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revision 1.1469 by ifenty, Wed Jun 29 21:44:26 2011 UTC revision 1.1530 by mlosch, Tue Nov 8 17:00:37 2011 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/obcs/obcs_calc_stevens.F:
8      - add code for northern and southern boundaries.
9      - reorder some loops to save some operations and so that drFBar can be scalar
10    o model/src:
11      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
12        truncation) and add diagnostics for Adams-Bashforth tendency increment.
13      - update test-exp. AD output:
14        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
15      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
16        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
17        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
18        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
19        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
20        tutorial_plume_on_slope.
21    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
22      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
23      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
24      does not even come with an F77 compiler anymore, this should not be
25      a limitation
26    
27    checkpoint63e (2011/11/06)
28    o pkg/seaice adjoint of LSR:
29      - substantially rework STORE dirs.
30      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
31        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
32        and only perform SOLV_MAX_FIXED adjoint iters.
33        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
34        always goes to same record, meaning that the last forward field will be
35        the one used in the adjoint - an approximation.
36      - now produces non-zero LSR-related gradients, and acceptable gradients for
37        An's zonal (x-z) test case (to be checked in)
38      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
39        (but these are screwed up by the thermodynamics in the first place);
40        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
41        output_adm.txt also reflects changes to seaice_lsr
42      - global_ocean.cs32x15:
43        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
44          (output_adm.seaice.txt was updated)
45        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
46          (output_adm.seaice_dynmix.txt)
47    o test-exp. exp4+stevens:
48      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
49    o pkg/seaice (lsr solver):
50      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
51        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
52      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
53      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
54        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
55      - compute (with new S/R) and print initial (+ free-driff sol. if available)
56        and final residual of linearised system.
57    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
58      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
59    o pkg/obcs: Stevens BCs (still only for east and west)
60      - fix Stevens BCs by using intermediate velocities of previous
61        time step as "baroclinic" contribution rather velocity of one grid cell
62        inside the boundaries; more consistent but makes the entire treatment
63        more complicated, requires new pickup files and two new S/Rs:
64        obcs_copy_uv_n and obcs_save_uv_n
65        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
66        (undefined by default)
67      - silently move computation of some grid factors into separate loops to
68        save some recomputations
69      - add a hack for non-linear free surface
70      - add a verification experiment to exp4 that tests this code
71    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
72    
73    checkpoint63d (2011/10/25)
74    o pkg/obcs + seaice-dynamics:
75      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
76        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
77        values (consistent with an implicit method).
78      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
79        return to older implementation (same results as before); note that none of
80        the "experimental" OBCS_SEAICE options are implemented in the new version.
81      - switch test exp. seaice_obcs to use new version (update output).
82    o pkg/seaice:
83      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
84      - add parenthesis in Water-Ice drag calculations (evp & lsr);
85      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
86        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
87      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
88        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
89    o pkg/layers:
90      - Include potential density as new coordinate (Thanks to David Munday)
91    o pkg/dic:
92      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
93        carbonate computation/output to CALC_PCO2_APPROX
94    o pkg/generic_advdiff
95      - make TAF generate code that vectorizes:
96        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
97    o model/src:
98      - improve vectorization also for adjoint code of
99        solve_tridiagonal and solve_pentadiagonal. As this requires up to
100        5 new 3D-fields, this code is only turned on for the combination of
101        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
102        for singular matrix check (only for TARGET_NEC_SX).
103      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
104        ALLOW_AUTODIFF. This flag now needs to be set outside of
105        solve_tri/pentadiagonal.F
106    o pkg/exf:
107      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
108        optional namelist EXF_NML_OBCS).
109      - add many debug-print (to trace down where pkg/cal error msg comes from)
110    o pkg/mom_vecinv/mom_vi_hdissip.F
111      - rearrange loops so that vectorization is improved and in particular
112        the adjoint routine vectorizes. The code is a little longer now, but I
113        think easier to read.
114        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
115    o pkg/seaice:
116      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
117    o pkg/exch2:
118      - alternative code (without tile x tile matrix) for cumulated (global) sum;
119        used as default; keep using matrix version in adjustment.cs-32x32x1.
