ) CLOSE( numnam ) ! oce namelist
	513	IF( numnam_ice /= -1 ) CLOSE( numnam_ice ) ! ice namelist
	514	IF( numevo_ice /= -1 ) CLOSE( numevo_ice ) ! ice variables (temp. evolution)
	515	IF( numout /= 6 ) CLOSE( numout ) ! standard model output file
	516	IF( numdct_vol /= -1 ) CLOSE( numdct_vol ) ! volume transports
	517	IF( numdct_heat /= -1 ) CLOSE( numdct_heat ) ! heat transports
	518	IF( numdct_salt /= -1 ) CLOSE( numdct_salt ) ! salt transports
	519
[1593]	520	!
[2442]	521	numout = 6 ! redefine numout in case it is used after this point...
	522	!
[2496]	523	END SUBROUTINE nemo_closefile
[467]	524
[2715]	525
	526	SUBROUTINE nemo_alloc
	527	!!----------------------------------------------------------------------
	528	!! * ROUTINE nemo_alloc *
	529	!!
	530	!! ** Purpose : Allocate all the dynamic arrays of the OPA modules
	531	!!
	532	!! ** Method :
	533	!!----------------------------------------------------------------------
	534	USE diawri , ONLY: dia_wri_alloc
	535	USE dom_oce , ONLY: dom_oce_alloc
	536	USE ldfdyn_oce, ONLY: ldfdyn_oce_alloc
	537	USE ldftra_oce, ONLY: ldftra_oce_alloc
	538	USE trc_oce , ONLY: trc_oce_alloc
[3680]	539	#if defined key_diadct
	540	USE diadct , ONLY: diadct_alloc
	541	#endif
[2715]	542	!
	543	INTEGER :: ierr
	544	!!----------------------------------------------------------------------
	545	!
	546	ierr = oce_alloc () ! ocean
	547	ierr = ierr + dia_wri_alloc ()
	548	ierr = ierr + dom_oce_alloc () ! ocean domain
	549	ierr = ierr + ldfdyn_oce_alloc() ! ocean lateral physics : dynamics
	550	ierr = ierr + ldftra_oce_alloc() ! ocean lateral physics : tracers
	551	ierr = ierr + zdf_oce_alloc () ! ocean vertical physics
	552	!
	553	ierr = ierr + lib_mpp_alloc (numout) ! mpp exchanges
	554	ierr = ierr + trc_oce_alloc () ! shared TRC / TRA arrays
	555	!
[3680]	556	#if defined key_diadct
	557	ierr = ierr + diadct_alloc () !
	558	#endif
	559	!
[2715]	560	IF( lk_mpp ) CALL mpp_sum( ierr )
	561	IF( ierr /= 0 ) CALL ctl_stop( 'STOP', 'nemo_alloc : unable to allocate standard ocean arrays' )
	562	!
	563	END SUBROUTINE nemo_alloc
	564
	565
	566	SUBROUTINE nemo_partition( num_pes )
	567	!!----------------------------------------------------------------------
	568	!! * ROUTINE nemo_partition *
	569	!!
	570	!! ** Purpose :
	571	!!
	572	!! ** Method :
	573	!!----------------------------------------------------------------------
	574	INTEGER, INTENT(in) :: num_pes ! The number of MPI processes we have
	575	!
	576	INTEGER, PARAMETER :: nfactmax = 20
	577	INTEGER :: nfact ! The no. of factors returned
	578	INTEGER :: ierr ! Error flag
	579	INTEGER :: ji
	580	INTEGER :: idiff, mindiff, imin ! For choosing pair of factors that are closest in value
	581	INTEGER, DIMENSION(nfactmax) :: ifact ! Array of factors
	582	!!----------------------------------------------------------------------
	583
	584	ierr = 0
	585
	586	CALL factorise( ifact, nfactmax, nfact, num_pes, ierr )
	587
	588	IF( nfact <= 1 ) THEN
	589	WRITE (numout, *) 'WARNING: factorisation of number of PEs failed'
	590	WRITE (numout, *) ' : using grid of ',num_pes,' x 1'
	591	jpnj = 1
	592	jpni = num_pes
	593	ELSE
	594	! Search through factors for the pair that are closest in value
	595	mindiff = 1000000
	596	imin = 1
	597	DO ji = 1, nfact-1, 2
	598	idiff = ABS( ifact(ji) - ifact(ji+1) )
	599	IF( idiff < mindiff ) THEN
	600	mindiff = idiff
	601	imin = ji
	602	ENDIF
	603	END DO
	604	jpnj = ifact(imin)
	605	jpni = ifact(imin + 1)
	606	ENDIF
	607	!
	608	jpnij = jpni*jpnj
	609	!
	610	END SUBROUTINE nemo_partition
	611
	612
	613	SUBROUTINE factorise( kfax, kmaxfax, knfax, kn, kerr )
	614	!!----------------------------------------------------------------------
	615	!! * ROUTINE factorise *
	616	!!
