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revision 1.1621 by heimbach, Wed Mar 14 22:59:05 2012 UTC revision 1.1844 by heimbach, Fri Mar 29 23:21:39 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 ECCO-CLIVAR merge:  o verification/isomip, pkg/shelfic and OpenAD:
8    1. seaice AREA relaxation    - add OpenAD setup to this exp and make shelfice package work with OpenAD
9    o verification/offline_exf_seaice: replace adjoint experiment.
10    o verification/tutorial_tracer_adjsens, pkg/ptracers and OpenAD:
11      - add OpenAD setup to this exp and make ptracers package work with OpenAD
12    o pkg/seaice/seaice_evp.F: mask the asymmetric contribution of the ice-ocean
13      stress (when the turningAngle is non-zero) over open water to avoid
14      stripes in the EVP-solutions after many EVP-substeps. This does not change
15      the verification experiment (because turningAngle=0 in that experiment), but
16      will affect other EVP solutions with turningAngle.ne.0
17    o verification, AD & TLM output:
18      - new TAF version 2.3.10 (previously 2.3.8) add more parenthesis in multiple
19        additions and multiplications which affect results at machine truncation
20        level. Update few AD output (1D_ocean_ice_column, bottom_ctrl_5x5,
21        lab_sea.noseaicedyn & offline_exf_seaice) and TLM output
22        (1D_ocean_ice_column & tutorial_tracer_adjsens.som81) which had only 12
23        digits of matching.
24    o pkg/seaice:
25       modify lsr-algorithm so that it vectorizes AND converges by using a
26       "zebra" method: split vector loop into two with step size 2; this
27       solves a general convergence problem for the JFNK solver on a vector
28       computer. It has the potential to even improve convergence for
29       non-vector machines, but it does change the results so it is turned
30       off by default. To turn on define CPP-flags SEAICE_VECTORIZE_LSR and
31       SEAICE_VECTORIZE_LSR_ZEBRA in SEAICE_OPTIONS.h
32    
33    checkpoint64e (2013/03/05)
34    o pkg/ecco and several verification experiments:
35       Remove special versions of the_model_main.F, the_main_loop.F, forward_step.F
36       from ecco package, and revert to unified routine in model/src/
37       Adjust verification experiments accordingly, especially gloal_oce_llc90
38       Should conclude long-standing work by Gael to reconsile the_main_loop with
39       ECCO and will enable OpenAD's revolve loop in ECCO setup.
40    o pkg/generic_advdiff:
41      - implement compressible flow method for multi-dim advection (similar to
42        gad_som_advect.F); add new option "GAD_MULTIDIM_COMPRESSIBLE" (since
43        TAF generates many recomputations) to use it; no yet coded with implicit
44        vertical advection.
45      - change experiment advect_cs (new output) and advect_xy (same output)
46        to test compressible flow multi-dim advection.
47    o pkg/generic_advdiff:
48      - fix SOM advection for unusual cases (linear Free-Surf in r*, other
49        cases where linear Free-Surf is not @ k=1, e.g., useShelfIce)
50    o pkg/seaice:
51      - fix bug in the no-slip implementation in seaice_calc_strainrates.F, this
52        bug affects two verification experiments (lab_sea and lab_sea.hb87),
53        recover old (wrong) results by setting noSlipFac = 2. in
54        seaice_calc_strainrates.F;
55      - add another averaging method for etaZ (etaZmethod=3), a mix of 2 and 0
56      - add runtime parameter SEAICE_JFNKepsilon for that finite difference
57        gradient in the Jacobian times vector operation (s/r seaice_jacvec)
58      - fix line search in seaice_jfnk.F (s/r seaice_jfnk_update)
59    o pkg/seaice: reorganize seaice_lsr.F to be able to reuse more code:
60      - new subroutines seaice_lsr_tridiagu/v
61      - introduce loop bounds i/jmin/max to be able to use a restricted
62        additive Schwarz method, but not used for now.
63      - rename SEAICE_CALC_LSR_COEFFS into SEAICE_LSR_CALC_COEFFS
64      - use new subroutines seaice_lsr_tridiagu/v in s/r seaice_preconditioner
65    o OpenAD support
66       Reorganize S/R call for overall time-stepping loop to facilitate
67       OpenAD revolve loop replacement
68       (new S/R main_do_loop.F)
69    o model/src:
70      - add 3-D array 3rd dimension to argument list of S/R ADAMS_BASHFORTH2/3;
71      - pkg/cheapaml: remove local S/R ADAMS2d and use instead standard S/R
72        ADAMS_BASHFORTH2.
73    o pkg/cheapaml:
74      - add new parameter (default=F, same as before) to disable full domain
75        (including land) periodicity in X & Y dir.
76      - new S/R CHEAPAML_COPY_EDGES to copy relaxation field into edges of
77        prognostics field ; merge the 2 S/R cycle_2d_tracer and timestep_2d_tracer
78        into single S/R CHEAPAML_TIMESTEP.
79    
80    checkpoint64d (2013/02/17)
81    o pkg/monitor (angular momentum):
82      - do not add Eta contribution to the total AM if using rigid-lid;
83      - correct for Adams-Bashforth in zonal-wind part (instead of in AM_eta).
84      - horizontal discretisation: compute Zonal wind contribution separately for
85        each component (instead of from cell centered averaged) and use the 4
86        grid-cell corner averaged value of Omega*(R*cos_Phi)^2 in AM_eta part.
87      - Check that AM is conserved with linear dynamics (momAdvection=F and linear
88        FreeSurf) if using vectorInvariant momentum.
89    o model/src (horizontal grid):
90      - move initialisation of all horizontal grid arrays to null value
91        from specific horizontal grid S/R to main S/R INI_GRID;
92      - add 2 new arrays to project model C-grid velocity on to zonal direction
93        (similar to AngleCosC & -AngleSinC but at U and V point location) and
94        compute them in S/R CALC_GRID_ANGLES.
95    o pkg/seaice: replace a hard coded parameter by a runtime parameter
96        SEAICE_JFNK_tolIter
97    o pkg/seaice: introduce a restricted additive Schwarz (RAS) method in
98        preconditioner for JFNK (run LSR into the overlaps as far as possible,
99        i.e OLx/y-2, but overwrite the solution in the overlaps)
100      - extend loop range in seaice_calc_viscosity
101      - add new parameters SEAICE_OLx/y (default = OLx/y-2)
102      - add flexible loop ranges to seaice_preconditioner, seaice_calc_lsr_coeffs
103      - slightly modify loops in tridiagonal solver lsr-preconditioner
104      - by default remove the extra exchange in seaice_preconditioner with a
105        replacement of an undocumented CPP flag by SEAICE_PRECOND_EXTRA_EXCHANGE
106      - modify offline_exf_seaice so that old results without RAS are reproduced
107        for output.dyn_jfnk.txt
108      in seaice_fgmres.F (unrelated to RAS)
109      - add a cpp-flag option for a re-ordered mapping (potentially more
110        efficient), but because this changes the results, turn it off by
111        default
112      - replace the save statement by local common blocks
113    o utils/matlab:
114      - fix tile-offset in rdmnc.m when output was produced using EXCH2.
115      - update cs_grid/bk_line scripts to use load_grid.m (in utils/matlab)
116        instead of local script "load_cs.m".
117    o pkg/seaice:
118      - fix a serious bug in seaice_fgmres.F, s/r seaice_scalprod, connected
119        to the scalarProductMetric and the unrolling. By chance this does not
120        change the verification experiment, because of the particular domain
121        decomposition
122    o pkg/diagnostics:
123      - change default missing_value from UNSET_RL to -999.
124    o pkg/layers: improve vectorization of layers_fluxcalc.F
125      - step 1: split loops, make TatU/V 2D arrays. This alone reduces the cpu
126        time spent in this routine by more than a factor of 3 on an NEC-SX8
127      - step 2: replace search algorithm by a bisection algorithm found in
128        Press et al. Numerical Recipes in Fortran. This algorithm can be
129        vectorized and finds the correct bin in approx. log2(Nlayers) steps.
