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revision 1.1092 by jmc, Wed Apr 29 00:04:57 2009 UTC revision 1.1172 by mlosch, Fri Oct 9 11:15:45 2009 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o write_utils : change WRITE_1D_R8 to WRITE_1D_RL  o pkg autodiff
8    and add 3 other S/R for other types (R4,R8,RS).   - fix bug in autodiff_restore
9     - make genmake2 remove comments and empty lines from ad_input_code.f in
10       order to reduce file size (new script file remove_comments_sed)
11    o allows to specify vertical profile of vertical viscosity (viscArNr)
12    o pkg autodiff
13      autodiff_ini_model_io: comment out writing of grid information to netcdf
14      files, because at this time the grid fields are a bunch of zeros
15      (this is analogous to ini_mnc_vars.F)
16    o pkg seaice/autodiff:
17     left-over from removing the 3-time-level fields:
18     - small rearrangement of common blocks (SEAICE.h)
19     - fix field declaration in order to get meaningful output in
20       adseaice.*.nc (adcommon.h)
21    o pkg obcs:
22     - go through NH code only if nonHydrostatic=T
23     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
24     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obcields
25       => Update output of experiment seaice_obcs
26     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
27     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
28     - fix restart for useOBCSprescribe + useEXF
29    o pkg ctrl
30     - make obcs as control parameter work also with useSingleCPUio
31     - replace a few sny and snx by Ny and Nx to be consistent with
32       ctrl_set_globfld_x/yz.F
33    o pkg seaice
34     - re-introduce global field frWtrAtm for the case of
35       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
36     - catch the case of an empty filename in seaice_cost_init_fixed.F
37    o pkg ecco:
38     - small bug fixes in the_main_loop
39      . fix order of monitor arguments
40      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
41      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
42        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
43     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
44       imbalance diagnostics for wmean_h/sflux = 0
45     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
46     - catch the case of empty filenames in ecco_cost_init_fixed.F
47       and ecco_readparms.F
48     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
49       to make this statement meaningfull in ecco_cost_weights.F
50    o pkg zonal_filt:
51      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
52      - when using rStar, filter uVel*hFacW instead of uVel
53       (tested without topography: fix a Pb of growing instability with NLFS)
54    o pkg/aim/thsice:
55     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
56      (works as SST restoring)
57    o pkg/thsice:
58     -add specific parameter for salt restoring in slab mixed-layer
59       (by default equal to the temperature restoring)
60    
61    checkpoint61v
62    o pkg/kpp:
63     -add double diffusive contributions as a hack, turned off by default
64      for now, and the code can be excluded with a CPP-flag
65      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
66     -add a verification experiments to "vermix" to test this code
67    o pkg/mom_common:
68      Move computation of length scales to mom_init_fixed.F (avoid recomputation
69      at each time-steps*levels).
70    o pkg/layers:
71      Created a new package for computing volume fluxes in temperature or
72      [not yet implemented] density layers, e.g. for calculating residual
73      overturning circulations.
74    o pkg/diagnostics:
75      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
76    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
77    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
78      To avoid mixing type (RS/RL) of input/output array argument,
79      replace single mixed-type array with a pair from each type (RS/RL).
80    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
81      is now implemented for all pkgs (previously only done for the main pickup)
82    
83    checkpoint61u
84    o pkg/obcs:
85      - change OB?eta from _RS to _RL and put them into a separate commen block
86      - add code to read OB?eta from a file via obcs_prescribe_read: the code
87        compiles and does not destroy any other experiments, the data is read
88        properly, but the code is not tested in actual applications
89    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
90      create a meaningful unit attribute for the time coordinate variable
91    o pkg/ebm: add plenty of missing "_d 0" ;
92       update results of experiment global_ocean_ebm (fwd + adjoint tests)
93      Notes: several pieces of code only works for (very) specific set up
94       (domain size, lat range, etc ...); should be documented & stop if one
95       of those assumptions is not meet.
96    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
97       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
98          and offline_exf_seaice (seaicetd + adjoint).
