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revision 1.1921 by jmc, Fri Sep 20 00:45:38 2013 UTC revision 1.1976 by mlosch, Mon Apr 7 14:52:38 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o pkg/seaice:
8      - make deltaC a global variable, so that it can be used in ridging code
9      - first step towards ridging: introduce new routines that compute
10        ice strength based on ridging parameters
11    o verification/hs94.1x64x5:
12      - leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h
13      - do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests.
14    o autodiff:
15      - Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h,
16        and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h)
17        For now, only in pkgs used in verification/hs94.1x64x5.
18      - Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage
19        which are specific to TAF/TAMC).
20      - Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD:
21        since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad
22        is compiled), this simplifies/reduces which *_OPTIONS.h file to include.
23      - OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when
24        building mitgcmuv_ad (make adAll).
25    o pkg/ecco:
26      - cost_gencost_seaicev4.F:
27         reformulate proxy cost as function of sst and local param SEAICE_freeze
28         change cost names from siv4-[sst,vol] to siv4-[deconc,exconc]
29      - add stop statement if old names siv4-[sst,vol] are used
30      - add snapshots + cost reports for atmospheric longwave
31      - remove factor 0.1 in front of wtau[u,v]
32      - replace never used flag ALLOW_TMI_COST_CONTRIBUTION with
33         ALLOW_TMI_SST_COST_CONTRIBUTION
34    o pkg/atm_phys:
35      - add some diagnostics for Short-wave and for convection S/R.
36    o pkg/seaice/seaice_growth:
37      - fix a bug in the lateral melt parameterization for SEAICE_ITD
38        in seaice_growth; tempFrz needs to be computed inside the i/j-loop
39      - rearrange loop order for better vector code in the same code block
40      - rewrite the floeDiameter formula to have fewer divisions
41      -  (miraculously) none of this changes the results of seaice_itd
42    o pkg/smooth:
43      - move param smooth2Ddiffnbt to pkg/ecco
44    o pkg/salt_plume:
45      - salt_plume_frac.F:
46         clean up local param names
47         reformulate (1-frac) to frac; original 1-frac was based on swfrac code
48    o pkg/rw:
49      - add RS version of S/R READ_MFLDS_LEV.
50    o pkg/streamice:
51      - fix the restart test by writing/reading pickup_streamice files.
52    o pkg/seaice:
53      - refine checks for jfnk-related parameters
54      - comment out if statement with SEAICEuseIMEX parameter as long as there
55        is no IMEX code to avoid confusion and surprises
56    
57    checkpoint64u (2014/03/07)
58    o verification/MLAdjust:
59      - rename secondary test suffix:
60         1.leith  -> A4FlxF  + switch to flux-form & add side-drag
61         0.leithD -> AhFlxF  + switch to flux-form
62         0.smag   -> AhVrDv  (use Vorticity-Div. visc form) + add side-drag
63         0.leith  -> AhStTn  (use Strain-Tension visc form) + add side-drag
64    o pkg/mom_vecinv:
65      - remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used
66        to be before mom_calc_visc.F)
67      - skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed.
68      - add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip):
69        this is simpler for the adjoint and for diagnostics.
70    o model/src + pkg/momentum:
71      - add input files for  2-D additional Western and Southern cell-edge wall
72         (e.g., to add "thin-wall" where it is =1).
73      - fix sideDrag option for thin-walls with Non-Lin Free-Surf
74        using 2nd hFacZ that is computed from initial (fix domain) hFac
75      - known limitations of thin wall implementation: not yet coded for sigma
76        coords; not working with CD-scheme neither.
77    o pkg/seaice:
78      - rename recently introduced parameters from (wrong name) AB to
79        BDF (backward difference time discretisation)
80      - retire runtime parameters SEAICEuseAB2, SEAICE_abEps
81    o tools/adjoint_options:
82      - remove setting of "OPENAD=true" (now set by command line "genmake2 -oad")
83    
84    checkpoint64t (2014/02/01)
85    o pkg/ecco
86      - add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and
87        runtime logical flag gencost_timevaryweight to read daily sea-ice sigma
88      - replace hard-coded record number and period which only work for monthly
89        with read-in runtime param that works for other periods (month,day,year)
90    o pkg/thsice
91      - corrected store directive fixes thsice adjoint gradient checks
92    o genmake2 & testreport:
93      - add genmake2 option "-oad" to generate a Makefile for OpenAD built and
94        in this case, use tools/adjoint_options/adjoint_oad as default AD optfile.