130        For now, use this algorithm only for TARGET_NEC_SX defined.
131      - moved the search algorithm into a separate subroutine, that is kept
132        within the same file for automatic inlining.
133      - modified catching potential errors
134    o pkg/ecco:
135      - add compile switches ALLOW_SHALLOW_ALTIMETRY and ALLOW_HIGHLAT_ALTIMETRY.
136    o model/src, pkg/autodiff, pkg/ctrl, pkg/grdchk :
137      - modifications for ALLOW_GENTIM2D_CONTROL
138      -- forward_step.F, the_main_loop.F : pass options and arrays for adjoint tapes.
139      -- load_fields_driver.F : add call to CTRL_MAP_GENTIM2D( myTime, myIter, myThid )
140      -- add xx_gentim2d0/1 in ctrl_ad_check_lev1_dir.h checkpoint_lev1_directives.h etc
141      -- use ctrl_swapffields.F (new) instead of exf_SwapFFields.F in ctrl_get_gen.F
142    o model/src:
143      - account for moist thermodynamics in (dry) potential temperature equation;
144        update results of experiments: aim.5l_cs (x2), fizhi-cs (std + aqualev)
145        and cpl_aim+ocn.
146      - also switch to standard compiler (gfortran, was using ifort previously)
147        for fizhi-cs experiments reference output.
148    o pkg/ctrl:
149      - 1st step toward generic time-varying control variable (2D) via CPP option
150        ALLOW_GENTIM2D_CONTROL
151      - note new namelist ctrl_nml_genarr in data.ctrl
152    o verification/global_ocean.cs32x15:
153      - switch off OLD_THSICE_CALL_SEQUENCE (both forward and AD code) to use new
154        thsice calling sequence and update "output.icedyn.txt" output file.
155    o pkg/ptracers:
156      - from Ryan A.: code to allow to restart a tracer at regular time interval
157        specifying a reset frequency and a reset-phase (for each tracers).
158    o pkg/thsice:
159      - implement new sequence of calls for thsice+seaice:
160          previously:   ice-Dyn,ice-Advect,ice-Thermo(thsice)
161          new sequence: ice-Thermo(thsice),ice-Dyn,ice-Advect
162      - allows (with temporary CPP option "#define OLD_THSICE_CALL_SEQUENCE"
163        in CPP_OPTIONS.h) to recover old sequence;
164      - update diagnostics for Intermediate State thsice diagnostics: now filled
165        just before advection (instead of just after advection in old sequence);
166      - update output of experiment offline_exf_seaice (standard test);
167      - in global_ocean.cs32x15 exp., postpone output.icedyn.txt update
168        by setting #define OLD_THSICE_CALL_SEQUENCE in CPP_OPTIONS.h
169    o pkg/aim_v23:
170      - use tiled array for aim_CO2 and surface wind speed for export to coupler;
171      - use standard pkg/mdsio routines to read & write CO2 pickup file;
172      - in-line S/R AIM_AIM2DYN_EXCHANGES in aim_do_physics.F;
173      - Implement new sequence of calls for seaice advection (with thsice and
174        seaice diffusion): do ice advection after ice-Thermodynamic (previously
175        was done before); change aim_do_physics.F (split the bi,bj loops block);
176      - use same CPP option (OLD_THSICE_CALL_SEQUENCE) to recover old sequence;
177    o pkg/thsice:
178      - add a missing EXCH of sIceLoad in thsice_main.F (ocean set-up) for the case
179        where just seaice diffusion is used without seaice-dynamics.
180    
181    checkpoint64c (2013/01/18)
182    o pkg/seaice:
183      - add a parameter JFNKres_tFac that can replace JFNKres_t
184        (= JFNKres_tFac*JFNKresidual before JFNK solver)
185      - add a line search option to the JFNK solver
186      - move update of u/vIce and computation of initial residual into a separate
187        routine (same file); makes the code a little easier to read (?)
188      - the line search requires computation of the residual and for some reason
189        I cannot do the update of u/vIce at the beginning of the Newton loop
190        without changing the results, so we move computation of the new residual
191        also to the end of the Newton loop, even without the line search
192    o pkg/mdsio:
193      - write missing value (corresponding to undefined array value) to meta files;
194        skip this if missing value is one (UNSET_RL would be a better value for the
195        case of undefined missing value but it's current the default missing-value);
196        Also update mdsio_read_meta.F (reading timeInterval & missing-value).
197    o pkg/exf & thsice:
198      - for diagnostics purpose, fill-up and update Qsw array (+ fill the
199        diagnostics) even when SHORTWAVE_HEATING is #undef;
200    o verification/cfc_example:
201      - turn on pkg/layers with pkg/diagnostics (to test pkg/layers and to
202        illustrate how to use it).
203    o verification/offline_exf_seaice:
204      in input: add SEAICErestoreUnderIce=.TRUE., and reduce size of forcing
205        files to only one time-record.
206      in input.thermo: narrow the 2 bands of low initial ice-concentration near
207        N & S edges; switch on SEAICErestoreUnderIce=T; use pkg/diagnostics for
208        snapshot output; same mcPheePiston value as in thsice with
209        surf-current=0.2m/s.
210      in input.thsice: similar set-up as in input.thermo (channel with same seaice
211        initial conditions).
212    o verification/cfc_example:
213      - update file "data" with more standard choice (default rotationPeriod,
214        exactConserv=T, reduce ivdc_kappa to 10, remove multiDimAdvection=F,
215        set deltaTFreeSurf to deltaTtracer) and update the output.
216    o pkg/layers:
217      - fix bolus part so that it compiles with #undef GM_BOLUS_ADVEC;
218      - ensure that "layers_bolus" is switched to False when useGMRedi=False.
219    o verification/offline_exf_seaice:
220      - set all {field}period to zero for constant-in-time forcing (not tested
221        anywhere else).
222    o verification/offline_exf_seaice:
223      - dyn_lsr  : use pkg/seaice S/R (instead of pkg/thsice) to advect sea-ice;
224      - dyn_jfnk : use pkg/thsice S/R (instead of pkg/seaice) to advect sea-ice.
225    o model/src:
226      - implement Finite-Volume method for (hydrostatic) presure gradient
227        from S.-J. Lin (QJRMS 1997), for atmosphere using sigma-coordinate.
228    o pkg/seaice: implement EVP* by Lemieux et al. (2012).
229      - In order to be compatible with the default EVP code, this requires changing
230        the EVP code around a little; and because any small change immediately
231        breaks the lab_sea.hb87 verification experiment, the reference output is
232        updated two times (each time the remaining aggrement was only 2 digits):
233        - after replacing 1/dt by 1*recip_dt with a precomputed recip_dt
234        - after replacing 1/(1+0.5*dt/tau) by a/(a+1), with a=2*tau/dt
235        The adjoint test lab_sea.evp also needed to be updated.
236      - Turn on EVP* by setting SEAICE_deltaTevp as before, and setting
237        SEAICEuseEVPstar=.true.; for EVP* SEAICE_deltaTevp does not need to be
238        a factor of SEAICE_deltaTdyn, and you can set the number of EVP steps
239        explicitly with SEAICEnEVPstarSteps (thereby overriding the default of
240        INT(SEAICE_deltaTdyn/SEAICE_deltaTevp)). Controlling EVP* is deliberately
241        kept obscure, because I need to test it a little more.
242    o pkg/cheapaml:
243      - fix few incorrect type (_RL/_RS) in subroutine calls.
244    o pkg/seaice:
245      - new S/R SEAICE_MAP_RS2VEC (similar to SEAICE_MAP2VEC) to map _RS arrays
246        to _RL vector; this fixes JFNK code when compiling with "-use_r4" option.
247    o model/src:
248      - add a warning if using select_rStar=2 with nonlinFreeSurf <> 4;
249        change (in input_ad*/data) select_rStar from 2 to 1 for AD verification
250        experiments global_ocean.cs32x15 & tutorial_tracer_adjsens (+ update output)
251    o pkg/cheapaml:
252      - replace "273.1 _d 0" by celsius2K in pkg/cheapaml/cheapaml.F and
253        update output of experiment cheapAML_box.
