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revision 1.1889 by dimitri, Mon Jul 1 16:55:57 2013 UTC revision 1.2028 by jmc, Fri Jul 18 13:37:32 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint65 (2014/07/18)
8    o pkg/fizhi:
9      - add parenthesis around fizhi tendencies in fizhi_tendency_apply.F: this
10        affects results at machine truncation level. Update output of experiments
11        fizhi-cs-32x32x40 (12 digits for cg2d) & fizhi-cs-aqualev20 (13 digits).
12    o pkg/seaice: more clean up
13      - rename TAF common block tapes to be more consistent and remove
14        unnecessary duplicates
15      - add store directives to remove more recomputations, but use smaller
16        tapes (and adjust keys) when SEAICE_LSR_ADJOINT_ITER is undefined.
17        The idea behind this flag is to reduce the memory footprint when the
18        adjoint of the LSR is not required. As of now, defining the flag
19        SEAICE_LSR_ADJOINT_ITER increases 4 common block tapes for 2D field by
20        a factor of SOLV_MAX_FIXED (=500 by default in SEAICE_SIZE.h).
21        For experiment offline_exf_seaice, this means on a linux box with gfortran
22        nearly a factor of 10 (but keep in mind there is mostly seaice code in
23        this experiment):
24        > size mitgcmuv_ad
25        text    data        bss     dec        hex  
26        5100659 1216  220458952  225560827  d71c8fb
27        5339425 1200 1868783272 1874123897 6fb4dc79 (SEAICE_LSR_ADJOINT_ITER)
28        but only a moderate increase of 36% for global_ocean.cs32x15:
29        text    data        bss     dec        hex
30        6695027 1648 1014578664 1021275339 3cdf6ccb
31        6695203 1648 1382505320 1389202171 52cd8afb (SEAICE_LSR_ADJOINT_ITER)
32      - note: there are still recomputations in global_ocean.cs32x15 and
33        offline_exf_seaice and the gradient agreement changes (gets a
34        little worse) for global_ocean.cs32x15 (-> update output_adm.seaice.txt)
35      - in general, the AD gradients still are wrong
36    o OpenAD
37      - clean up code_oad/ directories somewhat by moving files
38        dontCompile, dontTransform, keepOriginal to OAD_support/
39    o model/src:
40      - using MOM fluxform and Non-Lin Free-Surf with momDissip_In_AB=F
41        (not currently tested): add dissipation terms before NLFS rescaling of
42        tendencies (previously done after).
43    o pkg/diagnostics:
44      - write stats-diags in ascii file with more digits (same as in monitor).
45    o pkg/down_slope:
46      - drop the bi,bj dimension of argument recip_hFac in S/R DWNSLP_APPLY; with
47        NLFS (not tested), use new recip_hFac value in order to conserve tracer.
48    o model/src:
49      - new file "apply_forcing.F" containing all the code previously in
50        external_forcing.F, but with new argument list: pass, as new argument,
51        the current level tendency array to update (instead of a direct update
52        of the common bloc array). Change the corresponding calls.
53      - add CPP option USE_OLD_EXTERNAL_FORCING (default is undef) to use
54        EXTERNAL_FORCING_U,V,T,S subroutines (for backward compatibility).
55    o pkg/seaice/seaice_lsr, a little bit of clean up
56      - rearrange some code blocks, so that now all calculations for
57        setting up the right-hand-sides done within one single block
58        (I find that easier to read and understand)
59      - rearrange freedrift-code to reduce the number of ifdefs
60      - adjust some indentations and comments
61    
62    checkpoint64z (2014/07/10)
63    o model/src and several pkgs:
64      - change argument list of all S/R called from external_forcing.F and
65        called from ptracers_forcing.F (renamed to ptracers_apply_forcing.F)
66        to pass, as argument, the current level tendency array to update
67        (instead of a direct update of the common bloc array).
