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revision 1.1462 by jmc, Wed Jun 22 19:17:36 2011 UTC revision 1.1495 by jmc, Fri Aug 26 20:27:15 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 verification/matrix_example:
8      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
9        MPI and mutlti-threaded testing.
10    o pkg/matrix:
11      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
12      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
13      - fix for multi-threaded (remove DATA statement);
14      - use standard DIFFERENT_MULTIPLE function;
15      - add MATRIX_OPTIONS.h
16    o verification/matrix_example:
17       To allow to split the domain in several tiles, change the domain size
18        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
19        Western side) of land points.
20    o (*_)write_pickup:
21      - fix few bugs in mypackage_read/write_pickup.F
22      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
23        array of length 1 (was caught by compiler syntax-check).
24    o pkg/diagnostics (velocity potential solver):
25      - fix initialisation of main diagonal matrix (for overlap values)
26    o tools/build_options:
27      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
28        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
29      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
30        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
31        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
32        and use "-devel" testreport option for standard testing on baudelaire.
33    o pkg/grdchk:
34      - Assume that all gradient-check position are within the same tile
35        corresponding to global indices (iGloTile,jGloTile) and that
36        positions (i,j indices or nbeg) are local to this tile;
37      - set tile local-indices and proc. number according to tile global-indices;
38      - remove grdchkwhichproc from namelist (retired param);
39      - send adjoint gradient to all procs so that all procs print it to STDOUT;
40      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
41    o adding package bbl (Bottom Boundary Layer)
42      description in MITgcm/pkg/bbl/bbl_description.tex
43      example/test experiment in MITgcm_contrib/bbl
44    o adjoint verifications
45      - changed 5 experiments to multi-tiles
46        * global_ocean.90x40x15
47        * obcs_ctrl
48        * offline_exf_seaice
49        * tutorial_dic_adjoffline
50        * tutorial_tracer_adjsens
51        changed reference output for those that crossed tile boundaries
52        (changed choices of gradient check positions)
53      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
54      - temporary bug fix in grdchk_loc.F for obcs
55    o genmake2 & testreport
56      - add target "obj" (just for OBJFILES files) to Makefile;
57      - add option to specify FEXTRAFLAGS on command line.
58    o pkg/mypackage:
59      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
60    
61    checkpoint63a (2011/08/02)
62    o pkg/diagnostics (velocity potential):
63      - fix velocity-potential calculation when using OBCS: balance net inflow
64        at each level (new S/R OBCS_DIAG_BALANCE).
65      - fix some of the problems with OBCS in stream-function calculation.
66    o pkg/exf/exf_readparms.F
67      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
68        EXF_NML_OBCS) more consistent, so that you need not have these lists
69        in data.exf when they are not used.
70    o optim/optim_readdata.F:
71      - add some output about obcs variables that might help debugging
72      - add a check about nvarlength
73    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
74    o pkg/diagnostics (velocity potential):
75      - fix mask for OBCS (still problems in stream-function with OBCS);
76      - add specific parameter (default = main code CG2D params) for solver;
77      - in case of poor convergence, use solution corresponding to lowest residual.
78    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
79      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
80      and should be avoided where possible.
81    o model/src (rStar):
82      - include r* effect on reference-state (PhiRef) in totPhiHyd
83        (so that it's really the potential anomaly at the cell center);
84        affect solution only if z* with full pressure in EOS.
85      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
86        update output (because of z* in totPhiHyd and viscA4 changes);
87      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
88        @ constant r) until interpolation at constant r is implemented.
89    o pkg/diagnostics
90      - fix RCENTER diagnostics in case cell center is not at interface middle
91    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
92      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
93      that THETA and SALT are "conservative temperature" and "absolute
94      salinity"
95    o pkg/ctrl
96      - fix computation of endrec in s/r ctrl_init_rec
97      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
98    o pkg/seaice/seaice_growth.F
99      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
100        remove then obsolete STORE directives
101      - fix STORE directives for tice and tices, so that only the
102        appropriate part of the fields are stored (and not the entire
103        field); update global_ocean.cs32x15.seaice AD output.
104      - cosmetic changes: adjust CPP flags and indentation for better
105        legibilty
106    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
107      Chris Wilson)
108    o pkg/gmredi:
109       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
110       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
111    
112    checkpoint63  (2011/07/11)
113    o pkg/exch2:
114     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
115     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
116       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
117       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
118    o pkg/diagnostics:
119     - deal with pairs of post-processed diags which are computed together; in
120       particular, re-order list of diags within 1 file to save 2nd computation.
121     - add S/R to compute velocity stream-function (called after velocity-potential
122       calculation) from divergence free transport -> new diagnostics "PsiVEL".
123     - add parameter to select grid-point location where PsiVEL == 0.
124    o eesupp/src:
125       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
126       (specific S/R needed with exch2 topology - for now, just print an error msg)
127    o pkg/shelfice
128     - Implement friction velocity-dependent transfer coefficients following
129       Holland and Jenkins, JPO, 1999
130       Original code by M. Losch with small modifs.
131       Enable with CPP option SHI_ALLOW_GAMMAFRICT
132       and runtime flag SHELFICEuseGammaFrict
133    o verification lab_sea & global_ocean.cs32x15:
134     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
135       does not miss some dependencies (but is slower) and also works with many files
136       (default makedepend limitation for AD built).
137     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
138    o pkg/diagnostics:
139     - add run-time parameter "useMissingValue" (def=False) to fill land-point
140        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
141       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
142     - Extend the use of "missing_value" setting from data.diagnostics for the case
143       of counter-diagnostics (where fraction-weight is zero). This applies both to
144       MNC and MDS output files.
145    o pkg/seaice/seaice_growth.F:
146      - add 'a priori' cap of latent heat flux based on actual mass considerations
147        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
148        non-legacy seaice_solve4temp.
149      - add diagnostic of the residual sublimation freshwater flux (the freshwater
150        flux taken from the ocean if the total actual latent heat fluxes exceed
151        the maximum)
152      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
153       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
154      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
155       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
156      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
157      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
158    o verification 1D_ocean_ice_column:
159       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
160       update results
161  o pkg/diagnostics:  o pkg/diagnostics:
162   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
163     which are not filled-up but computed from other diags ; In this case, the mate     which are not filled-up but computed from other diags ; In this case, the mate
164     diag points to the primary (filled-up) diag to used for post processing.     diag points to the primary (filled-up) diag to used for post processing.
165   - Update Velocity-potential computation using post-processed diag framework.   - Update Velocity-potential computation using post-processed diag framework.
166   Change the ordering of fields and time-periods in MDS output file   ==> Change the ordering of fields and time-periods in MDS output file
167     when using periodic averaging: now writes one time record with the full set     when using periodic averaging: now writes one time record with the full set
168     of fields for this time period, then the next time reccord (it used to be     of fields for this time period, then the next time reccord (it used to be
169     one field with the full set of time records then the next field).     one field with the full set of time records then the next field).
170     Note: this is now similar to NetCDF (MNC) output file.       Note: this is now similar to NetCDF (MNC) output file. <==
171    
172  checkpoint62z (2011/06/21)  checkpoint62z (2011/06/21)
173  o adjoint monitor:  o adjoint monitor:
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