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revision 1.1774 by mlosch, Fri Nov 23 15:54:18 2012 UTC revision 1.1839 by mlosch, Thu Mar 7 08:34:26 2013 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:
8      modify lsr-algorithm so that it vectorizes AND converges by using a
9      "zebra" method: split vector loop into two with step size 2; this
10      solves a general convergence problem for the JFNK solver on a vector
11      computer. It has the potential to even improve convergence for
12      non-vector machines, but it does change the results so it is turned
13      off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
14      SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
15    
16    checkpoint64e (2013/03/05)
17    o pkg/ecco and several verification experiments:
18       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
19       from ecco package, and revert to unified routine in model/src/
20       Adjust verification experiments accordingly, especially gloal_oce_llc90
21       Should conclude long-standing work by Gael to reconsile the_main_loop with
22       ECCO and will enable OpenAD's revolve loop in ECCO setup.
23    o pkg/generic_advdiff:
24      - implement compressible flow method for multi-dim advection (similar to
25        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
26        TAF generates many recomputations) to use it; no yet coded with implicit
27        vertical advection.
28      - change experiment advect_cs (new output) and advect_xy (same output)
29        to test compressible flow multi-dim advection.
30    o pkg/generic_advdiff:
31      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
32        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
33    o pkg/seaice:
34      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
35        bug affects two verification experiments (lab_sea and lab_sea.hb87),
36        recover old (wrong) results by setting noSlipFac = 2. in
37        seaice_calc_strainrates.F;
38      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
39      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
40        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
41      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
42    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
43      - new subroutines seaice_lsr_tridiagu/v
44      - introduce loop bounds i/jmin/max to be able to use a restricted
45        additive Schwarz method, but not used for now.
46      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
47      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
48    o OpenAD support
49       Reorganize S/R call for overall time-stepping loop to facilitate
50       OpenAD revolve loop replacement
51       (new S/R main_do_loop.F)
52    o model/src:
53      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
54      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
55        ADAMS_BASHFORTH2.
56    o pkg/cheapaml:
57      - add new parameter (default=F, same as before) to disable full domain
58        (including land) periodicity in X & Y dir.
59      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
60        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
61        into single S/R CHEAPAML_TIMESTEP.
62    
63    checkpoint64d (2013/02/17)
64    o pkg/monitor (angular momentum):
65      - do not add Eta contribution to the total AM if using rigid-lid;
66      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
67      - horizontal discretisation: compute Zonal wind contribution separately for
68        each component (instead of from cell centered averaged) and use the 4
69        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
70      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
71        FreeSurf) if using vectorInvariant momentum.
72    o model/src (horizontal grid):
73      - move initialisation of all horizontal grid arrays to null value
74        from specific horizontal grid S/R to main S/R INI_GRID;
75      - add 2 new arrays to project model C-grid velocity on to zonal direction
76        (similar to AngleCosC & -AngleSinC but at U and V point location) and
77        compute them in S/R CALC_GRID_ANGLES.
78    o pkg/seaice: replace a hard coded parameter by a runtime parameter
79        SEAICE_JFNK_tolIter
80    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
81        preconditioner for JFNK (run LSR into the overlaps as far as possible,
82        i.e OLx/y-2, but overwrite the solution in the overlaps)
83      - extend loop range in seaice_calc_viscosity
84      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
85      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
86      - slightly modify loops in tridiagonal solver lsr-preconditioner
87      - by default remove the extra exchange in seaice_preconditioner with a
88        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
89      - modify offline_exf_seaice so that old results without RAS are reproduced
90        for output.dyn_jfnk.txt
91      in seaice_fgmres.F (unrelated to RAS)
92      - add a cpp-flag option for a re-ordered mapping (potentially more
93        efficient), but because this changes the results, turn it off by
94        default
95      - replace the save statement by local common blocks
96    o utils/matlab:
97      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
98      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
99        instead of local script "load_cs.m".
100    o pkg/seaice:
101      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
102        to the scalarProductMetric and the unrolling. By chance this does not
103        change the verification experiment, because of the particular domain
104        decomposition
105    o pkg/diagnostics:
106      - change default missing_value from UNSET_RL to -999.
107    o pkg/layers: improve vectorization of layers_fluxcalc.F
108      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
109        time spent in this routine by more than a factor of 3 on an NEC-SX8
110      - step 2: replace search algorithm by a bisection algorithm found in
111        Press et al. Numerical Recipes in Fortran. This algorithm can be
112        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
113        For now, use this algorithm only for TARGET_NEC_SX defined.
114      - moved the search algorithm into a separate subroutine, that is kept
115        within the same file for automatic inlining.
