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revision 1.2025 by mlosch, Wed Jul 16 12:03:54 2014 UTC revision 1.2054 by jmc, Wed Aug 27 03:03:27 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 verification:
8      - new experiment testing OBCS and DIC pkgs, using params & output from
9        tutorial_global_oce_biogeo but limited to a sub-domain around Drake
10        passage: take OBCS from the last year of a 2 yrs simulation and initial
11        conditions from t=1.yr while keeping the same forcing.
12    o model/src:
13      - when allowFreezing=T, only reset below freezing initial Temp to Tfreezing
14        (at any k) if checkIniTemp is not set to FALSE (default checkIniTemp=T).
15    o pkg/diagnostics (Stats-Diags):
16      - re-write S/R DIAGSTATS_CALC (more similar to TARGET_NEC_SX part) to:
17        a) refine region where stats are computed, excluding where arrhFac=0 ;
18        b) fix missing interior mask (use with OBCS) in 3-D fields statistics;
19        c) extend regional stats over the region edges (for U or V pt location).
20    o pkg/gchem:
21      - add a (2nd) call to OBCS_APPLY_PTRACER in gchem_forcing_sep.F (needed since
22        pkg/dic is currently changing/updating ptracers values beyond the OB).
23    o verification (hs94):
24      - convert Held & Suarez external_forcing.F (from hs94.cs, with Sigma-coords
25        bits) to apply_forcing.F and undef USE_OLD_EXTERNAL_FORCING in experiments
26        hs94.cs-32x32x5 and tutorial_held_suarez_cs ; also use the same version of
27        apply_forcing.F in 2D hs94 (fwd, ad & oad) but keep LatLon hs94 unchanged.
28    o pkg/ptracers:
29      - implement Adams-Bashforth on pTracers (instead of on tracer tendency),
30        switched on by setting PTRACERS_doAB_onGpTr=F (default set to doAB_onGtGs)
31      - change exp4 secondary test (input.nlfs) to test AB on T & S & pTracer
32        with AB-2 code (so that it get tested).
33    o model/src:
34      - allow to apply Adams-Bashforth on Temp & Salt (instead of on gT,gS)
35        with AB-2 code (previously only available with AB-3 code).
36        Also move the code (call to ADAMS_BASHFORTH S/R) form thermodynamics.F
37        to temp/salt_integrate.F (since the 2nd part of gt/sNm1 update is done
38        there, by calling CYCLE_AB_TRACER).
39    o pkg/generic_advdiff:
40      - change Tracer argument (drop bi,bj indices) in S/R GAD_CALC_RHS,
41        GAD_C2_ADV_R, GAD_U3_ADV_R, GAD_C4_ADV_R, GAD_DIFF_R, GAD_BIHARM_R
42        + also in GMREDI_X/Y/RTRANSPORT ; and update corresponding calls in
43        S/R temp/salt/ptracers_integrate.F
44    o model/src & pkg/ptracers:
45      - remove common block variables gT,gS (in DYNVARS.h), except when
46         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
47      - remove common block variable gPtr.
48    o model/src & pkgs:
49      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
50         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
51         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
52         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
53      + change accordingly all calling S/R.
54      - use local temperature/salinity/ptracer tendency array (without bi,bj)
55        in S/R temp/salt/ptracers_integrate.F
56    o pkg/seaice:
57      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
58        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
59      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
60        in seaice_lsr
61      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
62        in s/r seaice_lsr_calc_coeffs
63    o pkg/mdsio:
64      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
65        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
66        too long (e.g., > MAX_LEN_FNAM/2 )
67    
68    checkpoint65b (2014/08/12)
69    o pkg/matrix:
70      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
71    o model/src:
72      - fix initialisation of geothermalFile; compile geothermal-flux code in
73        natl_box verification experiment.
74    o model/src & pkg/down_slope:
75      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
76      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
77        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
78        results at machine truncation level: update output of experiments
79        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
80    o pkg/diagnostics (Stats-Diags):
81      - do not cumulate the full volume when DIAGNOSTICS_FILL is
82        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
83        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
84        times (but Min,Max and StD are still wrong).
85    o model/src:
86      - add geothermal flux forcing: read in ini_forcing.F as time-constant
87        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
88    o model/src:
89      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
90        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
91        arrays are already updated while adjustments (filters, conv.adjustment) are
92        still applied later, in S/R TRACERS_CORRECTION_STEP.
93    o model/src:
94      - store in common bloc array "rhoInSitu" the virtual potential temperature
95        anomaly that is used to compute geopotential: this make the atmos code
96        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
97    o pkg/seaice/seaice_lsr.F
98      - rename integer variable ilcall to ipass (that's what it is called
99        in the residual diagnostics
100      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
101        default) for improved non-linear convergence of the first few steps
102      - adjust a few comments and add new ones to explain some of the store
103        directives
104    o pkg/generic_advdiff (& ptracers):
105      - re-work the code to check for valid advection scheme and for minimum
106        size of overlap (now stored in local common bloc in gad_advscheme.F)
107    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
108      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
109      - add an auxilliary variable "bet" and fix store directives and keys in
110        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
111        less exact gradients in my tests); but there are still
112        recomputation warning (although gradients are sort of OK), when
113        SEAICE_LSR_VECTORIZE is not defined, so this flag and
114        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
115      - update verification experiments lab_sea.
