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revision 1.1089 by jmc, Tue Apr 21 16:48:31 2009 UTC revision 1.1174 by jmc, Sat Oct 10 17:09:58 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 move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)  o tutorial_global_oce_optim:
8      now tested with 4 tiles (change data.grdchk and update output_adm.txt)
9      and add SIZE.h_mpi for MPI testing
10    o pkg autodiff
11     - fix bug in autodiff_restore
12     - make genmake2 remove comments and empty lines from ad_input_code.f in
13       order to reduce file size (new script file remove_comments_sed)
14    o allows to specify vertical profile of vertical viscosity (viscArNr)
15    o pkg autodiff
16      autodiff_ini_model_io: comment out writing of grid information to netcdf
17      files, because at this time the grid fields are a bunch of zeros
18      (this is analogous to ini_mnc_vars.F)
19    o pkg seaice/autodiff:
20     left-over from removing the 3-time-level fields:
21     - small rearrangement of common blocks (SEAICE.h)
22     - fix field declaration in order to get meaningful output in
23       adseaice.*.nc (adcommon.h)
24    o pkg obcs:
25     - go through NH code only if nonHydrostatic=T
26     - fix restart for Orlanski (Hydrostatic; still to fix NH+Orlanski restart)
27     - move call to OBCS_CALC before SEAICE_MODEL which needs seaice-obc fields
28       => Update output of experiment seaice_obcs
29     - useOBCSbalance: code is wrong with multi-tile / proc: add a stop.
30     - fix NH+Orlanski restart (add wvel OBC value in pickup file)
31     - fix restart for useOBCSprescribe + useEXF
32    o pkg ctrl
33     - make obcs as control parameter work also with useSingleCPUio
34     - replace a few sny and snx by Ny and Nx to be consistent with
35       ctrl_set_globfld_x/yz.F
36    o pkg seaice
37     - re-introduce global field frWtrAtm for the case of
38       ALLOW_MEAN_SFLUX_COST_CONTRIBUTION defined (SEAICE.h, seaice_growth.F)
39     - catch the case of an empty filename in seaice_cost_init_fixed.F
40    o pkg ecco:
41     - small bug fixes in the_main_loop
42      . fix order of monitor arguments
43      . change SEAICE_MULTILEVEL to SEAICE_MULTICATEGORY
44      . move include DYNVARS.h up outside the ALLOW_AUTODIFF_TAMC block so
45        that ALLOW_ECCO_FORWARD_RUN works with NONLIN_FRSURF
46     - replace cos(yc*deg2rad) by _rA in cost_mean_heat/saltflux.F, fix the
47       imbalance diagnostics for wmean_h/sflux = 0
48     - add actual values to f_obcsn/s/w/e in ecco_cost_final.F
49     - catch the case of empty filenames in ecco_cost_init_fixed.F
50       and ecco_readparms.F
51     - fix the logic of wsalt=0.and.wsalt2=0 to wsalt=0.or.wsalt2=0 (and theta)
52       to make this statement meaningfull in ecco_cost_weights.F
53    o pkg zonal_filt:
54      - change ZONAL_FILTER S/R interface (allows to filter 2-D fields)
55      - when using rStar, filter uVel*hFacW instead of uVel
56       (tested without topography: fix a Pb of growing instability with NLFS)
57    o pkg/aim/thsice:
58     -Add capacity to read a Q-Flux to be applied in slab-mixed layer thsice_slab_ocean.F
59      (works as SST restoring)
60    o pkg/thsice:
61     -add specific parameter for salt restoring in slab mixed-layer
62       (by default equal to the temperature restoring)
63    
64    checkpoint61v
65    o pkg/kpp:
66     -add double diffusive contributions as a hack, turned off by default
67      for now, and the code can be excluded with a CPP-flag
68      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
69     -add a verification experiments to "vermix" to test this code
70    o pkg/mom_common:
71      Move computation of length scales to mom_init_fixed.F (avoid recomputation
72      at each time-steps*levels).
73    o pkg/layers:
74      Created a new package for computing volume fluxes in temperature or
75      [not yet implemented] density layers, e.g. for calculating residual
76      overturning circulations.
77    o pkg/diagnostics:
78      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
79    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
80    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
81      To avoid mixing type (RS/RL) of input/output array argument,
82      replace single mixed-type array with a pair from each type (RS/RL).