68      - change also (in the same way) argument list of PTRACERS_APPLY_FORCING;
69      - rename taueddy_external_forcing.f to taueddy_tendency_apply.F
70    o pkg/seaice/seaice_lsr.F
71      - always initialize local arrays in seaice_lsr_tridiagu/v
72      - add more local tapes to seaice_lsr_tridiagu/v
73      - move storing u/vice(:,:,bi,bj) out of seaice_lsr_tridiagu/v, but
74        keep it in bi/bj loop; this seems to be essential
75      - gradients are still wrong but only by 4-7 orders of magnitude
76        instead of 15 orders of magnitude, lab_sea improves a little
77    o pkg/seaice
78      - (pkg/autodiff) remove storing/restoring of seaiceMaskU/V that
79        generates unnecessary code in seaice_lsr_ad
80      - add more store directives in seaice_lsr to avoid unnecessary code
81        in seaice_lsr_ad
82      - exclude some residual computations in seaice_lsr when
83        ALLOW_AUTODIFF_TAMC is defined in order to avoid unnecessary code
84        in seaice_lsr_ad
85      - add more storing, a new tape (model/src/the_main_loop.F) and
86        another key for SEAICE_LSR_VECTORIZE_ZEBRA (the local keys ilockey
87        and klockey should be checked by a specialist)
88      - modify ( define SEAICE_VECTORIZE_LSR and SEAICE_LSR_ADJOINT_ITER )
89        and update lab_sea after previous changes in pkg/seaice below
90    o pkg/autodiff:
91      - introduce useSmoothCorrel2DinAdMode, SEAICEapproxLevInAd, and
92        viscFacInAd : run time parameters allowing for adjoint switches
93        note : logic for useSmoothCorrel2DinAdMode is in ctrl_readparms.F
94    o pkg/ecco:
95      - introduce cost_gencost_boxmean.F that computes a box mean
96        temperature (for use in adjoint sensitivity studies).
97    o model/src/set_defaults.F : initialize viscFacAdj to 1.
98    o pkg/mom_common/mom_calc_visc.F:
99      - ifdef ALLOW_AUTODIFF then include viscFacAdj factor.
100    o pkg/seaice/seaice_summary.F:
101      - statement for SEAICEadjMODE now in autodiff_readparms.F
102    o pkg/seaice:
103      - remove some store directives and add new ones in an effort to get
104        finally rid off the recomputation warnings. This is successful
105        when SEAICE_VECTORIZE_LSR ***and*** SEAICE_LSR_ADJOINT_ITER are
106        defined (i.e. no extensive recomputation warnings left), but there
107        are still too many recomputations on the solver iteration level
108      - define SEAICE_VECTORISZE_LSR in offline_exf_seaice/code_ad/SEAICE_OPTIONS.h
109      - move definition of MPSEUDOTIMESTEPS into TAMC-block in
110        SEAICE_SIZE.h
111      - add a store directive in S/R seaice_calc_viscosities
112    o pkg/seaice (ITD code):
113      - fix definition of Hlimit for multi-threaded case
114      - use double precision arithmetic to compute Hlimit: this affects results;
115        update output of experiment seaice_itd.
116    o replace content of verification/seaice_itd
117      - instead of a 1D column use the configuration of offline_exf_seaice
118        to test the ice thickness distribution code with ridging
119      - this is a first shot at this experiment
120      - change of some defaults of ridging parameters SEAICEhStar (from
121        100 to 25) and SEAICEmuRidging (from 5 to 3) in seaice_readparms.F
122        and lot of new comments.
123    
124    checkpoint64y (2014/06/20)
125    o pkg/seaice/seaice_reg_ridge.F:
126      - modify the regularization of very small volumes of ice; only check
127        total volume HEFF, and do not apply correction to individual ice
128        classes because that leads to funny patterns in the heat and fw-fluxes
129        into the ocean. Adjust seaice_itd/results/output.txt
130      - replace nITD by SEAICE_multDim in loop-ranges
131    o pkg/exf:
132      - add code to process the case field period = -12. with UV interpolation.
133      - move debug print (formerly active when exf_verbose=T) from EXF_getFFieldRec
134        into S/R that calls it (i.e., exf_set_gen.F, exf_set_uv.F & obcs_exf_load.F)
135    o verification/global_with_exf:
136      - switch all fields period to -12. (was previously untested) in input/data.exf
137        (but keep secondary test ".yearly" unchanged); update the reference output.
138    o pkg/cal:
139      - new calendar type "noLeapYear" for 365 days calendar without any leap year.
140    o pkg/exf:
141      - new integer parameter "exf_debugLev" (default set to main model debugLevel)
142        to replace logical switch "exf_verbose"
143      - report in STDOUT when loading a new record (if exf_debugLev >= 3)
144    o pkg/sbo:
145      - update from Katherine Quinn: evaluate mass directly from density and SSH
146        (budget using Finite Volume method) instead of from bottom pressure.
147      - allow testreport to collect few selected SBO output ; tested in exp.
148        global_ocean.90x40x15 (after updating the results, to include SBO output).
149      - fix some multi-threading issues (in output part).
150    o model/src & most packages:
151      - always call {PKG}_READPARMS even if corresponding use{PKG}=F;
152      - in {PKG}_READPARMS, in case use{PKG}=F: add a call to new S/R
153        PACKAGES_UNUSED_MSG to print a weak warning when parameter file
154        "data.{pkg}" exist ; and leave the S/R (return) just after.
155      - more standard LAND pkg interface (land_init_fixed.F, land_check.F).
