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revision 1.1267 by mlosch, Tue May 11 15:48:00 2010 UTC revision 1.1305 by jmc, Sun Sep 26 13:48:19 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/seaice:
8      -fix the USE_ORIGINAL_SBI version (for variable freezing point);
9      -use "celsius2K" in SEAICE_VARIABLE_FREEZING_POINT and in new
10       version (with USE_ORIGINAL_SBI undef);
11    o add hooks for new packages OASIS, the package will follow
12      (hooks exclude the seaice pkg for now)
13    o pkg/autodiff: ALLOW_AUTODIFF_WHTAPEIO
14      Option to use mdsio_read_whalos.F/mdsio_write_whalos.F,
15      rather than mdsio_readvector.F/mdsio_writevector.F, within
16      adread_adwrite.F to read/write adjoint-related tapes to disk.
17    o eesupp and pkg/mdsio: ALLOW_WHIO
18      Option to write/read 2D fields to files including tiles halos.
19      The main purpose is for adjoint related "tape I/O".
20      The secondary purpose is for debugging phases.
21      A word on those rather specifically intended purposes.
22      The code was meant to be stripped down to the bare minimum.
23      Typically, there is a unique and basic mapping to the global
24      buffer (tile by tile, then proc by proc, then level by level), and
25      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
26      meant to generate user friendly outputs of various shapes and forms.
27      Rather it is intended, for the knowledgeabale developers,
28      to be largely independent of the many mdsio options, to allow
29      outputs of tiles+halos in debugging phases and in adjoint runs,
30      and to allow some flexibility in tuning (adoint) I/O depending on each
31      file system behavior. With regard to tuning, most of the potential knobs
32      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
33      to specify directories, to specify the typical size of I/O calls, etc.)
34      are not yet included, and will be added if they prove useful.
35    o pkg/seaice:
36       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
37    o pkg/seaice:
38       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
39       code (seaice_budget_ice_if.F) which enable to recover old standard
40       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
41       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
42    o model/src (rStar):
43       use simple average (not area weighted) of rStarFac at U,V point when using
44       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
45       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
46    
47    checkpoint62k (2010/09/17)
48    o adjoint
49       * changed verification/global_ocean.cs32x15 ; adjoint now tests
50         Adams-Bashforth 3 + NLFS + RSTAR
51       * some more modifs required for ECCO-GODAE v4
52    o pkg/seaice
53       add SEAICE_AGE_VOL option to use volume instead of area for
54       integrating SEAICE_AGE
55    o model/src:
56       first check-in of sigma & hybrid-sigma coordinate code ; also includes
57       non-linear free-surface parts ; but pressure-gradient not yet coded.
58    o pkg/ptracers:
59       option for ptracer to convert Salt Relax into additional EmP.
60        tested in exp. global_ocean.90x40x15.dwnslp (update output)
61    
62    checkpoint62j (2010/08/25)
63    o pkg/ggl90:
64       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
65    o pkg/dic: car_flux.F, phos_flux.F
66      - reduce number of exp-calls in order to improve performance
67      - clean up a little (replace fields by their macros, etc., fix
68        typo in CPP-flag)
69    o pkg/ggl90: minor changes
70      - GGL90diffKrS was removed --> always use GGL90diffKr
71      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
72      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
73        (commented out for now)
74      - change in max/min operations to ensure that smoothing is ok
75      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
76      - always use diffKrNrT as background profile (i.e. never use diffKr field)
77    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
78    o pkg/dic:
79      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
80        vectorization
81      - small bug fix in insol for the unlikely case of a cartesian grid
82      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
83        + now vectorize, which also removes adjoint recomputations;
84        + replace integer maksp1 by _RL maskp1
85        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
86    
87    checkpoint62i (2010/07/21)
88    o pkg/flt:
89      - with OBCS: stop floats which enter the OB region
90    o model/src:
91      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
92        for implicit vertical advection.
93    o pkg/seaice:
94     - account for melting in seaice age evolution.
95     - remove double counting of seaice ridging effect on seaice age.
96    
97    checkpoint62h (2010/06/18)
98    o pkg/exch2:
99     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
100    o tools/genmake2
101      - remove "-pdefault" option: redundant with the use of "packages.conf";
102      - remove file pkg/pkg_default : set the default as a pkg group
103        ("default_pkg_list") defined in pkg/pkg_groups;
104      - fix for case pkg/pkg_depend is missing (was hanging before);
105      - add option "-pgroups" to specify a different pkg_groups than the default.
106    o verification/adjustment.cs-32x32x1:
107       add a "minimal" set-up test (code_min & input_min) which only compiles
108       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
109    o tools/genmake2
110      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
111      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
112    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
113      files are nearly the same anyway.
114      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
115       - redefinition of tau(i,i) (by a factor of ustar)
116       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
117       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
118       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
119       - replace
120         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
121         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
122         by
123         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
124         (changes results)
125       -> exf_bulkformulae v1.22,
126          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
127          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
128                    output.txt 1.63
129           offline_exf_seaice: output.seaicetd.txt 1.7
130           seaice_obcs: output.txt 1.10)
131      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
132       -> exf_bulkformulae v1.23,
133          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
134          and global_ocean.cs32x15.icedyn (only 11 matching digits)
135      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
136    o adjoint of exch-1:
137     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
138       (note: was already like this when using EXCH-2) and remove flow dir
139       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
140     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
141     - update pkg/exch2 diff list.
142    
143    checkpoint62g (2010/05/19)
144    o eesupp/src (exch-1):
145     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
146       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
147       (renamed to exch1_*rx_cube.F).
148     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
149       to call new exch1 S/R ; update Makefile and .cvsignore.
150     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
151       exch2_xy_rx later)
152      Note: after updating your code, need to run "make clean" in eesupp/src
153    o test experiment bottom_ctrl_5x5:
154       new output_adm.txt with fewer grdchk & less monitor output.
155    o model/src:
156      remove the call to ini_cori in initialise_varia.F (just keep the usual one
157       in initialise_fixed.F). More consistent with coriolis & horizontal grid
158       beeing treated in the same way (ini_grid is not called a 2nd time).
159    o pkg/exf:
160      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
161      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
162      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
163      - cosmetic changes to exf_bulkformulae.F to make it look more like
164        exf_bulk_largeyeager04.F
165    o eesupp/src (exch-1):
166      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
167      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
168        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
169        (even without using MPI).
170      - Message mode: move RecvAck setting (indicator of buffer being ready)
171        from send_put to recv_get S/R (was useless before, but not sure if
172        it's much more useful now);
173      - Switch the order of sync: MPI-proc 1rst and then threads;
174      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
175      - fix AD code for communication mode ='get' (but not used).
176    o model/src:
177      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
178      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
179    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
180  o pkg/ctrl: require a specific set of control variables and exf-flags for  o pkg/ctrl: require a specific set of control variables and exf-flags for
181    adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)    adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
182  o model/src:  o model/src:

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