120    o tools/build_options:
121      - after merging some MPI and/or multi-threads specific optfiles so that
122        the modified default optfile support both built (using genmake2 -mpi
123        for the MPI built, using genmake2 -omp for OpenMP built),
124        move now obsolete optfiles to tools/build_options/unsupported/
125       (add copy of email sent to support list in doc/optfiles_changes.txt)
126    
127    checkpoint63c (2011/09/28)
128    o pkg/ebm:
129      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
130        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
131    o pkg/seaice (SItracer pickup)
132    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
133      To be done:
134      - thorough testing of missing fields in S/R seaice_read_pickup
135      - thorough matching between generic tracers and specific fields used
136        (e.g. volume-weighted age, area-weighted age, salinity, ...)
137    o pkg/grdchk:
138      - all procs calculate and print finite-difference gradient (for testreport)
139      - change description output used by testreport;
140      - AD testing: also compare and report Finite-difference gradient;
141        => update all output_adm*.txt
142    o test exp. global_ocean_ebm:
143      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
144        and turn on exactConserve; update (fwd) output.
145    o pkg/seaice (LSR):
146      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
147      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
148        * identical results with non-CS topology (but save up to half of EXCH calls)
149        * no much changes in cs-32 verification tests since no ice at face edges
150         (differences due to convergence criteria, since nb of iterations changed)
151        * expect some differences on lat-lon-cap grid.
152        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
153    o pkg/exch2:
154      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
155        many tiles); until alternative coding is added, just add a stop.
156    o pkg/kpp:
157      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
158        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
159    o optfiles:
160      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
161        into corresponding standard one, which now support different build:
162        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
163      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
164    o pkg/obcs (seaice):
165      - add missing EXCH for uIce,vIce after applying OBCS;
166      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
167        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
168        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
169      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
170      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
171        and eedata.mth for MPI and mutlti-threaded testing.
172    o pkg/flt:
173      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
174      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
175      - fix pickup and trajectories + profiles output with multi-threads;
176      - add parameter to select group of fields to write along trajectory and
177        profile (default unchanged);
178      - only call PORT_RAND* function when flt_noise <> 0;
179      - add multi-threaded test for verification exp. flt_example.
180    o eesupp/src:
181      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
182      - USE_OMP_THREADING: check that number of threads (from eedata) matches
183        actual number (from env.var. setting).
184    o pkg/ebm:
185      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
186      - add multi-threaded test for verification exp. global_ocean_ebm
187    
188    checkpoint63b (2011/08/29)
189    o pkg/ebm:
190      - fix sign of runoff;
191      - update directly forcing fields (Qnet,EmPmR) to use standard
192        external_forcing_surf.F (remove ebm_forcing_surf.F);
193      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
194      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
195        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
196      - update global_ocean_ebm parameters file data and update output (fwd+ad).
197    o verification/matrix_example:
198      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
199        MPI and mutlti-threaded testing.
200    o pkg/matrix:
201      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
202      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
203      - fix for multi-threaded (remove DATA statement);
204      - use standard DIFFERENT_MULTIPLE function;
205      - add MATRIX_OPTIONS.h
206    o verification/matrix_example:
207       To allow to split the domain in several tiles, change the domain size
208        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
209        Western side) of land points.
210    o (*_)write_pickup:
211      - fix few bugs in mypackage_read/write_pickup.F
212      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
213        array of length 1 (was caught by compiler syntax-check).
214    o pkg/diagnostics (velocity potential solver):
215      - fix initialisation of main diagonal matrix (for overlap values)
216    o tools/build_options:
217      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
218        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
219      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
220        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
221        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
222        and use "-devel" testreport option for standard testing on baudelaire.
