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revision 1.1258 by mlosch, Wed Apr 28 08:37:41 2010 UTC revision 1.1354 by gforget, Tue Dec 21 23:36:55 2010 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o global_ocean.cs32x15: additional input_ad.seaice experiment
8        that uses pkg/seaice rather than pkg/thsice.
9        (using multidim advection for seaice)
10    o towards more F95 syntax for array specification in namelist:
11      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
12        of all verification experiments.
13           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
14          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
15      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
16    o global_ocean.cs32x15: additional input.seaice experiment
17        that uses pkg/seaice rather than pkg/thsice.
18    
19    checkpoint62p (2010/12/17)
20    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
21        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
22    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
23        allow for use of multim. advection in seaice adjoint.
24    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
25      - first attempt to close budgets by taking into account the freshwater
26        flux implied by the sublimation of snow and ice. So far only the
27        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
28        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
29    o eesupp/src:
30      new S/R with new option (NML_EXTENDED_F77) to change array specification
31      from F95 standard to commonly accepted extended F77 form.
32      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
33      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
34      for less tolerant f77 compiler (e.g., pgf77, g77).
35    o globalFiles:
36      commented out in parameter file "data" since it's not safe with MPI
37      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
38      in this case); no longer commented out in restart test (tst_2+2).
39    o add adTapeDir to specify a special directory where adjoint tapes are
40      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
41      and cannot be used together with mdsioLocalDir.
42    o nesting pkgs:
43      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
44      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
45      - add parameter files + utils dir + output from short run on beagle.
46    o pkg/seaice:
47        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
48    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
49      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
50    
51    checkpoint62o (2010/11/25)
52    o pkg/exf:
53      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
54    o pkg/seaice:
55      - seaice_ocean_stress: split a loop for better vectorization of the
56        adjoint code
57      - seaice_growth.F: fix bug in conservation of freshwater connected to
58        capping of heff, put contribution into d_HEFFbyNEG
59      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
60        by something more sensible (parameters that are what their name implies)
61      - change some defaults, so that by default exf-parameters are used for
62        things like rhoAir, cpAir,latent/sensible heat parameters, in order
63        to reproduce the old results, many data.seaice now contain funny values
64        for cpAir and latent heat of sublimation
65    o packages_readparms.F: move exf_readparms up in line so that
66        exf-parameters are visible for other packages (e.g. seaice)
67    o debugMode & debugLevel=2:
68      - differentiate between debugMode & debugLevel=2:
69        debugMode: controls printing of debug messages (sequence of S/R calls).
70        debugLevel: controls printing of algorithm intermediate results and stats.
71      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
72        => allows to print debug-stats without all sequence of call messages.
73      - switch control of debug print from debugLevel to debugMode in many S/R.
74    o pkg/obcs (obcs-sponge):
75        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
76        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
77    o pkg/generic_advdiff:
78      - record overlap minimum size for each advection scheme;
79      - refine criteria on overlap minimum size;
80      - check and stop (in gad_check) if overlap size is too small.
81    o pkg/obcs:
82      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
83        once, in ptracers_implicit.F)
84      - with seaice: remove test on empty file name in obcs_apply_seaice (always
85        apply OB values when tile has OB)
86    o model/src, coriolis setting:
87      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
88        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
89        files (selectCoriMap=3) with any grid.
90      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
91    o pkg/seaice/seaice_growth.F:
92        a few cosmetic changes that reduce the number of lines of code
93    o pkg/obcs: add boundary conditions following Stevens (1990)
94      - the code follows old MOM/NAOSIM code
95      - so far it is only implemented for the eastern and western boundaries
96        and NOT for pTracers
97    o pkg/rbcs:
98      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
99        beginning of the first rbcs forcing period.
100      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
101        offline package, i.e., one file per time, labeled by iteration number;
102        deltaTrbcs sets the timestep with which the data was generated;
103        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
104      - rbcsForcingCycle=0 makes forcing non-cyclic.
105      - make arithmetic safe for negative times and odd forcing periods.
106    
107    checkpoint62n (2010/11/09)
108    o pkg/seaice:
109        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
110    o pkg/obcs:
111       New S/R to copy tracer value from the OB location to narrow band region
112        (width = same as overlap) beyond the OB: preserve OB value (needed for
113        high-order scheme) which were overwritten by EXCH call if in overlap
114        region. Applied to theta, salt, ptracer and advected seaice variables.
115       With seaice: use maskInC in similar way as in gad_advection.F,
116        in seaice_advection.F and advect.F.
117       Update output of experiment seaice_obcs and change exp4 to test OBCS with
118        4th order Adv.Scheme. for pasive salt and ptracer.
119    o tools/genmake2:
120      - when looking for an optfile (not specified), only search for Fortran compiler
121        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
122      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
123        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
124      - set default for CPP to "cpp -traditional -P" (was the case without specifying
125        an optfile, but otherwise default was just "cpp".
