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revision 1.53 by adcroft, Fri Sep 28 17:53:37 2001 UTC revision 1.53.4.53 by heimbach, Tue Jul 8 15:18:29 2003 UTC
# Line 3  $Header$ Line 3  $Header$
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    
6    ecco_c51_e34c
7    o introducing integer flag debugLevel
8      - debLevZero: suppress all output
9      - debLevA: standard
10      - debLevB: equivalent to current debugMode=.TRUE.
11    o introducing pathname variable mdsioLocalDir for mdsio
12      that can be specified at runtime
13      (relevant for cluster I/O to local disk)
14    
15    ecco_c51_e34b
16    o Modifications of obcs
17      - bug fixes in cost package
18      - bug fixes in grdchk package
19    o new parameter maxKPPhbl in KPP
20    o added input for obcs verification
21    
22    ecco_c51_e34a
23    o Modifications to pkg/seaice, verification/lab_sea, and
24      verification/natl_box_adjoint for testing sea-ice adjoint code.
25    
26    ecco_c51_e34
27    o merging c51 into ecco-branch
28    
29    ecco_c50_e33a
30    o first step in c51 merge
31      - redundant update in model/src/
32      - merge back's in autodiff, ctrl, kpp, seaice
33    
34    ecco_c50_e33
35    o minor changes to pkg/seaice pkg/cost/cost_ice.F
36      and verification/natl_box_adjoint/README
37    o Modif's to enable tangent linear run in ECCO environment
38      including time-dependent forcing
39      * main problem is missing call mdsreadfield out of exf_set_gen
40        (i.e. computation of trajectory in TLM mode)
41      * incorrect g_active_write_...
42      * (re-) init of bar files and g_bar files
43    o Reverted back to 3-dim. tbar, sbar for SST, SSS bar files.
44    o MERGES:
45      * obcs/ ctrl/ G. Gebbie code
46        (major changes in ctrl handling, volume flux balancing etc.)
47      * cost/ ctrl/ A. Koehl code
48        - new cost contributions (new data types)
49        - efficient pack/unpack for time-dependent 2-d fields
50    o replaced mutiple ctrl_get... by single generic ctrl_get_gen.F
51      (except obcs)
52    o somewhat cleaned package initialisation sequence for
53      ctrl/ cost/ ecco/
54    o extended grdchk to enable obcs gradient checks
55    o some generalizations for easier TLM <-> ADM switches
56    o added configuration example for parallel divided adjoint
57      (see verification/natl_box_adjoint/code_diva_mpi/README )
58    o started verification exp. for obcs control
59      (still needs checking)
60    
61    ecco_c50_e32
62    o Patrick's adjoint-model storage directives for pkg/seaice
63    o merged with checkpoint50g_post (pkg/seaice and verification/lab_sea)
64      - added SEAICE_MULTILEVEL for 8-category sea-ice thermodynamics
65      - LSR sea-ice dynamic solver moved to SouthWest B-grid location and
66        made the default because of faster convergence than ADI
67    o Modifications for adjoint of SEAICE_ALLOW_DYNAMICS
68      - extended state in checkpoint_lev...
69      - in lsr.F, replaced GO TO by fixed loop index (also avoid DO WHILE)
70      - YEAH: in lsr.F, (first) successful use of CADJ LOOP = ITERATION
71      - avoid stoing in S/R budget for now
72      - in dynsolver.F, avoid NPSEUDO loop for adjoint
73      - new comlev1_lsr in the_main_loop
74    o Small modif's in lsopt/, optim/ to ease compilation
75      New script to run optim (lsopt)
76    
77    ecco_c50_e31
78    o exf totally restructured
79      - replaced all exf_set_ routines by one generic exf_set_gen.F
80        and made sure it's still differentiable
81      - split exf_getffields.F into new exf_bulkformulae.F
82      - exf_inscal_/exf_outscal_ suffixes consistent with field names
83    o New cost function: Tini-Tfin to do model spinup optimization.
84    o Started new verification exp for Tini-Tfin optimization.
85    
86    ecco_c50_e30
87    o corrected CPP option mismatch in exf_Bulk... functions for case
88      #define ALLOW_ATM_WIND && #undef ALLOW_ATM_TEMP
89    o Merging from release1_p13 and from icebear5
90      - bug fix for pkg/seaice dynamic solver
91      - Added SEAICE_initialHEFF to pkg/seaice
92      - Additional options for pkg/cost/cost_ice.F
93      - Updates to verification/natl_box_adjoint
94      - pkg/ctrl/ctrl_init.F
95        Fix for determination of startrec and endrec.
96      - pkg/cal/cal_toseconds.F
97        Fix for negative intervals shorter than 1 day.
98    
99    ecco_c50_e29
100    Bug fix for merging between c50 and KPP.
101    ikey was passed from thermodynamics to kpp_calc via
102    common block rather than being recomputed in kpp_calc,
103    in contradiction with new key itdkey.