156        + call LAND_READPARMS from packages_readparms.F
157    o pkg/seaice:
158      - remove code that resets useThSice in S/R seaice_readparms and
159        replace it by a warning in S/R seaice_check
160      - remove parameter MULTDIM, replace with nITD and runtime
161        parameter SEAICE_multDim (still hard-wired to nITD if
162        SEAICE_ITD is defined)
163    
164    checkpoint64x (2014/05/24)
165    o verification/lab_sea:
166      - update adjoint and TLM output following changes to pkg/salt_plume
167      - un-do the update after putting back local recip_Cp in few places.
168    o pkg/salt_plume: modifications by An Nguyen:
169      - add capability to do brine rejection (salt-plume) as function of
170        volume+tracers (instead of only salinity tracer).
171      - conserve volume by exchanging volume from each kLev to above to
172        accommodate in-coming brine volume
173      - store surface and klev exchanged fraction + volume in 4 new 3-d arrays
174      - switch KPP surf buoyancy due to brine forcing to 3-d
175        (3 more 3-d arrays, 2 for SPforcing[T,S], 1 for boplume)
176      - add salt_plume_volfrac, salt_plume_apply, salt_plume_tendency_apply_t
177      - unrelatedly, also add ad-hoc capability to vary salt_plume scheme
178        in East/West Arctic.
179    o pkg/sbo:
180      - incorporate modifications from Katherine Quinn to enable the use of sbo
181        pkg in ECCO-v4 set-up ; remove SBO-TimeAve output ; add monitor-like
182        output for future testreport verification (unfinished).
183    o pkg/atm_phys:
184      - change diagnostics (AtPh_Trf & AtPh_Qrf) of DARGAN_BETTSMILLER S/R:
185        skip the reseting of t_ref & q_ref to initial t & q ; this preserve the
186        output of S/R CAPECALCNEW (Parcel temp & q) for diagnostics.
187    o pkg/seaice
188      seaice_calc_ice_strength.F: modify expression to avoid divisions
189        (affects truncation)
190      seaice_do_ridging.F: clean up the insectarium
191      - fix a bug that was compensated by areaScaling (-> remove areaScaling code)
192      - added SEAICEsnowFracRidge to redistributed snow (2nd bug)
193      - set closing/openingRate to zero where no extra iteration is need (3rd bug)
194      - add some debugging information and error messages (warnings)
195    o model/src: modifications relatd to atmosphere p*:
196      - Switch to more accurate p* coordinate slope term (calc_grad_phi_hyd.F)
197      - With p* or Sigma-P, use constant reference Pot.Temp (thetaConst) instead
198        of vertical profile tRef in geopotential background and anomaly.
199      - Acount for true p* correction in theta <-> T conversion in pkg/aim_v23
200        and pkg/atm_phys.
201      - Update FWD output of experiments: aim.5l_cs (x2), fizhi-cs-32x32x40,
202        fizhi-cs-aqualev20, fizhi-gridalt-hs, tutorial_held_suarez_cs, cpl_aim+ocn.
203    o pkg/seaice: fix a bug in seaice_prepare_ridging.F, forgot a sqrt
204    o pkg/ptracers: compute ptracer source/sink due to linear free surface.
205        not used right now, but can be used in BGC packages to fix conservation.
206    o pkg/dic, pkg/gchem: move tracer_meanarea to gchem, so it can be used by
207        other packages too.
208    o pkg/seaice/seaice_calc_ice_strength.F: replace SEAICE_rhoSnow by
209        SEAICE_rhoIce in the Rothrock (1975)-type strength calculations (bug fix)
210    o model/src:
211      - since we have several heat capacity (even in model/src), define "recip_Cp"
212        as local variable (no longer in common block) to avoid any confusion.
213      - add thetaConst in PARAMS.h (to be used with pStar or sigma-P coords).
214    o pkg/exf:
215      - from Jeff Scott: add option (#define EXF_CALC_ATMRHO) to calculate local
216        air density as function of air Temp, Humidity and atm pressure.
217    
218    checkpoint64w (2014/05/02)
219    o verification:
220      - update output_adm.txt files for experiment global_ocean.cs32x15 (seaice &
221        seaice_dynmix) and lab_sea (primary test & noseaicedyn): moving/changing
222        code from seaice_growth.F & seaice_advdiff.F to new ridging routines
223        seaice_reg_ridge.F seaice_do_ridging.F affects AD gradient
224        (down to 8-7 matching digits for global_ocean and 5-6 for lab_sea).
225    o model/src: for atmosphere in p* coords:
226      - store factor rStarFacC**atm_kappa (= pStarFacK) in common block
227      - implement more accurate p* coordinate slope term (in calc_grad_phi_hyd.F),
228        but not yet activated.