116      - modified catching potential errors
117    o pkg/ecco:
118      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
119    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
120      - modifications for ALLOW_GENTIM2D_CONTROL
121      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
122      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
123      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
124      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
125    o model/src:
126      - account for moist thermodynamics in (dry) potential temperature equation;
127        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
128        and cpl_aim+ocn.
129      - also switch to standard compiler (gfortran, was using ifort previously)
130        for fizhi-cs experiments reference output.
131    o pkg/ctrl:
132      - 1st step toward generic time-varying control variable (2D) via CPP option
133        ALLOW_GENTIM2D_CONTROL
134      - note new namelist ctrl_nml_genarr in data.ctrl
135    o verification/global_ocean.cs32x15:
136      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
137        thsice calling sequence and update "output.icedyn.txt" output file.
138    o pkg/ptracers:
139      - from Ryan A.: code to allow to restart a tracer at regular time interval
140        specifying a reset frequency and a reset-phase (for each tracers).
141    o pkg/thsice:
142      - implement new sequence of calls for thsice+seaice:
143          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
144          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
145      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
146        in CPP_OPTIONS.h) to recover old sequence;
147      - update diagnostics for Intermediate State thsice diagnostics: now filled
148        just before advection (instead of just after advection in old sequence);
149      - update output of experiment offline_exf_seaice (standard test);
150      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
151        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
152    o pkg/aim_v23:
153      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
154      - use standard pkg/mdsio routines to read & write CO2 pickup file;
155      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
156      - Implement new sequence of calls for seaice advection (with thsice and
157        seaice diffusion): do ice advection after ice-Thermodynamic (previously
158        was done before); change aim_do_physics.F (split the bi,bj loops block);
159      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
160    o pkg/thsice:
161      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
162        where just seaice diffusion is used without seaice-dynamics.
163    
164    checkpoint64c (2013/01/18)
165    o pkg/seaice:
166      - add a parameter JFNKres_tFac that can replace JFNKres_t
167        (= JFNKres_tFac*JFNKresidual before JFNK solver)
168      - add a line search option to the JFNK solver
169      - move update of u/vIce and computation of initial residual into a separate
170        routine (same file); makes the code a little easier to read (?)
171      - the line search requires computation of the residual and for some reason
172        I cannot do the update of u/vIce at the beginning of the Newton loop
173        without changing the results, so we move computation of the new residual
174        also to the end of the Newton loop, even without the line search
175    o pkg/mdsio:
176      - write missing value (corresponding to undefined array value) to meta files;
177        skip this if missing value is one (UNSET_RL would be a better value for the
178        case of undefined missing value but it's current the default missing-value);
179        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
180    o pkg/exf & thsice:
181      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
182        diagnostics) even when SHORTWAVE_HEATING is #undef;
183    o verification/cfc_example:
184      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
185        illustrate how to use it).
186    o verification/offline_exf_seaice:
187      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
188        files to only one time-record.
189      in input.thermo: narrow the 2 bands of low initial ice-concentration near
190        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
191        snapshot output; same mcPheePiston value as in thsice with
192        surf-current=0.2m/s.
193      in input.thsice: similar set-up as in input.thermo (channel with same seaice
194        initial conditions).
195    o verification/cfc_example:
196      - update file "data" with more standard choice (default rotationPeriod,
197        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
198        set deltaTFreeSurf to deltaTtracer) and update the output.
199    o pkg/layers:
200      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
201      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
202    o verification/offline_exf_seaice:
203      - set all {field}period to zero for constant-in-time forcing (not tested
204        anywhere else).
205    o verification/offline_exf_seaice:
206      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
207      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
208    o model/src:
209      - implement Finite-Volume method for (hydrostatic) presure gradient
210        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
211    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
212      - In order to be compatible with the default EVP code, this requires changing
213        the EVP code around a little; and because any small change immediately
214        breaks the lab_sea.hb87 verification experiment, the reference output is
215        updated two times (each time the remaining aggrement was only 2 digits):
216        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
217        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
218        The adjoint test lab_sea.evp also needed to be updated.
219      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
220        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
221        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
222        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
223        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
224        kept obscure, because I need to test it a little more.