104    New key ikppkey created, and tamc.h headers updated.
105    
106    ecco_c50_e28
107    o major merge:
108      ecco-branch merged with checkpoint50
109      gmredi now available, grdchk, DIVA up-to-date for MPI
110      However, two outstanding problems:
111      - kpp adjoint is broken, needs fixing!
112      - a few minor modif's in handling of CPP option
113        ALLOW_TANGENTLINEAR_RUN in conjunction with
114        ALLOW_ECCO_OPTIMIZATION are necessary to enable
115        TLM runs with ECCO setup
116    
117    ecco_c44_e27
118    o exf:
119      - Enable initialisation of forcing fields to constant
120        (runtime) values.
121      - in exf_getffields.F
122        Reduce i-/j-loop to interior domain, discarding overlaps.
123        That also fixes wrong TAF-key computations for key_1, key_2
124        with bulf formulae.
125      - exf_init.F modify #ifdef for exf_init_evap
126      - exf_getffieldrec.F, ctrl_getrec.F
127        The following INT-usages are not safe:
128          fldsecs  = int(fldsecs/fldperiod)*fldperiod
129          fldcount = int(fldsecs/fldperiod) + 1
130        and were modified.
131      - added repeatPeriod (from MAIN branch)
132    o grdchk: updated and merged
133      - has both ADM and TLM checks
134      - works for single- and multi-proc.
135      - output cleaned
136      - worked successfully for parallel DIVA
137      Needed one update in EEPARAMS.h and updates in ctrl package
138      More modif's may be necessary for ECCO code to support TLM.
139    o autodiff: checkpoint_lev...
140      - updated storing for bulk formulae (some arrays were missing)
141      - added state for seaice package
142      - synchronized with main branch
143    o DIVA:
144      Modif.s in
145      - cost_init.F
146      - cost_averagesfields.F
147      - ecco_the_main_loop.F
148      - ecco_the_model_main.F
149      and added cost_final_restore.F cost_final_store.F
150      o With these changes, it is possible to fully separate
151        the first forward run to compute the cost function (mdthe_main_loop)
152        and adjoint runs over individual DIVA intervals (adthe_main_loop)
153        into separate model executions.
154        This enables better tuning of DIVA to given queue sizes.
155      o Loss of cost function value in consecutive DIVA runs is
156        fixed by storing to 'costfinal' file.
157      o Appropriate call of ctrl_unpack/_pack,grdchk_main at
158        beginning/end of adjoint integration is accounted for.
159      The current changes apply to TAF-1.4.26.
160      TAF has one remaining bug, requiring one manual change
161      (see MITgcm manual).
162    o bug fix plus modif for ubar, vbar in cost_averagesfields
163    o cal: synchronized between MAIN and ecco-branch
164    
165    icebear4
166    o Added cost_ice for sea-ice volume sensitivity experiment.
167    o ecco_the_model_main.F: SEAICE_WRITE_PICKUP must precede WRITE_CHECKPOINT
168    o Reduced derivative singularities in pkg/seaice.
169    o Updated verification/natl_box_adjoint
170    
171    icebear3
172    o Removed spurious iikey and idkey
173    o pkg/exf
174      - bug fix in treatment of downward radiation
175    o pkg/seaice
176      - added initial sea-ice thickness parameter SEAICE_initialHEFF
177    o updated verification/natl_box_adjoint
178    
179    icebear2
180    o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf,
181      kpp_transport_t.F,and ecco_the_main_loop.F
182    o adjoint-friendly modifications to pkg/seaice
183    o added verification/lab_sea as per release1_p12_pre
184    
185    ecco_c44_e26
186    o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2
187    o exf: Modifications to correctly handle evap field for adjoint
188    o grdchk:
189      Added code to perform gradient checks for bulk formulae/atmos. state
190      (atemp, aqh, uwind, vwind).
191      NOTE:
192      This package is out of synch with c48 package.
193      The latter also has the tangent linear gradient checks.
194      Need to be merged.
195    o verification/natl_box_adjoint:
196      * added new setup: code_bulk/, input_bulk, results_bulk
197        (Experiment 2, described in README)
198        uses bulk formulae and atmos. state as control instead of
199        air-sea fluxes.
200        Performs gradient checks for first 4 elements of atemp control.
201      * changed standard verification to perform
202        gradient checks on first 4 elements on hflux control.
203      * gmredi switched off (will come after merge with c48).
204    
205    ecco_c44_e25
206    o Merging some GM changes from main trunk (c47) to ecco-branch.