229    o pkg/seaice: fix restart problem for ITD with new ice strength parameterisation:
230      - move computation of opnWtrFrac = 1-AREA to before computing ice strength
231      - this changes the results (but not for any verification experiment, because
232        none tests this), but avoids having an extra field in the restart files
233    o pkg/seaice: remove global variable TICE (not needed)
234      - replace by TICES or local variable where necessary (cost_seaice_test,
235        seaice_diagnostics_state)
236      - move copying TICE to TICES from seaice_check_pickup to seaice_read_pickup
237      - use specific read/write routines for reading and writing individual leves
238        of a multilevel field
239    o pkg/ctrl & model/inc:
240      - move additional anomaly fields of control vars (related to options:
241         ALLOW_KAPGM_CONTROL, ALLOW_KAPREDI_CONTROL and ALLOW_BOTTOMDRAG_CONTROL)
242        from DYNVARS.h into new header file: CTRL_FIELDS.h
243    o pkg/seaice: some small modifications to the ridging code
244      - make fw2ObyRidge a global variable and add the freshwater flux to
245        seaice_growth
246      - pass actual thickness from seaice_prepare_ridging, so that it is
247        computed only in one place and compute it in the same way as in
248        seaice_growth
249      - initialise more fields in seaice_do_ridging that where cause floating
250        point exceptions over land
251    o pkg/seaice: preparations for ridging code and first real ridging code
252      - move most of "PART 1" of S/R seaice_growth into a new and separate
253        S/R seaice_reg_ridge that will both regularize the state variable after
254        advection call the actual ridging routine;
255      - requires to make 5 fields global fields: d_HEFFbyNEG,d_HSNWbyNEG,
256        d_AREAbyRLX,d_HEFFbyRLX,saltFluxAdjust;
257      - remove ridging code from seaice_advdiff
258      - clean up remaining part 1 of seaice_growth in an attempt to make it
259        more readable (this is probably subjective)
260      - call seaice_itd_redist once in the initialisation phase to have the initial
261        conditions in the correct category
262      - finally: add new ridging routine for ITD code
263    
264    checkpoint64v (2014/04/11)
265    o pkg/ecco:
266      - add runtime parameters mdt[start,end]date[1,2]
267      - rename variable "tpmean" as "mdt" and "topexmeanfile" as "mdtdatfile"
268    o pkg/seaice:
269      - make deltaC a global variable, so that it can be used in ridging code
270      - first step towards ridging: introduce new routines that compute
271        ice strength based on ridging parameters
272      - add diagnostic for HSNOWITD
273      - add opnWtrFrac as a global variable (required for ridging scheme)
274    o pkg/salt_plume + pkg/seaice/seaice_growth.F
275      - add SALT_PLUME_IN_LEADS flag to activate pkg/salt_plume only when ice
276        AREA exceeds a threshold (code contributed by I.Fenty in 2011)
277    o verification/hs94.1x64x5:
278      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
279      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
280    o autodiff:
281      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
282        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
283        For now, only in pkgs used in verification/hs94.1x64x5.
284      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
285        which are specific to TAF/TAMC).
286      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
287        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
288        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
289      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
290        building mitgcmuv_ad (make adAll).
291    o pkg/ecco:
292      - cost_gencost_seaicev4.F:
293         reformulate proxy cost as function of sst and local param SEAICE_freeze
294         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
295      - add stop statement if old names siv4-[sst,vol] are used
296      - add snapshots + cost reports for atmospheric longwave
297      - remove factor 0.1 in front of wtau[u,v]
298      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
299         ALLOW_TMI_SST_COST_CONTRIBUTION
300    o pkg/atm_phys:
301      - add some diagnostics for Short-wave and for convection S/R.
302    o pkg/seaice/seaice_growth:
303      - fix a bug in the lateral melt parameterization for SEAICE_ITD
304        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
305      - rearrange loop order for better vector code in the same code block
306      - rewrite the floeDiameter formula to have fewer divisions
307      -  (miraculously) none of this changes the results of seaice_itd
308    o pkg/smooth:
309      - move param smooth2Ddiffnbt to pkg/ecco
310    o pkg/salt_plume:
311      - salt_plume_frac.F:
312         clean up local param names
313         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
314    o pkg/rw:
315      - add RS version of S/R READ_MFLDS_LEV.
316    o pkg/streamice:
317      - fix the restart test by writing/reading pickup_streamice files.