254      - store in CHEAPAML.h coeffs ssq[0:2] for saturation specific humidity,
255        and set them only in one place (cheapaml_readparms.F).
256      - replace "273.16 _d 0" by celsius2K & replace "3.14159 _d 0" by constant "PI"
257      - remove re-setting of main-model parameter "celsius2K" (in cheapaml_readparms)
258        and re-setting of cheapAML params "lath" & "p0" (in cheapaml_init_varia).
259    o model/src/the_main_loop.F:
260      - fix revision 129 : need both ALLOW_ECCO and ALLOW_ECCO_EVOLUTION.
261    o pkg/seaice:
262      - remove legacy branch code.
263      - retire SEAICE_GROWTH_LEGACY and SEAICE_CAP_HEFF accordingly.
264    o verification/*/code*/SEAICE_OPTIONS.h:
265      - remove documentation for retired CPP flags (SEAICE_GROWTH_LEGACY,
266        SEAICE_CAP_HEFF).
267    o pkg/cheapaml:
268      - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
269        to load new forcing fields.
270      - add missing "_d 0" where it's needed; + some editing (improve indentation).
271      - remove switch to "-r8" compiler option (no longer needed) in verification
272        cheapAML_box, keep same output (small trucation error differences).
273    o verification/offline_exf_seaice:
274      - add thermodynamics only test.
275    o verification/cheapAML_box:
276      - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
277        keep same output (same 14 digits for cg2d).
278      - switch on "-r8" compiler option (some numerical values are missing
279        the "_d 0") and update output (only 6 digits for cg2d were preserved).
280    
281    checkpoint64b (2012/12/24)
282    o pkg/cheapaml:
283      - remove un-used variables (Qnet,EmPmR) from pickup files.
284      - store tendency of advected variables into cheapaml pickup file
285        and fix the AB-2 restart.
286    o verification/offline_exf_seaice and lab_sea adjoint:
287      - switch to new code (#undef SEAICE_GROWTH_LEGACY).
288      - switch to 4 time steps in offline, consistent with lab_sea.
289      - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
290      - update results after change of experiment seaice.
291    o pkg/seaice:
292      - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
293        parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
294        still defined since SEAICE_multDim needs to be set to MULTDIM value (from
295        SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
296    o model/src:
297      - add run-time parameter to select CG2D solver minimum-residual solution
298        (in case of a poor convergence).
299    o pkg/seaice/seaice_lsr.F
300      - move calculation of matrix coefficients into new
301        S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
302        file; the main purpose of this change is to be able to reuse the code
303        in S/R SEAICE_PRECONDITIONER
304      - modify the computation of the residual so that the mass of sea-ice
305        is not used twice; this simplifies the calculations, but since
306        the residual is never used except when LSR_mixIniGuess.ge.4---and this is
307        not tested in testreport---this does not affect the testreport results.
308    o verification/seaice_obcs:
309      - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
310        verification/lab_sea/input.salt_plume; changes results/output.txt*
311    o model/src:
312      - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
313    o pkg/seaice:
314      - improve description of parameters in seaice_fgmres.F and start
315        cleaning up the code
316      - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
317        second argument
318      - add a metric based on grid cell area to SEAICE_SCALPROD; update
319        results of offline_exf_seaice.dyn_jfnk
320      - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
321    o pkg/aim_v23:
322      - fix an other bug in dissipation heating (grid-cell area was missing).
323    o model/src + pkg/seaice:
324      - add global (multi-tile) linear solver for pair of tri-diagonal system
325        along X and Y lines, respectively for U and V component.
326        Note: 1) MPI and cube-exchange not yet coded.
327            2) probably not accurate for poorly conditioned / large size problem.
328      - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
329        default: not compiled and not used.
330    o pkg/seaice:
331      - first attempt at a multi-threaded fgmres solver for the JFNK solver:
332        introduce bi/bj loops and use global_sum_tile_rl instead of
333        mpi_allreduce in seaice_fgmres.F
334      - improve diagnostics output for fgmres solver (seaice_fgmres.F)
335      - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
336      - add a verification experiment for JFNK in offline_exf_seaice
337    o verification:
338      - change (for now, only fwd test) offline_exf_seaice experiment:
339        use a re-entrant channel with idealized coastline (trapezoidal shape)
340        at southern boundary to explore seaice dynamics and thermodynamics
341        with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
342        secondary test (input.thsice) use thermodynamics only with SST relaxation.
343      - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
344    o pkg/exf:
345      - disable "sstExtrapol" when Nr=1
346    o verification:
347      - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
348        to test pkg/cheapaml.
349    o pkg/aim_v23 & pkg/shap_filt:
350      - fix dissipation heating (erroneous gravity multiplication factor).
351    o pkg/seaice:
352      - remove unused field pressPre from jfnk solver
353      - rename two subroutines in seaice_preconditioner.F
354    o eesupp/src:
355       - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
356    o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
357       - remove wrong parts of the rhs and the lhs (were in there
358         because I did not understand the concept of this preconditioner)
359       - add an exchange between u- and v-sweep. This increases communication
360         by a factor of two but improves the convergence of jfnk. Ideally,
361         one would like the u- and v-sweep to be independent. So far within
362         undocumented ifdefs
363       - reorganize the extra computations for printing the residuals
364    o tools/genmake2:
365      - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
366        since it's not necessary (and was preventing to use MNC in some cases).
367    
368    checkpoint64a (2012/11/16)
369    o pkg/autodiff:
370      - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
371        autodiff_readparms.F no longer depends on calling order (within
372        packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
373        rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
374        and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
375    o pkg/obcs:
376      - adding tidal velocity forcing capability to obcs
377        for usage example, see verification/seaice_obcs/input.tides
378    o pkg/seaice:
379      - turn the LSR-relaxation parameters WFAU/V into runtime parameters
380        SEAICE_LSRrelaxU/V
381      - introduce runtime parameter SEAICEetaZmethod (=0 by default)
382    o pkg/aim_v23:
383      - implement heating from friction (bottom friction and stratospheric drag).
384    o pkg/shap_filt:
385      - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
386        dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
387    o model/src:
388      - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
389        time-constant addMass field from file (addMassFile);
390      - support for heating due to friction (and Kinetic Energy dissipation):
391        add option, run-time switch and 3-D field array + support code ; each pkg
392        or S/R can add heating contribution (if there is a sink of KE); the sum is
393        accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
394    o pkg/seaice:
395      - complete merge of ITD code into seaice_growth.F
396        from MITgcm_contrib/torge/itd/code/
397        no verification so far, but Torge Martin tested
398        "1-D test case and Beaufort set up;
399        deliver okay results after 1 model year."
400      - complete merge of SEAICE_SIZE.h into all relevant routines
401      - move computation of eta at Z-points into calc_viscosities
402        + introduce global field etaZ
403        + add different methods for computing etaZ, for now the old
404          method (simple averages of eta to Z-points) is hardwired
405        + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
406          seaice_preconditioner
407      - simplify computations for SEAICE_ZETA_SMOOTHREG
408      - seaice_preconditioner:
409        + replace one remaining press by pressLoc (mistake)
410        + adjust printing of residuals
411      - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
412        + add (SEAICE.h) and rename some counters (initiliased in
413          seaice_init_fixed.F)
414        + add _BEGIN/END_MASTER (myThid)  around print statements
415        + print total number of iterations and failures over SEAICE_monFreq
416          interval to STDOUT
417      - move control over output-messages by fgmres to seaice_jfnk to save
418        some operations
419      - move resetting initial guess for fgmres outside of seaice_fgmres_driver
420        in order to make restarts with sol .ne. zero (fgmres with restarts)
421        (seaice_jfnk.F, seaice_fgmres.F)
422      - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
423        a serious convergence problem when open boundaries are involved
424    o pkg/ggl90: fix computation of control volumes for the case of
425      ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
426      up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
427    o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
428    o pkg/autodiff
429      - Add inAdMode switch for SEAICEuseDYNAMICS:
430        SEAICEuseDYNAMICSinAdMode
431        (extend logic in ADAUTODIFF_INADMODE_SET)
432    o pkg/seaice
433      - Step 1 of merging ice-thickness distribution (ITD) code from
434        MITgcm_contrib/torge/itd/ (author: Torge Martin)
435        The code implements concept laid out in Thorndike et al. (1975);
436        code is enabled via CPP flag SEAICE_ITD
437        nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
438        code is not complete yet!!
