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revision 1.1664 by jmc, Mon Jun 4 21:05:46 2012 UTC revision 1.1719 by gforget, Tue Aug 21 14:28:07 2012 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/autodiff/ctrl/grdchk :
8      - attempt to sort out what works and what does not,
9        with regard to I/O, and to warn/stop accordingly.
10    o pkg/grdchk :
11      - attempt to fix grdchk in the case of useSingleCpuIO.
12      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
13       statements were moved from grdchk_main.F and into
14       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
15      - a global sum is applied to record numbers icvrec/layer
16       out of grdchk_loc so that they be passed to I/O routines.
17    o pkg/smooth :
18      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
19        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
20    o verification/testreport:
21      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
22      - can also use compressed (gzip) reference output file;
23      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
24        to be easier to collect by testreport.
25      - update existing TLM output (half out-of-date by more than 3 yrs).
26      - report NETCDF & LAPACK settings (from genmake2) in output dir.
27      - report run-time in each individual summary (previously only for AD test);
28        for TLM test, add also TAF version.
29      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
30    
31    checkpoint63r (2012/08/15)
32    o tools/genmake2:
33      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
34    o pkg/ecco/ecco_cost_final.F :
35      - fix fc print statements (to stdout and costfunction0000) so
36        that the printed value is always after the global sum.
37    o pkg/seaice/seaice_dynsolver.F :
38      - fix ice strength assymptote at SEAICE_area_max<1
39        (no change for the standard case of SEAICE_area_max=1)
40    o some cleaning:
41      - pkg source files: ensure that all *.F files from each pkg included the
42        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
43        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
44        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
45        includes;
46      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
47      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
48        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
49        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
50      - update option-file CPP_OPTIONS.h of all AD experiments:
51        * no longer include PACKAGES_CONFIG.h ;
52        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
53        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
54          including ECCO_CPPOPTIONS.h).
55    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
56      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
57        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
58        not necessary accurate).
59      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
60        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
61        deliberately break compilation (a remainder that it needs to be customized)
62      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
63      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
64      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
65    o tools/genamke2:
66      - check for lapack.
67    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
68      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
69        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
70        from both packages.
71      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
72      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
73      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
74        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
75    o pkg/cost : add comments to explain special and/or untested setups.
76    o pkg/exf:
77      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
78        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
79    o verification/*/code_ad:
80      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
81      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
82      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
83        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
84    o pkg/seaice :
85      - added possibility to change ice strength/PRESS0 relationship to
86        HEFF, according to the following run time parameters
87        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
88        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
89        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
90    o pkg/ggl90 :
91      - added run time flag mxlSurfFlag to include the code that ensure
92        mixing between first and second level (previously included as a comment)
93    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
94      - add test of newly added dumpAdByRec=T option where
95        we write all records to one file per variable.
96    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
97      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
98        to check that this code is ok with taf and compiles in adjoint.
99    o pkg/autodiff :
100      - added run time param dumpAdByRec : ad dump format switch.
101        If true then write all records to one file per variable.
102        Else write one file per record (remains the default).
103      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
104    o pkg/seaice:
105     - Added SEAICEuseTILT run time switch : if set to
106       false then omit the tilt term in seaice dynamics.
107     - Fix free drift calculation.
108    o pkg/shelfice:
109      When initializing SHELFICEDragQuadratic, set default to be
110      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
111      but retain option to set it independently
112      (inconsistenty spotted by Veronique Dansereau)
113    o eesupp/inc:
114      - in EEPARAMS.h, add real-type constant for some frequently used simple number
115         (0,1,2,1/2), with name explicitly referring to RS/RL type.
116    o model/src:
117      - move balancing of relaxation terms to new S/R balance_relax.F.
118    o pkg/autodiff:
119      re-write active I/O high-level (control) S/R:
120      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
121      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
122      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
123        MDS_READ/WRITE_FIELD); change loops to multi-threads.
124      - update and merge active_file_control_slice.flow into active_file_control.flow
125      - update the calls in lower level S/R (active_file.F, active_file_g.F and
126        active_file_ad.F) keeping the argument list and function unchanged.
127      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
128        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
129      - new low-level active I/O routines, one for each type (RL/RS), for active var
130        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
131        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
132        right type.
133    o autodiff and RS=real*4:
134      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
135        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
136      - change argument type of 3-D mask argument to _RS to match type in the call
137        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
138    o pkg/thsice:
139      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
140      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
141        fresh-water flux: uniform correction or proportional to local precip.
142    o pkg/ctrl:
143      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
144      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
145                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
146      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
147    
148    checkpoint63q (2012/07/30)
149    o pkg/autodiff:
150      note about monitor and snap-shot of ad-variables:
151      a) need to apply ADEXCH before monitor or output of ad-vars to include
152       overlap contributions (was done for adjDump but missing for monitor).
153      b) since ADEXCH implies adding overlap values to interior array, machine
154       truncation error is expected when adding an ADEXCH call in the middle of
155       the time-stepping (although mathematically identical).
156      modifs:
157      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
158        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
159      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
160        apply ADEXCH before monitor or snap-shot of ad-variables:
161           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
162      - implement new method (copy+adexch) for snap-shot and monitor of main model
163        ad-vars (initially not used by default -> output unchanged).
164      - change default (set to 2) to use new method and update few output_adm.txt
165        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
166        and both tutorial_tracer_adjsens tests).
