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revision 1.1474 by jmc, Thu Jul 14 17:06:12 2011 UTC revision 1.1509 by jmc, Mon Oct 3 12:48:20 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/exch2:
8      - alternative code (without tile x tile matrix) for cumulated (global) sum;
9        used as default; keep using matrix version in adjustment.cs-32x32x1.
10    o tools/build_options:
11      - after merging some MPI and/or multi-threads specific optfiles so that
12        the modified default optfile support both built (using genmake2 -mpi
13        for the MPI built, using genmake2 -omp for OpenMP built),
14        move now obsolete optfiles to tools/build_options/unsupported/
15       (add copy of email sent to support list in doc/optfiles_changes.txt)
16    
17    checkpoint63c (2011/09/28)
18    o pkg/ebm:
19      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
20        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
21    o pkg/seaice (SItracer pickup)
22    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
23      To be done:
24      - thorough testing of missing fields in S/R seaice_read_pickup
25      - thorough matching between generic tracers and specific fields used
26        (e.g. volume-weighted age, area-weighted age, salinity, ...)
27    o pkg/grdchk:
28      - all procs calculate and print finite-difference gradient (for testreport)
29      - change description output used by testreport;
30      - AD testing: also compare and report Finite-difference gradient;
31        => update all output_adm*.txt
32    o test exp. global_ocean_ebm:
33      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
34        and turn on exactConserve; update (fwd) output.
35    o pkg/seaice (LSR):
36      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
37      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
38        * identical results with non-CS topology (but save up to half of EXCH calls)
39        * no much changes in cs-32 verification tests since no ice at face edges
40         (differences due to convergence criteria, since nb of iterations changed)
41        * expect some differences on lat-lon-cap grid.
42        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
43    o pkg/exch2:
44      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
45        many tiles); until alternative coding is added, just add a stop.
46    o pkg/kpp:
47      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
48        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
49    o optfiles:
50      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
51        into corresponding standard one, which now support different build:
52        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
53      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
54    o pkg/obcs (seaice):
55      - add missing EXCH for uIce,vIce after applying OBCS;
56      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
57        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
58        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
59      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
60      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
61        and eedata.mth for MPI and mutlti-threaded testing.
62    o pkg/flt:
63      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
64      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
65      - fix pickup and trajectories + profiles output with multi-threads;
66      - add parameter to select group of fields to write along trajectory and
67        profile (default unchanged);
68      - only call PORT_RAND* function when flt_noise <> 0;
69      - add multi-threaded test for verification exp. flt_example.
70    o eesupp/src:
71      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
72      - USE_OMP_THREADING: check that number of threads (from eedata) matches
73        actual number (from env.var. setting).
74    o pkg/ebm:
75      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
76      - add multi-threaded test for verification exp. global_ocean_ebm
77    
78    checkpoint63b (2011/08/29)
79    o pkg/ebm:
80      - fix sign of runoff;
81      - update directly forcing fields (Qnet,EmPmR) to use standard
82        external_forcing_surf.F (remove ebm_forcing_surf.F);
83      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
84      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
85        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
86      - update global_ocean_ebm parameters file data and update output (fwd+ad).
87    o verification/matrix_example:
88      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
89        MPI and mutlti-threaded testing.
90    o pkg/matrix:
91      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
92      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
93      - fix for multi-threaded (remove DATA statement);
94      - use standard DIFFERENT_MULTIPLE function;
95      - add MATRIX_OPTIONS.h
96    o verification/matrix_example:
97       To allow to split the domain in several tiles, change the domain size
98        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
99        Western side) of land points.
100    o (*_)write_pickup:
101      - fix few bugs in mypackage_read/write_pickup.F
102      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
103        array of length 1 (was caught by compiler syntax-check).
104    o pkg/diagnostics (velocity potential solver):
105      - fix initialisation of main diagonal matrix (for overlap values)
106    o tools/build_options:
107      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
108        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
109      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
110        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
111        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
112        and use "-devel" testreport option for standard testing on baudelaire.
113    o pkg/grdchk:
114      - Assume that all gradient-check position are within the same tile
115        corresponding to global indices (iGloTile,jGloTile) and that
116        positions (i,j indices or nbeg) are local to this tile;
117      - set tile local-indices and proc. number according to tile global-indices;
118      - remove grdchkwhichproc from namelist (retired param);
119      - send adjoint gradient to all procs so that all procs print it to STDOUT;
120      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
121    o adding package bbl (Bottom Boundary Layer)
122      description in MITgcm/pkg/bbl/bbl_description.tex
123      example/test experiment in MITgcm_contrib/bbl
124    o adjoint verifications
125      - changed 5 experiments to multi-tiles
126        * global_ocean.90x40x15
127        * obcs_ctrl
128        * offline_exf_seaice
129        * tutorial_dic_adjoffline
130        * tutorial_tracer_adjsens
131        changed reference output for those that crossed tile boundaries
132        (changed choices of gradient check positions)
133      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
134      - temporary bug fix in grdchk_loc.F for obcs
135    o genmake2 & testreport
136      - add target "obj" (just for OBJFILES files) to Makefile;
137      - add option to specify FEXTRAFLAGS on command line.
138    o pkg/mypackage:
139      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
140    
141    checkpoint63a (2011/08/02)
142    o pkg/diagnostics (velocity potential):
143      - fix velocity-potential calculation when using OBCS: balance net inflow
144        at each level (new S/R OBCS_DIAG_BALANCE).
145      - fix some of the problems with OBCS in stream-function calculation.
146    o pkg/exf/exf_readparms.F
147      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
148        EXF_NML_OBCS) more consistent, so that you need not have these lists
149        in data.exf when they are not used.
150    o optim/optim_readdata.F:
151      - add some output about obcs variables that might help debugging
152      - add a check about nvarlength
153    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
154    o pkg/diagnostics (velocity potential):
155      - fix mask for OBCS (still problems in stream-function with OBCS);
156      - add specific parameter (default = main code CG2D params) for solver;
157      - in case of poor convergence, use solution corresponding to lowest residual.
158    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
159      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
160      and should be avoided where possible.
161    o model/src (rStar):
162      - include r* effect on reference-state (PhiRef) in totPhiHyd
163        (so that it's really the potential anomaly at the cell center);
164        affect solution only if z* with full pressure in EOS.
165      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
166        update output (because of z* in totPhiHyd and viscA4 changes);
167      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
168        @ constant r) until interpolation at constant r is implemented.
169    o pkg/diagnostics
170      - fix RCENTER diagnostics in case cell center is not at interface middle
171    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
172      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
173      that THETA and SALT are "conservative temperature" and "absolute
174      salinity"
175    o pkg/ctrl
176      - fix computation of endrec in s/r ctrl_init_rec
177      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
178    o pkg/seaice/seaice_growth.F
179      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
180        remove then obsolete STORE directives
181      - fix STORE directives for tice and tices, so that only the
182        appropriate part of the fields are stored (and not the entire
183        field); update global_ocean.cs32x15.seaice AD output.
184      - cosmetic changes: adjust CPP flags and indentation for better
185        legibilty
186    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
187      Chris Wilson)
188  o pkg/gmredi:  o pkg/gmredi:
189     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
190     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)
191    
192  checkpoint63 (2011/07/11)  checkpoint63  (2011/07/11)
193  o pkg/exch2:  o pkg/exch2:
194   - 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
195   - 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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