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revision 1.1474 by jmc, Thu Jul 14 17:06:12 2011 UTC revision 1.1505 by jmc, Mon Sep 26 19:00:49 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/seaice (SItracer pickup)
8    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
9      To be done:
10      - thorough testing of missing fields in S/R seaice_read_pickup
11      - thorough matching between generic tracers and specific fields used
12        (e.g. volume-weighted age, area-weighted age, salinity, ...)
13    o pkg/grdchk:
14      - all procs calculate and print finite-difference gradient (for testreport)
15      - change description output used by testreport;
16      - AD testing: also compare and report Finite-difference gradient;
17        => update all output_adm*.txt
18    o test exp. global_ocean_ebm:
19      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
20        and turn on exactConserve; update (fwd) output.
21    o pkg/seaice (LSR):
22      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
23      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
24        * identical results with non-CS topology (but save up to half of EXCH calls)
25        * no much changes in cs-32 verification tests since no ice at face edges
26         (differences due to convergence criteria, since nb of iterations changed)
27        * expect some differences on lat-lon-cap grid.
28        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
29    o pkg/exch2:
30      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
31        many tiles); until alternative coding is added, just add a stop.
32    o pkg/kpp:
33      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
34        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
35    o optfiles:
36      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
37        into corresponding standard one, which now support different build:
38        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
39      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
40    o pkg/obcs (seaice):
41      - add missing EXCH for uIce,vIce after applying OBCS;
42      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
43        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
44        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
45      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
46      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
47        and eedata.mth for MPI and mutlti-threaded testing.
48    o pkg/flt:
49      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
50      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
51      - fix pickup and trajectories + profiles output with multi-threads;
52      - add parameter to select group of fields to write along trajectory and
53        profile (default unchanged);
54      - only call PORT_RAND* function when flt_noise <> 0;
55      - add multi-threaded test for verification exp. flt_example.
56    o eesupp/src:
57      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
58      - USE_OMP_THREADING: check that number of threads (from eedata) matches
59        actual number (from env.var. setting).
60    o pkg/ebm:
61      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
62      - add multi-threaded test for verification exp. global_ocean_ebm
63    
64    checkpoint63b (2011/08/29)
65    o pkg/ebm:
66      - fix sign of runoff;
67      - update directly forcing fields (Qnet,EmPmR) to use standard
68        external_forcing_surf.F (remove ebm_forcing_surf.F);
69      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
70      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
71        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
72      - update global_ocean_ebm parameters file data and update output (fwd+ad).
73    o verification/matrix_example:
74      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
75        MPI and mutlti-threaded testing.
76    o pkg/matrix:
77      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
78      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
79      - fix for multi-threaded (remove DATA statement);
80      - use standard DIFFERENT_MULTIPLE function;
81      - add MATRIX_OPTIONS.h
82    o verification/matrix_example:
83       To allow to split the domain in several tiles, change the domain size
84        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
85        Western side) of land points.
86    o (*_)write_pickup:
87      - fix few bugs in mypackage_read/write_pickup.F
88      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
89        array of length 1 (was caught by compiler syntax-check).
90    o pkg/diagnostics (velocity potential solver):
91      - fix initialisation of main diagonal matrix (for overlap values)
92    o tools/build_options:
93      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
94        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
95      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
96        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
97        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
98        and use "-devel" testreport option for standard testing on baudelaire.
99    o pkg/grdchk:
100      - Assume that all gradient-check position are within the same tile
101        corresponding to global indices (iGloTile,jGloTile) and that
102        positions (i,j indices or nbeg) are local to this tile;
103      - set tile local-indices and proc. number according to tile global-indices;
104      - remove grdchkwhichproc from namelist (retired param);
105      - send adjoint gradient to all procs so that all procs print it to STDOUT;
106      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
107    o adding package bbl (Bottom Boundary Layer)
108      description in MITgcm/pkg/bbl/bbl_description.tex
109      example/test experiment in MITgcm_contrib/bbl
110    o adjoint verifications
111      - changed 5 experiments to multi-tiles
112        * global_ocean.90x40x15
113        * obcs_ctrl
114        * offline_exf_seaice
115        * tutorial_dic_adjoffline
116        * tutorial_tracer_adjsens
117        changed reference output for those that crossed tile boundaries
118        (changed choices of gradient check positions)
119      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
120      - temporary bug fix in grdchk_loc.F for obcs
121    o genmake2 & testreport
122      - add target "obj" (just for OBJFILES files) to Makefile;
123      - add option to specify FEXTRAFLAGS on command line.
124    o pkg/mypackage:
125      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
126    
127    checkpoint63a (2011/08/02)
128    o pkg/diagnostics (velocity potential):
129      - fix velocity-potential calculation when using OBCS: balance net inflow
130        at each level (new S/R OBCS_DIAG_BALANCE).
131      - fix some of the problems with OBCS in stream-function calculation.
132    o pkg/exf/exf_readparms.F
133      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
134        EXF_NML_OBCS) more consistent, so that you need not have these lists
135        in data.exf when they are not used.
136    o optim/optim_readdata.F:
137      - add some output about obcs variables that might help debugging
138      - add a check about nvarlength
139    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
140    o pkg/diagnostics (velocity potential):
141      - fix mask for OBCS (still problems in stream-function with OBCS);
142      - add specific parameter (default = main code CG2D params) for solver;
143      - in case of poor convergence, use solution corresponding to lowest residual.
144    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
145      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
146      and should be avoided where possible.
147    o model/src (rStar):
148      - include r* effect on reference-state (PhiRef) in totPhiHyd
149        (so that it's really the potential anomaly at the cell center);
150        affect solution only if z* with full pressure in EOS.
151      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
152        update output (because of z* in totPhiHyd and viscA4 changes);
153      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
154        @ constant r) until interpolation at constant r is implemented.
155    o pkg/diagnostics
156      - fix RCENTER diagnostics in case cell center is not at interface middle
157    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
158      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
159      that THETA and SALT are "conservative temperature" and "absolute
160      salinity"
161    o pkg/ctrl
162      - fix computation of endrec in s/r ctrl_init_rec
163      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
164    o pkg/seaice/seaice_growth.F
165      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
166        remove then obsolete STORE directives
167      - fix STORE directives for tice and tices, so that only the
168        appropriate part of the fields are stored (and not the entire
169        field); update global_ocean.cs32x15.seaice AD output.
170      - cosmetic changes: adjust CPP flags and indentation for better
171        legibilty
172    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
173      Chris Wilson)
174  o pkg/gmredi:  o pkg/gmredi:
175     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
176     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)     and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
177    
178  checkpoint63 (2011/07/11)  checkpoint63  (2011/07/11)
179  o pkg/exch2:  o pkg/exch2:
180   - 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
181   - 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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