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revision 1.1265 by jmc, Sun May 9 17:05:14 2010 UTC revision 1.1314 by jmc, Sat Oct 16 17:23:12 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 eesupp/src:
8       fix flow dir for exch1_z_RX_cube, exch1_uv_RX_cube & exch1_bg_RX_cube
9    o pkg/seaice/seaice_growth.F
10      Revision 1.89 of seaice_growth.F completes the overall october 2010 revision and
11      merging process. The merged routine has two branches, and one activates the 'evolution'
12      branch by setting SEAICE_GROWTH_LEGACY to undef (at the top of the routine for now).
13      In summary, here is what the '10/10 revision' did consist of
14        part 1: seaice_growth.F revisions 1.71 to 1.75
15          - Preliminary seaice_growth.F clean-up, keeping test results strictly unchanged.
16            The emphasis here was on improving readability (e.g. by trying to use meaningful
17            variable names) and modularity (e.g. by adding arrays to store heff etc. updates).
18        part 1.5:
19          - revising the lab_sea experiment to make it a more useful (i.e. stable
20            and representative of an actual model run). This was done by generating a
21            (winter) pickup to start from, switching back the main experiment dynamic
22            solver from evp to lsr, having one of the experiments use the free drift solution.
23        part 2: seaice_growth.F revisions 1.76 to 1.85
24          - Sorting out hard-coded constants that prevented heat and fresh water conservation.
25          - Sorting out the various fields units and sign (set early on and reset at the end)
26            to avoid numerous scalings/re-scalings. By v1.85 the basic unit for ice, heat and
27            fresh water stock is 'effective ice meters', and >0 implies more ice/snow.
28          - Using tendency terms arrays (d_HEFF* etc.) to alleviate remaining code locks,
29            and simplifying logical expressions to further improve readibility.
30        part 3: seaice_growth.F revisions 1.86 to 1.89
31          - Re-organize the blocks of code more logically.
32          - Merging the '_if.F' pieces that add something new.
33    o pkg/thsice:
34      - vectorize thsice_solve4temp and thsice_get_exf.
35        Problem: thsice_solve4temp has an unvectorizable statement that
36        might also be problematic for TAF
37      - thsice_get_exf: add the ALLOW_BULK_LARGEYEAGER04 CPP-flag. This
38        does not change the verifcation experiment, but will change all
39        experiments that have this flag undefined (not tested in verification);
40        a little reorganization to save a few 2D fields and recomputations
41    o pkg/obcs: add support for exch2
42      - the position of the boundary and prescribed values are specified using
43        a global domain with exch2 facets stacked
44        - in x for N,S boundaries (like W2_mapIO=-1)
45        - in y for E,W boundaries (so E,W boundaries do not overlap)
46    o pkg/mdsio: add support for writing global sections with exch2
47        file layout is as for obcs described above:
48        - for x-z sections, facets are stacked in x (like W2_mapIO=-1)
49        - for y-z sections, facets are stacked in y
50    o pkg/thsice:
51       - change a few routines for better vectorization: thsice_albedo.F,
52         thsice_step_temp.F, and in thsice_calc_thickn.F. Results are
53         not affected, but in particular the latter routine has changed
54         dramatically (not necessarily easier to read now).
55       - re-arrange calculation in THSICE_SOLVE4TEMP: move outside of i,j loops
56       iteration loop and call to S/R THSICE_GET_BULKF & THSICE_GET_EXF.
57    o verification/lab_sea:
58      - overhaul of the forward model experiments. The main motivation
59        for this revision is that lab_sea has proven quite fragile (when
60        changing the sea-ice code, and switching platforms) to a point
61        when failures were very hard to attribute to specific code problems.
62      - the suspected reason for this fragility is noise amplification by evp so,
63        to start with, we decided to replace evp with lsr in the main experiment.
64      - the input.lsr experiment thus became obsolete and was removed.
65      - it was replaced with the input.fd experiment that uses an
66        analytical "free drift" solution as the ice velocity field.
