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revision 1.1093 by jmc, Wed Apr 29 18:10:27 2009 UTC revision 1.1173 by jmc, Fri Oct 9 21:08:38 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 tutorial_global_oce_optim:
8      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
9    o pkg autodiff
10     - fix bug in autodiff_restore
11     - make genmake2 remove comments and empty lines from ad_input_code.f in
12       order to reduce file size (new script file remove_comments_sed)
13    o allows to specify vertical profile of vertical viscosity (viscArNr)
14    o pkg autodiff
15      autodiff_ini_model_io: comment out writing of grid information to netcdf
16      files, because at this time the grid fields are a bunch of zeros
17      (this is analogous to ini_mnc_vars.F)
18    o pkg seaice/autodiff:
19     left-over from removing the 3-time-level fields:
20     - small rearrangement of common blocks (SEAICE.h)
21     - fix field declaration in order to get meaningful output in
22       adseaice.*.nc (adcommon.h)
23    o pkg obcs:
24     - go through NH code only if nonHydrostatic=T
25     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
26     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obcields
27       => Update output of experiment seaice_obcs
28     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
29     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
30     - fix restart for useOBCSprescribe + useEXF
31    o pkg ctrl
32     - make obcs as control parameter work also with useSingleCPUio
33     - replace a few sny and snx by Ny and Nx to be consistent with
34       ctrl_set_globfld_x/yz.F
35    o pkg seaice
36     - re-introduce global field frWtrAtm for the case of
37       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
38     - catch the case of an empty filename in seaice_cost_init_fixed.F
39    o pkg ecco:
40     - small bug fixes in the_main_loop
41      . fix order of monitor arguments
42      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
43      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
44        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
45     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
46       imbalance diagnostics for wmean_h/sflux = 0
47     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
48     - catch the case of empty filenames in ecco_cost_init_fixed.F
49       and ecco_readparms.F
50     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
51       to make this statement meaningfull in ecco_cost_weights.F
52    o pkg zonal_filt:
53      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
54      - when using rStar, filter uVel*hFacW instead of uVel
55       (tested without topography: fix a Pb of growing instability with NLFS)
56    o pkg/aim/thsice:
57     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
58      (works as SST restoring)
59    o pkg/thsice:
60     -add specific parameter for salt restoring in slab mixed-layer
61       (by default equal to the temperature restoring)
62    
63    checkpoint61v
64    o pkg/kpp:
65     -add double diffusive contributions as a hack, turned off by default
66      for now, and the code can be excluded with a CPP-flag
67      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
68     -add a verification experiments to "vermix" to test this code
69    o pkg/mom_common:
70      Move computation of length scales to mom_init_fixed.F (avoid recomputation
71      at each time-steps*levels).
72    o pkg/layers:
73      Created a new package for computing volume fluxes in temperature or
74      [not yet implemented] density layers, e.g. for calculating residual
75      overturning circulations.
76    o pkg/diagnostics:
77      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
78    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
79    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
80      To avoid mixing type (RS/RL) of input/output array argument,
81      replace single mixed-type array with a pair from each type (RS/RL).
82    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
83      is now implemented for all pkgs (previously only done for the main pickup)
84    
85    checkpoint61u
86    o pkg/obcs:
87      - change OB?eta from _RS to _RL and put them into a separate commen block
88      - add code to read OB?eta from a file via obcs_prescribe_read: the code
89        compiles and does not destroy any other experiments, the data is read
90        properly, but the code is not tested in actual applications
91    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
92      create a meaningful unit attribute for the time coordinate variable
93    o pkg/ebm: add plenty of missing "_d 0" ;
94       update results of experiment global_ocean_ebm (fwd + adjoint tests)
95      Notes: several pieces of code only works for (very) specific set up
96       (domain size, lat range, etc ...); should be documented & stop if one
97       of those assumptions is not meet.
98    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
99       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
100          and offline_exf_seaice (seaicetd + adjoint).