207    o Updating verif. natl_box_adjoint with GMRedi.
208    o Adding setup with explicit differentiaton of pressure solver.
209    o Bug fix: missing OBCS_OPTIONS.h for sponge layer code.
210    o (Re-?) Commiting old bug fixes in kpp to ecco-branch
211      (kpp_calc.F, kpp_routines.F)
212    o exf:
213      updated external forcing package
214      - cleaned old exfa stuff
215      - bug fixes
216        (missing OBCS_OPTIONS.h in two routines)
217      - enable easy to use "no forcing".
218      - added exf I/O for atmospheric loading
219      - added exf I/O for runoff data
220      - transfered scaling between exf <-> MITgcm to exf namelist
221    
222    ecco_c44_e24
223    o modifications to gradient check package (Martin Losch)
224      - enable centered differences
225      - modified format of standard output
226    o bug fix for nwettile contents
227      so far assumed global sum  in first entry (1,1,k),
228      needed for global control vector
229      -> introduced new variable nwet[c/w/s]global(nr)
230    o shifts of calls to cal/exf package to be accessible
231      in MITgcm stand-alone
232    o shifted packages_init_variables before convective_adjustment_ini
233      (corresponding update of TAF tape initialisation).
234    o removed auxiliary field in impldiff
235      (caused numerical differences for GMRedi cases)
236    o updated obcs control part (G. Gebbie)
237    o removed some f90 comments ("!")
238    o Bug fixes and updates in cost package
239     * cost_final: correct multiplier mult_tauv, mult_sflux
240     * cost_hyd: added call cost_ssh
241     * cost_init_barfiles.F: replaced arrays by tmpfld's
242     * cost_readtopexmean.F: ersmask -> tpmeanmask
243     * cost_weights.F: corrected wtheta[2], wsalt[2]
244    o cleaned exchanges in cg2d.F
245    
246    ecco_c44_e23
247    merged patches between release1_p1 and release1_p2:
248    o fixed array boundary problem for adjoint
249      (related to partial recomputation within subroutine
250      related to dynamics -> calc_viscosity -> mom_...
251    o fixed recomputation in thermodynamics
252    o prepare (but not complete) recomputation problem in impldiff
253    o fixed problem for adjoint of global_max
254    o switched off sponge layer code in external_forcing
255    Bug fix in ctrl_mask_set_yz (spotted by G. Gebbie)
256    
257    ecco_c44_e22
258    o Finally, the merges with the Scripps cost function terms:
259      Various additions, modifications, quality checks.
260    o Plus: Included switch ALLOW_AUTODIFF_MONITOR to handle
261      monitoring of adjoint state.
262    o Plus: removed comm_stats, ini_communication_patterns from diff. list
263      (no more need to "keep" MPI headers for adjoint generation)
264    o Plus: exf changes:
265      o added run-off routine
266      o additional storing needed for ustress,vstess
267        because of state-dependent quality check
268      o added missing initialisations
269    o Plus: genmake with MAKEDEPEND variable was still missing in ecco-branch
270    NB: - verification/natl_box_adjoint/ 240 steps run
271          * looks ok under Linux (twain.lcs.mit.edu)
272          * looks ok on MIT SUN's (fjord.mit.edu)
273          * NaN in reverse mode on Scripps SUN's at iter=214
274          * NaN in reverse mode on IBM SP3 (BlueHorizon) at iter=204
275        - 1 year forward int. global 2x2 deg. produces similar cost functions
276          * all cost terms of new code are slightly smaller (0.5 to 3%).
277    
278    ecco_c44_e21
279    o reversed order of ctrl/cost initialisation
280    o gmredi_slope_psi.F: Inconsistent types in MIN/MAX expressions
281    o modified to enable ctrl field swapping
282    o bug fix for global sum of ncvarlength in ctrl_init
283    o no more call to ctrl_unpack from ctrl_init
284    o no more write of ctrl vector in ctrl_pack
285      however, init. of control vector from ctrl_unpack
286    o various bug fixes & consistent nobcs handling in
287      ctrl_pack/unpack routines (by G. Gebbie)
288    o optim package: Added obcs control part for lsopt I/O
289      (by G. Gebbie)
290    o missing call to obcs_diags
291    o moved calls in packages_init_fixed to packages_readparms
292      because some quantities are needed earlier.
293    
294    ecco_c44_e20
295    o before major merges from the Scripps setup
296      here are two small updates:
297      - field swapping for surface flux controls enabled
298        (remains t.b.d. for atmos. state plus obcs)
299      - bug fix in active_file.F for xz-/yz- routines
300      - added missing xz-/yz- routines to active_file_ad.F
301    
302    ecco_c44_e19
303    o merged necessary patches:
304      - AD-related changes for GMRedi
305      - fixes i KPP (delZ -> drF)
306      - hook to OBCS songe layer code in external_forcing
307      - errorMessageUnit non-zero in eeboot.F
308      - included GMREDI, EXACT_CONSERV to natl_box_adjoint verif.