67      - Taken together, input (lsr), input.fd (free drift) and input.hb87 (evp)
68        will hopefully allow us to discriminate problems due to dynamic solvers
69        from problems due to the thermodynamic code. input.salt_plume (lsr) allows
70        us to test additional options, along with the salt plume package.
71      - Finally a pickup was generated (at the end of a one year run) to
72        make the tests more representative of an actual model run. Previously
73        the tests starting point was a 1m thickness of ice everywhere.
74    o pkg/seaice:
75      - introducing S\R seaice_freedrift.F that compute the
76        analytical solution to an approximate ice momentum
77        equation (i.e. the simple stress/coriolis balance).
78      - define SEAICE_ALLOW_FREEDRIFT to trigger the computation
79        of the free drift velocity field, and enable its use.
80        To actually use the free drift solution as the model ice
81        velocity field set SEAICEuseFREEDRIFT to .TRUE. in data.seaice.
82    o move "useOASIS" from PARAMS.h to EEPARAMS.h and read it from "eedata"
83    
84    checkpoint62l (2010/10/04)
85    o pkg/seaice:
86      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
87      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
88       version (with USE_ORIGINAL_SBI undef);
89    o add hooks for new packages OASIS, the package will follow
90      (hooks exclude the seaice pkg for now)
91    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
92      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
93      rather than mdsio_readvector.F/mdsio_writevector.F, within
94      adread_adwrite.F to read/write adjoint-related tapes to disk.
95    o eesupp and pkg/mdsio: ALLOW_WHIO
96      Option to write/read 2D fields to files including tiles halos.
97      The main purpose is for adjoint related "tape I/O".
98      The secondary purpose is for debugging phases.
99      A word on those rather specifically intended purposes.
100      The code was meant to be stripped down to the bare minimum.
101      Typically, there is a unique and basic mapping to the global
102      buffer (tile by tile, then proc by proc, then level by level), and
103      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
104      meant to generate user friendly outputs of various shapes and forms.
105      Rather it is intended, for the knowledgeabale developers,
106      to be largely independent of the many mdsio options, to allow
107      outputs of tiles+halos in debugging phases and in adjoint runs,
108      and to allow some flexibility in tuning (adoint) I/O depending on each
109      file system behavior. With regard to tuning, most of the potential knobs
110      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
111      to specify directories, to specify the typical size of I/O calls, etc.)
112      are not yet included, and will be added if they prove useful.
113    o pkg/seaice:
114       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
115    o pkg/seaice:
116       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
117       code (seaice_budget_ice_if.F) which enable to recover old standard
118       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
119       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
120    o model/src (rStar):
121       use simple average (not area weighted) of rStarFac at U,V point when using
122       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
123       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
124    
125    checkpoint62k (2010/09/17)
126    o adjoint
127       * changed verification/global_ocean.cs32x15 ; adjoint now tests
128         Adams-Bashforth 3 + NLFS + RSTAR
129       * some more modifs required for ECCO-GODAE v4
130    o pkg/seaice
131       add SEAICE_AGE_VOL option to use volume instead of area for
132       integrating SEAICE_AGE
133    o model/src:
134       first check-in of sigma & hybrid-sigma coordinate code ; also includes
135       non-linear free-surface parts ; but pressure-gradient not yet coded.
136    o pkg/ptracers:
137       option for ptracer to convert Salt Relax into additional EmP.
138        tested in exp. global_ocean.90x40x15.dwnslp (update output)
139    
140    checkpoint62j (2010/08/25)
141    o pkg/ggl90:
142       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
143    o pkg/dic: car_flux.F, phos_flux.F
144      - reduce number of exp-calls in order to improve performance
145      - clean up a little (replace fields by their macros, etc., fix
146        typo in CPP-flag)
147    o pkg/ggl90: minor changes
148      - GGL90diffKrS was removed --> always use GGL90diffKr
149      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
150      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
151        (commented out for now)
152      - change in max/min operations to ensure that smoothing is ok
153      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
154      - always use diffKrNrT as background profile (i.e. never use diffKr field)
155    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
156    o pkg/dic:
157      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
158        vectorization
159      - small bug fix in insol for the unlikely case of a cartesian grid
160      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
161        + now vectorize, which also removes adjoint recomputations;
162        + replace integer maksp1 by _RL maskp1
163        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
164    
165    checkpoint62i (2010/07/21)
166    o pkg/flt:
167      - with OBCS: stop floats which enter the OB region
168    o model/src:
169      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
170        for implicit vertical advection.