101    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
102       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
103        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
104    o few changes to pass when compiling with strick checking of arguments
105       across S/R (allow to find few bugs in S/R calls).
106    o pkg/seaice:
107     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
108       2d-fields, for slightly better performance
109    
110    checkpoint61t
111    o pkg/seaice:
112     - remove unused variables in seaice_evp
113     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
114    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
115       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
116       each processor opens a different file (a fix from Matt).
117    o cg2d:
118       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
119       this reduces number of EXCH calls by 2 when using exch2.
120       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
121       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
122    o pkg/thsice:
123       add code for Near Infra-Red albedo (from Jeff)
124       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
125    o ini_model_io:
126       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
127       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
128       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
129    
130    checkpoint61s
131    o pkg/exch2 (exch2_rxN_cube*):
132       remove last BARRIER (no need to synchronise after getting data from shared
133       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
134    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
135      and generate new output (for the 2 tests) using default rotationPeriod.
136    o pkg/exch2:
137      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
138        (was already the case with AUTODIFF_EXCH2 defined)
139      - add bj in exch2 arrays and S/R.
140      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
141        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
142    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
143      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
144        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
145      - verification experiment natl_box.longstep
146    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
147      allow different versions of ifort (8 or 9) and different versions
148       of mpi (mpich or mpich2) to be used with the same optfile.
149      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
150       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
151    o pkg/seaice:
152      fix previous modif (3-level field removed) for old-pickup reading
153    
154    checkpoint61r
155    o pkg/seaice:
156     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
157      1. introduce fields for time step (N-1)
158      2. do not use levels 2 and 3 anymore (but keep them)
159      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
160         includes changes to pkg/thsice/thsice_get_velocity.F,
161         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
162         pkg/obcs/obcs_apply_uvice.F.
163     - completely remove code for leap-frog time stepping for second order
164       advection
165     - adjusted adjoint accordingly;
166       gradient checks have improved by an order of magnitude!
167    
168    checkpoint61q
169    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
170     - the boundary conditions along open boundaries are unclear, because the
171       associated masks are set to zero and are thus treated as closed when
172       applying the slip-boundary conditions.
173     - move initialisation of grid variables from seaice_init_varia to _fixed
174    o adding doc/diags_changes.txt
175    o model/src:
176      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
177       to avoid "_diags" naming if no relation to pkg/diagnostics.
178      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
179       file and only call PLOT_FIELD_XYZ if debugMode=T.
180      remove few PLOT_FIELD_XY calls outside initialisation.
181      remove few unnecessary BARRIER.
182    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
183      of salt_plume package in Southern Ocean
184    o pkg/thsice:
185     - fix hOceMxL in overlap (needed for sea-ice advection);
186       update output of experiment global_ocean.cs32x15.icedyn.
187    o pkg/seaice:
188     - make the (placeholder-)tracer IceAge a little more meaningful
189      by avoiding ridging of age due to convergent ice flow
190     - add diagnostics for surface temperature, atmospheric and oceanic
191       heat flux, and atmospheric and oceanic ice growth
192    
193    checkpoint61p
194    o eesupp (global_max & global_sum):
195     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
196     - remove starting & endding barrier (no longer needed)
197    o pkg/mdsio, writelocal:
198       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
199       (remove the STOP): uses shared buffer IO to store data from all threads
200       and then let master-thread write nThreads tiles.
201    o pkg/mdsio (read/write field):
202     - tiled IO done in 1 piece (all levels at a time);
203     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
204     - multi-threaded: allow to read/write local (non-shared) array
205       (was already working with singleCpuIO ; now works also without);
206       => no longer needs barrier call after reading a file (added inside
207       mds_read/write field).
208     - move barrier calls outside gather/scatter_2d to mds_read/write_field
209    o pkg/obcs/exf
210      - exf_getffieldrec.F: add a few ". _d 0" and
211                            add code to catch the case fldperiod = 0.  