167      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
168        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
169    o pkg/ctrl:
170      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
171      generic control variables via
172      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
173      Only required customization should be S/R ctrl_map_ini_genarr.F
174      (routine in repository contains example)
175    o pkg/exf:
176      - fix and refine checking of surface-relaxation setting when using EXF
177    o verification (adjoint exp):
178      - reduce length of simulation by half for experiment global_ocean.cs32x15
179        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
180    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
181      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
182        of KE that can occur with aggressive optimization
183      + put quadratic bottom drag calculation in separated loops (only done if
184        using bottomDragQuadratic)
185    o model/src: CG2D_NSA
186      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
187         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
188      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
189         change cg2d residual target to be expressed in Wunits (=> do not normalise
190         RHS ; this fix global_max Pb with TAF); update output.
191    o verification/tutorial_tracer_adjsens:
192       improve parameter consistency (and get rid of warnings):
193       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
194       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
195       - use staggerTimeStep (for stability) in som81; use default rotation period.
196    o pkg/exch2:
197      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
198        reset to 0 = 1 long line in X)
199    o pkg/mdsio:
200      - fix reading of dimensions from meta file for large-size domain
201    o model/src:
202      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
203      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
204        Cubed-Sphere Exch with CS-corners inside the domain;
205        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
206        globalArea and to set hasWetCSCorners.
207      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
208        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
209      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
210        useCDscheme and useCubedSphereExchange).
211    o pkg/seaice/seaice_growth.F :
212      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
213        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
214        when the previous code was not correct.
215      - in all cases diagnoze the boundary condition mismatch to SIaaflux
216      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
217        that term to QNET (essentially to set the melt/freeze water to 0degC).
218        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
219    o verification/global_ocean.cs32x15/input.seaice :
220      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
221      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
222      - update results (output.seaice.txt) accordingly.
223    o verification/lab_sea/input/data.seaice :
224      - remove SEAICEheatConsFix, which is now be tested
225        in global_ocean.cs32x15. The presently coded fix
226        is only consistent with real fresh water + nlfs.
227      - update results (output.txt) accordingly.
228    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
229    o AD_CONFIG.h file:
230      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
231      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
232        add it explicitly in each fortran src file where it is needed.
233        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
234        thus introducing potentially wrong dependency; therefore, better to include
235        it only where it's really needed, and after any other included OPTIONS file
236        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
237        or ALLOW_TANGENTLINEAR_RUN).
238    
239    checkpoint63p (2012/07/06)
240    o pkg/autodiff:
241      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
242      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
243        which are now read from new parameter file "data.autodiff" (inAdExact
244        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
245      - add file "data.autodiff" in all verification/*/input_ad/ directories.
246      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
247        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
248    o verification/tutorial_tracer_adjsens/
249      - add extra sub-verification which uses "SOM" advection scheme
250        (2nd Order-Moment Advection Scheme, Prather Limiter) with
251          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
252        and in data:
253          multiDimAdvection=.TRUE.,
254          tempAdvScheme=81,
255          saltAdvScheme=81,
256    o model/src:
257      - introduce ALLOW_BALANCE_RELAX which allow the removal
258       of the global mean of relaxation terms by setting
259       balanceThetaClimRelax and balanceSaltClimRelax
260      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
261       This case is now treated appropriately in seaice_growth.F
262    o pkg/seaice:
263      - do balanceEmPmR and balanceQnet based on the net fluxes
264        (SItflux) that enter the ocean+ice system rather than QNET
265        and EMPMR. Works best in real fresh water.
266      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
267        out of the diagnotics bloc, and stored in global arrays.
268    
269    checkpoint63o (2012/06/29)
270    o vertical mixing schemes:
271      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
272      - replace computation of density (in Function STATE1, opps_calc.F) by a call
273        to S/R FIND_RHO_SCALAR
274      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
275        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
276        affects output (vermix.ggl90) at truncation level.
277    o testreport:
278      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
279        (nSx,nSy) for the number of threads (from eedata.mth)
280    o model/src:
281      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
282        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
283    o verification/tutorial_tracer_adjsens/
284      - compile with ALLOW_CG2D_NSA
285      - run with nonlinFreeSurf=3
286      - update reference output_adm.txt
287    o tools/genmake2:
288      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
289        refine usePROFILES switching off (only when NetCDF is not available).
290    o verification (atmospheric set-up):
291      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
292    o pkg/profiles : refine profiles and files handling.
293    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
294    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
295      - changes to use model/src/the_main_loop.F rather than the ecco version
296        in ecco type adjoint runs.
297    o model/src:
298      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
299      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
300      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
301    o model/src:
302      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
303        update output of test experiment bottom_ctrl_5x5.
304    o pkg/generic_advdiff:
305      - implement vertical bi-harmonic diffusion (for now, only for T & S and
306        only explicitly).
307    o verification/bottom_ctrl_5x5/
308      update reference output (results changed quite some time ago,
309      not sure when; but new reference results look ok in terms of grdchk)
310    o verification/1D_ocean_ice_column/
311      For verification purposes, the exact adjoint rather than an approx.
312      should be used (e.g., to comare against F.D. or TLM).
313      removed autodiff_inadmode*_ad.F routines in code_ad/
314      Update results/ accordingly.
315    o pkg/cal:
316      - change cal_getdate.F so that output date is function of input time only
317        (less ambiguous, not mixed up with input iteration number).
318      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
319    o pkg/diagnostics:
320      - implement calendarDumps also for stats-diags
321      - implement calendarDumps also for snap-shot output (negative freq)
322      - for now, ignores calendarDumps if non-zero phase-lag.
323    
324  checkpoint63n (2012/06/04)  checkpoint63n (2012/06/04)
325  o model/src:  o model/src:
326    - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)    - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)

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