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revision 1.1447 by heimbach, Wed Jun 1 22:41:34 2011 UTC revision 1.1503 by jmc, Thu Sep 22 20:12:10 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice (LSR):
8      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
9      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
10        * identical results with non-CS topology (but save up to half of EXCH calls)
11        * no much changes in cs-32 verification tests since no ice at face edges
12         (differences due to convergence criteria, since nb of iterations changed)
13        * expect some differences on lat-lon-cap grid.
14        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
15    o pkg/exch2:
16      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
17        many tiles); until alternative coding is added, just add a stop.
18    o pkg/kpp:
19      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
20        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
21    o optfiles:
22      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
23        into corresponding standard one, which now support different build:
24        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
25      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
26    o pkg/obcs (seaice):
27      - add missing EXCH for uIce,vIce after applying OBCS;
28      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
29        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
30        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
31      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
32      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
33        and eedata.mth for MPI and mutlti-threaded testing.
34    o pkg/flt:
35      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
36      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
37      - fix pickup and trajectories + profiles output with multi-threads;
38      - add parameter to select group of fields to write along trajectory and
39        profile (default unchanged);
40      - only call PORT_RAND* function when flt_noise <> 0;
41      - add multi-threaded test for verification exp. flt_example.
42    o eesupp/src:
43      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
44      - USE_OMP_THREADING: check that number of threads (from eedata) matches
45        actual number (from env.var. setting).
46    o pkg/ebm:
47      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
48      - add multi-threaded test for verification exp. global_ocean_ebm
49    
50    checkpoint63b (2011/08/29)
51    o pkg/ebm:
52      - fix sign of runoff;
53      - update directly forcing fields (Qnet,EmPmR) to use standard
54        external_forcing_surf.F (remove ebm_forcing_surf.F);
55      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
56      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
57        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
58      - update global_ocean_ebm parameters file data and update output (fwd+ad).
59    o verification/matrix_example:
60      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
61        MPI and mutlti-threaded testing.
62    o pkg/matrix:
63      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
64      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
65      - fix for multi-threaded (remove DATA statement);
66      - use standard DIFFERENT_MULTIPLE function;
67      - add MATRIX_OPTIONS.h
68    o verification/matrix_example:
69       To allow to split the domain in several tiles, change the domain size
70        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
71        Western side) of land points.
72    o (*_)write_pickup:
73      - fix few bugs in mypackage_read/write_pickup.F
74      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
75        array of length 1 (was caught by compiler syntax-check).
76    o pkg/diagnostics (velocity potential solver):
77      - fix initialisation of main diagonal matrix (for overlap values)
78    o tools/build_options:
79      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
80        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
81      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
82        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
83        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
84        and use "-devel" testreport option for standard testing on baudelaire.
85    o pkg/grdchk:
86      - Assume that all gradient-check position are within the same tile
87        corresponding to global indices (iGloTile,jGloTile) and that
88        positions (i,j indices or nbeg) are local to this tile;
89      - set tile local-indices and proc. number according to tile global-indices;
90      - remove grdchkwhichproc from namelist (retired param);
91      - send adjoint gradient to all procs so that all procs print it to STDOUT;
92      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
93    o adding package bbl (Bottom Boundary Layer)
94      description in MITgcm/pkg/bbl/bbl_description.tex
95      example/test experiment in MITgcm_contrib/bbl
96    o adjoint verifications
97      - changed 5 experiments to multi-tiles
98        * global_ocean.90x40x15
99        * obcs_ctrl
100        * offline_exf_seaice
101        * tutorial_dic_adjoffline
102        * tutorial_tracer_adjsens
103        changed reference output for those that crossed tile boundaries
104        (changed choices of gradient check positions)
105      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
106      - temporary bug fix in grdchk_loc.F for obcs
107    o genmake2 & testreport
108      - add target "obj" (just for OBJFILES files) to Makefile;
109      - add option to specify FEXTRAFLAGS on command line.