439      - SEAICE_SIZE.h now included in almost all seaice routines
440    o verification (using seaice):
441      - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
442        global_ocean.cs32x15.seaice ; update results.
443      - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
444      - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
445        offline_exf_seaice (previously compiling B-grid).
446    o pkg/exf:
447      - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
448        to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
449        forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
450    o pkg/layers (adjust changes from Sept 19):
451      - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
452        this allows to remove "layers_maxNum" dimension from all layers arrays.
453    o pkg/layers (adjust changes from Sept 19):
454      - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
455      - snap-shot extended to all type of layers (not just the 1rst type);
456      - remove layers variables when corresponding CPP option is undef.
457    o pkg/layers:
458      - rename pkg/layers variable and add new output (layer exist & un-weighted
459        velocity in layer)
460    o pkg/seaice:
461      - simplify (?) ocean-drag coefficent computations by using
462        the same routine in all three solvers (saves some code lines)
463      - remove global fields DRAGA and DRAGS from C-grid code and
464        declare them locally in lsr.F (the only place where they are
465        still used)
466      - update AD output of lab_sea.evp (very sensitive anyway).
467    o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
468      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
469      and SEAICEuseJFNK=.true. A few things to note:
470      - involves a FGMRES, that is parallel but very inefficient,
471        because of many scalar products (global sums) in the Gram-Schmidt
472        orthogonalization method. Needs to be replaced. Original code
473        from J.-F. Lemieux
474      - preconditioner for FGMRES is a stripped down version of LSOR
475      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
476        preconditioner. For the preconditioner, the default is set to 10.
477      - Jacobian times vector is computed with finite differences
478      - marginally related to JFNK-solver: add a smooth regularization for
479        zeta with tanh that will improve convergence (Lemieux and Tremblay,
480        2009) for any implicit solver (not implemented for EVP because EVP
481        does not need this regularization in the first place). Define
482        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
483    o eesupp/src:
484      - check in genmake2 that intrinsic S/R flush is available.
485      - add S/R to flush IO unit (if intrinsic S/R flush is available)
486      - flush standard & error msg unit before MPI termination
487      - if debugMode, flush IO unit after printing msg
488    o pkg/ctrl:
489      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
490        to ctrl_set_unpack_xyz.
491    
492    checkpoint64 (2012/10/09)
493    o pkg/shelfice
494      - in mom_fluxform.F, mom_vecinv.F:
495        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
496        Bug fix KappaRU -> KappaRV
497        does not change verification/isomip but may change other setups
498        (presumably constant KappaRU=KappaRV)
499      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
500    o pkg/obcs:
501      - fixed some indexing bugs in obcs_seaice_sponge.F
502      - added obcs relaxation subroutines for HSALT and HSNOW
503      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
504    o pkg/seaice:
505      - add "multicategory" parameterization for snow in analogy to ice,
506        default is off for now.
507    o pkg/obcs:
508      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
509        see verification/seaice_obcs/input.seaiceSponge for example application.
510      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
511        index setting by master-thread. This fix multi-threads Pb in previous modifs.
512    o pkg/layers :
513      - add diagnostics to pkg/layers
514      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
515        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
516    o pkg/generic_advdiff/gad_implicit_r.F :
517      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
518    o pkg/seaice/seaice_growth.F:
519      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
520    o pkg/obcs:
521      - change default setting of OBCS_UVICE_OLD from defined to undef;
522      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
523        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
524      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
525      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
526        with Southern & Western OB at a tile edge (at least in a simple set-up).
527    o pkg/obcs:
528      - change settings of OB index in case OB coincides with tile edge (shared by
529        2 tiles), so that common OB location is registered by both tiles (instead of
530        only 1). However, for Southern and Western OB, index value = 0 is not
531        recognized as valid OB index (=default null value) and needs to be fixed.
532      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
533      - new parameter "OB_indexNone" for null index value (for now, still zero)
534        to replace hard-coded null index value of zero.
535    o pkg/exch2:
536      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
537        always check buffer-size (but outside the loop); move checking for valid
538        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
539        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
540    o pkg/ctrl (pack & unpack):
541      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
542        (locally defined) for different variables (+ remove the variable-specific
543        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
544        (to be extended to other local file names in ctrl.h).
545    o pkg/flt:
546      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
547    o pkg/mdsio:
548      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
549    o tools/genmake2:
550      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
551        (added by Alistair in version 1.51 for building without make depend);
552      - remove Header files list (H_SRC_FILES) from the dependence of targets
553         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
554        place in version 1.23): this save going through staf when unrelated header
555        file has been modified.
556       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
557        "make depend" step, still need to do "make links" before "make adtaf".
558    o eesupp/src (+ few pkg src files) & genmake2:
559      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
560      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
561      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
562         upper/lower case ; account for space between "#" and undef/define)
563    o pkg/flt (with exch2):
564      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
565      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
566    
567    checkpoint63s (2012/09/05)
568    o pkg/ecco:
569      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
570      - add more relevant #ifdef ALLOW_SMOOTH ones.
571      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
572    o pkg/ctrl:
573      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
574        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
575      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
576        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
577        ctrlSmoothCorrel3D (new).
578        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
579      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
580      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
581        controls when useAtmWind, and vice versa.
582      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
583      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
584          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
585      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
586          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
587      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
588        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
589    o pkg/smooth:
590      - remove un-necessary includes.
591      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
592        Those CPP options were never defined, and not necessary.
593    o model/src:
594      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
595      - standard treatment of useSMOOTH.
596    o pkg/autodiff:
597      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
598        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
599    o pkg/exch2:
600      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
601        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
602      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
603        and tiles to process mapping.
604      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
605        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
606        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
607        from w2_eeboot.F to w2_readparms.F.
608    o eesupp/src:
609      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
610        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
611        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
612      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
613        is defined (remove condition on usingMPI) to match cases where MPI_INIT
614        has been called.
615      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
616      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
617        (so that on 1 proc, get same myPid independently of usingMPI)
618      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
619        useCubedSphereExchange with EXCH-1 (safer).
620      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
621    o pkg/ggl90:
622      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
623        used in ALLOW_GGL90_SMOOTH code.
624    o pkg/flt:
625      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
626        floats at the Southern end of the domain).
627    o eesupp/inc:
628      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
629        but not used (and not to be used) anywhere, just for documentation.
630    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
631      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
632        a) can damage previously written records in any other multi-record files.
633        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
634    o tools/genmake2:
635      - define variable MAKE within Makefile and use it in place of 'make';
636      - update AD_CONFIG.h (if needed) before building any of the executable
637        (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
638        and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
639      - always print usual warning comment 'this file is automatically generated'
640        from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
641    o pkg/cheapaml:
642      - updated to correspond to the code used in accepted paper (Nico Wienders).
643    o pkg/exf:
644        added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
645        ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
646        and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
647    o pkg/exf, autodiff, ctrl, ecco and seaice:
648        remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
649    o pkg/ctrl, ecco:
650        allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
651        Depending on useAtmWind, one is inactive, and the other is active (see
652        exf_getffields.F/exf_getsurfacefluxes.F).
653    o tools/genmake2:
654      - improve error msg when failing in 2nd test of check_for_broken_Ff
655      - fix option '-makefile' short-name (-mf according to genmake2 -help)
656      - source local config file "genmake_local" just after processing the genmake2
657        command arguments (previously done before processing arg).
658    o pkg/grdchk:
659      - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
660        to this routine from cost_final has been dropped in g_cost_final)
661      - improve printed information (more explicit msg, no longer using "print *,"
662         fix fcpertminus printed value).
663    o model/src:
664      - move call to COST_INIT_VARIA out of packages_init_variables.F directly
665        into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
666        this prevents getting cost-funct reset in adinitialise_varia recomputations.