	617	!! ** Purpose : return the prime factors of n.
	618	!! knfax factors are returned in array kfax which is of
	619	!! maximum dimension kmaxfax.
	620	!! ** Method :
	621	!!----------------------------------------------------------------------
	622	INTEGER , INTENT(in ) :: kn, kmaxfax
	623	INTEGER , INTENT( out) :: kerr, knfax
	624	INTEGER, DIMENSION(kmaxfax), INTENT( out) :: kfax
	625	!
	626	INTEGER :: ifac, jl, inu
	627	INTEGER, PARAMETER :: ntest = 14
	628	INTEGER :: ilfax(ntest)
	629
	630	! lfax contains the set of allowed factors.
	631	data (ilfax(jl),jl=1,ntest) / 16384, 8192, 4096, 2048, 1024, 512, 256, &
	632	& 128, 64, 32, 16, 8, 4, 2 /
	633	!!----------------------------------------------------------------------
	634
	635	! Clear the error flag and initialise output vars
	636	kerr = 0
	637	kfax = 1
	638	knfax = 0
	639
	640	! Find the factors of n.
	641	IF( kn == 1 ) GOTO 20
	642
	643	! nu holds the unfactorised part of the number.
	644	! knfax holds the number of factors found.
	645	! l points to the allowed factor list.
	646	! ifac holds the current factor.
	647
	648	inu = kn
	649	knfax = 0
	650
	651	DO jl = ntest, 1, -1
	652	!
	653	ifac = ilfax(jl)
	654	IF( ifac > inu ) CYCLE
	655
	656	! Test whether the factor will divide.
	657
	658	IF( MOD(inu,ifac) == 0 ) THEN
	659	!
	660	knfax = knfax + 1 ! Add the factor to the list
	661	IF( knfax > kmaxfax ) THEN
	662	kerr = 6
	663	write (,) 'FACTOR: insufficient space in factor array ', knfax
	664	return
	665	ENDIF
	666	kfax(knfax) = ifac
	667	! Store the other factor that goes with this one
	668	knfax = knfax + 1
	669	kfax(knfax) = inu / ifac
	670	!WRITE (,) 'ARPDBG, factors ',knfax-1,' & ',knfax,' are ', kfax(knfax-1),' and ',kfax(knfax)
	671	ENDIF
	672	!
	673	END DO
	674
	675	20 CONTINUE ! Label 20 is the exit point from the factor search loop.
	676	!
	677	END SUBROUTINE factorise
	678
[3294]	679	#if defined key_mpp_mpi
	680	SUBROUTINE nemo_northcomms
	681	!!======================================================================
	682	!! * ROUTINE nemo_northcomms *
	683	!! nemo_northcomms : Setup for north fold exchanges with explicit peer to peer messaging
	684	!!=====================================================================
	685	!!----------------------------------------------------------------------
	686	!!
	687	!! ** Purpose : Initialization of the northern neighbours lists.
	688	!!----------------------------------------------------------------------
	689	!! 1.0 ! 2011-10 (A. C. Coward, NOCS & J. Donners, PRACE)
	690	!!----------------------------------------------------------------------
	691
	692	INTEGER :: ji, jj, jk, ij, jtyp ! dummy loop indices
	693	INTEGER :: ijpj ! number of rows involved in north-fold exchange
	694	INTEGER :: northcomms_alloc ! allocate return status
	695	REAL(wp), ALLOCATABLE, DIMENSION ( :,: ) :: znnbrs ! workspace
	696	LOGICAL, ALLOCATABLE, DIMENSION ( : ) :: lrankset ! workspace
	697
	698	IF(lwp) WRITE(numout,*)
	699	IF(lwp) WRITE(numout,*) 'nemo_northcomms : Initialization of the northern neighbours lists'
	700	IF(lwp) WRITE(numout,*) '~~~~~~~~~~'
	701
	702	!!----------------------------------------------------------------------
	703	ALLOCATE( znnbrs(jpi,jpj), stat = northcomms_alloc )
	704	ALLOCATE( lrankset(jpnij), stat = northcomms_alloc )
	705	IF( northcomms_alloc /= 0 ) THEN
	706	WRITE(numout,cform_war)
	707	WRITE(numout,*) 'northcomms_alloc : failed to allocate arrays'
	708	CALL ctl_stop( 'STOP', 'nemo_northcomms : unable to allocate temporary arrays' )
	709	ENDIF
	710	nsndto = 0
	711	isendto = -1
	712	ijpj = 4
	713	!
	714	! This routine has been called because ln_nnogather has been set true ( nammpp )
	715	! However, these first few exchanges have to use the mpi_allgather method to
	716	! establish the neighbour lists to use in subsequent peer to peer exchanges.
	717	! Consequently, set l_north_nogather to be false here and set it true only after
	718	! the lists have been established.
