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revision 1.2012 by mlosch, Fri Jun 27 14:37:03 2014 UTC revision 1.2041 by heimbach, Thu Aug 7 18:47:03 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o model/src:
8      - store in common bloc array "rhoInSitu" the virtual potential temperature
9        anomaly that is used to compute geopotential: this make the atmos code
10        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
11      - add geothermal flux
12        read in ini_forcing.F as time-constant field geothermalFlux
13        applied in S/R APPLY_FORCING_T (apply_forcing.F)
14    o pkg/seaice/seaice_lsr.F
15      - rename integer variable ilcall to ipass (that's what it is called
16        in the residual diagnostics
17      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
18        default) for improved non-linear convergence of the first few steps
19      - adjust a few comments and add new ones to explain some of the store
20        directives
21    o pkg/generic_advdiff (& ptracers):
22      - re-work the code to check for valid advection scheme and for minimum
23        size of overlap (now stored in local common bloc in gad_advscheme.F)
24    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
25      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
26      - add an auxilliary variable "bet" and fix store directives and keys in
27        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
28        less exact gradients in my tests); but there are still
29        recomputation warning (although gradients are sort of OK), when
30        SEAICE_LSR_VECTORIZE is not defined, so this flag and
31        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
32      - update verification experiments lab_sea.
33      - change some comments in S/R seaice_calc_viscosities
34    o model/src:
35      - if staggerTimeStep=T, always apply exchange to velocity field in
36        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
37        (independent of using multi-dim advection or not); no effect on FWD run
38        but affects AD results (at machine truncation level): update output of
39        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
40        and isomip (oad: 12.d).
41    o pkg/generic_advdiff:
42      - stop if doAB_onGtGs is set to FALSE but ignored
43      - refine warning related to stability of tracer time-stepping
44        regarding internal wave dynamics.
45      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
46        on staggerTimeStep & implicitIntGravWave (will now get a warning
47        if potentially unstable).
48    o pkg/kl10:
49      - add new pkg "kl10" for mixing due to internal wave breaking, from
50        http://www.sciencedirect.com/science/article/pii/S1463500310000144
51        (contribution from Jody Klymak), tested in verification experiment
52        verification/internal_wave/input.kl10/
53    o isomip experiment:
54      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
55        (input.htd) and update the output.
56    o cd_code experiments:
57      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
58        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
59        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
60        update the corresponding output.
61    o pkg/seaice:
62      - reduce the number of include files and store directives in
63        S/R seaice_lsr_tridiagu/v
64      - change the order of loops in one case in S/R seaice_lsr_tridiagv
65        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
66        get rid off one store directive (a TAF bug?)
67      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
68        S/R seaice_lsr_tridiagv to change the loop range for consistency
69      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
70      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
71        S/R seaice_lsr_tridiagu/v (requires update of
72        offline_exf_seaice/input.dyn_jfnk)
73    
74    checkpoint65a (2014/07/27)
75    o model/src:
76      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
77        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
78        (topo in p-coords, ice-shelf in z-coords); update output of experiments
79        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
80    o model/src:
81      - collect momentum forcing tendency into local 2-D array (passed as argument
82        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
83        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
84        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
85      - collect T & S forcing tendency into local 2-D array (passed as argument to
86        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
87        affects results at machine truncation level (e.g., ocean: if using
88        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
89        moist correction due to vertical advection).
90      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
91        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
92        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
93        obcs_ctrl (ad & fwd grd @ 12 & 7).
94    o pkg/ptracers & diagnostics:
95      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
96        title (to avoid some unexpected truncation); sort out ptracers diags units.