318    o pkg/seaice:
319      - refine checks for jfnk-related parameters
320      - comment out if statement with SEAICEuseIMEX parameter as long as there
321        is no IMEX code to avoid confusion and surprises
322    
323    checkpoint64u (2014/03/07)
324    o verification/MLAdjust:
325      - rename secondary test suffix:
326         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
327         0.leithD -> AhFlxF  + switch to flux-form
328         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
329         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
330    o pkg/mom_vecinv:
331      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
332        to be before mom_calc_visc.F)
333      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
334      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
335        this is simpler for the adjoint and for diagnostics.
336    o model/src + pkg/momentum:
337      - add input files for  2-D additional Western and Southern cell-edge wall
338         (e.g., to add "thin-wall" where it is =1).
339      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
340        using 2nd hFacZ that is computed from initial (fix domain) hFac
341      - known limitations of thin wall implementation: not yet coded for sigma
342        coords; not working with CD-scheme neither.
343    o pkg/seaice:
344      - rename recently introduced parameters from (wrong name) AB to
345        BDF (backward difference time discretisation)
346      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
347    o tools/adjoint_options:
348      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
349    
350    checkpoint64t (2014/02/01)
351    o pkg/ecco
352      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
353        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
354      - replace hard-coded record number and period which only work for monthly
355        with read-in runtime param that works for other periods (month,day,year)
356    o pkg/thsice
357      - corrected store directive fixes thsice adjoint gradient checks
358    o genmake2 & testreport:
359      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
360        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
361        Update testreport accordingly. No need to set "export OPENAD=true"
362        in adjoint_options/adjoint_oad anymore (will be removed later).
363    o pkg/shelfice:
364      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
365        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
366        so that surface forcing applies to k=kSurf if using pkg/shelfice.
367    o pkg/ctrl, pkg/grdchk, pkg/ecco:
368      - Changes to make GENARR more modular (i.e. invisible if not used)
369    o model/src/temp_integrate.F and salt_integrate.F
370      - re-include store directives that were removed on Dec 27th.
371    o model/src/external_forcing_surf.F
372      - add storage directives for EmPmR and PmEpR to avoid recomputation of
373        seaice_model in the adjoint that is problematic when seaice_model is
374        turned off in the adjoint. The resolved issue dated back to July when
375        EXTERNAL_FORCING_SURF call was moved.
376        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
377    o pkg/exf/exf_check.F
378      - fix a small bug again (originally found by Wentao Liu, now found again)
379      - streamline error output
380    o pkg/streamice and aim_v23:
381      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
382        Apple's /usr/bin/cpp knows what to do:
383        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
384        Target: x86_64-apple-darwin13.0.0
385    
386    checkpoint64s (2014/01/05)
387    o tools/adjoint_options:
388      - switch to fastopt.net TAF server (instead of default fastopt.de) for
389        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
390    o model/src:
391      - remove some unnecessary TAF storage directives in forward_step.F and
392        in dynamics.F (note: not always removed by TAF, e.g., double storage
393        of kappaRU,kappaRV in former version of dynamics.F).
394    o model/src & pkg/ptracers:
395      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
396        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
397        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
398      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
399      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
400      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
401    o useSingleCpuInput separates single-CPU input from single-CPU output;
402        for now only implemented for in exf_interp_read.F
403    o verification/advect_xy:
404      - fix missing EXCH call in local version of ini_salt.F and update output.
405    o momentum diagnostics:
406      - fix which deltaT is used in Total-Tendency diagnostics.
407      - fix typo in diagnostics for momentum tendency from AB.
408    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
409        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
410    
411    checkpoint64r (2013/12/08)
412    o verification/*/results:
413      - Update reference output of experiments that were passing with just 13 digits
414         (make it easier to detect future changes in results)
415    o model/src & pkg/ptracers:
416      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
417        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
418        to inside ptracers_integrate.F ; remove ptracers_advection.F
419    o coupling interface pkgs:
420        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
421      - change the config check to test the agreement of Ocean Depth
422        with ATM land/sea mask (instead of ATM orography);
423      - send to coupler the number of coupler time-steps to do for this run:
424        this allows to check for consistency and don't need anymore to be
425        specified in parameter file "data";
426      in coupler:
427      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
428      - improve report to log-file of config setting (pass log-file unit to few S/R)
429    o pkg/compon_communic:
430      - add coupling send/receive for non-tiled integer vector;
431      - add S/R to check and stop if any proc has an error (similar to
432        eesupp/src/stop_if_error.F but single thread and across Comm_World).
433    o pkg/exch2:
434      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
435        through list of all tiles my proc owns.
436    o model/src:
437      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
438        from rTrans) to simplify dependencies (no need to store rTrans anymore in
439        calling S/R); this affects AD results at machine truncation level:
440        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
441        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
442    o tools/build_options:
443      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
444    o coupling interface pkgs:
445        [compon_communic, atm_compon_interf & ocn_compon_interf]
446      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
447        to each S/R that needs it; remove un-used variables.
