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revision 1.1462 by jmc, Wed Jun 22 19:17:36 2011 UTC revision 1.1510 by jmc, Wed Oct 5 18:35:02 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:
8      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
9    o pkg/exch2:
10      - alternative code (without tile x tile matrix) for cumulated (global) sum;
11        used as default; keep using matrix version in adjustment.cs-32x32x1.
12    o tools/build_options:
13      - after merging some MPI and/or multi-threads specific optfiles so that
14        the modified default optfile support both built (using genmake2 -mpi
15        for the MPI built, using genmake2 -omp for OpenMP built),
16        move now obsolete optfiles to tools/build_options/unsupported/
17       (add copy of email sent to support list in doc/optfiles_changes.txt)
18    
19    checkpoint63c (2011/09/28)
20    o pkg/ebm:
21      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
22        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
23    o pkg/seaice (SItracer pickup)
24    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
25      To be done:
26      - thorough testing of missing fields in S/R seaice_read_pickup
27      - thorough matching between generic tracers and specific fields used
28        (e.g. volume-weighted age, area-weighted age, salinity, ...)
29    o pkg/grdchk:
30      - all procs calculate and print finite-difference gradient (for testreport)
31      - change description output used by testreport;
32      - AD testing: also compare and report Finite-difference gradient;
33        => update all output_adm*.txt
34    o test exp. global_ocean_ebm:
35      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
36        and turn on exactConserve; update (fwd) output.
37    o pkg/seaice (LSR):
38      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
39      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
40        * identical results with non-CS topology (but save up to half of EXCH calls)
41        * no much changes in cs-32 verification tests since no ice at face edges
42         (differences due to convergence criteria, since nb of iterations changed)
43        * expect some differences on lat-lon-cap grid.
44        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
45    o pkg/exch2:
46      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
47        many tiles); until alternative coding is added, just add a stop.
48    o pkg/kpp:
49      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
50        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
51    o optfiles:
52      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
53        into corresponding standard one, which now support different build:
54        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
55      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
56    o pkg/obcs (seaice):
57      - add missing EXCH for uIce,vIce after applying OBCS;
58      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
59        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
60        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
61      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
62      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
63        and eedata.mth for MPI and mutlti-threaded testing.
64    o pkg/flt:
65      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
66      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
67      - fix pickup and trajectories + profiles output with multi-threads;
68      - add parameter to select group of fields to write along trajectory and
69        profile (default unchanged);
70      - only call PORT_RAND* function when flt_noise <> 0;
71      - add multi-threaded test for verification exp. flt_example.
72    o eesupp/src:
73      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
74      - USE_OMP_THREADING: check that number of threads (from eedata) matches
75        actual number (from env.var. setting).
76    o pkg/ebm:
77      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
78      - add multi-threaded test for verification exp. global_ocean_ebm
79    
80    checkpoint63b (2011/08/29)
81    o pkg/ebm:
82      - fix sign of runoff;
83      - update directly forcing fields (Qnet,EmPmR) to use standard
84        external_forcing_surf.F (remove ebm_forcing_surf.F);
85      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
86      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
87        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
88      - update global_ocean_ebm parameters file data and update output (fwd+ad).
89    o verification/matrix_example:
90      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
91        MPI and mutlti-threaded testing.
92    o pkg/matrix:
93      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
94      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
95      - fix for multi-threaded (remove DATA statement);
96      - use standard DIFFERENT_MULTIPLE function;
97      - add MATRIX_OPTIONS.h
98    o verification/matrix_example:
99       To allow to split the domain in several tiles, change the domain size
100        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
101        Western side) of land points.
102    o (*_)write_pickup:
103      - fix few bugs in mypackage_read/write_pickup.F
104      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
105        array of length 1 (was caught by compiler syntax-check).
106    o pkg/diagnostics (velocity potential solver):
107      - fix initialisation of main diagonal matrix (for overlap values)
108    o tools/build_options:
109      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
110        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
111      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
112        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
113        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
114        and use "-devel" testreport option for standard testing on baudelaire.
115    o pkg/grdchk:
116      - Assume that all gradient-check position are within the same tile
117        corresponding to global indices (iGloTile,jGloTile) and that
118        positions (i,j indices or nbeg) are local to this tile;
119      - set tile local-indices and proc. number according to tile global-indices;
120      - remove grdchkwhichproc from namelist (retired param);
121      - send adjoint gradient to all procs so that all procs print it to STDOUT;
122      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
123    o adding package bbl (Bottom Boundary Layer)
124      description in MITgcm/pkg/bbl/bbl_description.tex
125      example/test experiment in MITgcm_contrib/bbl
126    o adjoint verifications
127      - changed 5 experiments to multi-tiles
128        * global_ocean.90x40x15
129        * obcs_ctrl
130        * offline_exf_seaice
131        * tutorial_dic_adjoffline
132        * tutorial_tracer_adjsens
133        changed reference output for those that crossed tile boundaries
134        (changed choices of gradient check positions)
135      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
136      - temporary bug fix in grdchk_loc.F for obcs
137    o genmake2 & testreport
138      - add target "obj" (just for OBJFILES files) to Makefile;
139      - add option to specify FEXTRAFLAGS on command line.