97      - collect ptracer forcing tendency into local 2-D array (passed as argument
98        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
99    
100    checkpoint65 (2014/07/18)
101    o pkg/fizhi:
102      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
103        affects results at machine truncation level. Update output of experiments
104        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
105    o pkg/seaice: more clean up
106      - rename TAF common block tapes to be more consistent and remove
107        unnecessary duplicates
108      - add store directives to remove more recomputations, but use smaller
109        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
110        The idea behind this flag is to reduce the memory footprint when the
111        adjoint of the LSR is not required. As of now, defining the flag
112        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
113        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
114        For experiment offline_exf_seaice, this means on a linux box with gfortran
115        nearly a factor of 10 (but keep in mind there is mostly seaice code in
116        this experiment):
117        > size mitgcmuv_ad
118        text    data        bss     dec        hex  
119        5100659 1216  220458952  225560827  d71c8fb
120        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
121        but only a moderate increase of 36% for global_ocean.cs32x15:
122        text    data        bss     dec        hex
123        6695027 1648 1014578664 1021275339 3cdf6ccb
124        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
125      - note: there are still recomputations in global_ocean.cs32x15 and
126        offline_exf_seaice and the gradient agreement changes (gets a
127        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
128      - in general, the AD gradients still are wrong
129    o OpenAD
130      - clean up code_oad/ directories somewhat by moving files
131        dontCompile, dontTransform, keepOriginal to OAD_support/
132    o model/src:
133      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
134        (not currently tested): add dissipation terms before NLFS rescaling of
135        tendencies (previously done after).
136    o pkg/diagnostics:
137      - write stats-diags in ascii file with more digits (same as in monitor).
138    o pkg/down_slope:
139      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
140        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
141    o model/src:
142      - new file "apply_forcing.F" containing all the code previously in
143        external_forcing.F, but with new argument list: pass, as new argument,
144        the current level tendency array to update (instead of a direct update
145        of the common bloc array). Change the corresponding calls.
146      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
147        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
148    o pkg/seaice/seaice_lsr, a little bit of clean up
149      - rearrange some code blocks, so that now all calculations for
150        setting up the right-hand-sides done within one single block
151        (I find that easier to read and understand)
152      - rearrange freedrift-code to reduce the number of ifdefs
153      - adjust some indentations and comments
154    
155    checkpoint64z (2014/07/10)
156    o model/src and several pkgs:
157      - change argument list of all S/R called from external_forcing.F and
158        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
159        to pass, as argument, the current level tendency array to update
160        (instead of a direct update of the common bloc array).
161      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
162      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
163    o pkg/seaice/seaice_lsr.F
164      - always initialize local arrays in seaice_lsr_tridiagu/v
165      - add more local tapes to seaice_lsr_tridiagu/v
166      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
167        keep it in bi/bj loop; this seems to be essential
168      - gradients are still wrong but only by 4-7 orders of magnitude
169        instead of 15 orders of magnitude, lab_sea improves a little
170  o pkg/seaice  o pkg/seaice
171    - remove unnecessary u/vTmp from subroutine call of    - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
172      seaice_lsr_tridiagu/v      generates unnecessary code in seaice_lsr_ad
173      - add more store directives in seaice_lsr to avoid unnecessary code
174        in seaice_lsr_ad
175      - exclude some residual computations in seaice_lsr when
176        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
177        in seaice_lsr_ad
178      - add more storing, a new tape (model/src/the_main_loop.F) and
179        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
180        and klockey should be checked by a specialist)
181      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
182        and update lab_sea after previous changes in pkg/seaice below
183    o pkg/autodiff:
184      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
185        viscFacInAd : run time parameters allowing for adjoint switches
186        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
187    o pkg/ecco:
188      - introduce cost_gencost_boxmean.F that computes a box mean
189        temperature (for use in adjoint sensitivity studies).
190    o model/src/set_defaults.F : initialize viscFacAdj to 1.
191    o pkg/mom_common/mom_calc_visc.F:
192      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
193    o pkg/seaice/seaice_summary.F:
194      - statement for SEAICEadjMODE now in autodiff_readparms.F
195    o pkg/seaice:
196    - remove some store directives and add new ones in an effort to get    - remove some store directives and add new ones in an effort to get
197      finally rid off the recomputation warnings. This is successful      finally rid off the recomputation warnings. This is successful
198      for SEAICE_VECTORIZE_LSR defined (i.e. no extensive recomputation      when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
199      warnings left), but there are still too many recomputations on the      defined (i.e. no extensive recomputation warnings left), but there
200      solver iteration level      are still too many recomputations on the solver iteration level
201      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
202    - move definition of MPSEUDOTIMESTEPS into TAMC-block in    - move definition of MPSEUDOTIMESTEPS into TAMC-block in
203      SEAICE_SIZE.h      SEAICE_SIZE.h
204    - add a store directive in S/R seaice_calc_viscosities    - add a store directive in S/R seaice_calc_viscosities
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