448      - change component tile registration (cpl_register.F in both compon_interf
449        and mitcomponent_tile_register.F) to pass the full list of tiles
450        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
451      - with pkg/exch2: adopt the same convention used for I/O to define mapping
452        towards coupler global array (unless W2_useE2ioLayOut=F):
453         a) can now use different tiling between atm & ocn comp.
454         b) no needs to modify the run-Off map when changing tiling (was needed
455            even if using the same tiling between atm & ocn).
456         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
457            full land tiles); not yet tested.
458      - check for valid mapping from comp. tile to coupler global array
459      - improve report of tile registration results to log file.
460    o pkg/exch2:
461      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
462        tile-registration (CPL_REGISTER);
463      - activate (un-comment) definition and setting of "W2_tileIndex" list to
464        store the local bi,bj indices of each tile;
465      - also print bi,bj in local report to log file;
466      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
467        Jun 2009 modif of pkg/exch2).
468    o testing on baudelaire:
469      - run 2 tests at a time: no significant slow down (since enough cpu) and
470        get the full set of test done earlier
471      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
472    o model/src/thermodynamics.F and routines called from it:
473      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
474        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
475        velocity (outp) by adding bolus velocity.
476      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
477        mass transport from velocity + lateral grid cell area
478      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
479      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
480     in thermodynamics.F
481      - remove k from thermodynamics.F and move it to temp_integrate.F
482        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
483        loop).
484      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
485        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
486        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
487        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
488      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
489        global_ocean.90x40x15, tutorial_global_oce_biogeo and
490        tutorial_tracer_adjsens (+ TLM output).
491    o tools/OAD_support and (verification/*/) code_oad:
492      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
493        module conversion ; remove unneeded CPP_EEOPTIONS.h.
494      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
495        version (closer to model/inc/CPP_OPTIONS.h).
496    o model/src:
497      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
498        retired list of parameters (routine FREEZE has been replace by surface
499        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
500    o pkg/gmredi:
501      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
502        velocity (same scheme but affects machine truncation) for GM_AdvForm.
503      - update output of FWD experiments: front_relax.bvp,
504        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
505    
506    checkpoint64q (2013/11/17)
507    o verification:
508      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
509        tutorial_global_oce_biogeo and global_ocean.90x40x15.
510      - generate new output (growth & melt) for seaice_itd experiment after
511        updating the input pickup_seaice files (previously wrong).
512    o pkg/cost:
513      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
514        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
515        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
516          cannot be applied to var in common block).
517        o allows to get results independent of tile-per-proc setting (if using
518          slower GLOBAL_SUM_SEND_RECV option).
519      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
520        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
521        forward gradients: update output).
522      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
523        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
524    o pkg/mom_common:
525      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
526        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
527        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
528        ensure that all field value that are used are set.
529    o tutorial_deep_convection (smag3d):
530      - add missing scaling in mom_calc_smag_3d.F;
531      - set smag3D_coeff in input.smag3d such that results do not change.
532    o pkg/dic:
533      - change dic_cost.F to compute cost on each tile first and then apply
534        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
535        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
536      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
537    o eesupp/src & pkg/mdsio:
538      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
539        (from pkg/mdsio) since they are no longer used for tape IO.
540      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
541        (+ keep a copy in pkg/atm_ocn_coupler).
542    o verification/isomip:
543      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
544    o tools/build_options:
545      - optfile linux_amd64_ifort11, fast (no ieee) case:
546        to get a working restart for all experiments, add "-fp-model source"
547        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
548    
549    checkpoint64p (2013/10/20)
550    o pkg/autodiff:
551      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
552        criteria, return to simple (default) tape IO format.
553    o pkg/mdsio (+ eesupp/src):
554      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
555        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
556      - fix globalFile and singleCpuIO options using simpler global mapping.
557      - new pairs of scatter/gather vector S/R (one for each type, generated from
558        template) corresponding to simpler global mapping.
559      - adread_write.F: switch to new S/R (but leave old calls commented) and write
560        to globalFile when parameter globalFiles is set to True.
561      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
562    o pkg/autodiff:
563      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
564        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
565        missing, just add a STOP if array type do not match.
566    o pkg/exf:
567      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
568         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
569         and rename array obsSIce to exf_iceFraction.
570    o tutorial_deep_convection:
571      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
572        for now all in this exp. code dir.
573      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
574        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
575    o eesupp/src:
576      - added SINGLE_DISK_IO option because reading of parameter files on
577        very large number of processors did not work with existing set-up
578    
579    checkpoint64o (2013/09/25)
580    o pkg/atm_phys & atm_compon_interf:
581      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
582    o tools/build_options:
583      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
584        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
585        remove CPP setting (was identical to genmake2 default).