140    o pkg/mypackage:
141      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
142    
143    checkpoint63a (2011/08/02)
144    o pkg/diagnostics (velocity potential):
145      - fix velocity-potential calculation when using OBCS: balance net inflow
146        at each level (new S/R OBCS_DIAG_BALANCE).
147      - fix some of the problems with OBCS in stream-function calculation.
148    o pkg/exf/exf_readparms.F
149      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
150        EXF_NML_OBCS) more consistent, so that you need not have these lists
151        in data.exf when they are not used.
152    o optim/optim_readdata.F:
153      - add some output about obcs variables that might help debugging
154      - add a check about nvarlength
155    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
156    o pkg/diagnostics (velocity potential):
157      - fix mask for OBCS (still problems in stream-function with OBCS);
158      - add specific parameter (default = main code CG2D params) for solver;
159      - in case of poor convergence, use solution corresponding to lowest residual.
160    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
161      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
162      and should be avoided where possible.
163    o model/src (rStar):
164      - include r* effect on reference-state (PhiRef) in totPhiHyd
165        (so that it's really the potential anomaly at the cell center);
166        affect solution only if z* with full pressure in EOS.
167      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
168        update output (because of z* in totPhiHyd and viscA4 changes);
169      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
170        @ constant r) until interpolation at constant r is implemented.
171    o pkg/diagnostics
172      - fix RCENTER diagnostics in case cell center is not at interface middle
173    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
174      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
175      that THETA and SALT are "conservative temperature" and "absolute
176      salinity"
177    o pkg/ctrl
178      - fix computation of endrec in s/r ctrl_init_rec
179      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
180    o pkg/seaice/seaice_growth.F
181      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
182        remove then obsolete STORE directives
183      - fix STORE directives for tice and tices, so that only the
184        appropriate part of the fields are stored (and not the entire
185        field); update global_ocean.cs32x15.seaice AD output.
186      - cosmetic changes: adjust CPP flags and indentation for better
187        legibilty
188    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
189      Chris Wilson)
190    o pkg/gmredi:
191       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
192       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
193    
194    checkpoint63  (2011/07/11)
195    o pkg/exch2:
196     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
197     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
198       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
199       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
200    o pkg/diagnostics:
201     - deal with pairs of post-processed diags which are computed together; in
202       particular, re-order list of diags within 1 file to save 2nd computation.
203     - add S/R to compute velocity stream-function (called after velocity-potential
204       calculation) from divergence free transport -> new diagnostics "PsiVEL".
205     - add parameter to select grid-point location where PsiVEL == 0.
206    o eesupp/src:
207       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
208       (specific S/R needed with exch2 topology - for now, just print an error msg)
209    o pkg/shelfice
210     - Implement friction velocity-dependent transfer coefficients following
211       Holland and Jenkins, JPO, 1999
212       Original code by M. Losch with small modifs.
213       Enable with CPP option SHI_ALLOW_GAMMAFRICT
214       and runtime flag SHELFICEuseGammaFrict
215    o verification lab_sea & global_ocean.cs32x15:
216     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
217       does not miss some dependencies (but is slower) and also works with many files
218       (default makedepend limitation for AD built).
219     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
220    o pkg/diagnostics:
221     - add run-time parameter "useMissingValue" (def=False) to fill land-point
222        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
223       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
224     - Extend the use of "missing_value" setting from data.diagnostics for the case
225       of counter-diagnostics (where fraction-weight is zero). This applies both to
226       MNC and MDS output files.
227    o pkg/seaice/seaice_growth.F:
228      - add 'a priori' cap of latent heat flux based on actual mass considerations
229        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
230        non-legacy seaice_solve4temp.
231      - add diagnostic of the residual sublimation freshwater flux (the freshwater
232        flux taken from the ocean if the total actual latent heat fluxes exceed
233        the maximum)
234      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
235       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
236      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
237       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
238      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
239      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
240    o verification 1D_ocean_ice_column:
241       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
242       update results
243  o pkg/diagnostics:  o pkg/diagnostics:
244   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
245     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
246     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.
247   - Update Velocity-potential computation using post-processed diag framework.   - Update Velocity-potential computation using post-processed diag framework.
248   Change the ordering of fields and time-periods in MDS output file   ==> Change the ordering of fields and time-periods in MDS output file
249     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
250     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
251     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).
252     Note: this is now similar to NetCDF (MNC) output file.       Note: this is now similar to NetCDF (MNC) output file. <==
253    
254  checkpoint62z (2011/06/21)  checkpoint62z (2011/06/21)
255  o adjoint monitor:  o adjoint monitor:
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