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revision 1.1473 by jmc, Mon Jul 11 12:03:37 2011 UTC revision 1.1535 by mlosch, Thu Nov 17 12:52:17 2011 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  checkpoint63 (2011/07/11)  o pkg/seaice/seaice_init_fixed.F
8      - fix a bug in the initialisation of the second metric terms
9        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
10      - this affects all seaice configurations with useCurviLinearGrid = .true.
11        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
12        = .true. (default)
13      - the only verification experiment affected is global_ocean.cs32x15:
14        icedyn, seaice, and seaice_dynmix (AD)
15    o pkg/thsice/thsice_diagnostics_state.F
16      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
17        not contain garbage that can lead to surprises in diagstats_calc.F
18    o model/src:
19      - move bi,bj loops inside INTEGR_CONTINUITY ;
20      - call INTEGR_CONTINUITY directly from forward_step.F
21        (previously called from momentum_correction_step.F)
22      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
23        forward_step.F and pkg/ecco/the_main_loop.F
24    o model/src/do_oceanic_phys.F:
25      - reset addMass to zero only if useICEFRONT ;
26      - separated k-loop for rhoInSitu calculation ;
27      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
28        and at constant T,S (= WdRHOdP);
29      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
30        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
31        transport of locally-referenced potential density);
32        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
33    o gluemnc:
34      - replace ncrcat with ncks when adding variables to *.glob.nc
35      - change the way variables without record dimensions are handled so that
36        files that have variables with and without record variables can be glued:
37        add a record dimension with a new unique name to be able to differentiate
38        between variable with and without a-prior record dimensions. Remove
39        this record dimension before adding the variable to the *.glob.nc file.
40        This procedure automatically works also for grid.*.nc files that do not
41        have any record dimension.
42    o verification/cpl_aim+ocn:
43      - generate new reference output on baudelaire (gfortran, mpich2) (previously
44        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
45    o pkg/obcs/obcs_calc_stevens.F:
46      - add code for northern and southern boundaries.
47      - reorder some loops to save some operations and so that drFBar can be scalar
48    o model/src:
49      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
50        truncation) and add diagnostics for Adams-Bashforth tendency increment.
51      - update test-exp. AD output:
52        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
53      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
54        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
55        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
56        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
57        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
58        tutorial_plume_on_slope.
59    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
60      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
61      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
62      does not even come with an F77 compiler anymore, this should not be
63      a limitation
64    
65    checkpoint63e (2011/11/06)
66    o pkg/seaice adjoint of LSR:
67      - substantially rework STORE dirs.
68      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
69        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
70        and only perform SOLV_MAX_FIXED adjoint iters.
71        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
72        always goes to same record, meaning that the last forward field will be
73        the one used in the adjoint - an approximation.
74      - now produces non-zero LSR-related gradients, and acceptable gradients for
75        An's zonal (x-z) test case (to be checked in)
76      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
77        (but these are screwed up by the thermodynamics in the first place);
78        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
79        output_adm.txt also reflects changes to seaice_lsr
80      - global_ocean.cs32x15:
81        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
82          (output_adm.seaice.txt was updated)
83        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
84          (output_adm.seaice_dynmix.txt)
85    o test-exp. exp4+stevens:
86      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
87    o pkg/seaice (lsr solver):
88      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
89        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
90      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
91      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
92        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
93      - compute (with new S/R) and print initial (+ free-driff sol. if available)
94        and final residual of linearised system.
95    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
96      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
97    o pkg/obcs: Stevens BCs (still only for east and west)
98      - fix Stevens BCs by using intermediate velocities of previous
99        time step as "baroclinic" contribution rather velocity of one grid cell
100        inside the boundaries; more consistent but makes the entire treatment
101        more complicated, requires new pickup files and two new S/Rs:
102        obcs_copy_uv_n and obcs_save_uv_n
103        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
104        (undefined by default)
105      - silently move computation of some grid factors into separate loops to
106        save some recomputations
107      - add a hack for non-linear free surface
108      - add a verification experiment to exp4 that tests this code
109    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
110    
111    checkpoint63d (2011/10/25)
112    o pkg/obcs + seaice-dynamics:
113      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
114        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
115        values (consistent with an implicit method).
116      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
117        return to older implementation (same results as before); note that none of
118        the "experimental" OBCS_SEAICE options are implemented in the new version.