223    o pkg/grdchk:
224      - Assume that all gradient-check position are within the same tile
225        corresponding to global indices (iGloTile,jGloTile) and that
226        positions (i,j indices or nbeg) are local to this tile;
227      - set tile local-indices and proc. number according to tile global-indices;
228      - remove grdchkwhichproc from namelist (retired param);
229      - send adjoint gradient to all procs so that all procs print it to STDOUT;
230      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
231    o adding package bbl (Bottom Boundary Layer)
232      description in MITgcm/pkg/bbl/bbl_description.tex
233      example/test experiment in MITgcm_contrib/bbl
234    o adjoint verifications
235      - changed 5 experiments to multi-tiles
236        * global_ocean.90x40x15
237        * obcs_ctrl
238        * offline_exf_seaice
239        * tutorial_dic_adjoffline
240        * tutorial_tracer_adjsens
241        changed reference output for those that crossed tile boundaries
242        (changed choices of gradient check positions)
243      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
244      - temporary bug fix in grdchk_loc.F for obcs
245    o genmake2 & testreport
246      - add target "obj" (just for OBJFILES files) to Makefile;
247      - add option to specify FEXTRAFLAGS on command line.
248    o pkg/mypackage:
249      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
250    
251    checkpoint63a (2011/08/02)
252    o pkg/diagnostics (velocity potential):
253      - fix velocity-potential calculation when using OBCS: balance net inflow
254        at each level (new S/R OBCS_DIAG_BALANCE).
255      - fix some of the problems with OBCS in stream-function calculation.
256    o pkg/exf/exf_readparms.F
257      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
258        EXF_NML_OBCS) more consistent, so that you need not have these lists
259        in data.exf when they are not used.
260    o optim/optim_readdata.F:
261      - add some output about obcs variables that might help debugging
262      - add a check about nvarlength
263    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
264    o pkg/diagnostics (velocity potential):
265      - fix mask for OBCS (still problems in stream-function with OBCS);
266      - add specific parameter (default = main code CG2D params) for solver;
267      - in case of poor convergence, use solution corresponding to lowest residual.
268    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
269      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
270      and should be avoided where possible.
271    o model/src (rStar):
272      - include r* effect on reference-state (PhiRef) in totPhiHyd
273        (so that it's really the potential anomaly at the cell center);
274        affect solution only if z* with full pressure in EOS.
275      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
276        update output (because of z* in totPhiHyd and viscA4 changes);
277      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
278        @ constant r) until interpolation at constant r is implemented.
279    o pkg/diagnostics
280      - fix RCENTER diagnostics in case cell center is not at interface middle
281    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
282      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
283      that THETA and SALT are "conservative temperature" and "absolute
284      salinity"
285    o pkg/ctrl
286      - fix computation of endrec in s/r ctrl_init_rec
287      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
288    o pkg/seaice/seaice_growth.F
289      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
290        remove then obsolete STORE directives
291      - fix STORE directives for tice and tices, so that only the
292        appropriate part of the fields are stored (and not the entire
293        field); update global_ocean.cs32x15.seaice AD output.
294      - cosmetic changes: adjust CPP flags and indentation for better
295        legibilty
296    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
297      Chris Wilson)
298    o pkg/gmredi:
299       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
300       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
301    
302    checkpoint63  (2011/07/11)
303    o pkg/exch2:
304     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
305     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
306       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
307       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
308    o pkg/diagnostics:
309     - deal with pairs of post-processed diags which are computed together; in
310       particular, re-order list of diags within 1 file to save 2nd computation.
311     - add S/R to compute velocity stream-function (called after velocity-potential
312       calculation) from divergence free transport -> new diagnostics "PsiVEL".
313     - add parameter to select grid-point location where PsiVEL == 0.
314    o eesupp/src:
315       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
316       (specific S/R needed with exch2 topology - for now, just print an error msg)
317  o pkg/shelfice  o pkg/shelfice
318   - Implement friction velocity-dependent transfer coefficients following   - Implement friction velocity-dependent transfer coefficients following
319     Holland and Jenkins, JPO, 1999     Holland and Jenkins, JPO, 1999
# Line 27  o pkg/seaice/seaice_growth.F: Line 337  o pkg/seaice/seaice_growth.F:
337      when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the      when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
338      non-legacy seaice_solve4temp.      non-legacy seaice_solve4temp.
339    - add diagnostic of the residual sublimation freshwater flux (the freshwater    - add diagnostic of the residual sublimation freshwater flux (the freshwater
340      flux taken from the ocean if the total actual latent heat fluxes exceed      flux taken from the ocean if the total actual latent heat fluxes exceed
341      the maximum)      the maximum)
342    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic    - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
343     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.     fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.

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