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revision 1.1091 by jmc, Sun Apr 26 02:56:36 2009 UTC revision 1.1181 by mlosch, Wed Oct 21 13:54:55 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 adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi  o autodiff: fix seaice fields in g_common.h (left over from 3 to 1 level
8      transition in checkpoint61r)
9    
10    checkpoint61x
11    o adjoint: adding two new verification experiments
12      * tutorial_global_biogeo: an online dic sensitivity experiment
13        (work with G. Forget)
14      * tutorial_dic_adjoffline: an offline dic sensitivity experiment
15        (an update of the Dutkiewicz et al., 2006 paper)
16      Both use the same CO2FLUX cost function, but different controls
17      Gradient checks look good, but some recomp. could still be traightened out
18      Should add xx_dic control variable to test at some point
19    o model/src:
20      add run-time parameters to check and/or mask initial Temp & Salt
21    o pkg/ptracers:
22      apply zonal filter (if used) to all passive tracers
23    
24    checkpoint61w
25    o adjoint:
26      * update and finish work on adjoint of dic package (G. Forget)
27      * start adjoint of offline package
28      * bug fix for cube-sphere TLM code (active_file_g.F)
29    o tutorial_global_oce_optim:
30      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
31      and add SIZE.h_mpi for MPI testing
32    o pkg autodiff
33     - fix bug in autodiff_restore
34     - make genmake2 remove comments and empty lines from ad_input_code.f in
35       order to reduce file size (new script file remove_comments_sed)
36    o allows to specify vertical profile of vertical viscosity (viscArNr)
37    o pkg autodiff
38      autodiff_ini_model_io: comment out writing of grid information to netcdf
39      files, because at this time the grid fields are a bunch of zeros
40      (this is analogous to ini_mnc_vars.F)
41    o pkg seaice/autodiff:
42     left-over from removing the 3-time-level fields:
43     - small rearrangement of common blocks (SEAICE.h)
44     - fix field declaration in order to get meaningful output in
45       adseaice.*.nc (adcommon.h)
46    o pkg obcs:
47     - go through NH code only if nonHydrostatic=T
48     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
49     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
50       => Update output of experiment seaice_obcs
51     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
52     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
53     - fix restart for useOBCSprescribe + useEXF
54    o pkg ctrl
55     - make obcs as control parameter work also with useSingleCPUio
56     - replace a few sny and snx by Ny and Nx to be consistent with
57       ctrl_set_globfld_x/yz.F
58    o pkg seaice
59     - re-introduce global field frWtrAtm for the case of
60       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
61     - catch the case of an empty filename in seaice_cost_init_fixed.F
62    o pkg ecco:
63     - small bug fixes in the_main_loop
64      . fix order of monitor arguments
65      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
66      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
67        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
68     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
69       imbalance diagnostics for wmean_h/sflux = 0
70     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
71     - catch the case of empty filenames in ecco_cost_init_fixed.F
72       and ecco_readparms.F
73     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
74       to make this statement meaningfull in ecco_cost_weights.F
75    o pkg zonal_filt:
76      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
77      - when using rStar, filter uVel*hFacW instead of uVel
78       (tested without topography: fix a Pb of growing instability with NLFS)
79    o pkg/aim/thsice:
80     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
81      (works as SST restoring)
82    o pkg/thsice:
83     -add specific parameter for salt restoring in slab mixed-layer
84       (by default equal to the temperature restoring)
85    
86    checkpoint61v
87    o pkg/kpp:
88     -add double diffusive contributions as a hack, turned off by default
89      for now, and the code can be excluded with a CPP-flag
90      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
91     -add a verification experiments to "vermix" to test this code
92    o pkg/mom_common:
93      Move computation of length scales to mom_init_fixed.F (avoid recomputation
94      at each time-steps*levels).
95    o pkg/layers:
96      Created a new package for computing volume fluxes in temperature or
97      [not yet implemented] density layers, e.g. for calculating residual
98      overturning circulations.
99    o pkg/diagnostics:
100      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
101    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
102    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
103      To avoid mixing type (RS/RL) of input/output array argument,
104      replace single mixed-type array with a pair from each type (RS/RL).