99    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
100       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
101        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
102    o few changes to pass when compiling with strick checking of arguments
103       across S/R (allow to find few bugs in S/R calls).
104    o pkg/seaice:
105     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
106       2d-fields, for slightly better performance
107    
108    checkpoint61t
109    o pkg/seaice:
110     - remove unused variables in seaice_evp
111     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
112    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
113       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
114       each processor opens a different file (a fix from Matt).
115    o cg2d:
116       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
117       this reduces number of EXCH calls by 2 when using exch2.
118       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
119       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
120    o pkg/thsice:
121       add code for Near Infra-Red albedo (from Jeff)
122       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
123    o ini_model_io:
124       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
125       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
126       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
127    
128    checkpoint61s
129    o pkg/exch2 (exch2_rxN_cube*):
130       remove last BARRIER (no need to synchronise after getting data from shared
131       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
132    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
133      and generate new output (for the 2 tests) using default rotationPeriod.
134    o pkg/exch2:
135      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
136        (was already the case with AUTODIFF_EXCH2 defined)
137      - add bj in exch2 arrays and S/R.
138      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
139        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
140    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
141      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
142        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
143      - verification experiment natl_box.longstep
144    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
145      allow different versions of ifort (8 or 9) and different versions
146       of mpi (mpich or mpich2) to be used with the same optfile.
147      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
148       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
149    o pkg/seaice:
150      fix previous modif (3-level field removed) for old-pickup reading
151    
152    checkpoint61r
153    o pkg/seaice:
154     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
155      1. introduce fields for time step (N-1)
156      2. do not use levels 2 and 3 anymore (but keep them)
157      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
158         includes changes to pkg/thsice/thsice_get_velocity.F,
159         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
160         pkg/obcs/obcs_apply_uvice.F.
161     - completely remove code for leap-frog time stepping for second order
162       advection
163     - adjusted adjoint accordingly;
164       gradient checks have improved by an order of magnitude!
165    
166    checkpoint61q
167    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
168     - the boundary conditions along open boundaries are unclear, because the
169       associated masks are set to zero and are thus treated as closed when
170       applying the slip-boundary conditions.
171     - move initialisation of grid variables from seaice_init_varia to _fixed
172    o adding doc/diags_changes.txt
173    o model/src:
174      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
175       to avoid "_diags" naming if no relation to pkg/diagnostics.
176      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
177       file and only call PLOT_FIELD_XYZ if debugMode=T.
178      remove few PLOT_FIELD_XY calls outside initialisation.
179      remove few unnecessary BARRIER.
180    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
181      of salt_plume package in Southern Ocean
182    o pkg/thsice:
183     - fix hOceMxL in overlap (needed for sea-ice advection);
184       update output of experiment global_ocean.cs32x15.icedyn.
185    o pkg/seaice:
186     - make the (placeholder-)tracer IceAge a little more meaningful
187      by avoiding ridging of age due to convergent ice flow
188     - add diagnostics for surface temperature, atmospheric and oceanic
189       heat flux, and atmospheric and oceanic ice growth
190    
191    checkpoint61p
192    o eesupp (global_max & global_sum):
193     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
194     - remove starting & endding barrier (no longer needed)
195    o pkg/mdsio, writelocal:
196       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
197       (remove the STOP): uses shared buffer IO to store data from all threads
198       and then let master-thread write nThreads tiles.
199    o pkg/mdsio (read/write field):
200     - tiled IO done in 1 piece (all levels at a time);
201     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
202     - multi-threaded: allow to read/write local (non-shared) array
203       (was already working with singleCpuIO ; now works also without);
204       => no longer needs barrier call after reading a file (added inside
205       mds_read/write field).
206     - move barrier calls outside gather/scatter_2d to mds_read/write_field
207    o pkg/obcs/exf
208      - exf_getffieldrec.F: add a few ". _d 0" and
209                            add code to catch the case fldperiod = 0.  