171    o pkg/seaice:
172     - account for melting in seaice age evolution.
173     - remove double counting of seaice ridging effect on seaice age.
174    
175    checkpoint62h (2010/06/18)
176    o pkg/exch2:
177     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
178    o tools/genmake2
179      - remove "-pdefault" option: redundant with the use of "packages.conf";
180      - remove file pkg/pkg_default : set the default as a pkg group
181        ("default_pkg_list") defined in pkg/pkg_groups;
182      - fix for case pkg/pkg_depend is missing (was hanging before);
183      - add option "-pgroups" to specify a different pkg_groups than the default.
184    o verification/adjustment.cs-32x32x1:
185       add a "minimal" set-up test (code_min & input_min) which only compiles
186       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
187    o tools/genmake2
188      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
189      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
190    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
191      files are nearly the same anyway.
192      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
193       - redefinition of tau(i,i) (by a factor of ustar)
194       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
195       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
196       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
197       - replace
198         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
199         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
200         by
201         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
202         (changes results)
203       -> exf_bulkformulae v1.22,
204          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
205          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
206                    output.txt 1.63
207           offline_exf_seaice: output.seaicetd.txt 1.7
208           seaice_obcs: output.txt 1.10)
209      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
210       -> exf_bulkformulae v1.23,
211          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
212          and global_ocean.cs32x15.icedyn (only 11 matching digits)
213      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
214    o adjoint of exch-1:
215     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
216       (note: was already like this when using EXCH-2) and remove flow dir
217       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
218     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
219     - update pkg/exch2 diff list.
220    
221    checkpoint62g (2010/05/19)
222    o eesupp/src (exch-1):
223     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
224       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
225       (renamed to exch1_*rx_cube.F).
226     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
227       to call new exch1 S/R ; update Makefile and .cvsignore.
228     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
229       exch2_xy_rx later)
230      Note: after updating your code, need to run "make clean" in eesupp/src
231    o test experiment bottom_ctrl_5x5:
232       new output_adm.txt with fewer grdchk & less monitor output.
233    o model/src:
234      remove the call to ini_cori in initialise_varia.F (just keep the usual one
235       in initialise_fixed.F). More consistent with coriolis & horizontal grid
236       beeing treated in the same way (ini_grid is not called a 2nd time).
237    o pkg/exf:
238      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
239      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
240      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
241      - cosmetic changes to exf_bulkformulae.F to make it look more like
242        exf_bulk_largeyeager04.F
243    o eesupp/src (exch-1):
244      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
245      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
246        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
247        (even without using MPI).
248      - Message mode: move RecvAck setting (indicator of buffer being ready)
249        from send_put to recv_get S/R (was useless before, but not sure if
250        it's much more useful now);
251      - Switch the order of sync: MPI-proc 1rst and then threads;
252      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
253      - fix AD code for communication mode ='get' (but not used).
254    o model/src:
255      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
256      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
257    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
258    o pkg/ctrl: require a specific set of control variables and exf-flags for
259      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
260  o model/src:  o model/src:
261    1rst version of a new driver S/R to turn-off output freq and flags after the   a) 1rst version of a new driver S/R to turn-off output freq and flags after the
262    1rst forward sweep, to avoid over-writing output files during recomputations     1rst forward sweep, to avoid over-writing output files during recomputations
263    (& grdchk); called from cost_final.F (and ctrl_init_ctrlvar.F ?).     recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
264     b) 2nd version:
265      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
266      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
267         writePickupAtEnd) + seaice & ptracers output;
268      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
269  o model/src:  o model/src:
270    - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.    - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
271  o pkg/exch2:  o pkg/exch2:

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