126      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
127      - when "CC" is not set in the optfile, look for possible C compiler
128        (instead of just setting CC=cc)
129      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
130        => add a ".F" to ".o" rule for source files with no "#include" (such as
131           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
132      - move gfortran before g77 in list of possible Fortran compiler (consistent
133        with reference compiler switch from g77 to gfortran)
134    o pkg/seaice:
135      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
136        seaice_check that stops the model, when the CPP flag is used.
137      o seaice_growth.F: make capping of ice volume conserving by returning the
138        capped ice as freshwater to EmPmR. This does not change the verification
139        experiments but will change runs where the capping is acutally active
140    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
141      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
142         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
143         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
144    o tools/genmake2:
145      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
146      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
147      - clean previous genmake log files before anything else.
148      - change Makefile to remove testreport log files (*.tr_log) and genmake log
149        files only with "CLEAN" target (instead of "Clean");
150    o pkg/generic_advdiff:
151      Change OBCS in multiDim advection (gad_advection.F):
152       Use maskInC to prevent intermediate update of tracer-field in OB regions,
153       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
154       which were applying future time-step OB values.
155      This way, all explicit calculations use current-time-step OB values
156       (simpler and more consistent).
157      Affects results when set-up uses time-varying OBC and multi-dim advection;
158       update output of experiment seaice_obcs.
159    o pkg/seaice:
160      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
161       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
162         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
163      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
164       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
165       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
166    o pkg aim (2010/10/26):
167      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
168        formulation with obliquity, eccentricity, ... as run-time parameters,
169      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
170        upward shortwave radition at the surface (all-sky and clear-sky).
171    o pkg/obcs:
172      - writing sections with globalFiles=T does not work: switch to tiled-files
173        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
174      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
175      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
176    
177    checkpoint62m (2010/10/21)
178    o pkg/seaice: vectorize seaice_solve4temp.F
179      - move iterations loops outside of i/j-loops
180      - requires 2D arrays for TB and effConduct
181      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
182        modified in this routine
183      - a little bit of clean up, adjusting indentation, etc.
184      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
185        performance and '**TWO' by '**2' (because TWO is a float),
186        replaced ONE, ZERO
187    o eesupp/src:
188       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
189    o pkg/seaice/seaice_growth.F
190      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
191      merging process. The merged routine has two branches, and one activates the 'evolution'
192      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
193      In summary, here is what the '10/10 revision' did consist of
194        part 1: seaice_growth.F revisions 1.71 to 1.75
195          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
196            The emphasis here was on improving readability (e.g. by trying to use meaningful
197            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
198        part 1.5:
199          - revising the lab_sea experiment to make it a more useful (i.e. stable
200            and representative of an actual model run). This was done by generating a
201            (winter) pickup to start from, switching back the main experiment dynamic
202            solver from evp to lsr, having one of the experiments use the free drift solution.
203        part 2: seaice_growth.F revisions 1.76 to 1.85
204          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
205          - Sorting out the various fields units and sign (set early on and reset at the end)
206            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
207            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
208          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
209            and simplifying logical expressions to further improve readibility.
210        part 3: seaice_growth.F revisions 1.86 to 1.89
211          - Re-organize the blocks of code more logically.
212          - Merging the '_if.F' pieces that add something new.
213    o pkg/thsice:
214      - vectorize thsice_solve4temp and thsice_get_exf.
215        Problem: thsice_solve4temp has an unvectorizable statement that
216        might also be problematic for TAF
217      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
218        does not change the verifcation experiment, but will change all
219        experiments that have this flag undefined (not tested in verification);
220        a little reorganization to save a few 2D fields and recomputations
221      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
222      - 2nd step:  fix some store dirs
223        o seems to work somewhat, i.e. using ifort but not g77
224        o likely cause are incomplete init. or recomputation
225        o start verification/global_ocean.cs32x15/input_ad.thsice
226    o pkg/obcs: add support for exch2
227      - the position of the boundary and prescribed values are specified using
228        a global domain with exch2 facets stacked
229        - in x for N,S boundaries (like W2_mapIO=-1)
230        - in y for E,W boundaries (so E,W boundaries do not overlap)
231    o pkg/mdsio: add support for writing global sections with exch2
232        file layout is as for obcs described above:
233        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
234        - for y-z sections, facets are stacked in y
235    o pkg/thsice:
236       - change a few routines for better vectorization: thsice_albedo.F,
237         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
238         not affected, but in particular the latter routine has changed
239         dramatically (not necessarily easier to read now).
240       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
241       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
242    o verification/lab_sea:
243      - overhaul of the forward model experiments. The main motivation
244        for this revision is that lab_sea has proven quite fragile (when
245        changing the sea-ice code, and switching platforms) to a point
246        when failures were very hard to attribute to specific code problems.