83    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
84      is now implemented for all pkgs (previously only done for the main pickup)
85    
86    checkpoint61u
87    o pkg/obcs:
88      - change OB?eta from _RS to _RL and put them into a separate commen block
89      - add code to read OB?eta from a file via obcs_prescribe_read: the code
90        compiles and does not destroy any other experiments, the data is read
91        properly, but the code is not tested in actual applications
92    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
93      create a meaningful unit attribute for the time coordinate variable
94    o pkg/ebm: add plenty of missing "_d 0" ;
95       update results of experiment global_ocean_ebm (fwd + adjoint tests)
96      Notes: several pieces of code only works for (very) specific set up
97       (domain size, lat range, etc ...); should be documented & stop if one
98       of those assumptions is not meet.
99    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
100       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
101          and offline_exf_seaice (seaicetd + adjoint).
102    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
103       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
104        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
105    o few changes to pass when compiling with strick checking of arguments
106       across S/R (allow to find few bugs in S/R calls).
107    o pkg/seaice:
108     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
109       2d-fields, for slightly better performance
110    
111    checkpoint61t
112    o pkg/seaice:
113     - remove unused variables in seaice_evp
114     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
115    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
116       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
117       each processor opens a different file (a fix from Matt).
118    o cg2d:
119       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
120       this reduces number of EXCH calls by 2 when using exch2.
121       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
122       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
123    o pkg/thsice:
124       add code for Near Infra-Red albedo (from Jeff)
125       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
126    o ini_model_io:
127       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
128       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
129       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
130    
131    checkpoint61s
132    o pkg/exch2 (exch2_rxN_cube*):
133       remove last BARRIER (no need to synchronise after getting data from shared
134       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
135    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
136      and generate new output (for the 2 tests) using default rotationPeriod.
137    o pkg/exch2:
138      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
139        (was already the case with AUTODIFF_EXCH2 defined)
140      - add bj in exch2 arrays and S/R.
141      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
142        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
143    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
144      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
145        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
146      - verification experiment natl_box.longstep
147    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
148      allow different versions of ifort (8 or 9) and different versions
149       of mpi (mpich or mpich2) to be used with the same optfile.
150      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
151       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
152    o pkg/seaice:
153      fix previous modif (3-level field removed) for old-pickup reading
154    
155    checkpoint61r
156    o pkg/seaice:
157     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
158      1. introduce fields for time step (N-1)
159      2. do not use levels 2 and 3 anymore (but keep them)
160      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
161         includes changes to pkg/thsice/thsice_get_velocity.F,
162         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
163         pkg/obcs/obcs_apply_uvice.F.
164     - completely remove code for leap-frog time stepping for second order
165       advection
166     - adjusted adjoint accordingly;
167       gradient checks have improved by an order of magnitude!
168    
169    checkpoint61q
170    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
171     - the boundary conditions along open boundaries are unclear, because the
172       associated masks are set to zero and are thus treated as closed when
173       applying the slip-boundary conditions.
174     - move initialisation of grid variables from seaice_init_varia to _fixed
175    o adding doc/diags_changes.txt
176    o model/src:
177      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
178       to avoid "_diags" naming if no relation to pkg/diagnostics.
179      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
180       file and only call PLOT_FIELD_XYZ if debugMode=T.
181      remove few PLOT_FIELD_XY calls outside initialisation.
182      remove few unnecessary BARRIER.
183    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
184      of salt_plume package in Southern Ocean
185    o pkg/thsice:
186     - fix hOceMxL in overlap (needed for sea-ice advection);
187       update output of experiment global_ocean.cs32x15.icedyn.
188    o pkg/seaice:
189     - make the (placeholder-)tracer IceAge a little more meaningful
190      by avoiding ridging of age due to convergent ice flow
191     - add diagnostics for surface temperature, atmospheric and oceanic
192       heat flux, and atmospheric and oceanic ice growth
193    
194    checkpoint61p
195    o eesupp (global_max & global_sum):
196     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
197     - remove starting & endding barrier (no longer needed)
198    o pkg/mdsio, writelocal:
199       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
200       (remove the STOP): uses shared buffer IO to store data from all threads
201       and then let master-thread write nThreads tiles.
202    o pkg/mdsio (read/write field):
203     - tiled IO done in 1 piece (all levels at a time);
204     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
205     - multi-threaded: allow to read/write local (non-shared) array
206       (was already working with singleCpuIO ; now works also without);
207       => no longer needs barrier call after reading a file (added inside
208       mds_read/write field).
209     - move barrier calls outside gather/scatter_2d to mds_read/write_field
210    o pkg/obcs/exf
211      - exf_getffieldrec.F: add a few ". _d 0" and
212                            add code to catch the case fldperiod = 0.  
