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revision 1.1462 by jmc, Wed Jun 22 19:17:36 2011 UTC revision 1.1525 by heimbach, Mon Oct 31 03:30:19 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 adjoint of LSR:
8      - substantially rework STORE dirs.
9      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
10        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
11        and only perform SOLV_MAX_FIXED adjoint iters.
12      - now produces non-zero LSR-related gradients, and acceptable gradients for
13        An's zonal (x-z) test case (to be checked in)
14      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
15        (but these are screwed up by the thermodynamics in the first place);
16        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
17        output_adm.txt also reflects changes to seaice_lsr
18      - global_ocean.cs32x15:
19        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
20          (output_adm.seaice.txt was updated)
21        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
22          (output_adm.seaice_dynmix.txt)
23    o test-exp. exp4+stevens:
24      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
25    o pkg/seaice (lsr solver):
26      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
27        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
28      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
29      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
30        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
31      - compute (with new S/R) and print initial (+ free-driff sol. if available)
32        and final residual of linearised system.
33    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
34      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
35    o pkg/obcs: Stevens BCs (still only for east and west)
36      - fix Stevens BCs by using intermediate velocities of previous
37        time step as "baroclinic" contribution rather velocity of one grid cell
38        inside the boundaries; more consistent but makes the entire treatment
39        more complicated, requires new pickup files and two new S/Rs:
40        obcs_copy_uv_n and obcs_save_uv_n
41        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
42        (undefined by default)
43      - silently move computation of some grid factors into separate loops to
44        save some recomputations
45      - add a hack for non-linear free surface
46      - add a verification experiment to exp4 that tests this code
47    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
48    
49    checkpoint63d (2011/10/25)
50    o pkg/obcs + seaice-dynamics:
51      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
52        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
53        values (consistent with an implicit method).
54      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
55        return to older implementation (same results as before); note that none of
56        the "experimental" OBCS_SEAICE options are implemented in the new version.
57      - switch test exp. seaice_obcs to use new version (update output).
58    o pkg/seaice:
59      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
60      - add parenthesis in Water-Ice drag calculations (evp & lsr);
61      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
62        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
63      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
64        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
65    o pkg/layers:
66      - Include potential density as new coordinate (Thanks to David Munday)
67    o pkg/dic:
68      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
69        carbonate computation/output to CALC_PCO2_APPROX
70    o pkg/generic_advdiff
71      - make TAF generate code that vectorizes:
72        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
73    o model/src:
74      - improve vectorization also for adjoint code of
75        solve_tridiagonal and solve_pentadiagonal. As this requires up to
76        5 new 3D-fields, this code is only turned on for the combination of
77        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
78        for singular matrix check (only for TARGET_NEC_SX).
79      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
80        ALLOW_AUTODIFF. This flag now needs to be set outside of
81        solve_tri/pentadiagonal.F
82    o pkg/exf:
83      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
84        optional namelist EXF_NML_OBCS).
85      - add many debug-print (to trace down where pkg/cal error msg comes from)
86    o pkg/mom_vecinv/mom_vi_hdissip.F
87      - rearrange loops so that vectorization is improved and in particular
88        the adjoint routine vectorizes. The code is a little longer now, but I
89        think easier to read.
90        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
91    o pkg/seaice:
92      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
93    o pkg/exch2:
94      - alternative code (without tile x tile matrix) for cumulated (global) sum;
95        used as default; keep using matrix version in adjustment.cs-32x32x1.
96    o tools/build_options:
97      - after merging some MPI and/or multi-threads specific optfiles so that
98        the modified default optfile support both built (using genmake2 -mpi
99        for the MPI built, using genmake2 -omp for OpenMP built),
100        move now obsolete optfiles to tools/build_options/unsupported/
101       (add copy of email sent to support list in doc/optfiles_changes.txt)
102    
103    checkpoint63c (2011/09/28)
104    o pkg/ebm:
105      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
106        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
107    o pkg/seaice (SItracer pickup)
108    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
109      To be done:
110      - thorough testing of missing fields in S/R seaice_read_pickup
111      - thorough matching between generic tracers and specific fields used
112        (e.g. volume-weighted age, area-weighted age, salinity, ...)
113    o pkg/grdchk:
114      - all procs calculate and print finite-difference gradient (for testreport)
115      - change description output used by testreport;
116      - AD testing: also compare and report Finite-difference gradient;
117        => update all output_adm*.txt
118    o test exp. global_ocean_ebm:
119      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
120        and turn on exactConserve; update (fwd) output.
121    o pkg/seaice (LSR):
122      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
123      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
124        * identical results with non-CS topology (but save up to half of EXCH calls)
125        * no much changes in cs-32 verification tests since no ice at face edges
126         (differences due to convergence criteria, since nb of iterations changed)
127        * expect some differences on lat-lon-cap grid.
128        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
129    o pkg/exch2:
130      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
131        many tiles); until alternative coding is added, just add a stop.
