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revision 1.1295 by jmc, Sat Sep 11 21:39:13 2010 UTC revision 1.1357 by jmc, Thu Dec 23 18:08:53 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 pkg/mdsio:
8      - add 2 arguments to S/R MDS_PASS_R4/8toRL/S for overlap size of buffer
9        to copy to/from, so that it can be used to replace MDS_PASS_WH_R8toRL/RS.
10      - change barrier call for safe multi-threads access to 3-D shared buffer.
11      - MDS_READ/WRITEVEC_LOC use buffers from MDSIO_BUFF_3D.h (instead of local ones)
12      - replace call to MDS_PASS_WH_R4/8toRL with call to MDS_PASS_R4/8toRL and
13        remove the 4 S/R MDS_PASS_WH_R4/8toRL/S.
14    o pkg/flt:
15      - add fourth-order Runge-Kutta integration
16      - add basic exch2 support (only 1 facet supported so far!)
17    o pkg/mdsio+rw:
18      new S/R to read local (or tile independent) vector (read counterpart of
19       mds_writevec_loc, and front-end write_glvec_rl/rs).
20    o global_ocean.cs32x15: additional input_ad.seaice experiment
21        that uses pkg/seaice rather than pkg/thsice.
22        (using multidim advection for seaice)
23    o towards more F95 syntax for array specification in namelist:
24      - change "data.diagnostics" (data.ptracers was changed before checkpoint62p)
25        of all verification experiments.
26           e.g.:    line: fields(1,3)='ETAN    ','ETANSQ  ',
27          was changed to: fields(1:2,3)='ETAN    ','ETANSQ  ',
28      - finish adding "-DNML_EXTENDED_F77" to DEFINES list in pgf77 and g77 optfiles
29    o global_ocean.cs32x15: additional input.seaice experiment
30        that uses pkg/seaice rather than pkg/thsice.
31    
32    checkpoint62p (2010/12/17)
33    o pkg/thsice: rename (ad tape index) iicekey as ticekey, and move it
34        to THSICE_SIZE.h to avoid conflict with pkg/seaice.
35    o pkg/seaice: add seaice_diffusion.f seaice_map_thsice.f to adjoint.
36        allow for use of multim. advection in seaice adjoint.
37    o pkg/seaice: add diagnostics for snow precipitation and sublimation flux
38      - first attempt to close budgets by taking into account the freshwater
39        flux implied by the sublimation of snow and ice. So far only the
40        volume budget is closed, turn on with soon-to-be-retired-again CPP-Flag
41        SEAICE_ADD_SUBLIMATION_TO_FWBUDGET
42    o eesupp/src:
43      new S/R with new option (NML_EXTENDED_F77) to change array specification
44      from F95 standard to commonly accepted extended F77 form.
45      This would allow to use F95 syntax in namelist (needed with gfortran 4.4.5)
46      and to revert back to the original syntax (with -DNML_EXTENDED_F77)
47      for less tolerant f77 compiler (e.g., pgf77, g77).
48    o globalFiles:
49      commented out in parameter file "data" since it's not safe with MPI
50      (e.g., wrong on aces); keep it if useSingleCpuIO=T (but not doing much
51      in this case); no longer commented out in restart test (tst_2+2).
52    o add adTapeDir to specify a special directory where adjoint tapes are
53      written/read (adread_adwrite.F). adTapeDir is specified in data/PARM05
54      and cannot be used together with mdsioLocalDir.
55    o nesting pkgs:
56      - packages_init_variables : put call to OBCS_INIT_VARIABLES in last position
57      - update Gianmaria's Nesting pkgs (from Contrib/nesting_sannino)
58      - add parameter files + utils dir + output from short run on beagle.