210      - obcs_precribe_read.F: change if statements so that they match
211                              the variable type (_RL)
212      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
213        exf_iprec) as part of namelist EXF_NML_01
214    o pkg/mdsio:
215      - read/write tiled (local) files: read/write 1-level tile chunk at a time
216        (instead of segment of length sNx); expected to speed up tiled IO.
217    o pkg/exch2:
218      - take buffer copy from/to array out of S/R exch2_send/recv into new
219        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
220        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
221      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
222      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
223        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
224        including Topology header file (and common blocks).
225      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
226        remove 2nd exch call in exch2_s3d_rx (no longer needed).
227      - document S/R arg. list (+ update some comments)
228    o pkg/seaice:
229      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
230        temperature and humidity over sea ice based on climatological values.
231      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
232        of LSR (this change is expected to change the results slightly because now
233        it uses slightly difference moduli from the second last LSR solution, but
234        that is more consistent with the stress computations; this part of the code
235        is not tested in the verification experiments)
236      - fix diagnostics for flux of ice in case of B-grid
237      - turn strain rates eij and press into global fields within global
238        common block in SEAICE.h for more straighforward diagnostics
239      - fix diagnostics for principal stress components, press, zeta, eta
240        to give something meaning full
241    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
242      new output (all 4 tests) using default rotationPeriod.
243    o pkg KPP:
244      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
245      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
246        and normal grid from 1 to Nr)
247    o Fix computations of L4rdt in mom_calc_visc.F
248    o eesupp:
249      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
250      should be called before a "stop" if we know that all process are going
251      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
252    
253    checkpoint61o
254    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
255    o model/src/ini_curvilinear_grid.F:
256       compute angleSin/CosC when they are not read from a file
257    o pkg/seaice:
258       add pseudo time stepping for LSOR
259    o pkg/exch2:
260       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
261    o pkg/seaice:
262       Adding separate sea ice albedo, drag coefficients, and HO in Southern
263       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
264    o SingleCpuIO:
265       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
266    o pkg/seaice:
267       put exchanged variable in (local) common block for MPI+Multi-Threads
268       to work (necessary with exch1, and for now with exch2 too).
269    o verification: to get more experiments tested with mpi, mth and mpi+mth,
270      change tiling of:
271       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
272       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
273      update output of exp:
274       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
275       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
276      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
277                       (note: output.txt generated on faulks using only 1 tile)
278    o eesupp & mdsio (SingleCpuIO):
279     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
280       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
281       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
282     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
283     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
284       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
285    o pkg/exch2:
286     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
287       read parameter file "data.exch2" if it exists; otherwise try default regular
288       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
289     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
290       with new code (not to be used, just as a backup solution).
291     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
292       in utils/exch2/input.
293    
294    checkpoint61n
295    o eesupp & mdsio (SingleCpuIO):
296      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
297        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
298        receive real*4 array (instead of real*8) to read/write 32.bit files.
299        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
300         and remove new mapping S/R)
301    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
302      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
303        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
304        when using exch2. Add S/R to map global io-buffer to global model array.
305      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
306    
307    checkpoint61m
308    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
309      and add 3 other S/R for other types (R4,R8,RS).
310    Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.    Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
311  o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):  o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
312   - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;   - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
313   - reduce number of macro definitions (keep only those which are used);   - reduce number of macro definitions (keep only those which are used);
314     can always call directly the corrresponding S/R if needed.     can always call directly the corrresponding S/R if needed.
315   - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix   - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
316     _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.     _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
317   Fixed wrong type of arg in:   Fixed wrong type of arg in:
318     atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F     atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
319     ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F     ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
320   To fix: global_sum of var in common block is wrong (multi-threaded) in:   To fix: global_sum of var in common block is wrong (multi-threaded) in:
321     dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F     dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
322   To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)   To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
323  o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi  o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
324      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
325  o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error  o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
326  o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile  o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
327    edges are closed (zero depth); might happen with "blank tiles";    edges are closed (zero depth); might happen with "blank tiles";
328    for now, disable if using OBCS.    for now, disabled if using OBCS.
329  o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":  o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
330    link *_mpi files from "MODS" dir) to return to a strait-forward behavior.    link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
331  o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)  o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)

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