212      - obcs_precribe_read.F: change if statements so that they match
213                              the variable type (_RL)
214      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
215        exf_iprec) as part of namelist EXF_NML_01
216    o pkg/mdsio:
217      - read/write tiled (local) files: read/write 1-level tile chunk at a time
218        (instead of segment of length sNx); expected to speed up tiled IO.
219    o pkg/exch2:
220      - take buffer copy from/to array out of S/R exch2_send/recv into new
221        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
222        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
223      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
224      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
225        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
226        including Topology header file (and common blocks).
227      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
228        remove 2nd exch call in exch2_s3d_rx (no longer needed).
229      - document S/R arg. list (+ update some comments)
230    o pkg/seaice:
231      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
232        temperature and humidity over sea ice based on climatological values.
233      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
234        of LSR (this change is expected to change the results slightly because now
235        it uses slightly difference moduli from the second last LSR solution, but
236        that is more consistent with the stress computations; this part of the code
237        is not tested in the verification experiments)
238      - fix diagnostics for flux of ice in case of B-grid
239      - turn strain rates eij and press into global fields within global
240        common block in SEAICE.h for more straighforward diagnostics
241      - fix diagnostics for principal stress components, press, zeta, eta
242        to give something meaning full
243    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
244      new output (all 4 tests) using default rotationPeriod.
245    o pkg KPP:
246      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
247      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
248        and normal grid from 1 to Nr)
249    o Fix computations of L4rdt in mom_calc_visc.F
250    o eesupp:
251      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
252      should be called before a "stop" if we know that all process are going
253      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
254    
255    checkpoint61o
256    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
257    o model/src/ini_curvilinear_grid.F:
258       compute angleSin/CosC when they are not read from a file
259    o pkg/seaice:
260       add pseudo time stepping for LSOR
261    o pkg/exch2:
262       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
263    o pkg/seaice:
264       Adding separate sea ice albedo, drag coefficients, and HO in Southern
265       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
266    o SingleCpuIO:
267       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
268    o pkg/seaice:
269       put exchanged variable in (local) common block for MPI+Multi-Threads
270       to work (necessary with exch1, and for now with exch2 too).
271    o verification: to get more experiments tested with mpi, mth and mpi+mth,
272      change tiling of:
273       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
274       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
275      update output of exp:
276       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
277       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
278      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
279                       (note: output.txt generated on faulks using only 1 tile)
280    o eesupp & mdsio (SingleCpuIO):
281     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
282       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
283       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
284     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
285     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
286       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
287    o pkg/exch2:
288     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
289       read parameter file "data.exch2" if it exists; otherwise try default regular
290       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
291     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
292       with new code (not to be used, just as a backup solution).
293     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
294       in utils/exch2/input.
295    
296    checkpoint61n
297    o eesupp & mdsio (SingleCpuIO):
298      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
299        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
300        receive real*4 array (instead of real*8) to read/write 32.bit files.
301        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
302         and remove new mapping S/R)
303    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
304      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
305        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
306        when using exch2. Add S/R to map global io-buffer to global model array.
307      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
308    
309  checkpoint61m  checkpoint61m
310  o write_utils : change WRITE_1D_R8 to WRITE_1D_RL  o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
311    and add 3 other S/R for other types (R4,R8,RS).    and add 3 other S/R for other types (R4,R8,RS).
312    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.
313  o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):  o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
314   - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;   - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
315   - reduce number of macro definitions (keep only those which are used);   - reduce number of macro definitions (keep only those which are used);
316     can always call directly the corrresponding S/R if needed.     can always call directly the corrresponding S/R if needed.
317   - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix   - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
318     _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.     _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
319   Fixed wrong type of arg in:   Fixed wrong type of arg in:
320     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
321     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
322   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:
323     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
324   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)
325  o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi  o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
326      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
327  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
328  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
329    edges are closed (zero depth); might happen with "blank tiles";    edges are closed (zero depth); might happen with "blank tiles";
330    for now, disable if using OBCS.    for now, disabled if using OBCS.
331  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":
332    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.
333  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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