59    o pkg/seaice:
60        fix seaice_growth.F store directives; update results of exp. lab_sea.ad
61    o pkg/seaice: explicitly store tsurfloc in seaice_solve4temp.F to avoid
62      unnecessary copying in adjoint code, requires new parameter NMAX_ITER
63    
64    checkpoint62o (2010/11/25)
65    o pkg/exf:
66      - change CPP option EXF_VERBOSE to run-time logical param exf_verbose.
67    o pkg/seaice:
68      - seaice_ocean_stress: split a loop for better vectorization of the
69        adjoint code
70      - seaice_growth.F: fix bug in conservation of freshwater connected to
71        capping of heff, put contribution into d_HEFFbyNEG
72      - replace irritating parameters SEAICE_latentWater/Ice and SEAICE_sensHeat
73        by something more sensible (parameters that are what their name implies)
74      - change some defaults, so that by default exf-parameters are used for
75        things like rhoAir, cpAir,latent/sensible heat parameters, in order
76        to reproduce the old results, many data.seaice now contain funny values
77        for cpAir and latent heat of sublimation
78    o packages_readparms.F: move exf_readparms up in line so that
79        exf-parameters are visible for other packages (e.g. seaice)
80    o debugMode & debugLevel=2:
81      - differentiate between debugMode & debugLevel=2:
82        debugMode: controls printing of debug messages (sequence of S/R calls).
83        debugLevel: controls printing of algorithm intermediate results and stats.
84      - remove "if debugLevel=2 => debugMode" but keep "debugMode =>  debugLevel=2";
85        => allows to print debug-stats without all sequence of call messages.
86      - switch control of debug print from debugLevel to debugMode in many S/R.
87    o pkg/obcs (obcs-sponge):
88        fix bug that was introduced on Oct 25 (in dynamics.F v1.151): put back the
89        call to OBCS_PRESCRIBE_EXCHANGES (need to exch gU,gV when using obcs-sponge)
90    o pkg/generic_advdiff:
91      - record overlap minimum size for each advection scheme;
92      - refine criteria on overlap minimum size;
93      - check and stop (in gad_check) if overlap size is too small.
94    o pkg/obcs:
95      - with ptracers: remove multiple calls to obcs_apply_ptracer (only done
96        once, in ptracers_implicit.F)
97      - with seaice: remove test on empty file name in obcs_apply_seaice (always
98        apply OB values when tile has OB)
99    o model/src, coriolis setting:
100      - integer parameter "selectCoriMap" (=0,1,2) replaces 3 logical
101        useConstantF, useBetaPlaneF, useSphereF ; can now read coriolis from
102        files (selectCoriMap=3) with any grid.
103      - add parameter "fPrime" for constant second Coriolis coeff (default=0).
104    o pkg/seaice/seaice_growth.F:
105        a few cosmetic changes that reduce the number of lines of code
106    o pkg/obcs: add boundary conditions following Stevens (1990)
107      - the code follows old MOM/NAOSIM code
108      - so far it is only implemented for the eastern and western boundaries
109        and NOT for pTracers
110    o pkg/rbcs:
111      - replace rbcsInIter by rbcsForcingOffset, the time in seconds at the
112        beginning of the first rbcs forcing period.
113      - add option rbcsSingleTimeFiles that makes rbcs read forcing data like the
114        offline package, i.e., one file per time, labeled by iteration number;
115        deltaTrbcs sets the timestep with which the data was generated;
116        rbcsIter0 is the forcing iteration corresponding to rbcsForcingOffset.
117      - rbcsForcingCycle=0 makes forcing non-cyclic.
118      - make arithmetic safe for negative times and odd forcing periods.
119    
120    checkpoint62n (2010/11/09)
121    o pkg/seaice:
122        fix masking in free-drift S/R ; update results of exp. lab_sea.fd
123    o pkg/obcs:
124       New S/R to copy tracer value from the OB location to narrow band region
125        (width = same as overlap) beyond the OB: preserve OB value (needed for
126        high-order scheme) which were overwritten by EXCH call if in overlap
127        region. Applied to theta, salt, ptracer and advected seaice variables.