132    o pkg/kpp:
133      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
134        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
135    o optfiles:
136      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
137        into corresponding standard one, which now support different build:
138        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
139      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
140    o pkg/obcs (seaice):
141      - add missing EXCH for uIce,vIce after applying OBCS;
142      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
143        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
144        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
145      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
146      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
147        and eedata.mth for MPI and mutlti-threaded testing.
148    o pkg/flt:
149      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
150      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
151      - fix pickup and trajectories + profiles output with multi-threads;
152      - add parameter to select group of fields to write along trajectory and
153        profile (default unchanged);
154      - only call PORT_RAND* function when flt_noise <> 0;
155      - add multi-threaded test for verification exp. flt_example.
156    o eesupp/src:
157      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
158      - USE_OMP_THREADING: check that number of threads (from eedata) matches
159        actual number (from env.var. setting).
160    o pkg/ebm:
161      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
162      - add multi-threaded test for verification exp. global_ocean_ebm
163    
164    checkpoint63b (2011/08/29)
165    o pkg/ebm:
166      - fix sign of runoff;
167      - update directly forcing fields (Qnet,EmPmR) to use standard
168        external_forcing_surf.F (remove ebm_forcing_surf.F);
169      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
170      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
171        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
172      - update global_ocean_ebm parameters file data and update output (fwd+ad).
173    o verification/matrix_example:
174      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
175        MPI and mutlti-threaded testing.
176    o pkg/matrix:
177      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
178      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
179      - fix for multi-threaded (remove DATA statement);
180      - use standard DIFFERENT_MULTIPLE function;
181      - add MATRIX_OPTIONS.h
182    o verification/matrix_example:
183       To allow to split the domain in several tiles, change the domain size
184        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
185        Western side) of land points.
186    o (*_)write_pickup:
187      - fix few bugs in mypackage_read/write_pickup.F
188      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
189        array of length 1 (was caught by compiler syntax-check).
190    o pkg/diagnostics (velocity potential solver):
191      - fix initialisation of main diagonal matrix (for overlap values)
192    o tools/build_options:
193      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
194        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
195      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
196        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
197        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
198        and use "-devel" testreport option for standard testing on baudelaire.
199    o pkg/grdchk:
200      - Assume that all gradient-check position are within the same tile
201        corresponding to global indices (iGloTile,jGloTile) and that
202        positions (i,j indices or nbeg) are local to this tile;
203      - set tile local-indices and proc. number according to tile global-indices;
204      - remove grdchkwhichproc from namelist (retired param);
205      - send adjoint gradient to all procs so that all procs print it to STDOUT;
206      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
207    o adding package bbl (Bottom Boundary Layer)
208      description in MITgcm/pkg/bbl/bbl_description.tex
209      example/test experiment in MITgcm_contrib/bbl
210    o adjoint verifications
211      - changed 5 experiments to multi-tiles
212        * global_ocean.90x40x15
213        * obcs_ctrl
214        * offline_exf_seaice
215        * tutorial_dic_adjoffline
216        * tutorial_tracer_adjsens
217        changed reference output for those that crossed tile boundaries
218        (changed choices of gradient check positions)
219      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
220      - temporary bug fix in grdchk_loc.F for obcs
221    o genmake2 & testreport
222      - add target "obj" (just for OBJFILES files) to Makefile;
223      - add option to specify FEXTRAFLAGS on command line.
224    o pkg/mypackage:
225      - remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS
226    
227    checkpoint63a (2011/08/02)
228    o pkg/diagnostics (velocity potential):
229      - fix velocity-potential calculation when using OBCS: balance net inflow
230        at each level (new S/R OBCS_DIAG_BALANCE).
231      - fix some of the problems with OBCS in stream-function calculation.
232    o pkg/exf/exf_readparms.F
233      - make treatment of optional namelists (EXF_NML_04, EXF_NML_SGRUNOFF,
234        EXF_NML_OBCS) more consistent, so that you need not have these lists
235        in data.exf when they are not used.
236    o optim/optim_readdata.F:
237      - add some output about obcs variables that might help debugging
238      - add a check about nvarlength
239    o pkg/ctrl: once again, fix computation of endrec in s/r ctrl_init_rec
240    o pkg/diagnostics (velocity potential):
241      - fix mask for OBCS (still problems in stream-function with OBCS);
242      - add specific parameter (default = main code CG2D params) for solver;
243      - in case of poor convergence, use solution corresponding to lowest residual.
244    o pkg/seaice/seaice_growth.F: small changes that permit vectorizable
245      adjoint code. In general statements like tmpscal=fld(i,j) are problematic
246      and should be avoided where possible.
247    o model/src (rStar):
248      - include r* effect on reference-state (PhiRef) in totPhiHyd
249        (so that it's really the potential anomaly at the cell center);
250        affect solution only if z* with full pressure in EOS.
251      - test-exp global_ocean.90x40x15: reduce viscA4 (was not stable) and
252        update output (because of z* in totPhiHyd and viscA4 changes);
253      - keep the previous diagnostics as "PHIHYDcR" (closer to potential anomaly
254        @ constant r) until interpolation at constant r is implemented.