247      - the suspected reason for this fragility is noise amplification by evp so,
248        to start with, we decided to replace evp with lsr in the main experiment.
249      - the input.lsr experiment thus became obsolete and was removed.
250      - it was replaced with the input.fd experiment that uses an
251        analytical "free drift" solution as the ice velocity field.
252      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
253        will hopefully allow us to discriminate problems due to dynamic solvers
254        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
255        us to test additional options, along with the salt plume package.
256      - Finally a pickup was generated (at the end of a one year run) to
257        make the tests more representative of an actual model run. Previously
258        the tests starting point was a 1m thickness of ice everywhere.
259    o pkg/seaice:
260      - introducing S\R seaice_freedrift.F that compute the
261        analytical solution to an approximate ice momentum
262        equation (i.e. the simple stress/coriolis balance).
263      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
264        of the free drift velocity field, and enable its use.
265        To actually use the free drift solution as the model ice
266        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
267    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
268    
269    checkpoint62l (2010/10/04)
270    o pkg/seaice:
271      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
272      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
273       version (with USE_ORIGINAL_SBI undef);
274    o add hooks for new packages OASIS, the package will follow
275      (hooks exclude the seaice pkg for now)
276    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
277      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
278      rather than mdsio_readvector.F/mdsio_writevector.F, within
279      adread_adwrite.F to read/write adjoint-related tapes to disk.
280    o eesupp and pkg/mdsio: ALLOW_WHIO
281      Option to write/read 2D fields to files including tiles halos.
282      The main purpose is for adjoint related "tape I/O".
283      The secondary purpose is for debugging phases.
284      A word on those rather specifically intended purposes.
285      The code was meant to be stripped down to the bare minimum.
286      Typically, there is a unique and basic mapping to the global
287      buffer (tile by tile, then proc by proc, then level by level), and
288      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
289      meant to generate user friendly outputs of various shapes and forms.
290      Rather it is intended, for the knowledgeabale developers,
291      to be largely independent of the many mdsio options, to allow
292      outputs of tiles+halos in debugging phases and in adjoint runs,
293      and to allow some flexibility in tuning (adoint) I/O depending on each
294      file system behavior. With regard to tuning, most of the potential knobs
295      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
296      to specify directories, to specify the typical size of I/O calls, etc.)
297      are not yet included, and will be added if they prove useful.
298    o pkg/seaice:
299       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
300    o pkg/seaice:
301       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
302       code (seaice_budget_ice_if.F) which enable to recover old standard
303       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
304       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
305    o model/src (rStar):
306       use simple average (not area weighted) of rStarFac at U,V point when using
307       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
308       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
309    
310    checkpoint62k (2010/09/17)
311    o adjoint
312       * changed verification/global_ocean.cs32x15 ; adjoint now tests
313         Adams-Bashforth 3 + NLFS + RSTAR
314       * some more modifs required for ECCO-GODAE v4
315    o pkg/seaice
316       add SEAICE_AGE_VOL option to use volume instead of area for
317       integrating SEAICE_AGE
318    o model/src:
319       first check-in of sigma & hybrid-sigma coordinate code ; also includes
320       non-linear free-surface parts ; but pressure-gradient not yet coded.
321    o pkg/ptracers:
322       option for ptracer to convert Salt Relax into additional EmP.
323        tested in exp. global_ocean.90x40x15.dwnslp (update output)
324    
325    checkpoint62j (2010/08/25)
326    o pkg/ggl90:
327       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
328    o pkg/dic: car_flux.F, phos_flux.F
329      - reduce number of exp-calls in order to improve performance
330      - clean up a little (replace fields by their macros, etc., fix
331        typo in CPP-flag)
332    o pkg/ggl90: minor changes
333      - GGL90diffKrS was removed --> always use GGL90diffKr
334      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
335      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
336        (commented out for now)
337      - change in max/min operations to ensure that smoothing is ok
338      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
339      - always use diffKrNrT as background profile (i.e. never use diffKr field)
340    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
341    o pkg/dic:
342      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
343        vectorization
344      - small bug fix in insol for the unlikely case of a cartesian grid
345      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
346        + now vectorize, which also removes adjoint recomputations;
347        + replace integer maksp1 by _RL maskp1
348        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
349    
350    checkpoint62i (2010/07/21)
351    o pkg/flt:
352      - with OBCS: stop floats which enter the OB region
353    o model/src:
354      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
355        for implicit vertical advection.
356    o pkg/seaice:
357     - account for melting in seaice age evolution.
358     - remove double counting of seaice ridging effect on seaice age.