586    o pkg/gmredi & model/src: Some updating and work done on the residual model.
587      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
588      - fixed up the calculation of the eddy stress and how it is added to the
589        external forcing via taueddy_external_forcing.F
590      - at the moment, it is very experimental and only works with the variable eddy
591        diffusivity calculated in gmredi_k3d.F
592    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
593        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
594    o testreport (& tools/do_tst_2+2):
595      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
596    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
597      - remove CPP='cpp -traditional -P' (this is genmake2 default)
598      - add switch (for big setups) to use 'medium' memory-model (but leave it
599        commented out for now). Note: needed with FC 19 to compile big setups.
600    o pkg/atm_compon_interf:
601      - regroup per field origin (model & pkgs) the coupling storage routines
602         (which accumalate in time each coupling field)
603      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
604        update accordingly + simplify aim_do_physics.F
605    
606    checkpoint64n (2013/08/26)
607    o pkg/bbl:
608      - update formulation to reduce dispersion of tracer properties in bbl
609      - replaced horizontal and vertical transport parameters with velocities
610      - changes results for verification/global_with_exf.yearly
611    o verification/halfpipe_streamice:
612      - change to matrix construction; update both Fwd & AD output.
613    o verification/tutorial_tracer_adjsens:
614      - OpenAD test: switch to vector-invariant momentum since fluxform with
615        rStar causes problems with OpenAD; update output.
616    o tools:
617      - genmake2: define a common prefix for all temp-file names ; move them
618        to local /tmp disk (but would be easy to move them back);
619      - xmakedepend: apply the same switch for temp-files.
620    o pkg/offline:
621      - changes for use with rStar (NLFS): assume that we continue to provide
622        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
623        output files) and apply r* scaling at each time-step (function of the time
624        varying Eta field); use normal pickup files (needed for restart with NLFS).
625    o adjoint with OpenAD:
626      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
627        package openad.  This package has to be compiled for all runs with OpenAD
628        instead of specifying code_oad_all as a modification directory.
629      - link the fortran templates from tools/OAD_support to the build directory
630        for preprocessing to avoid conflicts between different setups compiled
631        simultaneously and simplify cleanup.
632    o pkg/exf:
633      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
634        main model or other pkgs are exchanged in EXF_MAPFIELDS).
635    o model/src:
636      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
637        (similar to do_fields_blocking_exchanges.F).
638    o tools/genmake2:
639      - remove TAF output src code just before calling staf (when not doing a fresh
640        built, will stop if things go wrong with staf).
641      - fix target "adobj" (left from TAF version-2 transition)
642    o pkg/diagnostics:
643      - add a parameter to track the status of pkg/diagnostics activation;
644        this replace/extend the use of logical param "settingDiags" (to check
645        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
646        New S/R to print error message and stop when pkgStatus is not right.
647      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
648    
649    checkpoint64m (2013/08/13)
650    o model/inc:
651      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
652        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
653    o pkg/kpp & aim_v23:
654      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
655    o pkg/seaice:
656      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
657        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
658      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
659    o eesupp/src:
660      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
661        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
662    o switch to TAF version-2:
663      - add flow directives to "freeze" naming convention for ad-routines that
664        are used in I/O routines of adjoint state and associated common blocks
665        that are used in adcommon.h (backward compatible with version-1)
666      - update all ad-optfiles (in tools/adjoint_options + few local to some
667        verification exp) to switch to latest TAF version (currently 2.5.5);
668        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
669        out except for diva).
670      - the major change with TAF version-2 is that both the differentiated
671        routines and the forward routines (new) are returned as part of the TAF
672        output source code. Update genmake2 accordingly.
673      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
674        with version-2 when compared to TLM or FWD gradient); other experiments
675        output show minor changes (machine truncation level); update the few AD &
676        TLM output with 12 matching digits only (some prior to version-2 switch).
677    
678    checkpoint64l (2013/08/05)
679    o model/src:
680      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
681      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
682        when using TAF but only if using OpenAD.
683    o pkg/mom_common+fluxform+vecinv:
684      - always set horiz. viscosity arrays to background value before calling
685        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
686        only when using variable horiz. viscosity (useVariableVisc=T);
687      - simplify mom_vecinv.F (only 1 block for momViscosity).
688    o pkg/mom_common: variable horiz. viscosity in NH code
689      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
690        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
691      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
692        useBiharmonicVisc & useVariableVisc.
693      - fix old bug (already in 1rst implementation of variable horizontal viscosity
694        in calc_gw.F, version 1.27, 2006/06/20):
695        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
696        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
697      - change background horiz viscosity in vertical momentum (gW) to always be
698        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
699        any type of variable viscosity, e.g., viscAh/4Grid)
700      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
701        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
702        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
703        default viscAh,viscA4 is zero).