116      - change some comments in S/R seaice_calc_viscosities
117    o model/src:
118      - if staggerTimeStep=T, always apply exchange to velocity field in
119        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
120        (independent of using multi-dim advection or not); no effect on FWD run
121        but affects AD results (at machine truncation level): update output of
122        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
123        and isomip (oad: 12.d).
124    o pkg/generic_advdiff:
125      - stop if doAB_onGtGs is set to FALSE but ignored
126      - refine warning related to stability of tracer time-stepping
127        regarding internal wave dynamics.
128      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
129        on staggerTimeStep & implicitIntGravWave (will now get a warning
130        if potentially unstable).
131    o pkg/kl10:
132      - add new pkg "kl10" for mixing due to internal wave breaking, from
133        http://www.sciencedirect.com/science/article/pii/S1463500310000144
134        (contribution from Jody Klymak), tested in verification experiment
135        verification/internal_wave/input.kl10/
136    o isomip experiment:
137      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
138        (input.htd) and update the output.
139    o cd_code experiments:
140      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
141        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
142        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
143        update the corresponding output.
144    o pkg/seaice:
145      - reduce the number of include files and store directives in
146        S/R seaice_lsr_tridiagu/v
147      - change the order of loops in one case in S/R seaice_lsr_tridiagv
148        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
149        get rid off one store directive (a TAF bug?)
150      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
151        S/R seaice_lsr_tridiagv to change the loop range for consistency
152      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
153      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
154        S/R seaice_lsr_tridiagu/v (requires update of
155        offline_exf_seaice/input.dyn_jfnk)
156    
157    checkpoint65a (2014/07/27)
158    o model/src:
159      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
160        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
161        (topo in p-coords, ice-shelf in z-coords); update output of experiments
162        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
163    o model/src:
164      - collect momentum forcing tendency into local 2-D array (passed as argument
165        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
166        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
167        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
168      - collect T & S forcing tendency into local 2-D array (passed as argument to
169        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
170        affects results at machine truncation level (e.g., ocean: if using
171        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
172        moist correction due to vertical advection).
173      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
174        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
175        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
176        obcs_ctrl (ad & fwd grd @ 12 & 7).
177    o pkg/ptracers & diagnostics:
178      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
179        title (to avoid some unexpected truncation); sort out ptracers diags units.
180      - collect ptracer forcing tendency into local 2-D array (passed as argument
181        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
182    
183    checkpoint65 (2014/07/18)
184    o pkg/fizhi:
185      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
186        affects results at machine truncation level. Update output of experiments
187        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
188  o pkg/seaice: more clean up  o pkg/seaice: more clean up
189    - rename TAF common block tapes to be more consistent and remove    - rename TAF common block tapes to be more consistent and remove
190      unnecessary duplicates      unnecessary duplicates
191    - add store directives to remove more recomputations,    - add store directives to remove more recomputations, but use smaller
192      but use smaller tapes (and adjust keys) when      tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
193      SEAICE_LSR_ADJOINT_ITER is undefined. The idea behind this flag is      The idea behind this flag is to reduce the memory footprint when the
194      to reduce the memory footprint when the adjoint of the LSR is not      adjoint of the LSR is not required. As of now, defining the flag
195      required. As of now, defining the flag SEAICE_LSR_ADJOINT_ITER      SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
196      increase 4 common block tapes for 2D field by a factor of      a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
197      SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h). For experiment      For experiment offline_exf_seaice, this means on a linux box with gfortran
198      offline_exf_seaice, this means on a linux box with gfortran nearly      nearly a factor of 10 (but keep in mind there is mostly seaice code in
199      a factor of 10 (but keep in mind there is mostly seaice code      this experiment):
     in this experiment)  
200      > size mitgcmuv_ad      > size mitgcmuv_ad
201      text    data        bss     dec        hex        text    data        bss     dec        hex  
202      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
203      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
204      but only a moderate increase of 36% for global_ocean.cs32x15      but only a moderate increase of 36% for global_ocean.cs32x15:
205      text    data        bss     dec        hex      text    data        bss     dec        hex
206      6695027 1648 1014578664 1021275339 3cdf6ccb      6695027 1648 1014578664 1021275339 3cdf6ccb
207      6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)      6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
208    - note: there are still recomputations in global_ocean.cs32x15 and    - note: there are still recomputations in global_ocean.cs32x15 and
209      the gradient agreement changes (gets a little worse)      offline_exf_seaice and the gradient agreement changes (gets a
210        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
211    - in general, the AD gradients still are wrong    - in general, the AD gradients still are wrong
212  o OpenAD  o OpenAD
213    - clean up code_oad/ directories somewhat by moving files    - clean up code_oad/ directories somewhat by moving files
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