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revision 1.1256 by heimbach, Tue Apr 27 17:43:30 2010 UTC revision 1.1286 by mlosch, Fri Jul 30 15:03:11 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 pkg/dic:
8      -small bug fix in insol for the unlikely case of a cartesian grid
9      -first step towards vectorizing the dic package: bio_export.F
10    
11    checkpoint62i (2010/07/21)
12    o pkg/flt:
13      - with OBCS: stop floats which enter the OB region
14    o model/src:
15      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
16        for implicit vertical advection.
17    o pkg/seaice:
18     - account for melting in seaice age evolution.
19     - remove double counting of seaice ridging effect on seaice age.
20    
21    checkpoint62h (2010/06/18)
22    o pkg/exch2:
23     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
24    o tools/genmake2
25      - remove "-pdefault" option: redundant with the use of "packages.conf";
26      - remove file pkg/pkg_default : set the default as a pkg group
27        ("default_pkg_list") defined in pkg/pkg_groups;
28      - fix for case pkg/pkg_depend is missing (was hanging before);
29      - add option "-pgroups" to specify a different pkg_groups than the default.
30    o verification/adjustment.cs-32x32x1:
31       add a "minimal" set-up test (code_min & input_min) which only compiles
32       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
33    o tools/genmake2
34      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
35      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
36    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
37      files are nearly the same anyway.
38      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
39       - redefinition of tau(i,i) (by a factor of ustar)
40       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
41       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
42       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
43       - replace
44         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
45         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
46         by
47         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
48         (changes results)
49       -> exf_bulkformulae v1.22,
50          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
51          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
52                    output.txt 1.63
53           offline_exf_seaice: output.seaicetd.txt 1.7
54           seaice_obcs: output.txt 1.10)
55      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
56       -> exf_bulkformulae v1.23,
57          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
58          and global_ocean.cs32x15.icedyn (only 11 matching digits)
59      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
60    o adjoint of exch-1:
61     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
62       (note: was already like this when using EXCH-2) and remove flow dir
63       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
64     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
65     - update pkg/exch2 diff list.
66    
67    checkpoint62g (2010/05/19)
68    o eesupp/src (exch-1):
69     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
70       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
71       (renamed to exch1_*rx_cube.F).
72     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
73       to call new exch1 S/R ; update Makefile and .cvsignore.
74     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
75       exch2_xy_rx later)
76      Note: after updating your code, need to run "make clean" in eesupp/src
77    o test experiment bottom_ctrl_5x5:
78       new output_adm.txt with fewer grdchk & less monitor output.
79    o model/src:
80      remove the call to ini_cori in initialise_varia.F (just keep the usual one
81       in initialise_fixed.F). More consistent with coriolis & horizontal grid
82       beeing treated in the same way (ini_grid is not called a 2nd time).
83    o pkg/exf:
84      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
85      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
86      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
87      - cosmetic changes to exf_bulkformulae.F to make it look more like
88        exf_bulk_largeyeager04.F
89    o eesupp/src (exch-1):
90      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
91      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
92        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
93        (even without using MPI).
94      - Message mode: move RecvAck setting (indicator of buffer being ready)
95        from send_put to recv_get S/R (was useless before, but not sure if
96        it's much more useful now);
97      - Switch the order of sync: MPI-proc 1rst and then threads;
98      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
99      - fix AD code for communication mode ='get' (but not used).
100    o model/src:
101      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
102      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
103    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
104    o pkg/ctrl: require a specific set of control variables and exf-flags for
105      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
106    o model/src:
107     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
108       1rst forward sweep, to avoid over-writing output files during recomputations
109       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
110     b) 2nd version:
111      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
112      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
113         writePickupAtEnd) + seaice & ptracers output;
114      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
115    o model/src:
116      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
117    o pkg/exch2:
118      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
119      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
120    o pkg/autodiff & exch2:
121      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
122      (for now, only if ALLOW_EXCH2 is defined).
123    o pkg/autodiff:
124      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
125        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
126       + clean-up comments (_RS is not always real*4)
127      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
128      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
129        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
130    o testreport (AD-tests):
131      no longer link files from dir "../input" (1rst link files from
132      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
133    
134    checkpoint62f (2010/04/29)
135    o model/src/the_main_loop.F:
136      adjust store directives for seaice evp and multicategory according to
137      pkg/ecco/the_main_loop.F
138  o adjoint:  o adjoint:
139    global_sum_ad was incomplete (noted many times by many people ;)    global_sum_ad was incomplete (noted many times by many people ;)
140    nice description by Jean U. as follows:    nice description by Jean U. as follows:
141    * allreduce(var) in global_sum.F can be interpreted as    * allreduce(var) in global_sum.F can be interpreted as
142      reduce(sum) followed by broadcast of sum.        reduce(sum) followed by broadcast of sum.
143    * The adjoint of that is    * The adjoint of that is
144      sum(adjoint) followed by broadcast(summed adjoint value)      sum(adjoint) followed by broadcast(summed adjoint value)
145      or in other words, allreduce(sum, adjoint vars)      or in other words, allreduce(sum, adjoint vars)
146    We were missing the sum(adjoint)!    We were missing the sum(adjoint)!
147    Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)    Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
# Line 19  o adjoint: Line 150  o adjoint:
150    single-CPU multi-tile (e.g. nSx=2, nPx=1) and    single-CPU multi-tile (e.g. nSx=2, nPx=1) and
151    multi-CPU single-tile (e.g. nSx=1, nPx-2)    multi-CPU single-tile (e.g. nSx=1, nPx-2)
152    We'll probably change this yet again shortly    We'll probably change this yet again shortly
153    o eesupp/src:
154      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
155  o pkg/icefront  o pkg/icefront
156    - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving    - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
157      specification of addmass array based on a 2D field, which is added      specification of addmass array based on a 2D field, which is added
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