667    o pkg/dic:
668      - move initialisation of "freefe" array from from dic_biotic_forcing.F to
669        fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
670    o pkg/grdchk:
671      - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
672      - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
673    o pkg/autodiff/ctrl/grdchk :
674      - attempt to sort out what works and what does not,
675        with regard to I/O, and to warn/stop accordingly.
676    o pkg/grdchk:
677      - attempt to fix grdchk in the case of useSingleCpuIO.
678      - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
679       statements were moved from grdchk_main.F and into
680       grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
681      - a global sum is applied to record numbers icvrec/layer
682       out of grdchk_loc so that they be passed to I/O routines.
683    o pkg/smooth:
684      - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
685        smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
686    o verification/testreport:
687      - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
688      - can also use compressed (gzip) reference output file;
689      - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
690        to be easier to collect by testreport.
691      - update existing TLM output (half out-of-date by more than 3 yrs).
692      - report NETCDF & LAPACK settings (from genmake2) in output dir.
693      - report run-time in each individual summary (previously only for AD test);
694        for TLM test, add also TAF version.
695      - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
696    
697    checkpoint63r (2012/08/15)
698    o tools/genmake2:
699      - fix Makefile for target ftlall (+ update files to clean after make ftlall)
700    o pkg/ecco/ecco_cost_final.F :
701      - fix fc print statements (to stdout and costfunction0000) so
702        that the printed value is always after the global sum.
703    o pkg/seaice/seaice_dynsolver.F :
704      - fix ice strength assymptote at SEAICE_area_max<1
705        (no change for the standard case of SEAICE_area_max=1)
706    o some cleaning:
707      - pkg source files: ensure that all *.F files from each pkg included the
708        corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
709        only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
710        code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
711        includes;
712      - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
713      - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
714        is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
715        ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
716      - update option-file CPP_OPTIONS.h of all AD experiments:
717        * no longer include PACKAGES_CONFIG.h ;
718        * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
719        * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
720          including ECCO_CPPOPTIONS.h).
721    o pkg/cost, pkg/ctrl, pkg/ecco option-file:
722      - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into
723        separated pkg option-file (done according to old doc from ECCO_CPPOPTIONS.h,
724        not necessary accurate).
725      - add a template for option-file ECCO_CPPOPTIONS.h, mostly empty, in
726        pkg/autodiff, i.e., the 1rst pkg to compile for adjoint built, with lines to
727        deliberately break compilation (a remainder that it needs to be customized)
728      - in pkg/ecco, includes ECCO_OPTIONS.h instead of COST_OPTIONS.h
729      - rename COST_CPPOPTIONS.h to COST_OPTIONS.h
730      - rename CTRL_CPPOPTIONS.h to CTRL_OPTIONS.h
731    o tools/genamke2:
732      - check for lapack.
733    o pkg/cost and pkg/ecco : attempt to sort out some of the limiting intricacies.
734      - pkg/cost.cost_final.F : allow for use of pkg/ecco and pkg/cost cost functions
735        jointly. The exclusive ifdefs were removed, to add costs terms (when defined)
736        from both packages.
737      - the fc global sum in pkg/ecco/ecco_cost_final.F was removed accordingly.
738      - for objf_atl we use either the pkg/ecco or the pkg/cost term depending on CPPs.
739      - pkg/ecco and model/src : add CPP brackets around pkg/cost and pkg/ctrl includes
740        of "CTRL_SIZE.h" "ctrl.h" "ctrl_dummy.h" "optim.h" / "cost.h" accordingly.
741    o pkg/cost : add comments to explain special and/or untested setups.
742    o pkg/exf:
743      - use EXF_OPTIONS.h to set pkg/exf options except if done in ECCO_CPPOPTIONS.h
744        (previously, ALLOW_AUTODIFF_TAMC was controling this switch).
745    o verification/*/code_ad:
746      mimimal cleaning of AD experiments ECCO_CPPOPTIONS.h option-file:
747      - reccord when this file is included (define ECCO_CPPOPTIONS_H)
748      - remove the most obvious obsolete features (e.g., #define ALLOW_COST not
749        allowed since Oct 2003 in any option-file except in PACKAGES_CONFIG.h)
750    o pkg/seaice :
751      - added possibility to change ice strength/PRESS0 relationship to
752        HEFF, according to the following run time parameters
753        SEAICEpresPow0 :: HEFF exponent for ice strength below SEAICEpresH0 (integer, >0)
754        SEAICEpresPow1 :: HEFF exponent for ice strength above SEAICEpresH0 (integer, >0)
755        SEAICEpresH0   :: HEFF threshold for ice strength            (m)
756    o pkg/ggl90 :
757      - added run time flag mxlSurfFlag to include the code that ensure
758        mixing between first and second level (previously included as a comment)
759    o verification/1D_ocean_ice_column/input_ad/data.autodiff :
760      - add test of newly added dumpAdByRec=T option where
761        we write all records to one file per variable.
762    o verification/global_ocean.cs32x15/code_ad/CPP_OPTIONS.h :
763      - switch to #define ALLOW_BALANCE_RELAX and ALLOW_BALANCE_FLUXES
764        to check that this code is ok with taf and compiles in adjoint.
765    o pkg/autodiff :
766      - added run time param dumpAdByRec : ad dump format switch.
767        If true then write all records to one file per variable.
768        Else write one file per record (remains the default).
769      - revise seaice_ad_dump.F and exf_adjoint_snapshots_ad.F accordingly.
770    o pkg/seaice:
771     - Added SEAICEuseTILT run time switch : if set to
772       false then omit the tilt term in seaice dynamics.
773     - Fix free drift calculation.
774    o pkg/shelfice:
775      When initializing SHELFICEDragQuadratic, set default to be
776      consistent with shiCdrag in case SHELFICEuseGammaFrict is used,
777      but retain option to set it independently
778      (inconsistenty spotted by Veronique Dansereau)
779    o eesupp/inc:
780      - in EEPARAMS.h, add real-type constant for some frequently used simple number
781         (0,1,2,1/2), with name explicitly referring to RS/RL type.
782    o model/src:
783      - move balancing of relaxation terms to new S/R balance_relax.F.
784    o pkg/autodiff:
785      re-write active I/O high-level (control) S/R:
786      - rename  S/R ACTIVE_READ/WRITE_RL to ACTIVE_READ/WRITE_3D_RL
787      - add 1 more argument (useCurrentDir) to replace the "_LOC" 2nd set of S/R.
788      - use standard pkg/mdsio I/O routines (MDS_READ/WRITE_SEC_XZ/YZ  and
789        MDS_READ/WRITE_FIELD); change loops to multi-threads.
790      - update and merge active_file_control_slice.flow into active_file_control.flow
791      - update the calls in lower level S/R (active_file.F, active_file_g.F and
792        active_file_ad.F) keeping the argument list and function unchanged.
793      - also update lower-level "_LOC" version (call same S/R with "useCurrentDir
794        =.TRUE.") and remove high-level (control) _loc version (not called anymore).
795      - new low-level active I/O routines, one for each type (RL/RS), for active var
796        of various (XY,XZ,YZ) shape and level number (arguments: arrShape, myNr);
797        fix ctrl_init_wet.F & ecco_cost_weights.F by calling the new S/R with the
798        right type.
799    o autodiff and RS=real*4:
800      - call the right type (_RS instead of _RL) of S/R in few output S/R (pkg/exf
801        ad-monitor and snapshots); disable arrType='RS' in mdsio_gl*.F ;
802      - change argument type of 3-D mask argument to _RS to match type in the call
803        (in seaice_cost*.F, ctrl_*_gen.F and *ctrl_bound.F); to be continued.
804    o pkg/thsice:
805      - re-anable balanceEmPmR when useSEAICE=T with useThSIce=T.
806      - option to correct ocean fresh-water flux for imbalance of Atmos+Land
807        fresh-water flux: uniform correction or proportional to local precip.