110    o pkg/mypackage:
111      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
112    
113    checkpoint63a (2011/08/02)
114    o pkg/diagnostics (velocity potential):
115      - fix velocity-potential calculation when using OBCS: balance net inflow
116        at each level (new S/R OBCS_DIAG_BALANCE).
117      - fix some of the problems with OBCS in stream-function calculation.
118    o pkg/exf/exf_readparms.F
119      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
120        EXF_NML_OBCS) more consistent, so that you need not have these lists
121        in data.exf when they are not used.
122    o optim/optim_readdata.F:
123      - add some output about obcs variables that might help debugging
124      - add a check about nvarlength
125    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
126    o pkg/diagnostics (velocity potential):
127      - fix mask for OBCS (still problems in stream-function with OBCS);
128      - add specific parameter (default = main code CG2D params) for solver;
129      - in case of poor convergence, use solution corresponding to lowest residual.
130    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
131      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
132      and should be avoided where possible.
133    o model/src (rStar):
134      - include r* effect on reference-state (PhiRef) in totPhiHyd
135        (so that it's really the potential anomaly at the cell center);
136        affect solution only if z* with full pressure in EOS.
137      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
138        update output (because of z* in totPhiHyd and viscA4 changes);
139      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
140        @ constant r) until interpolation at constant r is implemented.
141    o pkg/diagnostics
142      - fix RCENTER diagnostics in case cell center is not at interface middle
143    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
144      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
145      that THETA and SALT are "conservative temperature" and "absolute
146      salinity"
147    o pkg/ctrl
148      - fix computation of endrec in s/r ctrl_init_rec
149      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
150    o pkg/seaice/seaice_growth.F
151      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
152        remove then obsolete STORE directives
153      - fix STORE directives for tice and tices, so that only the
154        appropriate part of the fields are stored (and not the entire
155        field); update global_ocean.cs32x15.seaice AD output.
156      - cosmetic changes: adjust CPP flags and indentation for better
157        legibilty
158    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
159      Chris Wilson)
160    o pkg/gmredi:
161       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
162       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
163    
164    checkpoint63  (2011/07/11)
165    o pkg/exch2:
166     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
167     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
168       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
169       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
170    o pkg/diagnostics:
171     - deal with pairs of post-processed diags which are computed together; in
172       particular, re-order list of diags within 1 file to save 2nd computation.
173     - add S/R to compute velocity stream-function (called after velocity-potential
174       calculation) from divergence free transport -> new diagnostics "PsiVEL".
175     - add parameter to select grid-point location where PsiVEL == 0.
176    o eesupp/src:
177       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
178       (specific S/R needed with exch2 topology - for now, just print an error msg)
179    o pkg/shelfice
180     - Implement friction velocity-dependent transfer coefficients following
181       Holland and Jenkins, JPO, 1999
182       Original code by M. Losch with small modifs.
183       Enable with CPP option SHI_ALLOW_GAMMAFRICT
184       and runtime flag SHELFICEuseGammaFrict
185    o verification lab_sea & global_ocean.cs32x15:
186     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
187       does not miss some dependencies (but is slower) and also works with many files
188       (default makedepend limitation for AD built).
189     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
190    o pkg/diagnostics:
191     - add run-time parameter "useMissingValue" (def=False) to fill land-point
192        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
193       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
194     - Extend the use of "missing_value" setting from data.diagnostics for the case
195       of counter-diagnostics (where fraction-weight is zero). This applies both to
196       MNC and MDS output files.
197    o pkg/seaice/seaice_growth.F:
198      - add 'a priori' cap of latent heat flux based on actual mass considerations
199        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
200        non-legacy seaice_solve4temp.
201      - add diagnostic of the residual sublimation freshwater flux (the freshwater
202        flux taken from the ocean if the total actual latent heat fluxes exceed
203        the maximum)
204      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
205       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
206      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
207       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
208      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
209      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
210    o verification 1D_ocean_ice_column:
211       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
212       update results
213    o pkg/diagnostics:
214     - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
215       which are not filled-up but computed from other diags ; In this case, the mate
216       diag points to the primary (filled-up) diag to used for post processing.
