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revision 1.2025 by mlosch, Wed Jul 16 12:03:54 2014 UTC revision 1.2048 by jmc, Fri Aug 15 20:54:49 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 & pkg/ptracers:
8      - remove common block variables gT,gS (in DYNVARS.h), except when
9         USE_OLD_EXTERNAL_FORCING is defined; update TAF storage accordingly.
10      - remove common block variable gPtr.
11    o model/src & pkgs:
12      - change gTracer (and/or tracer) argument (drop bi,bj indices) in S/R
13         ADAMS_BASHFORTH(2&3), CYCLE_(AB_)TRACER, FREESURF_RESCALE_G,
14         IMPLDIFF, SOLVE_TRIDIAGONAL & _PENTADIAGONAL, GAD_SOM_ADVECT,
15         GAD_ADVECTION, GAD_CALC_RHS, GAD_IMPLICIT_R, TIMEAVE_CUMUL_DIF_1T
16      + change accordingly all calling S/R.
17      - use local temperature/salinity/ptracer tendency array (without bi,bj)
18        in S/R temp/salt/ptracers_integrate.F
19    o pkg/seaice:
20      - move computation of stress contributions to rhsU/V in s/r seaice_lsr
21        to separate s/r seaice_lsr_rhsu/v in order to be able to re-use code
22      - make u/vIceC local variables if SEAICE_CGRID is defined only to be used
23        in seaice_lsr
24      - seaice_lsr.F: make local 4D arrays UXX, VYY, etc 2D
25        in s/r seaice_lsr_calc_coeffs
26    o pkg/mdsio:
27      - in MDS_READ/WRITE_FIELD, stop if file-name (+prefix) is too long
28        (e.g., > MAX_LEN_MBUF -90 ) or, in INI_MODEL_IO, if mdsioLocalDir is
29        too long (e.g., > MAX_LEN_FNAM/2 )
30    
31    checkpoint65b (2014/08/12)
32    o pkg/matrix:
33      - pass, as argument, updated tracer field to S/R MATRIX_STORE_TENDENCY_EXP
34    o model/src:
35      - fix initialisation of geothermalFile; compile geothermal-flux code in
36        natl_box verification experiment.
37    o model/src & pkg/down_slope:
38      - push the k loop inside S/R TIMESTEP_TRACER (now called outside the k loop).
39      - in dwnslp_apply.F, update tracer tendency instead of the future tracer
40        field and call S/R DWNSLP_APPLY before TIMESTEP_TRACER; this affects
41        results at machine truncation level: update output of experiments
42        global_ocean.90x40x15.dwnslp (FWD) and lab_sea.noseaicedyn (AD).
43    o pkg/diagnostics (Stats-Diags):
44      - do not cumulate the full volume when DIAGNOSTICS_FILL is
45        called with bibjFlg < 0 (no increment of the counter for 2D/3D diag);
46        This fix the mean statistics when DIAGNOSTICS_FILL is called multiple
47        times (but Min,Max and StD are still wrong).
48    o model/src:
49      - add geothermal flux forcing: read in ini_forcing.F as time-constant
50        field "geothermalFlux" applied in S/R APPLY_FORCING_T (apply_forcing.F)
51    o model/src:
52      - move CYCLE_TRACER calls from tracers_correction_step.F to temp/salt/ptracer
53        _integrate.F so that, when leaving S/R THERMODYANMICS, theta,salt and pTrac
54        arrays are already updated while adjustments (filters, conv.adjustment) are
55        still applied later, in S/R TRACERS_CORRECTION_STEP.
56    o model/src:
57      - store in common bloc array "rhoInSitu" the virtual potential temperature
58        anomaly that is used to compute geopotential: this make the atmos code
59        more similar to ocean code which already uses rhoInSitu in calc_phi_hyd.F
60    o pkg/seaice/seaice_lsr.F
61      - rename integer variable ilcall to ipass (that's what it is called
62        in the residual diagnostics
63      - change time stepping for NPSEUDOTIMESTEP > 2 (does not change the
64        default) for improved non-linear convergence of the first few steps
65      - adjust a few comments and add new ones to explain some of the store
66        directives
67    o pkg/generic_advdiff (& ptracers):
68      - re-work the code to check for valid advection scheme and for minimum
69        size of overlap (now stored in local common bloc in gad_advscheme.F)
70    o pkg/seaice: another attempt to make the adjoint work for sea ice dynamics
71      - re-initialize more variables in seaice_lsr: u/vIceC, u/vIceNm1
72      - add an auxilliary variable "bet" and fix store directives and keys in
73        seaice_lsr_tridiagu/v, this seems to do the trick (i.e. more or
74        less exact gradients in my tests); but there are still
75        recomputation warning (although gradients are sort of OK), when
76        SEAICE_LSR_VECTORIZE is not defined, so this flag and
77        SEAICE_LSR_VECTORIZE_ZEBRA are recommended for efficiency.
78      - update verification experiments lab_sea.
79      - change some comments in S/R seaice_calc_viscosities
80    o model/src:
81      - if staggerTimeStep=T, always apply exchange to velocity field in
82        do_stagger_fields_exchanges.F instead of in do_fields_blocking_exchanges.F
83        (independent of using multi-dim advection or not); no effect on FWD run
84        but affects AD results (at machine truncation level): update output of
85        experiment 1D_ocean_ice_column (ad: 12 digits), hs94.1x64x5 (ad,oad: 13.d)
86        and isomip (oad: 12.d).
87    o pkg/generic_advdiff:
88      - stop if doAB_onGtGs is set to FALSE but ignored
89      - refine warning related to stability of tracer time-stepping
90        regarding internal wave dynamics.