309    
310    ecco_c44_e18
311    o sponge layer code for obcs was missing
312      - added hook in external_forcing.F
313      - added storing for TAF
314    o new routine cost_init_barfiles to initialise
315      adjoint fields adtbar, adsbar, adpsbar
316      (needed in conjunction with corrected ladinit for active I/O)
317    o cleaned up and corrected order in packages_readparms, ecco_readparms
318    o corrected and simplified weights for obcs controls
319      - weight fields simplified
320      - bug fix in ctrl_pack
321      - no more write of control vector in ctrl_pack
322    o i/j index bug fixes in cost_ssh_mean
323    
324    ecco_c44_e17
325    o bug fixes in cost package
326      * wrong identifier for active I/O of monthly mean psbar
327        (cost_averagesfields, cost_ssh) xx_psbar_dummy
328      * cleaned all identifier for active I/O of monthly fields
329      * wrong ladinit in various cost routines
330    o merge with interval (chkpt44c_post - chkpt44d_post)
331      * added missing EXCLUDE_MONITOR flags
332      * changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
333        (incompatible typ in MIN/MAX expressions caused problems
334        on IBM SP3)
335      * in genmake added variable MAKEDEPEND
336        plus resetting for case SunOS
337        added timer_stats.c routine for IBM SP3
338      * removed variables in dynamics
339    
340    ecco_c44_e16
341    o new ECCO checkpoint, the first since ecco_c43_e15
342      which is branched from MITgcm.
343      All changes were merged in between (see ecco-branch-mod? tags).
344    o last changes:
345      * assuming path for TAF and TAMC are known (e.g. in $path)
346      * genmake:
347        - added tools/xmakedepend to circumvene shortcoming of
348          SUN's makedepend (size too small)
349        - invoking ../tools/xmakedepend instead of makedepend
350        - changed compiler flags for case SunOS
351    
352    ecco-branch-mod5
353    o mod's to reproduce open boundary run
354    o enable field swapping for OB's and climatology
355    o update store directives for OB control
356    o added option ALLOW_OBCS_PRESCRIBE
357    o call of getobcs now out of obcs_calc (param. list modified)
358    
359    ecco-branch-mod4
360    o this is the second part of changes necessary to reconcile
361      the natl_box_adjoint verification (with and without grdchk).
362      >>>!!! CHANGES BETWEEN THE TAGS ecco-branch-mod3 !!!<<<
363      >>>!!!                      AND ecco-branch-mod4 !!!<<<
364      >>>!!! SHOULD BE MERGED INTO THE MAIN TRUNK      !!!<<<
365      - genmake: removed $S64 overwrite for case SunOS
366      - pkg/exf: update and corrections for field swapping and obcs
367      - pkg/ecco: parameter lists for the_model_main, the_main_loop
368                  harmonized between ECCO and MITgcm
369      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
370                      updated checkpointing_lev... lists for obcs
371      - model/src: minor changes in forward_step, plot_field
372      - pkg/mdsio: added mdsio_gl_slice
373    
374    ecco-branch-mod3
375    o this is the first part of changes necessary to reconcile
376      natl_box_adjoint verification (with and without grdchk).
377      This set of changes is relevant for ECCO only.
378      The next set/tag of changes (ecco-branch-mod4)
379      should be merged into the main trunk.
380      - update some options
381      - parameter lists of ecco_the_model_main and ecco_the_main_loop
382        differed from those of the MITgcm counterparts.
383    
384    ecco-branch-mod2
385    o update ecco-branch-mod1 to checkpoint44
386    o exclude from updates:
387      - verification/
388      - adjoint/
389      - pkg/cost
390      - pkg/ctrl
391      - pkg/ecco
392      - pkg/obcs
393      - model/src/the_model_main.F
394      - model/src/the_main_loop.F
395    
396    checkpoint44
397    o apply Shapiro filter on T&S before calc_PhiHyd (stagger time stepping)
398    o fix bug in mom_vi_del2uv
399    o added some stuff for AD
400    
401    ecco-branch-mod1
402    o based on c43
403    o replaced packages cost, ctrl, ecco, obcs
404    o removed MITgcm verif.'s, added ECCO verif.'s
405    o added lsopt, optim for line search optimization.
406    
407  checkpoint43  checkpoint43
408  o added two new advection tests  o added two new advection tests
409  o added global 4x4 degree ocean test  o added global 4x4 degree ocean test

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