255    o pkg/diagnostics
256      - fix RCENTER diagnostics in case cell center is not at interface middle
257    o add code for TEOS-10 (www.teos-10.org, McDougall et al. 2011). Use
258      this eos with eosType = 'TEOS10', in data (PARM01). This eos implies
259      that THETA and SALT are "conservative temperature" and "absolute
260      salinity"
261    o pkg/ctrl
262      - fix computation of endrec in s/r ctrl_init_rec
263      - ctrl_pack/unpack_*: remove unused variables and some obsolete code
264    o pkg/seaice/seaice_growth.F
265      - fix recomputation with FENTY_AREA_EXPANSION_CONTRACTION code,
266        remove then obsolete STORE directives
267      - fix STORE directives for tice and tices, so that only the
268        appropriate part of the fields are stored (and not the entire
269        field); update global_ocean.cs32x15.seaice AD output.
270      - cosmetic changes: adjust CPP flags and indentation for better
271        legibilty
272    o pkg/autodiff: add mnc-output of adBottomDragFld (code contributed by
273      Chris Wilson)
274    o pkg/gmredi:
275       Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF),
276       and test it in verification exp. "front_relax.bvp" (update output.bvp.txt)
277    
278    checkpoint63  (2011/07/11)
279    o pkg/exch2:
280     - rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h
281     - exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the
282       (2*nTiles)x(nTiles) Cumul-Sum matrix and Master Proc collects all tiles X,Y
283       increments, calculates Cumul-Sum @ tile origin and sends results to each tile.
284    o pkg/diagnostics:
285     - deal with pairs of post-processed diags which are computed together; in
286       particular, re-order list of diags within 1 file to save 2nd computation.
287     - add S/R to compute velocity stream-function (called after velocity-potential
288       calculation) from divergence free transport -> new diagnostics "PsiVEL".
289     - add parameter to select grid-point location where PsiVEL == 0.
290    o eesupp/src:
291       new S/R to calculate cumulated sum on tiled array, corner grid-cell location
292       (specific S/R needed with exch2 topology - for now, just print an error msg)
293    o pkg/shelfice
294     - Implement friction velocity-dependent transfer coefficients following
295       Holland and Jenkins, JPO, 1999
296       Original code by M. Losch with small modifs.
297       Enable with CPP option SHI_ALLOW_GAMMAFRICT
298       and runtime flag SHELFICEuseGammaFrict
299    o verification lab_sea & global_ocean.cs32x15:
300     - use tools/xmakedepend (instead of cyrus_makedepend, in genmake_local):
301       does not miss some dependencies (but is slower) and also works with many files
302       (default makedepend limitation for AD built).
303     - use cyrus_makedepend in adjustment.128x64x1 (so that it still tested).
304    o pkg/diagnostics:
305     - add run-time parameter "useMissingValue" (def=False) to fill land-point
306        (i.e., where mask=0) with MissingValue ; used only in MNC output file.
307       This replaces CPP-option DIAGNOSTICS_MISSING_VALUE.
308     - Extend the use of "missing_value" setting from data.diagnostics for the case
309       of counter-diagnostics (where fraction-weight is zero). This applies both to
310       MNC and MDS output files.
311    o pkg/seaice/seaice_growth.F:
312      - add 'a priori' cap of latent heat flux based on actual mass considerations
313        when SEAICE_ADD_SUBLIMATION_TO_FWBUDGET is used in conjunction with the
314        non-legacy seaice_solve4temp.
315      - add diagnostic of the residual sublimation freshwater flux (the freshwater
316        flux taken from the ocean if the total actual latent heat fluxes exceed
317        the maximum)
318      - remove the CPP switch around the *_FWbySublim unit change and move diagnostic
319       fill for SIatmQnt, SIfwSubl, SIatmFW to the end of seaice_growth.F.
320      - add diagnostic of the actual sublimation freshwater flux (that is 0. ifndef
321       SEAICE_ADD_SUBLIMATION_TO_FWBUDGET) and of the latent heat flux (evap+sublim).
322      - bug fix : frWtrAtm needs a_FWbySublim ifdef SEAICE_ADD_SUBLIMATION_TO_FWBUDGET.
323      - bug fix : missing part to Martin's r_FWbySublim pathological case fix.
324    o verification 1D_ocean_ice_column:
325       made model domain truly 1x1x23 instead of 5x5x23 with only center cell (3,3,:) wet
326       update results
327  o pkg/diagnostics:  o pkg/diagnostics:
328   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')   - Implement setting of "Post-Processed" diagnostics (corresponding to gdiag(5)='P')
329     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
330     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.
331   - Update Velocity-potential computation using post-processed diag framework.   - Update Velocity-potential computation using post-processed diag framework.
332   Change the ordering of fields and time-periods in MDS output file   ==> Change the ordering of fields and time-periods in MDS output file
333     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
334     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
335     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).
336     Note: this is now similar to NetCDF (MNC) output file.       Note: this is now similar to NetCDF (MNC) output file. <==
337    
338  checkpoint62z (2011/06/21)  checkpoint62z (2011/06/21)
339  o adjoint monitor:  o adjoint monitor:

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