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revision 1.1242 by heimbach, Wed Mar 24 21:56:45 2010 UTC revision 1.1277 by mlosch, Fri May 21 10:16:59 2010 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    
8    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
9      files are nearly the same anyway.
10      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
11       - redefinition of tau(i,i) (by a factor of ustar)
12       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
13       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
14       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
15       - replace
16         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
17         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
18         by
19         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
20         (changes results)
21       -> exf_bulkformulae v1.22,
22          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
23          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
24                    output.txt 1.63      
25           offline_exf_seaice: output.seaicetd.txt 1.7
26           seaice_obcs: output.txt 1.10)
27      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
28       -> exf_bulkformulae v1.23,
29          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
30          and global_ocean.cs32x15.icedyn (only 11 matching digits)
31    o adjoint of exch-1:
32     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
33       (note: was already like this when using EXCH-2) and remove flow dir
34       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
35     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
36     - update pkg/exch2 diff list.
37    
38    checkpoint62g (2010/05/19)
39    o eesupp/src (exch-1):
40     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
41       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
42       (renamed to exch1_*rx_cube.F).
43     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
44       to call new exch1 S/R ; update Makefile and .cvsignore.
45     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
46       exch2_xy_rx later)
47      Note: after updating your code, need to run "make clean" in eesupp/src
48    o test experiment bottom_ctrl_5x5:
49       new output_adm.txt with fewer grdchk & less monitor output.
50    o model/src:
51      remove the call to ini_cori in initialise_varia.F (just keep the usual one
52       in initialise_fixed.F). More consistent with coriolis & horizontal grid
53       beeing treated in the same way (ini_grid is not called a 2nd time).
54    o pkg/exf:
55      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
56      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
57      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
58      - cosmetic changes to exf_bulkformulae.F to make it look more like
59        exf_bulk_largeyeager04.F
60    o eesupp/src (exch-1):
61      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
62      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
63        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
64        (even without using MPI).
65      - Message mode: move RecvAck setting (indicator of buffer being ready)
66        from send_put to recv_get S/R (was useless before, but not sure if
67        it's much more useful now);
68      - Switch the order of sync: MPI-proc 1rst and then threads;
69      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
70      - fix AD code for communication mode ='get' (but not used).
71    o model/src:
72      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
73      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
74    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
75    o pkg/ctrl: require a specific set of control variables and exf-flags for
76      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
77    o model/src:
78     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
79       1rst forward sweep, to avoid over-writing output files during recomputations
80       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
81     b) 2nd version:
82      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
83      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
84         writePickupAtEnd) + seaice & ptracers output;
85      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
86    o model/src:
87      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
88    o pkg/exch2:
89      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
90      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
91    o pkg/autodiff & exch2:
92      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
93      (for now, only if ALLOW_EXCH2 is defined).
94    o pkg/autodiff:
95      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
96        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
97       + clean-up comments (_RS is not always real*4)
98      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
99      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
100        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
101    o testreport (AD-tests):
102      no longer link files from dir "../input" (1rst link files from
103      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
104    
105    checkpoint62f (2010/04/29)
106    o model/src/the_main_loop.F:
107      adjust store directives for seaice evp and multicategory according to
108      pkg/ecco/the_main_loop.F
109    o adjoint:
110      global_sum_ad was incomplete (noted many times by many people ;)
111      nice description by Jean U. as follows:
112      * allreduce(var) in global_sum.F can be interpreted as
113        reduce(sum) followed by broadcast of sum.
114      * The adjoint of that is
115        sum(adjoint) followed by broadcast(summed adjoint value)
116        or in other words, allreduce(sum, adjoint vars)
117      We were missing the sum(adjoint)!
118      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
119      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
120      The fix should produce 16-digit accuracy between
121      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
122      multi-CPU single-tile (e.g. nSx=1, nPx-2)
123      We'll probably change this yet again shortly
124    o eesupp/src:
125      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
126    o pkg/icefront
127      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
128        specification of addmass array based on a 2D field, which is added
129        at bottommost wet level at each horizontal location.
130    o model/src:
131     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
132     layout; (not always compatible with delX,delY setting; commented out for now).
133    o pkg/exch2:
134     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
135     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
136    
137    checkpoint62e (2010/04/15)
138    o pkg/obcs:
139      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
140    o pkg/dic:
141      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
142        (note: not presently tested in any forward verification exp.)
143       update tutorial_global_oce_biogeo AD output file.
144    o pkg/exf:
145      - account for the variation of albedo as a function of zenith angle
146        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
147    o build_options:
148     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
149    o pkg/dic:
150      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
151      - use binary pickup file for restart;
152      - initialise atmos-CO2 box from dic_pCO2 parameter;
153      - fix multi-threaded.
154    o pkg/rbcs:
155     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
156       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
157     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
158       and update output.txt
159    o pkg/kpp:
160     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
161     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
162       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
163       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
164     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
165       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
166    o pkg/offline:
167      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
168      (bug was added in version 1.10 on 2007-08-23).
169    o pkg/offline:
170      - no need to specify periodicExternalForcing, etc ... to use offline pack
171      - offline input files no longer just single prec --> parameter offlineLoadPrec
172  o verification/lab_sea:  o verification/lab_sea:
173    change to multi-tile setup.    change AD test to multi-tile setup and update all 4 AD output.
174    NOTE: while cost function values remain very similar,    NOTE: while cost function values remain very similar,
175    gradients are very different, although gradient checks are self-consistent    gradients are very different, although gradient checks are self-consistent
176    Should try to get to the bottom of this (cost function summation order?)    Should try to get to the bottom of this (cost function summation order?)
177  o pkg/dic:  o pkg/dic:
178    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid    in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
179    a weakness of TAF that drops part of double precision in log10 derivative.    a weakness of TAF that drops part of double precision in log10 derivative.
180      <= changes removed since problem has been fixed in current TAF version 1.9.71
181    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.    update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
182  o pkg/ecco:  o pkg/ecco:
183    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F    add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
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