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revision 1.1220 by jmc, Sat Jan 16 23:17:16 2010 UTC revision 1.1257 by jmc, Tue Apr 27 19:34:25 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 adjoint:
8      global_sum_ad was incomplete (noted many times by many people ;)
9      nice description by Jean U. as follows:
10      * allreduce(var) in global_sum.F can be interpreted as
11        reduce(sum) followed by broadcast of sum.  
12      * The adjoint of that is
13        sum(adjoint) followed by broadcast(summed adjoint value)
14        or in other words, allreduce(sum, adjoint vars)
15      We were missing the sum(adjoint)!
16      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
17      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
18      The fix should produce 16-digit accuracy between
19      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
20      multi-CPU single-tile (e.g. nSx=1, nPx-2)
21      We'll probably change this yet again shortly
22    o eesupp/src:
23      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
24    o pkg/icefront
25      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
26        specification of addmass array based on a 2D field, which is added
27        at bottommost wet level at each horizontal location.
28    o model/src:
29     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
30     layout; (not always compatible with delX,delY setting; commented out for now).
31    o pkg/exch2:
32     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
33     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
34    
35    checkpoint62e (2010/04/15)
36    o pkg/obcs:
37      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
38    o pkg/dic:
39      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
40        (note: not presently tested in any forward verification exp.)
41       update tutorial_global_oce_biogeo AD output file.
42    o pkg/exf:
43      - account for the variation of albedo as a function of zenith angle
44        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
45    o build_options:
46     - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
47    o pkg/dic:
48      change DIC atmos-CO2 box (method 3, dic_int1=3) initialisation & restart:
49      - use binary pickup file for restart;
50      - initialise atmos-CO2 box from dic_pCO2 parameter;
51      - fix multi-threaded.
52    o pkg/rbcs:
53     - clean-up RBCS code: add RBCS_OPTIONS.h file ; fix multi-threaded ;
54       change (+ fix IO calls) type of array RBC_mask from _RL to _RS.
55     - add RBCS to exp4 passive tracer 01 (rbcs was previously untested)
56       and update output.txt
57    o pkg/kpp:
58     - add diagnostics for KPP non-local flux of Temp, Salinity and pTracers;
59     - change diagnostic of KPP non-local term: output average of KPPghat*KPPdiffKzS
60       (= ratio of KPP non-local (salt) flux relative to surface-flux) when
61       using pkg/timeave & pkg/diagnostics (diag 'KPPghatK' replaces 'KPPghat ');
62     - change pkg/offline to read-in average KPPghat*KPPdiffKzS from file
63       KPP_ghatKFile (instead of the average of KPPghat from file KPP_ghatFile).
64    o pkg/offline:
65      fix bug in S/R OFFLINE_FIELDS_LOAD regarding surfaceForcing conversion factor
66      (bug was added in version 1.10 on 2007-08-23).
67    o pkg/offline:
68      - no need to specify periodicExternalForcing, etc ... to use offline pack
69      - offline input files no longer just single prec --> parameter offlineLoadPrec
70    o verification/lab_sea:
71      change AD test to multi-tile setup and update all 4 AD output.
72      NOTE: while cost function values remain very similar,
73      gradients are very different, although gradient checks are self-consistent
74      Should try to get to the bottom of this (cost function summation order?)
75    o pkg/dic:
76      in carbon_chem.F, replace log10 (AUTODIFF) with explicit form to avoid
77      a weakness of TAF that drops part of double precision in log10 derivative.
78      <= changes removed since problem has been fixed in current TAF version 1.9.71
79      update AD output of exp. tutorial_dic_adjoffline & tutorial_global_oce_biogeo.
80    o pkg/ecco:
81      add missing "_d 0" in cost_readers.F, cost_readtopex.F & cost_readtopexmean.F
82      update all 4 lab_sea AD output.
83    
84    checkpoint62d (2010/03/22)
85    o build_options:
86      remove '-r8' (and '-i4') from linux_*pgf and linux_*ifort optfiles.