217     - Update Velocity-potential computation using post-processed diag framework.
218     ==> Change the ordering of fields and time-periods in MDS output file
219       when using periodic averaging: now writes one time record with the full set
220       of fields for this time period, then the next time reccord (it used to be
221       one field with the full set of time records then the next field).
222         Note: this is now similar to NetCDF (MNC) output file. <==
223    
224    checkpoint62z (2011/06/21)
225    o adjoint monitor:
226     - Add adjoint monitor output for packages exf, seaice
227       and update relevant testreport output
228    o pkg/seaice:
229     - re-order diags inits so that they appear in order in available_diagnostics.log
230     - added diags: hsnow thermo. rates of change, area preceeding ridiging process,
231       area/heff/hsnow preceeding thermodynamic growth/melt.
232     - modified diag: SIdA; output actual effect, as the description states.
233     - modified description: SIqneti, SIqneto, SIuheff, SIvheff, SIdAb*, HSNOW.
234     - retired redundant diags: SIyneg, SIfice, SIsnwice, SIthdgrh.
235       (SIyneg->SIdHbOCN; SIfice->SIdHbATC; SIsnwice->SIdHbFLO;
236        and SIthdgrh->SIdHbOCN+SIdHbATC+SIdHbATO)
237     - modified diags (2) : switch all SIdA*, SIdH*, SIdS* from delta to rates.
238     - added diagnostics for seaice generic tracers (SItr*).
239     - added SItrUnit and SItrNameLong run time param (for SItr* diags).
240     - in diag names, replaced 'PrTh' abbrev. of 'preceeding thermo' with 'PT'.
241     I. Fenty: 18-Jun-2011:
242     Minor changes to seaice package:
243     1) Retired old variables (A22, SEAICE_lhsublim, areaMax, areaMin, hiceMin) and
244        added some new ones (SEAICE_area_reg, SEAICE_hice_reg, SEAICE_area_floor)
245       - Differentiated "regularization variables" from "floor variables"
246        * areaMin became SEAICE_area_reg (old A22) and SEAICE_area_floor
247        * hiceMin became SEAICE_hice_reg (old hiceMin)
248          (with _reg meaning regularization variable)
249       - SEAICE_lhSublim becomes lhSublim, the sum of SEAICE_lhEvap and SEAICE_lhFusion
250        so as to ensure energy conservation when going between phases
251      - A22 was not used anywhere
252     2) Changed regularization procedure for heffActual and hsnowActual to ensure
253        well-boundedness and smooth adjoint in seaice_growth.F
254     3) Fixed a bug where seaice_solve4temp would not recognize ice-free grid cells
255        because the old regularization always set heffActual >= 0.05 cm
256     4) Changed the model so that the default behavior is to put a small (10^-5) "floor"
257        on AREA when HEFF > 0.
258      - went from requiring ALLOW_PRECLUDE_INFINITESIMAL_AREA to be defined to
259        requiring that DISABLE_AREA_FLOOR *not* be defined
260     Affected verifications:
261      - 1D_ocean_ice_column (output.txt output_adm.txt)
262      - global_ocean.cs32x15 (output.seaice.txt output_adm.seaice.txt)
263    o pkg/diagnostics:
264      - move MNC code from diagnostics_out.F into new diagnostics_mnc_out.F (2 S/R).
265      - rename S/R GETDIAG to DIAGNOSTICS_GET_DIAG and change type of 1rst argument
266        (was _RL, now integer) with option = 0 to retrieve all levels.
267      - add pieces of code to compute velocity potential at each level (new diagnostics
268        PhiVEL, works only when UVELMASS & VVELMASS are also turned on);
269        for now, using same params as CG2D (target-resisual, max Nb of iter ...).