	719	!
	720	l_north_nogather = .FALSE.
	721	!
	722	! Exchange and store ranks on northern rows
	723
	724	DO jtyp = 1,4
	725
	726	lrankset = .FALSE.
	727	znnbrs = narea
	728	SELECT CASE (jtyp)
	729	CASE(1)
	730	CALL lbc_lnk( znnbrs, 'T', 1. ) ! Type 1: T,W-points
	731	CASE(2)
	732	CALL lbc_lnk( znnbrs, 'U', 1. ) ! Type 2: U-point
	733	CASE(3)
	734	CALL lbc_lnk( znnbrs, 'V', 1. ) ! Type 3: V-point
	735	CASE(4)
	736	CALL lbc_lnk( znnbrs, 'F', 1. ) ! Type 4: F-point
	737	END SELECT
	738
	739	IF ( njmppt(narea) .EQ. MAXVAL( njmppt ) ) THEN
	740	DO jj = nlcj-ijpj+1, nlcj
	741	ij = jj - nlcj + ijpj
	742	DO ji = 1,jpi
	743	IF ( INT(znnbrs(ji,jj)) .NE. 0 .AND. INT(znnbrs(ji,jj)) .NE. narea ) &
	744	& lrankset(INT(znnbrs(ji,jj))) = .true.
	745	END DO
	746	END DO
	747
	748	DO jj = 1,jpnij
	749	IF ( lrankset(jj) ) THEN
	750	nsndto(jtyp) = nsndto(jtyp) + 1
	751	IF ( nsndto(jtyp) .GT. jpmaxngh ) THEN
	752	CALL ctl_stop( ' Too many neighbours in nemo_northcomms ', &
	753	& ' jpmaxngh will need to be increased ')
	754	ENDIF
	755	isendto(nsndto(jtyp),jtyp) = jj-1 ! narea converted to MPI rank
	756	ENDIF
	757	END DO
	758	ENDIF
	759
	760	END DO
	761
	762	!
	763	! Type 5: I-point
	764	!
	765	! ICE point exchanges may involve some averaging. The neighbours list is
	766	! built up using two exchanges to ensure that the whole stencil is covered.
	767	! lrankset should not be reset between these 'J' and 'K' point exchanges
	768
	769	jtyp = 5
	770	lrankset = .FALSE.
	771	znnbrs = narea
	772	CALL lbc_lnk( znnbrs, 'J', 1. ) ! first ice U-V point
	773
	774	IF ( njmppt(narea) .EQ. MAXVAL( njmppt ) ) THEN
	775	DO jj = nlcj-ijpj+1, nlcj
	776	ij = jj - nlcj + ijpj
	777	DO ji = 1,jpi
	778	IF ( INT(znnbrs(ji,jj)) .NE. 0 .AND. INT(znnbrs(ji,jj)) .NE. narea ) &
	779	& lrankset(INT(znnbrs(ji,jj))) = .true.
	780	END DO
	781	END DO
	782	ENDIF
	783
	784	znnbrs = narea
	785	CALL lbc_lnk( znnbrs, 'K', 1. ) ! second ice U-V point
	786
	787	IF ( njmppt(narea) .EQ. MAXVAL( njmppt )) THEN
	788	DO jj = nlcj-ijpj+1, nlcj
	789	ij = jj - nlcj + ijpj
	790	DO ji = 1,jpi
	791	IF ( INT(znnbrs(ji,jj)) .NE. 0 .AND. INT(znnbrs(ji,jj)) .NE. narea ) &
	792	& lrankset( INT(znnbrs(ji,jj))) = .true.
	793	END DO
	794	END DO
	795
	796	DO jj = 1,jpnij
	797	IF ( lrankset(jj) ) THEN
	798	nsndto(jtyp) = nsndto(jtyp) + 1
	799	IF ( nsndto(jtyp) .GT. jpmaxngh ) THEN
	800	CALL ctl_stop( ' Too many neighbours in nemo_northcomms ', &
	801	& ' jpmaxngh will need to be increased ')
	802	ENDIF
	803	isendto(nsndto(jtyp),jtyp) = jj-1 ! narea converted to MPI rank
	804	ENDIF
	805	END DO
	806	!
	807	! For northern row areas, set l_north_nogather so that all subsequent exchanges
	808	! can use peer to peer communications at the north fold
	809	!
	810	l_north_nogather = .TRUE.
	811	!
	812	ENDIF
	813	DEALLOCATE( znnbrs )
	814	DEALLOCATE( lrankset )
	815
	816	END SUBROUTINE nemo_northcomms
	817	#else
	818	SUBROUTINE nemo_northcomms ! Dummy routine
	819	WRITE(,) 'nemo_northcomms: You should not have seen this print! error?'
	820	END SUBROUTINE nemo_northcomms
	821	#endif
[3]	822	!!======================================================================
[2496]	823	END MODULE nemogcm

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