128       With seaice: use maskInC in similar way as in gad_advection.F,
129        in seaice_advection.F and advect.F.
130       Update output of experiment seaice_obcs and change exp4 to test OBCS with
131        4th order Adv.Scheme. for pasive salt and ptracer.
132    o tools/genmake2:
133      - when looking for an optfile (not specified), only search for Fortran compiler
134        (remove sym-link test + setting of CPP + makedepend check + C-compiler check)
135      - in get_fortran_c_namemangling: use "$CC $CFLAG" to compile C test programm
136        (instead of "$MAKE genmake_test.o" since an existing Makefile can be wrong)
137      - set default for CPP to "cpp -traditional -P" (was the case without specifying
138        an optfile, but otherwise default was just "cpp".
139      - comment out PLATFORM=$p_PLATFORM (no idea where p_PLATFORM comes from)
140      - when "CC" is not set in the optfile, look for possible C compiler
141        (instead of just setting CC=cc)
142      - put back version v.169 modif (from 2008/02/15), was dropped in v.173 changes:
143        => add a ".F" to ".o" rule for source files with no "#include" (such as
144           port_rand.F); otherwise, default ignores FOPTIM and just uses FFLAGS.
145      - move gfortran before g77 in list of possible Fortran compiler (consistent
146        with reference compiler switch from g77 to gfortran)
147    o pkg/seaice:
148      o remove SEAICE_OLD_AND_BAD_DISCRETIZATION-code, add a test to
149        seaice_check that stops the model, when the CPP flag is used.
150      o seaice_growth.F: make capping of ice volume conserving by returning the
151        capped ice as freshwater to EmPmR. This does not change the verification
152        experiments but will change runs where the capping is acutally active
153    o change reference platform+compiler from faulks+g77 to baudelaire+gfortran
154      (except the 2 fizhi test exp.); update output of exp.: bottom_ctrl_5x5,
155         global_ocean.cs32x15 (icedyn, thsice, AD thsice), global_ocean_ebm (AD),
156         lab_sea (fd, hb87, salt_plume), MLAdjust (3/5) and vermix (dd)
157    o tools/genmake2:
158      - merge genmake_warnings & genmake_errors into 1 log file: "genmake.log")
159      - change DUMPSTATE default to false (can use "-ds" option to switch it to T)
160      - clean previous genmake log files before anything else.
161      - change Makefile to remove testreport log files (*.tr_log) and genmake log
162        files only with "CLEAN" target (instead of "Clean");
163    o pkg/generic_advdiff:
164      Change OBCS in multiDim advection (gad_advection.F):
165       Use maskInC to prevent intermediate update of tracer-field in OB regions,
166       thus keeping current-time-step OB values; and remove the call to OBCS_APPLY
167       which were applying future time-step OB values.
168      This way, all explicit calculations use current-time-step OB values
169       (simpler and more consistent).
170      Affects results when set-up uses time-varying OBC and multi-dim advection;
171       update output of experiment seaice_obcs.
172    o pkg/seaice:
173      move OPTIONS (formerly locally defined) to SEAICE_OPTIONS.h:
174       this includes SEAICE_GROWTH_LEGACY (+ SEAICE_DO_OPEN_WATER_GROWTH &
175         SEAICE_OCN_MELT_ACT_ON_AREA ) and SEAICE_SOLVE4TEMP_LEGACY.
176      Default (pkg/seaice/SEAICE_OPTIONS.h) is to define SEAICE_SOLVE4TEMP_LEGACY
177       but leave SEAICE_GROWTH_LEGACY undef ; For now, keep verification exp
178       unchanged (SEAICE_GROWTH_LEGACY defined in */code*/SEAICE_OPTIONS.h)
179    o pkg aim (2010/10/26):
180      - Introduce ALLOW_INSOLATION, moving toward a more general incoming solar radiation
181        formulation with obliquity, eccentricity, ... as run-time parameters,
182      - Introduce diagnostics for top-of-the-atmaophere incoming solar radiation and
183        upward shortwave radition at the surface (all-sky and clear-sky).