359    
360    checkpoint62h (2010/06/18)
361    o pkg/exch2:
362     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
363    o tools/genmake2
364      - remove "-pdefault" option: redundant with the use of "packages.conf";
365      - remove file pkg/pkg_default : set the default as a pkg group
366        ("default_pkg_list") defined in pkg/pkg_groups;
367      - fix for case pkg/pkg_depend is missing (was hanging before);
368      - add option "-pgroups" to specify a different pkg_groups than the default.
369    o verification/adjustment.cs-32x32x1:
370       add a "minimal" set-up test (code_min & input_min) which only compiles
371       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
372    o tools/genmake2
373      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
374      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
375    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
376      files are nearly the same anyway.
377      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
378       - redefinition of tau(i,i) (by a factor of ustar)
379       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
380       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
381       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
382       - replace
383         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
384         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
385         by
386         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
387         (changes results)
388       -> exf_bulkformulae v1.22,
389          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
390          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
391                    output.txt 1.63
392           offline_exf_seaice: output.seaicetd.txt 1.7
393           seaice_obcs: output.txt 1.10)
394      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
395       -> exf_bulkformulae v1.23,
396          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
397          and global_ocean.cs32x15.icedyn (only 11 matching digits)
398      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
399    o adjoint of exch-1:
400     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
401       (note: was already like this when using EXCH-2) and remove flow dir
402       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
403     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
404     - update pkg/exch2 diff list.
405    
406    checkpoint62g (2010/05/19)
407    o eesupp/src (exch-1):
408     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
409       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
410       (renamed to exch1_*rx_cube.F).
411     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
412       to call new exch1 S/R ; update Makefile and .cvsignore.
413     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
414       exch2_xy_rx later)
415      Note: after updating your code, need to run "make clean" in eesupp/src
416    o test experiment bottom_ctrl_5x5:
417       new output_adm.txt with fewer grdchk & less monitor output.
418    o model/src:
419      remove the call to ini_cori in initialise_varia.F (just keep the usual one
420       in initialise_fixed.F). More consistent with coriolis & horizontal grid
421       beeing treated in the same way (ini_grid is not called a 2nd time).
422    o pkg/exf:
423      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
424      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
425      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
426      - cosmetic changes to exf_bulkformulae.F to make it look more like
427        exf_bulk_largeyeager04.F
428    o eesupp/src (exch-1):
429      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
430      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
431        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
432        (even without using MPI).
433      - Message mode: move RecvAck setting (indicator of buffer being ready)
434        from send_put to recv_get S/R (was useless before, but not sure if
435        it's much more useful now);
436      - Switch the order of sync: MPI-proc 1rst and then threads;
437      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
438      - fix AD code for communication mode ='get' (but not used).
439    o model/src:
440      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
441      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
442    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
443    o pkg/ctrl: require a specific set of control variables and exf-flags for
444      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
445    o model/src:
446     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
447       1rst forward sweep, to avoid over-writing output files during recomputations
448       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
449     b) 2nd version:
450      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
451      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
452         writePickupAtEnd) + seaice & ptracers output;
453      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
454    o model/src:
455      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
456    o pkg/exch2:
457      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
458      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
459    o pkg/autodiff & exch2:
460      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
461      (for now, only if ALLOW_EXCH2 is defined).
462    o pkg/autodiff:
463      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
464        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
465       + clean-up comments (_RS is not always real*4)
466      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
467      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
468        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
469    o testreport (AD-tests):
470      no longer link files from dir "../input" (1rst link files from
471      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
472    
473    checkpoint62f (2010/04/29)
474  o model/src/the_main_loop.F:  o model/src/the_main_loop.F:
475    adjust store directives for seaice evp and multicategory according to    adjust store directives for seaice evp and multicategory according to
476    pkg/ecco/the_main_loop.F    pkg/ecco/the_main_loop.F
477  o adjoint:  o adjoint:
478    global_sum_ad was incomplete (noted many times by many people ;)    global_sum_ad was incomplete (noted many times by many people ;)
479    nice description by Jean U. as follows:    nice description by Jean U. as follows:
480    * allreduce(var) in global_sum.F can be interpreted as    * allreduce(var) in global_sum.F can be interpreted as
481      reduce(sum) followed by broadcast of sum.        reduce(sum) followed by broadcast of sum.
482    * The adjoint of that is    * The adjoint of that is
483      sum(adjoint) followed by broadcast(summed adjoint value)      sum(adjoint) followed by broadcast(summed adjoint value)
484      or in other words, allreduce(sum, adjoint vars)      or in other words, allreduce(sum, adjoint vars)
485    We were missing the sum(adjoint)!    We were missing the sum(adjoint)!
486    Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)    Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
# Line 117  o tools/build_options: Line 584  o tools/build_options:
584      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
585  o pkg/ecco  o pkg/ecco
586    - allow user defined cost function contributions    - allow user defined cost function contributions
587          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
588          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
589    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
590        the two options are complementary.        the two options are complementary.
591  o pkg/smooth  o pkg/smooth
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