213      - obcs_precribe_read.F: change if statements so that they match
214                              the variable type (_RL)
215      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
216        exf_iprec) as part of namelist EXF_NML_01
217    o pkg/mdsio:
218      - read/write tiled (local) files: read/write 1-level tile chunk at a time
219        (instead of segment of length sNx); expected to speed up tiled IO.
220    o pkg/exch2:
221      - take buffer copy from/to array out of S/R exch2_send/recv into new
222        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
223        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
224      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
225      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
226        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
227        including Topology header file (and common blocks).
228      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
229        remove 2nd exch call in exch2_s3d_rx (no longer needed).
230      - document S/R arg. list (+ update some comments)
231    o pkg/seaice:
232      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
233        temperature and humidity over sea ice based on climatological values.
234      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
235        of LSR (this change is expected to change the results slightly because now
236        it uses slightly difference moduli from the second last LSR solution, but
237        that is more consistent with the stress computations; this part of the code
238        is not tested in the verification experiments)
239      - fix diagnostics for flux of ice in case of B-grid
240      - turn strain rates eij and press into global fields within global
241        common block in SEAICE.h for more straighforward diagnostics
242      - fix diagnostics for principal stress components, press, zeta, eta
243        to give something meaning full
244    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
245      new output (all 4 tests) using default rotationPeriod.
246    o pkg KPP:
247      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
248      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
249        and normal grid from 1 to Nr)
250    o Fix computations of L4rdt in mom_calc_visc.F
251    o eesupp:
252      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
253      should be called before a "stop" if we know that all process are going
254      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
255    
256    checkpoint61o
257    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
258    o model/src/ini_curvilinear_grid.F:
259       compute angleSin/CosC when they are not read from a file
260    o pkg/seaice:
261       add pseudo time stepping for LSOR
262    o pkg/exch2:
263       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
264    o pkg/seaice:
265       Adding separate sea ice albedo, drag coefficients, and HO in Southern
266       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
267    o SingleCpuIO:
268       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
269    o pkg/seaice:
270       put exchanged variable in (local) common block for MPI+Multi-Threads
271       to work (necessary with exch1, and for now with exch2 too).
272    o verification: to get more experiments tested with mpi, mth and mpi+mth,
273      change tiling of:
274       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
275       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
276      update output of exp:
277       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
278       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
279      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
280                       (note: output.txt generated on faulks using only 1 tile)
281    o eesupp & mdsio (SingleCpuIO):
282     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
283       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
284       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
285     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
286     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
287       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
288    o pkg/exch2:
289     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
290       read parameter file "data.exch2" if it exists; otherwise try default regular
291       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
292     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
293       with new code (not to be used, just as a backup solution).
294     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
295       in utils/exch2/input.
296    
297    checkpoint61n
298    o eesupp & mdsio (SingleCpuIO):
299      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
300        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
301        receive real*4 array (instead of real*8) to read/write 32.bit files.
302        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
303         and remove new mapping S/R)
304    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
305      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
306        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
307        when using exch2. Add S/R to map global io-buffer to global model array.
308      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
309    
310    checkpoint61m
311    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
312      and add 3 other S/R for other types (R4,R8,RS).
313      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
314    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
315     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
316     - reduce number of macro definitions (keep only those which are used);
317       can always call directly the corrresponding S/R if needed.
318     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
319       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
320     Fixed wrong type of arg in:
321       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
322       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
323     To fix: global_sum of var in common block is wrong (multi-threaded) in:
324       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
325     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
326    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
327      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
328    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
329    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
330      edges are closed (zero depth); might happen with "blank tiles";
331      for now, disabled if using OBCS.
332    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
333      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
334    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
335    to reduce length of 1.D array print in STDOUT.    to reduce length of 1.D array print in STDOUT.
336  o adjustment.cs-32x32x1: changed to oceanic test with 1 continent  o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
337    + use 48 tiles (16x8): this will allow to test "blank tiles".    + use 48 tiles (16x8): this will allow to test "blank tiles".
# Line 37  o pkg/fizhi: Line 364  o pkg/fizhi:
364    (e.g., datein=dates(n) is overwritten by timein=times(n) since both    (e.g., datein=dates(n) is overwritten by timein=times(n) since both
365     datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"     datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
366     address) and produces error.     address) and produces error.
367    o tools/gemake2: (March 27-29 2009)
368      with option "-mpi": link *_mpi files from "MODS" dir (this is what
369      testreport does).
370  o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output  o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
371  o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:  o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
372     update lab_sea.lsr & lab_sea.salt_plume results     update lab_sea.lsr & lab_sea.salt_plume results

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