184    o pkg/obcs:
185      - writing sections with globalFiles=T does not work: switch to tiled-files
186        when writing sections for OBCS (change pkg/rw/write_rec.F accordingly).
187      - fix index bug (OB_Ie -> OB_Iw_) in obcs_apply_uvice.F
188      - apply OBCS_SEAICE_COMPUTE_UVICE to both uice and vice at all obcs
189    
190    checkpoint62m (2010/10/21)
191    o pkg/seaice: vectorize seaice_solve4temp.F
192      - move iterations loops outside of i/j-loops
193      - requires 2D arrays for TB and effConduct
194      - add 2D iceOrNot to replace HICE_ACTUAL.GT.0, as HICE_ACTUAL is
195        modified in this routine
196      - a little bit of clean up, adjusting indentation, etc.
197      - replaced a few TEN**a by exp(a*log(10.)) in new code for better
198        performance and '**TWO' by '**2' (because TWO is a float),
199        replaced ONE, ZERO
200    o eesupp/src:
201       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
202    o pkg/seaice/seaice_growth.F
203      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
204      merging process. The merged routine has two branches, and one activates the 'evolution'
205      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
206      In summary, here is what the '10/10 revision' did consist of
207        part 1: seaice_growth.F revisions 1.71 to 1.75
208          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
209            The emphasis here was on improving readability (e.g. by trying to use meaningful
210            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
211        part 1.5:
212          - revising the lab_sea experiment to make it a more useful (i.e. stable
213            and representative of an actual model run). This was done by generating a
214            (winter) pickup to start from, switching back the main experiment dynamic
215            solver from evp to lsr, having one of the experiments use the free drift solution.
216        part 2: seaice_growth.F revisions 1.76 to 1.85
217          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
218          - Sorting out the various fields units and sign (set early on and reset at the end)
219            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
220            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
221          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
222            and simplifying logical expressions to further improve readibility.
223        part 3: seaice_growth.F revisions 1.86 to 1.89
224          - Re-organize the blocks of code more logically.
225          - Merging the '_if.F' pieces that add something new.
226    o pkg/thsice:
227      - vectorize thsice_solve4temp and thsice_get_exf.
228        Problem: thsice_solve4temp has an unvectorizable statement that
229        might also be problematic for TAF
230      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
231        does not change the verifcation experiment, but will change all
232        experiments that have this flag undefined (not tested in verification);
233        a little reorganization to save a few 2D fields and recomputations
234      - 1st step of revisiting thsice adjoint (major recomp. sorted out)
235      - 2nd step:  fix some store dirs
236        o seems to work somewhat, i.e. using ifort but not g77
237        o likely cause are incomplete init. or recomputation
238        o start verification/global_ocean.cs32x15/input_ad.thsice
239    o pkg/obcs: add support for exch2
240      - the position of the boundary and prescribed values are specified using
241        a global domain with exch2 facets stacked
242        - in x for N,S boundaries (like W2_mapIO=-1)
243        - in y for E,W boundaries (so E,W boundaries do not overlap)
244    o pkg/mdsio: add support for writing global sections with exch2
245        file layout is as for obcs described above:
246        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
247        - for y-z sections, facets are stacked in y
248    o pkg/thsice:
249       - change a few routines for better vectorization: thsice_albedo.F,
250         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
251         not affected, but in particular the latter routine has changed
252         dramatically (not necessarily easier to read now).
253       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
254       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
255    o verification/lab_sea:
256      - overhaul of the forward model experiments. The main motivation
257        for this revision is that lab_sea has proven quite fragile (when
258        changing the sea-ice code, and switching platforms) to a point
259        when failures were very hard to attribute to specific code problems.
260      - the suspected reason for this fragility is noise amplification by evp so,
261        to start with, we decided to replace evp with lsr in the main experiment.
