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revision 1.1248 by jmc, Mon Apr 12 20:29:44 2010 UTC revision 1.1302 by gforget, Fri Sep 24 18:40:15 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 eesup and pkg/mdsio: ALLOW_WHIO
8    
9      Option to write/read 2D fields to files including tiles halos.
10      The main purpose is for adjoint related "tape I/O".
11      The secondary purpose is for debugging phases.
12    
13      A word on those rather specifically intended purposes.
14      The code was meant to be stripped down to the bare minimum.
15      Typically, there is a unique and basic mapping to the global
16      buffer (tile by tile, then proc by proc, then level by level), and
17      byteswaps and meta-files are omitted. Indeed the (*_WH*) code is not
18      meant to generate user friendly outputs of various shapes and forms.
19      Rather it is intended, for the knowledgeabale developers,
20      to be largely independent of the many mdsio options, to allow
21      outputs of tiles+halos in debugging phases and in adjoint runs,
22      and to allow some flexibility in tuning (adoint) I/O depending on each
23      file system behavior. With regard to tuning, most of the potential knobs
24      (to leave files open, to allocate the I/O indep. of usesinglecpuio,
25      to specify directories, to specify the typical size of I/O calls, etc.)
26      are not yet included, and will be added if they prove useful.
27    o pkg/seaice:
28       fix uninitialised arrays in USE_ORIGINAL_SBI version of seaice_solve4temp.F
29    o pkg/seaice:
30       new S/R seaice_solve4temp.F: this is the merged version of Ian Fenty
31       code (seaice_budget_ice_if.F) which enable to recover old standard
32       code (seaice_budget_ice.F) when option USE_ORIGINAL_SBI is defined.
33       temporary: add "#define USE_ORIGINAL_SBI" at the top of seaice_solve4temp.F.
34    o model/src (rStar):
35       use simple average (not area weighted) of rStarFac at U,V point when using
36       vectorInvariant and selectKEscheme=1,3 (consistent with mom. vertical advection)
37       update output of exp. fizhi-cs-32x32x40 and fizhi-cs-aqualev20.
38    
39    checkpoint62k (2010/09/17)
40    o adjoint
41       * changed verification/global_ocean.cs32x15 ; adjoint now tests
42         Adams-Bashforth 3 + NLFS + RSTAR
43       * some more modifs required for ECCO-GODAE v4
44    o pkg/seaice
45       add SEAICE_AGE_VOL option to use volume instead of area for
46       integrating SEAICE_AGE
47    o model/src:
48       first check-in of sigma & hybrid-sigma coordinate code ; also includes
49       non-linear free-surface parts ; but pressure-gradient not yet coded.
50    o pkg/ptracers:
51       option for ptracer to convert Salt Relax into additional EmP.
52        tested in exp. global_ocean.90x40x15.dwnslp (update output)
53    
54    checkpoint62j (2010/08/25)
55    o pkg/ggl90:
56       other minor changes: remove 3-D temp array gTKE (+ add argument myIter)
57    o pkg/dic: car_flux.F, phos_flux.F
58      - reduce number of exp-calls in order to improve performance
59      - clean up a little (replace fields by their macros, etc., fix
60        typo in CPP-flag)
61    o pkg/ggl90: minor changes
62      - GGL90diffKrS was removed --> always use GGL90diffKr
63      - GGL90viscAr was removed --> replaced with GGL90viscArU, GGL90viscArV
64      - hack of mxlMaxFlag=2 --> ensure mixing between first and second level
65        (commented out for now)
66      - change in max/min operations to ensure that smoothing is ok
67      - smoothing of GGL90viscAr was moved to ggl90_calc.F (as done for GGL90diffKr)
68      - always use diffKrNrT as background profile (i.e. never use diffKr field)
69    o pkg/cfc: bug fix, AREA(i,j,1,bi,bj) -> AREA(i,j,bi,bj)
70    o pkg/dic:
71      - model/src/impldiff.F: if TARGET_NEC_SX, extend loop ranges for better
72        vectorization
73      - small bug fix in insol for the unlikely case of a cartesian grid
74      - towards vectorizing the dic package: bio_export.F, car_flux.F, phos_flux.F
75        + now vectorize, which also removes adjoint recomputations;
76        + replace integer maksp1 by _RL maskp1
77        + replace a**x by exp(x*log(a)) in phos_flux.F for speed
78    
79    checkpoint62i (2010/07/21)
80    o pkg/flt:
81      - with OBCS: stop floats which enter the OB region
82    o model/src:
83      - use tempVertAdvScheme & saltVertAdvScheme (instead of horizontal ones)
84        for implicit vertical advection.
85    o pkg/seaice:
86     - account for melting in seaice age evolution.
87     - remove double counting of seaice ridging effect on seaice age.
88    
89    checkpoint62h (2010/06/18)
90    o pkg/exch2:
91     - remove exch2_*xy_rx files: call was replaced with exch2_*3d_rx(myNz=1).