95        Update testreport accordingly. No need to set "export OPENAD=true"
96        in adjoint_options/adjoint_oad anymore (will be removed later).
97    o pkg/shelfice:
98      - put T & S shelfice forcing into model surfaceForcing_T,_S (for now,
99        only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F
100        so that surface forcing applies to k=kSurf if using pkg/shelfice.
101    o pkg/ctrl, pkg/grdchk, pkg/ecco:
102      - Changes to make GENARR more modular (i.e. invisible if not used)
103    o model/src/temp_integrate.F and salt_integrate.F
104      - re-include store directives that were removed on Dec 27th.
105    o model/src/external_forcing_surf.F
106      - add storage directives for EmPmR and PmEpR to avoid recomputation of
107        seaice_model in the adjoint that is problematic when seaice_model is
108        turned off in the adjoint. The resolved issue dated back to July when
109        EXTERNAL_FORCING_SURF call was moved.
110        Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly.
111    o pkg/exf/exf_check.F
112      - fix a small bug again (originally found by Wentao Liu, now found again)
113      - streamline error output
114    o pkg/streamice and aim_v23:
115      - replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that
116        Apple's /usr/bin/cpp knows what to do:
117        Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
118        Target: x86_64-apple-darwin13.0.0
119    
120    checkpoint64s (2014/01/05)
121    o tools/adjoint_options:
122      - switch to fastopt.net TAF server (instead of default fastopt.de) for
123        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
124    o model/src:
125      - remove some unnecessary TAF storage directives in forward_step.F and
126        in dynamics.F (note: not always removed by TAF, e.g., double storage
127        of kappaRU,kappaRV in former version of dynamics.F).
128    o model/src & pkg/ptracers:
129      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
130        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
131        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
132      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
133      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
134      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
135    o useSingleCpuInput separates single-CPU input from single-CPU output;
136        for now only implemented for in exf_interp_read.F
137    o verification/advect_xy:
138      - fix missing EXCH call in local version of ini_salt.F and update output.
139    o momentum diagnostics:
140      - fix which deltaT is used in Total-Tendency diagnostics.
141      - fix typo in diagnostics for momentum tendency from AB.
142    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
143        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
144    
145    checkpoint64r (2013/12/08)
146    o verification/*/results:
147      - Update reference output of experiments that were passing with just 13 digits
148         (make it easier to detect future changes in results)
149    o model/src & pkg/ptracers:
150      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
151        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
152        to inside ptracers_integrate.F ; remove ptracers_advection.F
153    o coupling interface pkgs:
154        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
155      - change the config check to test the agreement of Ocean Depth
156        with ATM land/sea mask (instead of ATM orography);
157      - send to coupler the number of coupler time-steps to do for this run:
158        this allows to check for consistency and don't need anymore to be
159        specified in parameter file "data";
160      in coupler:
161      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
162      - improve report to log-file of config setting (pass log-file unit to few S/R)
163    o pkg/compon_communic:
164      - add coupling send/receive for non-tiled integer vector;
165      - add S/R to check and stop if any proc has an error (similar to
166        eesupp/src/stop_if_error.F but single thread and across Comm_World).
167    o pkg/exch2:
168      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
169        through list of all tiles my proc owns.
170    o model/src:
171      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
172        from rTrans) to simplify dependencies (no need to store rTrans anymore in
173        calling S/R); this affects AD results at machine truncation level:
174        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
175        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
176    o tools/build_options:
177      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
178    o coupling interface pkgs:
179        [compon_communic, atm_compon_interf & ocn_compon_interf]
180      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
181        to each S/R that needs it; remove un-used variables.
182      - change component tile registration (cpl_register.F in both compon_interf
183        and mitcomponent_tile_register.F) to pass the full list of tiles
184        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
185      - with pkg/exch2: adopt the same convention used for I/O to define mapping
186        towards coupler global array (unless W2_useE2ioLayOut=F):
187         a) can now use different tiling between atm & ocn comp.
188         b) no needs to modify the run-Off map when changing tiling (was needed
189            even if using the same tiling between atm & ocn).
190         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
191            full land tiles); not yet tested.
192      - check for valid mapping from comp. tile to coupler global array
193      - improve report of tile registration results to log file.
194    o pkg/exch2:
195      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
196        tile-registration (CPL_REGISTER);
197      - activate (un-comment) definition and setting of "W2_tileIndex" list to
198        store the local bi,bj indices of each tile;
199      - also print bi,bj in local report to log file;
200      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
201        Jun 2009 modif of pkg/exch2).
202    o testing on baudelaire:
203      - run 2 tests at a time: no significant slow down (since enough cpu) and
204        get the full set of test done earlier
205      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
206    o model/src/thermodynamics.F and routines called from it:
207      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
208        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
209        velocity (outp) by adding bolus velocity.