87    o remove unbalanced quote (single or double) in commented line of source code
88      (may cause some warning with some preprocessor/makedepend versions).
89    o pkg/seaice:
90      fix seaice_model.F for adjoint (gael) and update AD results of experiments
91       lab_sea (std + evp + noseaicedyn) and offline_exf_seaice.
92    o testreport:
93      add option '-runonly' (short: '-ro') to just do the run part (without make).
94    o eesupp: remove JAM communication code (obsolete).
95    o add option to genmake2 & testreport to switch "_RS" type to "real*4"
96      (if allowed in CPP_EEOPTIONS.h); update default CPP_EEOPTIONS.h and return
97      to default CPP_EEOPTIONS.h for exp. inverted_barometer & solid-body.cs-32x32x1
98      (update also the output).
99    
100    checkpoint62c (2010/03/02)
101    o tools/build_options :
102       move (some) old optfiles from build_options/ to build_options/unsupported/
103    o model/src and pkg/exf
104       surface relaxation -- separating data and data.exf options
105       The point is to ensure that we specify the surface relaxation
106       either in data or in data.exf (but not half and half) and to
107       avoid an accidental relaxation to 0 (which happened if a time
108       scale was specified but the file name was left empty)
109    o model/src model/inc and pkg/mom_common
110       ALLOW_3D_VISCAH/ALLOW_3D_VISCA4 => 3D specification of Viscosity
111       => addition to the viscosity field as computed by others schemes
112    o tools/build_options:
113      - rename "_generic_mpi" -> "+mpi_generic" (like other "+mpi" optfile)
114        but keep the former optfile for few weeks for smooth transition
115    o pkg/ecco
116      - allow user defined cost function contributions
117            CPP: ALLOW_USERCOST_CONTRIBUTION
118            USAGE: compute contributions in cost_usercost_all.F
119      - note: this is identical to what ALLOW_GENCOST_CONTRIBUTION once was.
120          the two options are complementary.
121    o pkg/smooth
122      - migration from contrib to the main repository
123    
124    checkpoint62b (2010/01/26)
125    o pkg/monitor:
126      - change back mon_printstats_rl.F & mon_stats_rl.F and add a stop
127        (in case someone forgot to update customized pieces of code)
128    o nonHydrostatic:
129      - add Non-hydrostatic free-surface form (selectNHfreeSurf=1)(not fully tested);
130      - add a simple 2-D experiment (short_surf_wave) to test it.
131    o pkg/icefront:
132       adding the shell of, and the hooks to, a new package that
133       will model melting and freezing of vertical glacier ice fronts
134    o momentum:
135      add diagnostics of momentum tendency from Hydrostatic pressure gradient
136       (without surf.pressure term: would need a 2nd filling since implicit term).
137    o add 3 "_d 0"s so that fizhi compiles with xlf on iblade, and replace
138      two " &end" by " &" (in fizhi-cs-*) because S/R NML_SET_TERMINATOR
139      cannot deal with the former
140  o cleaning:  o cleaning:
141      - remove all (except OpenAD) old TLM output from results_ad dirs.
142    - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)    - remove unused S/R (MDSWRITEMETA, DIAGNOSTICS_ADD2LIST, old DFILE IO S/R)
143    - comment out maskH definition (replaced by maskInC)    - comment out maskH definition (replaced by maskInC)
144  o pkg/monitor:  o pkg/monitor:
145    - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl    - change mon_printstats_rl.F & mon_stats_rl.F (were similar to mon_writestats_rl
146      & mon_calc_stats_rl) to be the RL pendant to mon_printstats_rs & mon_stats_rs.      & mon_calc_stats_rl) to be the RL equivalent of mon_printstats_rs & mon_stats_rs.
147    
148  checkpoint62a (2010/01/15)  checkpoint62a (2010/01/15)
149  o model/src:  o model/src:
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