105    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
106      is now implemented for all pkgs (previously only done for the main pickup)
107    
108    checkpoint61u
109    o pkg/obcs:
110      - change OB?eta from _RS to _RL and put them into a separate commen block
111      - add code to read OB?eta from a file via obcs_prescribe_read: the code
112        compiles and does not destroy any other experiments, the data is read
113        properly, but the code is not tested in actual applications
114    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
115      create a meaningful unit attribute for the time coordinate variable
116    o pkg/ebm: add plenty of missing "_d 0" ;
117       update results of experiment global_ocean_ebm (fwd + adjoint tests)
118      Notes: several pieces of code only works for (very) specific set up
119       (domain size, lat range, etc ...); should be documented & stop if one
120       of those assumptions is not meet.
121    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
122       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
123          and offline_exf_seaice (seaicetd + adjoint).
124    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
125       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
126        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
127    o few changes to pass when compiling with strick checking of arguments
128       across S/R (allow to find few bugs in S/R calls).
129    o pkg/seaice:
130     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
131       2d-fields, for slightly better performance
132    
133    checkpoint61t
134    o pkg/seaice:
135     - remove unused variables in seaice_evp
136     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
137    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
138       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
139       each processor opens a different file (a fix from Matt).
140    o cg2d:
141       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
142       this reduces number of EXCH calls by 2 when using exch2.
143       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
144       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
145    o pkg/thsice:
146       add code for Near Infra-Red albedo (from Jeff)
147       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
148    o ini_model_io:
149       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
150       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
151       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
152    
153    checkpoint61s
154    o pkg/exch2 (exch2_rxN_cube*):
155       remove last BARRIER (no need to synchronise after getting data from shared
156       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
157    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
158      and generate new output (for the 2 tests) using default rotationPeriod.
159    o pkg/exch2:
160      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
161        (was already the case with AUTODIFF_EXCH2 defined)
162      - add bj in exch2 arrays and S/R.
163      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
164        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
165    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
166      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
167        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
168      - verification experiment natl_box.longstep
169    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
170      allow different versions of ifort (8 or 9) and different versions
171       of mpi (mpich or mpich2) to be used with the same optfile.
172      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
173       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
174    o pkg/seaice:
175      fix previous modif (3-level field removed) for old-pickup reading
176    
177    checkpoint61r
178    o pkg/seaice:
179     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
180      1. introduce fields for time step (N-1)
181      2. do not use levels 2 and 3 anymore (but keep them)
182      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
183         includes changes to pkg/thsice/thsice_get_velocity.F,
184         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
185         pkg/obcs/obcs_apply_uvice.F.
186     - completely remove code for leap-frog time stepping for second order
187       advection
188     - adjusted adjoint accordingly;
189       gradient checks have improved by an order of magnitude!
190    
191    checkpoint61q
192    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
193     - the boundary conditions along open boundaries are unclear, because the
194       associated masks are set to zero and are thus treated as closed when
195       applying the slip-boundary conditions.
196     - move initialisation of grid variables from seaice_init_varia to _fixed
197    o adding doc/diags_changes.txt
198    o model/src:
199      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
200       to avoid "_diags" naming if no relation to pkg/diagnostics.
201      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
202       file and only call PLOT_FIELD_XYZ if debugMode=T.
203      remove few PLOT_FIELD_XY calls outside initialisation.
204      remove few unnecessary BARRIER.
205    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
206      of salt_plume package in Southern Ocean
207    o pkg/thsice:
208     - fix hOceMxL in overlap (needed for sea-ice advection);
209       update output of experiment global_ocean.cs32x15.icedyn.
210    o pkg/seaice:
211     - make the (placeholder-)tracer IceAge a little more meaningful
212      by avoiding ridging of age due to convergent ice flow
213     - add diagnostics for surface temperature, atmospheric and oceanic
214       heat flux, and atmospheric and oceanic ice growth
215    
216    checkpoint61p
217    o eesupp (global_max & global_sum):
218     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
219     - remove starting & endding barrier (no longer needed)
220    o pkg/mdsio, writelocal:
221       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
222       (remove the STOP): uses shared buffer IO to store data from all threads
223       and then let master-thread write nThreads tiles.