704    o model/src:
705      - extend length of drC & recip_drC from Nr to Nr+1.
706    o Divided Adjoint (DIVA) with MPI:
707      - genmake2: do not create local ./mpi_headers dir when no file to copy into.
708      - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT
709        and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h.
710    
711    checkpoint64k (2013/07/23)
712    o tools/OAD_support:
713      - avoid the need for file "oadtempflile" in insertTemplateDir.bash
714        and remove it from genmake2.
715    o tools/build_options:
716      - remove MPI_HEADER_FILES_INC setting (no longer used) and comment out
717        MPI_HEADER_FILES list (let genmake2 find the missing headers)
718    o verification/halfpipe_streamice:
719      - change to driving stress formulation; update both Fwd & AD output.
720    o tools/genmake2 and Divided Adjoint with MPI:
721      - remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken);
722      - only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set;
723      - add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in
724        Makefile, which is set by genmake2, and check which mpi-headers are needed.
725        Note: need to update adjoint_options/adjoint_diva_mpi accordingly.
726      - update target "CLEAN" (to also remove ./mpi_headers/ dir).
727    o testreport:
728      - changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present,
729        perform additional runs (number of additional runs is "add_DIVA_runs" taken
730        from file run_ADM_DIVA ; should match "nchklev_3" in file "code_ad/tamc.h").
731    o verification/lab_sea (AD test):
732      - change to test Divided Adjoint Run in this set-up (both standard AD test
733        and 2 secondary AD test: noseaice + noseaicedyn); drop the evp AD test.
734    o pkg atm_ & ocn_compon_interf:
735      - remove cpl_earlyExpImpCall=F option (was mainly a hack added for the old
736        staggerTimeStep implementation) and disable (retired) corresponding
737        parameter.
738    o pkg/offline:
739      - comment out unused field-array: ICEM, ConvectCount, hflx[01], icem[01];
740      - add S/R OFFLINE_CHECK to print offline parameter summary
741        and stop if loading a file that is not used;
742      - enable to calculate GMRedi tensor, KPP mixing and convective index
743        when the corresponding file(s) is/are not specified (but pkg is used).
744      - comment out resetting of monitorFreq (to endTime) since it still useful
745        for monitoring CFL numbers and checking offline fields.
746    o OpenAD:
747      - do not define OAD_DEBUG (in tools/adjoint_options/adjoint_oad) to get
748        smaller standard output) and generate new (smaller) output (on baudelaire
749        using gfortran with -ieee) for exp. tutorial_tracer_adjsens
750    o model/src:
751      - call EXTERNAL_FORCING_SURF outside bi,bj loops (in do_oceanic_phys.F),
752        (where external_forcing_adjust was called) and change list of arguments;
753      - merge external_forcing_adjust.F into external_forcing_surf.F
754      - put surface relaxation of SST & SSS in new S/R (forcing_surf_relax.F)
755        which also contains balancing surface relaxation (ALLOW_BALANCE_RELAX,
756        previously in file "balance_relax.F", now removed); remove corresponding
757        arrays in FFIELDS.h.
758      - EXTERNAL_FORCING_SURF is now called when using pkg/offline; implement
759        a hack for getting back surfaceForcingS (loaded from file) when using
760        ALLOW_OLD_VIRTUALFLUX (pkg/dic, in DIC_OPTIONS.h) in offline set-up.
761      - update output of AD test experiment global_ocean.cs32x15.seaice_dynmix
762        (was getting only 11 digits for AD-grad, due to different truncation
763         error in AD code).
764    
765    checkpoint64j (2013/07/04)
766    o pkg/offline:
767      - to enable the use of other features with pkg offline (e.g., obcs),
768        also call S/R DO_OCEANIC_PHYS in offline run - more modifs to come.
769      - comment out "allowFreezing" (now active) in 2 offline testing exp.
770  o pkg/exf ALLOW_RUNOFTEMP  o pkg/exf ALLOW_RUNOFTEMP
771    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL    - fix sign and make compatible with temp_EvPrRn .NE. UNSET_RL
772    - added RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice    - ahdded RUNOFTEMP test to verification/global_ocean.cs32x15/input.seaice
773    - changes verification/global_ocean.cs32x15/results/output.seaice.txt    - changes verification/global_ocean.cs32x15/results/output.seaice.txt
774  o pkg/atm_phys:  o pkg/atm_phys:
775    - allows to add some damping on uVel,vVel (strength only function of k).    - allows to add some damping on uVel,vVel (strength only function of k).
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