808    o pkg/ctrl:
809      - new header file CTRL_SIZE.h for parameters maxCtrlArr2D, maxCtrlArr3D
810      - redefine CPP option ALLOW_BOTTOMDRAG_CONTROL to
811                            ALLOW_BOTTOMDRAG_CONTROL_NONGENERIC
812      - verification/hs94.1x64x5/ tests ALLOW_GENARR{2D,3D}_CONTROL
813    
814    checkpoint63q (2012/07/30)
815    o pkg/autodiff:
816      note about monitor and snap-shot of ad-variables:
817      a) need to apply ADEXCH before monitor or output of ad-vars to include
818       overlap contributions (was done for adjDump but missing for monitor).
819      b) since ADEXCH implies adding overlap values to interior array, machine
820       truncation error is expected when adding an ADEXCH call in the middle of
821       the time-stepping (although mathematically identical).
822      modifs:
823      - fix some incorrect type (RL/RS, UV/scalar) in ADEXCH calls and ad-vars
824        declaration (adEddyPsiX,adEddyPsiY in adcommon.h).
825      - add new run-time params (dumpAdVarExch & mon_AdVarExch) to select how  to
826        apply ADEXCH before monitor or snap-shot of ad-variables:
827           =0 : no ADEXCH ; =1 : do ADEXCH ; =2 : apply ADEXCH on a local copy.
828      - implement new method (copy+adexch) for snap-shot and monitor of main model
829        ad-vars (initially not used by default -> output unchanged).
830      - change default (set to 2) to use new method and update few output_adm.txt
831        with accurate ad-monitor (global_ocean.90x40x15, tutorial_global_oce_biogeo
832        and both tutorial_tracer_adjsens tests).
833      - switch 2 global_ocean.cs32x15 AD-tests to AB-2 (seaice_dynmix & thsice)
834        and turn off momDissip_In_AB in the 2 other (needed for stable AB-3).
835    o pkg/ctrl:
836      enable the use of a variable number (maxCtrlArr2D, maxCtrlArr3D) of
837      generic control variables via
838      #define ALLOW_GENARR2D_CONTROL and/or #define ALLOW_GENARR3D_CONTROL
839      Only required customization should be S/R ctrl_map_ini_genarr.F
840      (routine in repository contains example)
841    o pkg/exf:
842      - fix and refine checking of surface-relaxation setting when using EXF
843    o verification (adjoint exp):
844      - reduce length of simulation by half for experiment global_ocean.cs32x15
845        (std, seaice & seaice_dynmix) and exp tutorial_dic_adjoffline; update output.
846    o pkg/mom_common (mom_u/v_bottomdrag), pkg/shelfice (shelfice_u/v_drag)
847      - replace if statements KE.ne.0 with KE.gt.0 to avoid sqrt of negative numbers
848        of KE that can occur with aggressive optimization
849      + put quadratic bottom drag calculation in separated loops (only done if
850        using bottomDragQuadratic)
851    o model/src: CG2D_NSA
852      - clean-up:  stop if cg2dNormaliseRHS=T and AUTODIFF
853         and replace GLOBAL_SUM calls with GLOBAL_SUM_TILE.
854      - in test-exp that uses CG2D_NSA (bottom_ctrl & tutorial_tracer_adjsens),
855         change cg2d residual target to be expressed in Wunits (=> do not normalise
856         RHS ; this fix global_max Pb with TAF); update output.
857    o verification/tutorial_tracer_adjsens:
858       improve parameter consistency (and get rid of warnings):
859       - use deltaTFreeSurf=deltaTtracer (better with NonLin FreeSurf);
860       - switch Temp Adv Scheme from 81 to 80 (no limiter since theta < 0 is physical)
861       - use staggerTimeStep (for stability) in som81; use default rotation period.
862    o pkg/exch2:
863      - with empty facet: fix compact-format (W2_mapIO=1) definition (was previously
864        reset to 0 = 1 long line in X)
865    o pkg/mdsio:
866      - fix reading of dimensions from meta file for large-size domain
867    o model/src:
868      - fix saltIsActiveTr setting for IdealGas eosType (eosType is 6 character long);
869      - to refine CS-grid check, add logical flag "hasWetCSCorners": true if using
870        Cubed-Sphere Exch with CS-corners inside the domain;
871        make new S/R INI_GLOBAL_DOMAIN from code in ini_linear_phisurf.F to calculate
872        globalArea and to set hasWetCSCorners.
873      - add warning if usingCurvilinearGrid and momAdvection in flux-form (missing
874        metric terms); stop if hasWetCSCorners=T and momAdvection in flux-form.
875      - re-activate the stop if useCDscheme and hasWetCSCorners=T (previously if
876        useCDscheme and useCubedSphereExchange).
877    o pkg/seaice/seaice_growth.F :
878      - compute the SEAICE_DISABLE_HEATCONSFIX term accordingly
879        for the (.NOT.useRealFreshWaterFlux).OR.(nonlinFreeSurf.EQ.0)
880        when the previous code was not correct.
881      - in all cases diagnoze the boundary condition mismatch to SIaaflux
882      - in the case of useRealFreshWaterFlux.AND.(nonlinFreeSurf.GT.0) add
883        that term to QNET (essentially to set the melt/freeze water to 0degC).
884        when SEAICEheatConsFix is true, so that the ocean+ice budget heat is closed.
885    o verification/global_ocean.cs32x15/input.seaice :
886      - add SEAICEheatConsFix in data.seaice, ensuring closed ocean+ice heat budget.
887      - add diagnostics (commented out) for budget test using my matlab codes (gcmfaces).
888      - update results (output.seaice.txt) accordingly.
889    o verification/lab_sea/input/data.seaice :
890      - remove SEAICEheatConsFix, which is now be tested
891        in global_ocean.cs32x15. The presently coded fix
892        is only consistent with real fresh water + nlfs.
893      - update results (output.txt) accordingly.
894    o pkg/salt_plume: added diagnotic for salt tendency (oceSPtnd).
895    o AD_CONFIG.h file:
896      - in genmake2: remove "#undef ALLOW_ECCO_OPTIMIZATION" from AD_CONFIG.h;
897      - remove #include "AD_CONFIG.h" from all included OPTIONS files and
898        add it explicitly in each fortran src file where it is needed.
899        motivation: header file AD_CONFIG.h is generated/modified after "make depend"
900        thus introducing potentially wrong dependency; therefore, better to include
901        it only where it's really needed, and after any other included OPTIONS file
902        (less tempting to bring conditional includes according to ALLOW_ADJOINT_RUN
903        or ALLOW_TANGENTLINEAR_RUN).
904    
905    checkpoint63p (2012/07/06)
906    o pkg/autodiff:
907      - rename S/R INI_AUTODIFF to AUTODIFF_INIT_VARIA ;
908      - create new header file "AUTODIFF_PARAMS.h" for pkg/autodiff parameters
909        which are now read from new parameter file "data.autodiff" (inAdExact
910        previously in "data", use{KPP/GMRedi/SEAICE}inAdMode previously in data.pkg)
911      - add file "data.autodiff" in all verification/*/input_ad/ directories.
912      - add run-time parameter to turn On/Off SEAICEuseFREEDRIFT in adjoint/forward
913        mode (used in global_ocean.cs32x15.seaice_dynmix test exp.)
914    o verification/tutorial_tracer_adjsens/
915      - add extra sub-verification which uses "SOM" advection scheme
916        (2nd Order-Moment Advection Scheme, Prather Limiter) with
917          #define GAD_ALLOW_TS_SOM_ADV in GAD_OPTIONS.h
918        and in data:
919          multiDimAdvection=.TRUE.,
920          tempAdvScheme=81,
921          saltAdvScheme=81,
922    o model/src:
923      - introduce ALLOW_BALANCE_RELAX which allow the removal
924       of the global mean of relaxation terms by setting
925       balanceThetaClimRelax and balanceSaltClimRelax
926      - disable balanceEmPmR and balanceQnet in the case when useSeaice.
927       This case is now treated appropriately in seaice_growth.F
928    o pkg/seaice:
929      - do balanceEmPmR and balanceQnet based on the net fluxes
930        (SItflux) that enter the ocean+ice system rather than QNET
931        and EMPMR. Works best in real fresh water.
932      - SIatmFW, SIatmQnet, and SItflux computations had to be moved
933        out of the diagnotics bloc, and stored in global arrays.