91      - setting of AdamsBashforth_T,S when doAB_onGtGs=F: remove condition
92        on staggerTimeStep & implicitIntGravWave (will now get a warning
93        if potentially unstable).
94    o pkg/kl10:
95      - add new pkg "kl10" for mixing due to internal wave breaking, from
96        http://www.sciencedirect.com/science/article/pii/S1463500310000144
97        (contribution from Jody Klymak), tested in verification experiment
98        verification/internal_wave/input.kl10/
99    o isomip experiment:
100      - test pkg/shelfice with Non-Lin Free-Surf in one of the FWD set-up
101        (input.htd) and update the output.
102    o cd_code experiments:
103      - use default cd_code options (#undef CD_CODE_NO_AB_MOMENTUM &
104        #undef CD_CODE_NO_AB_CORIOLIS) in experiments: cfc_example (fwd)
105        global_ocean.90x40x15 (ad & oad) and OpenAD (ad & oad) and
106        update the corresponding output.
107    o pkg/seaice:
108      - reduce the number of include files and store directives in
109        S/R seaice_lsr_tridiagu/v
110      - change the order of loops in one case in S/R seaice_lsr_tridiagv
111        (only for SEAICE_VECTORIZE_LSR_ZEBRA defined), which allows me to
112        get rid off one store directive (a TAF bug?)
113      - add one more instance of ifdef SEAICE_VECTORIZE_LSR_ZEBRA in
114        S/R seaice_lsr_tridiagv to change the loop range for consistency
115      - remove ilcall, m from parameter list of S/R seaice_lsr_tridiagu/v
116      - fix a bug that affects the JFNK solver: replace sNx/y by i/jMax in
117        S/R seaice_lsr_tridiagu/v (requires update of
118        offline_exf_seaice/input.dyn_jfnk)
119    
120    checkpoint65a (2014/07/27)
121    o model/src:
122      - Non-Lin Free-Surf in p/z coords: allows hFacW,S to be larger than
123        surrounding hFacC=1 @ edge of a step with different kSurfC on either side
124        (topo in p-coords, ice-shelf in z-coords); update output of experiments
125        tutorial_global_oce_in_p and isomip (both AD and OpenAD output).
126    o model/src:
127      - collect momentum forcing tendency into local 2-D array (passed as argument
128        to apply_forcing S/R); this simplifies mom. Forcing diagnostics and CD_CODE
129        parts in timestep.F (without CD_CODE_NO_AB_MOMENTUM defined = the default);
130        affects results at machine truncation level (e.g., if using OBCS_SPONGE).
131      - collect T & S forcing tendency into local 2-D array (passed as argument to
132        apply_forcing S/R); add 3-D diagnostics for temp & salt forcing tendency.
133        affects results at machine truncation level (e.g., ocean: if using
134        SHORTWAVE_HEATING and atmos:, if using FrictionHeating or (atm_Rq<>0)
135        moist correction due to vertical advection).
136      - update output of experiments: fizhi-cs-32x32x40 (13 digits),
137        global_ocean.cs32x15 (fwd: icedyn, seaice, thsice, all 3 @ 11d; adm & tml:
138        seaice_dynmix & thsice, fwd grd @ 3 & 8), hs94.1x64x5 (ad grd @ 13),
139        obcs_ctrl (ad & fwd grd @ 12 & 7).
140    o pkg/ptracers & diagnostics:
141      - use ptracers (short) name (instead of long one) to make ptracers diagnostics
142        title (to avoid some unexpected truncation); sort out ptracers diags units.
143      - collect ptracer forcing tendency into local 2-D array (passed as argument
144        to apply_forcing S/R); add 3-D diagnostics for ptracers forcing tendency.
145    
146    checkpoint65 (2014/07/18)
147    o pkg/fizhi:
148      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
149        affects results at machine truncation level. Update output of experiments
150        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
151  o pkg/seaice: more clean up  o pkg/seaice: more clean up
152    - rename TAF common block tapes to be more consistent and remove    - rename TAF common block tapes to be more consistent and remove
153      unnecessary duplicates      unnecessary duplicates
154    - add store directives to remove more recomputations,    - add store directives to remove more recomputations, but use smaller
155      but use smaller tapes (and adjust keys) when      tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
156      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
157      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
158      required. As of now, defining the flag SEAICE_LSR_ADJOINT_ITER      SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
159      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).
160      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
161      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
162      a factor of 10 (but keep in mind there is mostly seaice code      this experiment):
     in this experiment)  
163      > size mitgcmuv_ad      > size mitgcmuv_ad
164      text    data        bss     dec        hex        text    data        bss     dec        hex  
165      5100659 1216  220458952  225560827  d71c8fb      5100659 1216  220458952  225560827  d71c8fb
166      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)      5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
167      but only a moderate increase of 36% for global_ocean.cs32x15      but only a moderate increase of 36% for global_ocean.cs32x15:
168      text    data        bss     dec        hex      text    data        bss     dec        hex
169      6695027 1648 1014578664 1021275339 3cdf6ccb      6695027 1648 1014578664 1021275339 3cdf6ccb
170      6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)      6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
171    - note: there are still recomputations in global_ocean.cs32x15 and    - note: there are still recomputations in global_ocean.cs32x15 and
172      the gradient agreement changes (gets a little worse)      offline_exf_seaice and the gradient agreement changes (gets a
173        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
174    - in general, the AD gradients still are wrong    - in general, the AD gradients still are wrong
175  o OpenAD  o OpenAD
176    - clean up code_oad/ directories somewhat by moving files    - clean up code_oad/ directories somewhat by moving files
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