224    o pkg/mdsio (read/write field):
225     - tiled IO done in 1 piece (all levels at a time);
226     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
227     - multi-threaded: allow to read/write local (non-shared) array
228       (was already working with singleCpuIO ; now works also without);
229       => no longer needs barrier call after reading a file (added inside
230       mds_read/write field).
231     - move barrier calls outside gather/scatter_2d to mds_read/write_field
232    o pkg/obcs/exf
233      - exf_getffieldrec.F: add a few ". _d 0" and
234                            add code to catch the case fldperiod = 0.  
235      - obcs_precribe_read.F: change if statements so that they match
236                              the variable type (_RL)
237      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
238        exf_iprec) as part of namelist EXF_NML_01
239    o pkg/mdsio:
240      - read/write tiled (local) files: read/write 1-level tile chunk at a time
241        (instead of segment of length sNx); expected to speed up tiled IO.
242    o pkg/exch2:
243      - take buffer copy from/to array out of S/R exch2_send/recv into new
244        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
245        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
246      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
247      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
248        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
249        including Topology header file (and common blocks).
250      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
251        remove 2nd exch call in exch2_s3d_rx (no longer needed).
252      - document S/R arg. list (+ update some comments)
253    o pkg/seaice:
254      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
255        temperature and humidity over sea ice based on climatological values.
256      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
257        of LSR (this change is expected to change the results slightly because now
258        it uses slightly difference moduli from the second last LSR solution, but
259        that is more consistent with the stress computations; this part of the code
260        is not tested in the verification experiments)
261      - fix diagnostics for flux of ice in case of B-grid
262      - turn strain rates eij and press into global fields within global
263        common block in SEAICE.h for more straighforward diagnostics
264      - fix diagnostics for principal stress components, press, zeta, eta
265        to give something meaning full
266    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
267      new output (all 4 tests) using default rotationPeriod.
268    o pkg KPP:
269      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
270      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
271        and normal grid from 1 to Nr)
272    o Fix computations of L4rdt in mom_calc_visc.F
273    o eesupp:
274      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
275      should be called before a "stop" if we know that all process are going
276      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
277    
278    checkpoint61o
279    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
280    o model/src/ini_curvilinear_grid.F:
281       compute angleSin/CosC when they are not read from a file
282    o pkg/seaice:
283       add pseudo time stepping for LSOR
284    o pkg/exch2:
285       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
286    o pkg/seaice:
287       Adding separate sea ice albedo, drag coefficients, and HO in Southern
288       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
289    o SingleCpuIO:
290       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
291    o pkg/seaice:
292       put exchanged variable in (local) common block for MPI+Multi-Threads
293       to work (necessary with exch1, and for now with exch2 too).
294    o verification: to get more experiments tested with mpi, mth and mpi+mth,
295      change tiling of:
296       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
297       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
298      update output of exp:
299       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
300       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
301      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
302                       (note: output.txt generated on faulks using only 1 tile)
303    o eesupp & mdsio (SingleCpuIO):
304     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
305       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
306       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
307     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
308     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
309       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
310    o pkg/exch2:
311     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
312       read parameter file "data.exch2" if it exists; otherwise try default regular
313       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
314     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
315       with new code (not to be used, just as a backup solution).
316     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
317       in utils/exch2/input.
318    
319    checkpoint61n
320    o eesupp & mdsio (SingleCpuIO):
321      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
322        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
323        receive real*4 array (instead of real*8) to read/write 32.bit files.
324        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
325         and remove new mapping S/R)
326    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
327      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
328        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
329        when using exch2. Add S/R to map global io-buffer to global model array.
330      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
331    
332    checkpoint61m
333    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
334      and add 3 other S/R for other types (R4,R8,RS).
335      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
336    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
337     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
338     - reduce number of macro definitions (keep only those which are used);
339       can always call directly the corrresponding S/R if needed.
340     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
341       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
342     Fixed wrong type of arg in:
343       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
344       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
345     To fix: global_sum of var in common block is wrong (multi-threaded) in:
346       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
347     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
348    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
349      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
350  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
351  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
352    edges are closed (zero depth); might happen with "blank tiles";    edges are closed (zero depth); might happen with "blank tiles";
353    for now, disable if using OBCS.    for now, disabled if using OBCS.
354  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":
355    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.
356  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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