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revision 1.1484 by jmc, Mon Aug 1 20:47:39 2011 UTC revision 1.1516 by jmc, Fri Oct 21 18:33:58 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/obcs + seaice-dynamics:
8      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
9        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
10        values (consistent with an implicit method).
11      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
12        return to older implementation (same results as before); note that none of
13        the "experimental" OBCS_SEAICE options are implemented in the new version.
14    o pkg/seaice:
15      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
16      - add parenthesis in Water-Ice drag calculations (evp & lsr);
17      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
18        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
19      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
20        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
21    o pkg/layers:
22      - Include potential density as new coordinate (Thanks to David Munday)
23    o pkg/dic:
24      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
25        carbonate computation/output to CALC_PCO2_APPROX
26    o model/src:
27      - improve vectorization also for adjoint code of
28        solve_tridiagonal and solve_pentadiagonal. As this requires up to
29        5 new 3D-fields, this code is only turned on for the combination of
30        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX.
31      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
32        ALLOW_AUTODIFF. This flag now needs to be set outside of
33        solve_tri/pentadiagonal.F
34    o pkg/exf:
35      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
36        optional namelist EXF_NML_OBCS).
37      - add many debug-print (to trace down where pkg/cal error msg comes from)
38    o pkg/mom_vecinv/mom_vi_hdissip.F
39      - rearrange loops so that vectorization is improved and in particular
40        the adjoint routine vectorizes. The code is a little longer now, but I
41        think easier to read.
42        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
43    o pkg/seaice:
44      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
45    o pkg/exch2:
46      - alternative code (without tile x tile matrix) for cumulated (global) sum;
47        used as default; keep using matrix version in adjustment.cs-32x32x1.
48    o tools/build_options:
49      - after merging some MPI and/or multi-threads specific optfiles so that
50        the modified default optfile support both built (using genmake2 -mpi
51        for the MPI built, using genmake2 -omp for OpenMP built),
52        move now obsolete optfiles to tools/build_options/unsupported/
53       (add copy of email sent to support list in doc/optfiles_changes.txt)
54    
55    checkpoint63c (2011/09/28)
56    o pkg/ebm:
57      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
58        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
59    o pkg/seaice (SItracer pickup)
60    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
61      To be done:
62      - thorough testing of missing fields in S/R seaice_read_pickup
63      - thorough matching between generic tracers and specific fields used
64        (e.g. volume-weighted age, area-weighted age, salinity, ...)
65    o pkg/grdchk:
66      - all procs calculate and print finite-difference gradient (for testreport)
67      - change description output used by testreport;
68      - AD testing: also compare and report Finite-difference gradient;
69        => update all output_adm*.txt
70    o test exp. global_ocean_ebm:
71      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
72        and turn on exactConserve; update (fwd) output.
73    o pkg/seaice (LSR):
74      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
75      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
76        * identical results with non-CS topology (but save up to half of EXCH calls)
77        * no much changes in cs-32 verification tests since no ice at face edges
78         (differences due to convergence criteria, since nb of iterations changed)
79        * expect some differences on lat-lon-cap grid.
80        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
81    o pkg/exch2:
82      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
83        many tiles); until alternative coding is added, just add a stop.
84    o pkg/kpp:
85      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
86        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
87    o optfiles:
88      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
89        into corresponding standard one, which now support different build:
90        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
91      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
92    o pkg/obcs (seaice):
93      - add missing EXCH for uIce,vIce after applying OBCS;
94      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
95        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
96        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
97      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
98      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
99        and eedata.mth for MPI and mutlti-threaded testing.
100    o pkg/flt:
101      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
102      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
103      - fix pickup and trajectories + profiles output with multi-threads;
104      - add parameter to select group of fields to write along trajectory and
105        profile (default unchanged);
106      - only call PORT_RAND* function when flt_noise <> 0;
107      - add multi-threaded test for verification exp. flt_example.
108    o eesupp/src:
109      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
110      - USE_OMP_THREADING: check that number of threads (from eedata) matches
111        actual number (from env.var. setting).
112    o pkg/ebm:
113      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
114      - add multi-threaded test for verification exp. global_ocean_ebm
115    
116    checkpoint63b (2011/08/29)
117    o pkg/ebm:
118      - fix sign of runoff;
119      - update directly forcing fields (Qnet,EmPmR) to use standard
120        external_forcing_surf.F (remove ebm_forcing_surf.F);
121      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
122      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
123        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
124      - update global_ocean_ebm parameters file data and update output (fwd+ad).
125    o verification/matrix_example:
126      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
127        MPI and mutlti-threaded testing.
128    o pkg/matrix:
129      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
130      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
131      - fix for multi-threaded (remove DATA statement);
132      - use standard DIFFERENT_MULTIPLE function;
133      - add MATRIX_OPTIONS.h
134    o verification/matrix_example:
135       To allow to split the domain in several tiles, change the domain size
136        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
137        Western side) of land points.
138    o (*_)write_pickup:
139      - fix few bugs in mypackage_read/write_pickup.F
140      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
141        array of length 1 (was caught by compiler syntax-check).
142    o pkg/diagnostics (velocity potential solver):
143      - fix initialisation of main diagonal matrix (for overlap values)
144    o tools/build_options:
145      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
146        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
147      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
148        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
149        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
150        and use "-devel" testreport option for standard testing on baudelaire.
151    o pkg/grdchk:
152      - Assume that all gradient-check position are within the same tile
153        corresponding to global indices (iGloTile,jGloTile) and that
154        positions (i,j indices or nbeg) are local to this tile;
155      - set tile local-indices and proc. number according to tile global-indices;
156      - remove grdchkwhichproc from namelist (retired param);
157      - send adjoint gradient to all procs so that all procs print it to STDOUT;
158      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
159    o adding package bbl (Bottom Boundary Layer)
160      description in MITgcm/pkg/bbl/bbl_description.tex
161      example/test experiment in MITgcm_contrib/bbl
162    o adjoint verifications
163      - changed 5 experiments to multi-tiles
164        * global_ocean.90x40x15
165        * obcs_ctrl
166        * offline_exf_seaice
167        * tutorial_dic_adjoffline
168        * tutorial_tracer_adjsens
169        changed reference output for those that crossed tile boundaries
170        (changed choices of gradient check positions)
171      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
172      - temporary bug fix in grdchk_loc.F for obcs
173    o genmake2 & testreport
174      - add target "obj" (just for OBJFILES files) to Makefile;
175      - add option to specify FEXTRAFLAGS on command line.
176    o pkg/mypackage:
177      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
178    
179    checkpoint63a (2011/08/02)
180  o pkg/diagnostics (velocity potential):  o pkg/diagnostics (velocity potential):
181    - fix velocity-potential calculation when using OBCS: balance net inflow    - fix velocity-potential calculation when using OBCS: balance net inflow
182      at each level (new S/R OBCS_DIAG_BALANCE).      at each level (new S/R OBCS_DIAG_BALANCE).
# Line 54  o pkg/gmredi: Line 227  o pkg/gmredi:
227     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),     Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
228     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)
229    
230  checkpoint63 (2011/07/11)  checkpoint63  (2011/07/11)
231  o pkg/exch2:  o pkg/exch2:
232   - 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
233   - 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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