119      - switch test exp. seaice_obcs to use new version (update output).
120    o pkg/seaice:
121      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
122      - add parenthesis in Water-Ice drag calculations (evp & lsr);
123      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
124        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
125      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
126        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
127    o pkg/layers:
128      - Include potential density as new coordinate (Thanks to David Munday)
129    o pkg/dic:
130      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
131        carbonate computation/output to CALC_PCO2_APPROX
132    o pkg/generic_advdiff
133      - make TAF generate code that vectorizes:
134        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
135    o model/src:
136      - improve vectorization also for adjoint code of
137        solve_tridiagonal and solve_pentadiagonal. As this requires up to
138        5 new 3D-fields, this code is only turned on for the combination of
139        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
140        for singular matrix check (only for TARGET_NEC_SX).
141      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
142        ALLOW_AUTODIFF. This flag now needs to be set outside of
143        solve_tri/pentadiagonal.F
144    o pkg/exf:
145      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
146        optional namelist EXF_NML_OBCS).
147      - add many debug-print (to trace down where pkg/cal error msg comes from)
148    o pkg/mom_vecinv/mom_vi_hdissip.F
149      - rearrange loops so that vectorization is improved and in particular
150        the adjoint routine vectorizes. The code is a little longer now, but I
151        think easier to read.
152        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
153    o pkg/seaice:
154      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
155    o pkg/exch2:
156      - alternative code (without tile x tile matrix) for cumulated (global) sum;
157        used as default; keep using matrix version in adjustment.cs-32x32x1.
158    o tools/build_options:
159      - after merging some MPI and/or multi-threads specific optfiles so that
160        the modified default optfile support both built (using genmake2 -mpi
161        for the MPI built, using genmake2 -omp for OpenMP built),
162        move now obsolete optfiles to tools/build_options/unsupported/
163       (add copy of email sent to support list in doc/optfiles_changes.txt)
164    
165    checkpoint63c (2011/09/28)
166    o pkg/ebm:
167      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
168        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
169    o pkg/seaice (SItracer pickup)
170    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
171      To be done:
172      - thorough testing of missing fields in S/R seaice_read_pickup
173      - thorough matching between generic tracers and specific fields used
174        (e.g. volume-weighted age, area-weighted age, salinity, ...)
175    o pkg/grdchk:
176      - all procs calculate and print finite-difference gradient (for testreport)
177      - change description output used by testreport;
178      - AD testing: also compare and report Finite-difference gradient;
179        => update all output_adm*.txt
180    o test exp. global_ocean_ebm:
181      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
182        and turn on exactConserve; update (fwd) output.
183    o pkg/seaice (LSR):
184      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
185      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
186        * identical results with non-CS topology (but save up to half of EXCH calls)
187        * no much changes in cs-32 verification tests since no ice at face edges
188         (differences due to convergence criteria, since nb of iterations changed)
189        * expect some differences on lat-lon-cap grid.
190        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
191    o pkg/exch2:
192      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
193        many tiles); until alternative coding is added, just add a stop.
194    o pkg/kpp:
195      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
196        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
197    o optfiles:
198      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
199        into corresponding standard one, which now support different build:
200        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
201      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
202    o pkg/obcs (seaice):
203      - add missing EXCH for uIce,vIce after applying OBCS;
204      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
205        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
206        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
207      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
208      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
209        and eedata.mth for MPI and mutlti-threaded testing.
210    o pkg/flt:
211      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
212      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
213      - fix pickup and trajectories + profiles output with multi-threads;
214      - add parameter to select group of fields to write along trajectory and
215        profile (default unchanged);
216      - only call PORT_RAND* function when flt_noise <> 0;
217      - add multi-threaded test for verification exp. flt_example.
218    o eesupp/src:
219      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
220      - USE_OMP_THREADING: check that number of threads (from eedata) matches
221        actual number (from env.var. setting).
222    o pkg/ebm:
223      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
224      - add multi-threaded test for verification exp. global_ocean_ebm
225    
226    checkpoint63b (2011/08/29)
227    o pkg/ebm:
228      - fix sign of runoff;
229      - update directly forcing fields (Qnet,EmPmR) to use standard
230        external_forcing_surf.F (remove ebm_forcing_surf.F);
231      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
232      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
233        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
234      - update global_ocean_ebm parameters file data and update output (fwd+ad).