934    
935    checkpoint63o (2012/06/29)
936    o vertical mixing schemes:
937      - remove unused S/R CALC_BUOYANCY (left from branch-atmos merging)
938      - replace computation of density (in Function STATE1, opps_calc.F) by a call
939        to S/R FIND_RHO_SCALAR
940      - pass sigmaR to S/R PP81_CALC, MY82_CALC (but not yet used) and to GGL90_CALC
941        and use it for N^2 calculation in ggl90_calc.F (save 2 density computations);
942        affects output (vermix.ggl90) at truncation level.
943    o testreport:
944      - change adjustment of SIZE.h for mpi+mth testing: preserve enough tiles
945        (nSx,nSy) for the number of threads (from eedata.mth)
946    o model/src:
947      - remove 2nd set of calls at the top of initialise_varia.F (Adjoint part)
948        related to Non_Lin Free-Surf or Bottom-Control (but not longer necessary).
949    o verification/tutorial_tracer_adjsens/
950      - compile with ALLOW_CG2D_NSA
951      - run with nonlinFreeSurf=3
952      - update reference output_adm.txt
953    o tools/genmake2:
954      - add "-DHAVE_NETCDF" to the DEFINES list when NetCDF is available ;
955        refine usePROFILES switching off (only when NetCDF is not available).
956    o verification (atmospheric set-up):
957      - change eosType='IDEALGAS' to eosType='IDEALG' to match variable declaration
958    o pkg/profiles : refine profiles and files handling.
959    o model/src and pkg/ecco : introduce run-time switch usePROFILES.
960    o model/src/the_main_loop.F, forward_step.F and pkg/exf/EXF_OPTIONS.h :
961      - changes to use model/src/the_main_loop.F rather than the ecco version
962        in ecco type adjoint runs.
963    o model/src:
964      - move computation of recip of grid distance & area from INI_MASKS_ETC to INI_GRID
965      - move setting of h0Fac[C,W,S] from INI_LINEAR_PHISURF to INI_MASKS_ETC
966      - update_masks_etc.F: rename SMOOTH*_R4,R8 function to the corresponding type (RS,RL)
967    o model/src:
968      - fix S/R UPDATE_CG2D for ALLOW_DEPTH_CONTROL case (was empty before);
969        update output of test experiment bottom_ctrl_5x5.
970    o pkg/generic_advdiff:
971      - implement vertical bi-harmonic diffusion (for now, only for T & S and
972        only explicitly).
973    o verification/bottom_ctrl_5x5/
974      update reference output (results changed quite some time ago,
975      not sure when; but new reference results look ok in terms of grdchk)
976    o verification/1D_ocean_ice_column/
977      For verification purposes, the exact adjoint rather than an approx.
978      should be used (e.g., to comare against F.D. or TLM).
979      removed autodiff_inadmode*_ad.F routines in code_ad/
980      Update results/ accordingly.
981    o pkg/cal:
982      - change cal_getdate.F so that output date is function of input time only
983        (less ambiguous, not mixed up with input iteration number).
984      - fix calendarDumps for non-zero phase-lag (S/R CAL_TIME2DUMP).
985    o pkg/diagnostics:
986      - implement calendarDumps also for stats-diags
987      - implement calendarDumps also for snap-shot output (negative freq)
988      - for now, ignores calendarDumps if non-zero phase-lag.
989    
990    checkpoint63n (2012/06/04)
991    o model/src:
992      - recompute rSurfW & S to ensure consistent column thickness (needed for rStar)
993        between Sum_k(hFac*drF) and rSurf-rLow, for now only when using pkg/shelfice;
994      - use h0FacC, W & S to compute hFac_surfC, W & S in calc_surf_dr.F (more
995        similar to calc_r_star.F); update results of experiment internal_wave and
996        tutorial_global_oce_in_p (affected @ truncation level).
997    o pkg/shelfice:
998      - add parameterisation of advective-diffusive flux into the ice shelf
999        according to Holland and Jenkins (1999), eq.22-33, as suggested by Jan De Ryd
1000      - simply eps3/3a computation
1001    o eesupp:
1002     - add new CPP option (DISCONNECTED_TILES) to disconnect tiles (no exchange
1003       between tiles, just fill-in edges assuming locally periodic subdomain) and
1004       add corresponding exchange subroutines (EXCH0);
1005     - new CG-solver version (_EX0) for disconnected-tiles special case.
1006    o model/src (CG-solvers):
1007     - modify Single-Reduction version (CG2D_SR) in case cg2dMaxIters is reached
1008       (similar final residual output and max-Iter number as with standard version);
1009     - allows to store and use lowest-residual solution (standard & _SR versions);
1010     - cleaning up (remove old, commented out code, LETS_MAKE_JAM ...).
1011     - by default, also compile CG2D_SR version (define ALLOW_SRCG in CPP_OPTIONS.h)
1012    o eesup/src:
1013     - global_vec_sum.F cleaning: add a BARRIER ; update comments ; remove ndef
1014       ALWAYS_USE_MPI (no longer needed after fixing usingMPI settings - March 2012)
1015    o pkg/salt_plume added to lab_sea/input_ad.noseaicedyn
1016    
1017    checkpoint63m (2012/04/27)
1018    o pkg/shelfice:
1019     - account for partical cells in surface level below ice-shelf for hydrostatic
1020       pressure calculion (set uniformFreeSurfLev to F); update isomip experiments.
1021    o ad test experiments:
1022     - update and rename to "ad_optfile.local" local AD-optfile specific to a
1023       particular adjoint verification experiment (in verification/*/code_ad/)
1024    o pkg/seaice & pkg/exf:
1025     - Part two of ECCO-CLIVAR code merges.
1026       Completes merge of seaice area relax. code.
1027       Requires unified CPP option EXF_ALLOW_SEAICE_RELAX
1028       to be set in EXF_OPTIONS.h since this pkg controls its I/O
1029       (and avoids second CPP option in SEAICE_OPTIONS.h)
1030     - change default value of costIceStart & costIceEnd to a valid date.
1031     - add snowPrecip to HSNOW in seaice_growth
1032    o pkg/ptracers:
1033     - move ptracers summary and setup check into separated S/R ; add a check for
1034       valid PTRACERS_Iter0 value (error+stop or just warning).
1035    o pkg/cal (+ pkg/ecco):
1036     - avoid calling a S/R with 2 times the same arg (FWD: unless both are only used
1037       as input; and for AD, unless both are not differentiable (e.g., k index)).
1038    o model/src:
1039     - define internal flag "uniformFreeSurfLev" (=T when free-surface level-index
1040       is everywhere k=1) to speed-up some calculations (by pass kSurf reference);
1041       temporary set to usingZCoords value (to be changed to F when using shelfice).
1042     - hydrostatic pressure: implement partial cell near the surface also for
1043       Z-coordinates (for the case where uniformFreeSurfLev=F); replace test on
1044       usingZCoords with test on uniformFreeSurfLev where needed (in NonHyd code).
1045    o pkg/ctrl/ctrl_init.F:
1046     - add a formal parameter to s/r ctrl_init_rec to print
1047       xx_$(ctrl_valiable)_file for easier debugging
1048     - move call of cal_* routines into the if-block where they are really
1049       needed so that xx_$(ctrl_variable)_period can be 0 or -12 without having
1050       to specify a startdate
1051    o pkg/seaice:
1052     - update comments in SEAICE_OPTIONS.h (+ similar update of lab_sea/code and
1053       global_ocean.cs32x15/code versions).
1054     - turn on seaice Multi-category (in data.seaice, SEAICE_multDim=7) for
1055       verification experiment global_ocean.cs32x15.seaice and update results.
1056    o pkg/exf:
1057     - new S/R EXF_GETFIELD_START to return starting-time of a forcing field
1058       (according to useExfYearlyFields).
1059    o pkg/cal:
1060     - move calendar setting & summary (previously in cal_readparams.F) into new
1061       S/R CAL_INIT_FIXED to be called later in the initialisation process, once
1062       length of the simulation is set (after SET_PARMS call); This is an attempt
1063       to fix Pb when, e.g.: pkg/longstep, modifies the length of the run.