270      - fix few issues with counter diagnostics in diagnostics_setdiag.F &
271        diagstats_setdiag.F (if diagnostic counter is itself a counter diag)
272        and in diagnostics_fract_fill.F (do not need a valid pointer for the
273        diagnostics counter-mate); check that definition of counter-diagnostic
274        includes a valid counter-mate (in diagnostics_set_levels.F).
275    o model/src (rStar):
276      - add rStar scaling factor in diags_phi_hyd.F (similar to calc_grad_phi_hyd.F);
277        affect solution only if z* with full pressure in EOS;
278        update output of test-exp global_ocean.90x40x15.
279    o pkg/seaice:
280      - introduce siEps=1e-5 parameter
281      - use areaMax in AREA update (part 4), consistent with ridging step (part 2.5).
282      - re-organize SEAICE_ADD_SUBLIMATION_TO_FWBUDGET code.
283      - introduce ALLOW_SITRACER and seaice_tracer_phys.F to handle generic seaice tracer.
284        For now it covers, and was tested for, ice salinity and age (attached to HEFF),
285        as well as ice cover age and ridging index (attached to AREA).
286        For now the run time parameters (in data.seaice/SEAICE_PARM03) are
287        SItrName (e.g. 'age') and SItrMate ('HEFF', which is the default, or 'AREA').
288        Up to SItrMaxNum=3 tracers can be used simultaneously.
289    o pkg/salt_plume:
290      -introduce SPsalFRAC run time parameter that sets the fraction of the
291       salt by-product of ice growth (SPsalFRAC*(1-SIsalFRAC)*salt typically)
292       that gets vertically redistributed (fluxed down) by pkg/salt_plume.
293    o model debug options:
294      - Switch reading of debugMode from S/R INI_PARMS (parameter file "data", stored
295        in PARAMS.h) to S/R EESET_PARMS (parameter file "eedata", stored in EEPARAMS.h).
296      - Refine debug-msg printing selection (3 new levels):
297        debugMode  : controls printing of debug messages (sequence of S/R calls).
298        debugLevel : controls printing of algorithm-relevant auxiliary/debug messages
299         debLevZero =  0 ; /* level of disabled aux. msg printing */
300         debLevA =  1 ; /* level of minimum  aux. msg printing */
301         debLevB =  2 ; /* level of low aux. print (report read-file opening)*/
302         debLevC =  3 ; /* level of moderate debug prt (most pkgs debug msg) */
303         debLevD =  4 ; /* level of enhanced debug prt (add DEBUG_STATS prt) */
304         debLevE =  5 ; /* level of extensive debug printing */
305        New debugLevel default: with default debugMode value (=F),
306          = 2 (debLevB) or = 1 (debLevA) in case ALLOW_AUTODIFF is defined.;
307          and if debugMode=T, default debugLevel = 4 (debLevD).
308        Relation with previous settings:
309         debLevB (=2) corresponds to former debLevA (=1)
310         debLevD (=4) corresponds to former debLevB (=2)
311        Note:
312         a) if debugLevel=0, skip WRITE_GRID call when nIter0 > 0 (same as before);
313         b) default debugLevel=1 is convenient in AD runs (avoid many file opening msgs);
314            to recover previous default, set debugLevel=2 (e.g. AD-test hs94.1x64x5)
315      - Add new parameter (printResidualFreq, read from PARM02 namelist) to print
316        detailed CG solvers convergence; off (=0) by default, except if debugLevel=5.
317    o pkg/obcs:
318      - change OBCSfixTopo default from True to False (should not change the results);
319        keep OBCSfixTopo=T in verification-exp. seaice_obcs.
320    o pkg/thsice:
321      - fix bug in thsice_calc_thickn.F (was introduced in version 1.18) in
322        2nd layer seaice sublimation (unlikely to happen)
323      - use Interior mask for OBCS in thsice_advection.F (similar to what is
324        done in gad_advection & seaice_advection).
325  o adjoint:  o adjoint:
326    bug fix spotted by Gael Forget:    bug fix spotted by Gael Forget:
327    seaice_advection and thsice_advection still had    seaice_advection and thsice_advection still had

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