235    o verification/matrix_example:
236      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
237        MPI and mutlti-threaded testing.
238    o pkg/matrix:
239      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
240      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
241      - fix for multi-threaded (remove DATA statement);
242      - use standard DIFFERENT_MULTIPLE function;
243      - add MATRIX_OPTIONS.h
244    o verification/matrix_example:
245       To allow to split the domain in several tiles, change the domain size
246        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
247        Western side) of land points.
248    o (*_)write_pickup:
249      - fix few bugs in mypackage_read/write_pickup.F
250      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
251        array of length 1 (was caught by compiler syntax-check).
252    o pkg/diagnostics (velocity potential solver):
253      - fix initialisation of main diagonal matrix (for overlap values)
254    o tools/build_options:
255      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
256        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
257      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
258        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
259        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
260        and use "-devel" testreport option for standard testing on baudelaire.
261    o pkg/grdchk:
262      - Assume that all gradient-check position are within the same tile
263        corresponding to global indices (iGloTile,jGloTile) and that
264        positions (i,j indices or nbeg) are local to this tile;
265      - set tile local-indices and proc. number according to tile global-indices;
266      - remove grdchkwhichproc from namelist (retired param);
267      - send adjoint gradient to all procs so that all procs print it to STDOUT;
268      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
269    o adding package bbl (Bottom Boundary Layer)
270      description in MITgcm/pkg/bbl/bbl_description.tex
271      example/test experiment in MITgcm_contrib/bbl
272    o adjoint verifications
273      - changed 5 experiments to multi-tiles
274        * global_ocean.90x40x15
275        * obcs_ctrl
276        * offline_exf_seaice
277        * tutorial_dic_adjoffline
278        * tutorial_tracer_adjsens
279        changed reference output for those that crossed tile boundaries
280        (changed choices of gradient check positions)
281      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
282      - temporary bug fix in grdchk_loc.F for obcs
283    o genmake2 & testreport
284      - add target "obj" (just for OBJFILES files) to Makefile;
285      - add option to specify FEXTRAFLAGS on command line.
286    o pkg/mypackage:
287      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
288    
289    checkpoint63a (2011/08/02)
290    o pkg/diagnostics (velocity potential):
291      - fix velocity-potential calculation when using OBCS: balance net inflow
292        at each level (new S/R OBCS_DIAG_BALANCE).
293      - fix some of the problems with OBCS in stream-function calculation.
294    o pkg/exf/exf_readparms.F
295      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
296        EXF_NML_OBCS) more consistent, so that you need not have these lists
297        in data.exf when they are not used.
298    o optim/optim_readdata.F:
299      - add some output about obcs variables that might help debugging
300      - add a check about nvarlength
301    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
302    o pkg/diagnostics (velocity potential):
303      - fix mask for OBCS (still problems in stream-function with OBCS);
304      - add specific parameter (default = main code CG2D params) for solver;
305      - in case of poor convergence, use solution corresponding to lowest residual.
306    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
307      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
308      and should be avoided where possible.
309    o model/src (rStar):
310      - include r* effect on reference-state (PhiRef) in totPhiHyd
311        (so that it's really the potential anomaly at the cell center);
312        affect solution only if z* with full pressure in EOS.
313      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
314        update output (because of z* in totPhiHyd and viscA4 changes);
315      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
316        @ constant r) until interpolation at constant r is implemented.
317    o pkg/diagnostics
318      - fix RCENTER diagnostics in case cell center is not at interface middle
319    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
320      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
321      that THETA and SALT are "conservative temperature" and "absolute
322      salinity"
323    o pkg/ctrl
324      - fix computation of endrec in s/r ctrl_init_rec
325      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
326    o pkg/seaice/seaice_growth.F
327      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
328        remove then obsolete STORE directives
329      - fix STORE directives for tice and tices, so that only the
330        appropriate part of the fields are stored (and not the entire
331        field); update global_ocean.cs32x15.seaice AD output.
332      - cosmetic changes: adjust CPP flags and indentation for better
333        legibilty
334    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
335      Chris Wilson)
336    o pkg/gmredi:
337       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
338       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
339    
340    checkpoint63  (2011/07/11)
341  o pkg/exch2:  o pkg/exch2:
342   - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h   - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
343   - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the   - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the

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