210      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
211        mass transport from velocity + lateral grid cell area
212      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
213      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
214     in thermodynamics.F
215      - remove k from thermodynamics.F and move it to temp_integrate.F
216        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
217        loop).
218      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
219        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
220        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
221        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
222      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
223        global_ocean.90x40x15, tutorial_global_oce_biogeo and
224        tutorial_tracer_adjsens (+ TLM output).
225    o tools/OAD_support and (verification/*/) code_oad:
226      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
227        module conversion ; remove unneeded CPP_EEOPTIONS.h.
228      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
229        version (closer to model/inc/CPP_OPTIONS.h).
230    o model/src:
231      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
232        retired list of parameters (routine FREEZE has been replace by surface
233        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
234    o pkg/gmredi:
235      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
236        velocity (same scheme but affects machine truncation) for GM_AdvForm.
237      - update output of FWD experiments: front_relax.bvp,
238        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
239    
240    checkpoint64q (2013/11/17)
241    o verification:
242      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
243        tutorial_global_oce_biogeo and global_ocean.90x40x15.
244      - generate new output (growth & melt) for seaice_itd experiment after
245        updating the input pickup_seaice files (previously wrong).
246    o pkg/cost:
247      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
248        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
249        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL
250          cannot be applied to var in common block).
251        o allows to get results independent of tile-per-proc setting (if using
252          slower GLOBAL_SUM_SEND_RECV option).
253      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
254        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
255        forward gradients: update output).
256      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
257        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
258    o pkg/mom_common:
259      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
260        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
261        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
262        ensure that all field value that are used are set.
263    o tutorial_deep_convection (smag3d):
264      - add missing scaling in mom_calc_smag_3d.F;
265      - set smag3D_coeff in input.smag3d such that results do not change.
266    o pkg/dic:
267      - change dic_cost.F to compute cost on each tile first and then apply
268        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
269        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
270      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
271    o eesupp/src & pkg/mdsio:
272      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
273        (from pkg/mdsio) since they are no longer used for tape IO.
274      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
275        (+ keep a copy in pkg/atm_ocn_coupler).
276    o verification/isomip:
277      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
278    o tools/build_options:
279      - optfile linux_amd64_ifort11, fast (no ieee) case:
280        to get a working restart for all experiments, add "-fp-model source"
281        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
282    
283    checkpoint64p (2013/10/20)
284    o pkg/autodiff:
285      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
286        criteria, return to simple (default) tape IO format.
287    o pkg/mdsio (+ eesupp/src):
288      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
289        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
290      - fix globalFile and singleCpuIO options using simpler global mapping.
291      - new pairs of scatter/gather vector S/R (one for each type, generated from
292        template) corresponding to simpler global mapping.
293      - adread_write.F: switch to new S/R (but leave old calls commented) and write
294        to globalFile when parameter globalFiles is set to True.
295      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
296    o pkg/autodiff:
297      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
298        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
299        missing, just add a STOP if array type do not match.
300    o pkg/exf:
301      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
302         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
303         and rename array obsSIce to exf_iceFraction.
304    o tutorial_deep_convection:
305      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
306        for now all in this exp. code dir.
307      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
308        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
309    o eesupp/src:
310      - added SINGLE_DISK_IO option because reading of parameter files on
311        very large number of processors did not work with existing set-up
312    
313    checkpoint64o (2013/09/25)
314    o pkg/atm_phys & atm_compon_interf:
315      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
316    o tools/build_options:
317      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
318        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
319        remove CPP setting (was identical to genmake2 default).
320    o pkg/gmredi & model/src: Some updating and work done on the residual model.
321      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
322      - fixed up the calculation of the eddy stress and how it is added to the
323        external forcing via taueddy_external_forcing.F
324      - at the moment, it is very experimental and only works with the variable eddy
325        diffusivity calculated in gmredi_k3d.F
326    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
327        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
328    o testreport (& tools/do_tst_2+2):
329      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
330  o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:  o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
331    - remove CPP='cpp -traditional -P' (this is genmake2 default)    - remove CPP='cpp -traditional -P' (this is genmake2 default)
332    - add switch (for big setups) to use 'medium' memory-model (but leave it    - add switch (for big setups) to use 'medium' memory-model (but leave it

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