225    o pkg/cheapaml:
226      - fix few incorrect type (_RL/_RS) in subroutine calls.
227    o pkg/seaice:
228      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
229        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
230    o model/src:
231      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
232        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
233        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
234    o pkg/cheapaml:
235      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
236        update output of experiment cheapAML_box.
237      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
238        and set them only in one place (cheapaml_readparms.F).
239      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
240      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
241        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
242    o model/src/the_main_loop.F:
243      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
244    o pkg/seaice:
245      - remove legacy branch code.
246      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
247    o verification/*/code*/SEAICE_OPTIONS.h:
248      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
249        SEAICE_CAP_HEFF).
250    o pkg/cheapaml:
251      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
252        to load new forcing fields.
253      - add missing "_d 0" where it's needed; + some editing (improve indentation).
254      - remove switch to "-r8" compiler option (no longer needed) in verification
255        cheapAML_box, keep same output (small trucation error differences).
256    o verification/offline_exf_seaice:
257      - add thermodynamics only test.
258    o verification/cheapAML_box:
259      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
260        keep same output (same 14 digits for cg2d).
261      - switch on "-r8" compiler option (some numerical values are missing
262        the "_d 0") and update output (only 6 digits for cg2d were preserved).
263    
264    checkpoint64b (2012/12/24)
265    o pkg/cheapaml:
266      - remove un-used variables (Qnet,EmPmR) from pickup files.
267      - store tendency of advected variables into cheapaml pickup file
268        and fix the AB-2 restart.
269    o verification/offline_exf_seaice and lab_sea adjoint:
270      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
271      - switch to 4 time steps in offline, consistent with lab_sea.
272      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
273      - update results after change of experiment seaice.
274    o pkg/seaice:
275      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
276        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
277        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
278        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
279    o model/src:
280      - add run-time parameter to select CG2D solver minimum-residual solution
281        (in case of a poor convergence).
282    o pkg/seaice/seaice_lsr.F
283      - move calculation of matrix coefficients into new
284        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
285        file; the main purpose of this change is to be able to reuse the code
286        in S/R SEAICE_PRECONDITIONER
287      - modify the computation of the residual so that the mass of sea-ice
288        is not used twice; this simplifies the calculations, but since
289        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
290        not tested in testreport---this does not affect the testreport results.
291    o verification/seaice_obcs:
292      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
293        verification/lab_sea/input.salt_plume; changes results/output.txt*
294    o model/src:
295      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
296    o pkg/seaice:
297      - improve description of parameters in seaice_fgmres.F and start
298        cleaning up the code
299      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
300        second argument
301      - add a metric based on grid cell area to SEAICE_SCALPROD; update
302        results of offline_exf_seaice.dyn_jfnk
303      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
304    o pkg/aim_v23:
305      - fix an other bug in dissipation heating (grid-cell area was missing).
306    o model/src + pkg/seaice:
307      - add global (multi-tile) linear solver for pair of tri-diagonal system
308        along X and Y lines, respectively for U and V component.
309        Note: 1) MPI and cube-exchange not yet coded.
310            2) probably not accurate for poorly conditioned / large size problem.
311      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
312        default: not compiled and not used.
313    o pkg/seaice:
314      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
315        introduce bi/bj loops and use global_sum_tile_rl instead of
316        mpi_allreduce in seaice_fgmres.F
317      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
318      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
319      - add a verification experiment for JFNK in offline_exf_seaice
320    o verification:
321      - change (for now, only fwd test) offline_exf_seaice experiment:
322        use a re-entrant channel with idealized coastline (trapezoidal shape)
323        at southern boundary to explore seaice dynamics and thermodynamics
324        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
325        secondary test (input.thsice) use thermodynamics only with SST relaxation.
326      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
327    o pkg/exf:
328      - disable "sstExtrapol" when Nr=1
329    o verification:
330      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
331        to test pkg/cheapaml.
332    o pkg/aim_v23 & pkg/shap_filt:
333      - fix dissipation heating (erroneous gravity multiplication factor).
334    o pkg/seaice:
335      - remove unused field pressPre from jfnk solver
336      - rename two subroutines in seaice_preconditioner.F
337    o eesupp/src:
338       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
339  o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again  o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
340     - remove wrong parts of the rhs and the lhs (were in there     - remove wrong parts of the rhs and the lhs (were in there
341       because I did not understand the concept of this preconditioner)       because I did not understand the concept of this preconditioner)

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