262      - the input.lsr experiment thus became obsolete and was removed.
263      - it was replaced with the input.fd experiment that uses an
264        analytical "free drift" solution as the ice velocity field.
265      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
266        will hopefully allow us to discriminate problems due to dynamic solvers
267        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
268        us to test additional options, along with the salt plume package.
269      - Finally a pickup was generated (at the end of a one year run) to
270        make the tests more representative of an actual model run. Previously
271        the tests starting point was a 1m thickness of ice everywhere.
272    o pkg/seaice:
273      - introducing S\R seaice_freedrift.F that compute the
274        analytical solution to an approximate ice momentum
275        equation (i.e. the simple stress/coriolis balance).
276      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
277        of the free drift velocity field, and enable its use.
278        To actually use the free drift solution as the model ice
279        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
280    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
281    
282    checkpoint62l (2010/10/04)
283    o pkg/seaice:
284      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
285      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
286       version (with USE_ORIGINAL_SBI undef);
287    o add hooks for new packages OASIS, the package will follow
288      (hooks exclude the seaice pkg for now)
289    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
290      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
291      rather than mdsio_readvector.F/mdsio_writevector.F, within
292      adread_adwrite.F to read/write adjoint-related tapes to disk.
293    o eesupp and pkg/mdsio: ALLOW_WHIO
294      Option to write/read 2D fields to files including tiles halos.
295      The main purpose is for adjoint related "tape I/O".
296      The secondary purpose is for debugging phases.
297      A word on those rather specifically intended purposes.
298      The code was meant to be stripped down to the bare minimum.
299      Typically, there is a unique and basic mapping to the global
300      buffer (tile by tile, then proc by proc, then level by level), and
301      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
302      meant to generate user friendly outputs of various shapes and forms.
303      Rather it is intended, for the knowledgeabale developers,
304      to be largely independent of the many mdsio options, to allow
305      outputs of tiles+halos in debugging phases and in adjoint runs,
306      and to allow some flexibility in tuning (adoint) I/O depending on each
307      file system behavior. With regard to tuning, most of the potential knobs
308      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
309      to specify directories, to specify the typical size of I/O calls, etc.)
310      are not yet included, and will be added if they prove useful.
311    o pkg/seaice:
312       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
313    o pkg/seaice:
314       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
315       code (seaice_budget_ice_if.F) which enable to recover old standard
316       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
317       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
318    o model/src (rStar):
319       use simple average (not area weighted) of rStarFac at U,V point when using
320       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
321       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
322    
323    checkpoint62k (2010/09/17)
324    o adjoint
325       * changed verification/global_ocean.cs32x15 ; adjoint now tests
326         Adams-Bashforth 3 + NLFS + RSTAR
327       * some more modifs required for ECCO-GODAE v4
328    o pkg/seaice
329       add SEAICE_AGE_VOL option to use volume instead of area for
330       integrating SEAICE_AGE
331  o model/src:  o model/src:
332     first check-in of sigma & hybrid-sigma coordinate code ; also includes     first check-in of sigma & hybrid-sigma coordinate code ; also includes
333     non-linear free-surface parts ; but pressure-gradient not yet coded.     non-linear free-surface parts ; but pressure-gradient not yet coded.
# Line 273  o tools/build_options: Line 597  o tools/build_options:
597      but keep the former optfile for few weeks for smooth transition      but keep the former optfile for few weeks for smooth transition
598  o pkg/ecco  o pkg/ecco
599    - allow user defined cost function contributions    - allow user defined cost function contributions
600          CPP: ALLOW_USERCOST_CONTRIBUTION       CPP: ALLOW_USERCOST_CONTRIBUTION
601          USAGE: compute contributions in cost_usercost_all.F       USAGE: compute contributions in cost_usercost_all.F
602    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.    - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
603        the two options are complementary.        the two options are complementary.
604  o pkg/smooth  o pkg/smooth

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