1064     - For safety: keep a record of pkg/cal parameter settings status
1065               to allow to STOP if one pkg/cal S/R is called too early.
1066     - add a stop in all basic pkg/cal subroutines if called before setting is done.
1067     - modify cal_getdate.F: stop when nothing was returned;
1068       if called with myIter=-1, simply retrun modelBaseDate (1,2 = startDate_1,_2);
1069       this allows to remove "cal.h" from seaice_read_parms.F & init_mnc_vars.F.
1070    
1071    checkpoint63l (2012/04/04)
1072    o pkg/bbl:
1073      - fix call to FIND_RHO_2D in bbl_calc_rho.F (case multi-tiles per proc);
1074        update global_with_exf output.yearly.txt file.
1075    o pkg/cal:
1076      - start to clean-up cal_set.F ; fix for the case where baseTime is non-zero.
1077      - remove 2 unsused and very short (1 line only) functions ;
1078      - remove unsused subroutines from AD-Diff list.
1079    o model/src:
1080      - start to implement clean wait to stop in initialization S/R (config_check.F,
1081         packages_check.F, ini_parms.F and pkg/obcs/obcs_check.F + pkg/mypackage)
1082    o folowing PRINT_MESSAGE changes:
1083      - remove reminder multiple print to the same file (STDOUT) when multi-threads.
1084    o pkg/bbl:
1085      - modification so it can work with z*
1086      - replace deltaT with dTtracerLev(k) for asynchronous time stepping
1087      - global_with_exf/input.yearly verification; changes output.yearly.txt
1088    o eesupp/src:
1089      - PRINT_MESSAGE: use OpenMP critical instruction (similar to PRINT_ERROR);
1090        writing to unit 0 (if unit=errorMessageUnit) extended to the case myThid=1
1091      - CHECK_THREADS: specific code if using OpenMP threading: improve checking of
1092        # of threads across processors (e.g., different env OMP_NUM_THREADS setting)
1093      - improve special preliminary call to EESET_PARMS (if eedata is read 2 times).
1094      - when using MPI, always set usingMPI=T ; set default accordingly and stop
1095        if not consistent.
1096      - ALL_PROC_DIE: add a BARRIER after MPI_FINALIZE call ; skip this when thread
1097        argument is zero (in case called within single-thread section).
1098    o pkg/fizhi:
1099        clean-up turbulence cold-start switch: decided in fizhi_init_vars.F, stored
1100        in common bloc (fizhi_coms.h) and then passed as argument up to S/R TURBIO.
1101    o pkg/exch2:
1102      - add argument "updateCorners" to S/R exch2_get_uv_bounds (enable to
1103        activate EXCH_IGNORE_CORNERS in vector EXCH S/R).
1104      - switch 1rst EXCH call to IGNORE_CORNERS (instead of UPDATE_CORNERS)
1105        but keep the 2nd with UPDATE_CORNERS: this prevents overwriting good data
1106        with bad ones coming from a not-yet-updated halo.
1107        This should fix the problem when sNx <> sNy and GCD(sNx,sNy) < 2*Olx.
1108    o pkg/frazil:
1109        move FrzForcT diag from frazil_diagnostics_state.F to frazil_calc_rhs.F
1110        http://mitgcm.org/pipermail/mitgcm-devel/2012-March/005384.html
1111    o model/src/config_check.F: add a check for OLx>sNx/OLy>sNy
1112    o verification/lab_sea
1113      * #undef SEAICE_EXCLUDE_FOR_EXACT_AD_TESTING
1114      * #define ALLOW_SST_CONTROL & ALLOW_SST_CONTROL
1115      * nTimeSteps 3 -> 4
1116      * changed reference output accordingly
1117    o pkg/ctrl:
1118      * fix ctrl_get_gen for xx_sst, xx_sss
1119    o pkg/fizhi:
1120      - fix 2 calls to S/R GRD2MSC (argument igrd) in update_earth_exports.F
1121        update results of exp. fizhi-cs-32x32x40 (fail with only 6 digits for cg2d)
1122      - by default, use new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE);
1123        fix few out-of-bounds indices in referencing vars (initialise igrd to 1);
1124        clean-up fizhi_turb.F (remove unused & uninitialised qdiaglsm array).
1125    o pkg/gmredi:
1126      - add diagnostic of Redi (main diagnonal) vertical diffusive flux of Temp
1127    o pkg/fizhi:
1128      - fix few initialisation and multi-tile Pb: aqualev & gridalt now pass the
1129        (old)aces open64 tuv test.
1130    o pkg/icefront: fix bug and reorder loop in icefront_init_varia.F
1131    o pkg/mom_vecinv:
1132      - fix 1 loop range in mom_vecinv.F to be like all the other loops which
1133        set/update gu,gv/Diss (fix Pb of uninitialised fVerUkp in admom_vecinv
1134        with non-lin free-surf).
1135    o model/src: move k-loop outside of i/j-loops when (re-)computing R_low
1136      in ini/update_masks_etc.F in order to avoid -O3 optimization problems with
1137      some compilers (gfortran 4.6.0 on MacOS)
1138    o momentum:
1139      - separate fVer?(:,:,kUp) & fVer?(:,:,kDown) in argument list of MOM_FLUXFORM
1140        & MOM_VECINV subroutines (to help TAF). This fixes Pb of uninitialised
1141        fVer?(kUp) in admom_fluxform with non-lin free-surf or bottom control.
1142    
1143    checkpoint63k (2012/03/17)
1144    o model/src:
1145       - selectAddFluid (ALLOW_ADDFLUID): add missing term in horizontal momentum
1146         flux-form (mom_fluxform.F) and vertical momentum (calc_gw.F) equations.
1147       - SOLVE_DIAGONAL: switch default to use adjoinable & vectorized version
1148         (#undef SOLVE_DIAGONAL_LOWMEMORY); update output of exp. front_relax.bvp.
1149    o model/src: solve_*diagonal.F
1150       - replace division with multiplication by inverse (similar to original version)
1151         update output of AD exp. global_ocean.90x40x15.
1152       - fix pkg/gmredi/gmredi_calc_psi_bvp.F & pkg/ggl90/ggl90_calc.F
1153         to enable the use of the vectorized & differentiable solve_tridiagonal.F
1154       - test exp. global_ocean.90x40x15/input_ad: switch to advection scheme 20 for
1155         vertical advection (to get solve_tridiagonal tested in AD mode).
1156    o pkg/seaice: ECCO-CLIVAR merge:
1157      1. seaice AREA relaxation
1158       * CPP option: SEAICE_ALLOW_AREA_RELAXATION       * CPP option: SEAICE_ALLOW_AREA_RELAXATION
1159       * runtime flag: SEAICE_tauAreaObsRelax       * runtime flag: SEAICE_tauAreaObsRelax
1160    2. modified global mean cost imbalance code: CPP option ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION    2. modified global mean cost imbalance code: CPP option
1161          ALLOW_SSH_GLOBMEAN_COST_CONTRIBUTION
1162  o another iteration on solve_*diagonal.F  o another iteration on solve_*diagonal.F
1163    Make choices independent of AUTODIFF     Make choices independent of AUTODIFF
1164    Default is now the adjoinable vectorized version     Default will be the adjoinable vectorized version.
1165    Alternative choices are:     Alternative choices are:
1166    * still adjoinable but lower memory (k as inner-most loop)     * non-adjoinable original version with low memory footprint:
1167    SOLVE_DIAGONAL_KINNER       #define SOLVE_DIAGONAL_LOWMEMORY
1168    * non-adjoinable legacy version with low memory footprint     * still adjoinable but does not vectorize (k as inner-most loop):
1169    SOLVE_DIAGONAL_LOWMEMORY       #define SOLVE_DIAGONAL_KINNER (keeping SOLVE_DIAGONAL_LOWMEMORY undef)
1170  o testreport  o testreport
1171   - add option to use a home made wrapper around "make"   - add option to use a home made wrapper around "make"
1172   - remove MITGCM_IEEE env. variable (no longer active)   - remove MITGCM_IEEE env. variable (no longer active)
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