92    o tools/genmake2
93      - remove "-pdefault" option: redundant with the use of "packages.conf";
94      - remove file pkg/pkg_default : set the default as a pkg group
95        ("default_pkg_list") defined in pkg/pkg_groups;
96      - fix for case pkg/pkg_depend is missing (was hanging before);
97      - add option "-pgroups" to specify a different pkg_groups than the default.
98    o verification/adjustment.cs-32x32x1:
99       add a "minimal" set-up test (code_min & input_min) which only compiles
100       eesupp/src and the 2 pkgs (exch2 & debug) which don't need model/src & inc.
101    o tools/genmake2
102      - extend pkg_depend rules to model & eesupp (e.g., if model depend on [pkg]))
103      - fix details of checking for mnc & profile pkg when NetCDF is unavailable.
104    o pkg/exf: merge exf_bulk_largeyeager04 into exf_bulkformulae because these
105      files are nearly the same anyway.
106      Step 1: make exf_bulkformulae look like exf_bulk_largeyeager04:
107       - redefinition of tau(i,i) (by a factor of ustar)
108       - 1./exf(Const/T) -> exf(-Const/T) (big change in the results)
109       - replace rhonil by rhoConstFresh in computation of evap (bug fix)
110       - replace u/vstress=tau*rd*ws*cw by tau*rd*u/vwind (changes results)
111       - replace
112         rd(i,j)= rdn(i,j)/(exf_one - rdn(i,j)/karman*psimh )
113         shn    = sh(i,j,bi,bj)*rd(i,j)/rdn(i,j)
114         by
115         shn    = sh(i,j,bi,bj)/(exf_one - rdn(i,j)/karman*psimh )
116         (changes results)
117       -> exf_bulkformulae v1.22,
118          update verification experiments lab_sea, offline_exf_seaice, seaice_obcs
119          (lab_sea: output.hb87.txt 1.11, output.lsr.txt 1.25, output.salt_plume.txt 1.13,
120                    output.txt 1.63
121           offline_exf_seaice: output.seaicetd.txt 1.7
122           seaice_obcs: output.txt 1.10)
123      Step 2: do the actual merge and remove exf_bulk_largeyeager04.F
124       -> exf_bulkformulae v1.23,
125          unfortunately requires updating lab_sea.salt_plume (6 matching digits),
126          and global_ocean.cs32x15.icedyn (only 11 matching digits)
127      Also update output_adm of exp. lab_sea (all 4) and offline_exf_seaice.
128    o adjoint of exch-1:
129     - pass high-level EXCH S/R through TAF (eesupp/src/exch_ad_diff.list)
130       (note: was already like this when using EXCH-2) and remove flow dir
131       and hand-written AD version of high-level EXCH S/R (pkg/autodiff);
132     - provide flow-dir for low-level exch1 S/R (eesupp/src/exch1_ad.flow);
133     - update pkg/exch2 diff list.
134    
135    checkpoint62g (2010/05/19)
136    o eesupp/src (exch-1):
137     - split exch_rx.F into Forward S/R (exch1_rx.F) and Adjoint S/R (exch1_rx_ad.F)
138       and remove argument "simulationMode"; same thing for all exch_*rx_cube.F
139       (renamed to exch1_*rx_cube.F).
140     - change accordingly exch_*_rx.template and AD version in pkg/autodiff
141       to call new exch1 S/R ; update Makefile and .cvsignore.
142     - replace call to exch2_xy_rx S/R with exch2_*3d_rx(myNz=1) (will remove
143       exch2_xy_rx later)
144      Note: after updating your code, need to run "make clean" in eesupp/src
145    o test experiment bottom_ctrl_5x5:
146       new output_adm.txt with fewer grdchk & less monitor output.
147    o model/src:
148      remove the call to ini_cori in initialise_varia.F (just keep the usual one
149       in initialise_fixed.F). More consistent with coriolis & horizontal grid
150       beeing treated in the same way (ini_grid is not called a 2nd time).
151    o pkg/exf:
152      - rewrite exf_bulk_largeyeager04.F for better vectorization, changes
153      global_ocean.cs32x15/input.icedyn (11 digits of agreement), updated
154      - fix adjoint (used worked for ALLOW_ATM_WIND defined, works for this now)
155      - cosmetic changes to exf_bulkformulae.F to make it look more like
156        exf_bulk_largeyeager04.F
157    o eesupp/src (exch-1):
158      - Fix AD EXCH code for 2-D domain special cases (Nx=1 or Ny=1).
159      - Separate buffer filling and MPI sending: allow EXCH-1 to work for local
160        array (non-shared) when using MPI+MTH. Also reduces number of BARRIER
161        (even without using MPI).
162      - Message mode: move RecvAck setting (indicator of buffer being ready)
163        from send_put to recv_get S/R (was useless before, but not sure if
164        it's much more useful now);
165      - Switch the order of sync: MPI-proc 1rst and then threads;
166      - take out spin-waiting code (#undef EXCH_USE_SPINNING), use BARRIER instead.
167      - fix AD code for communication mode ='get' (but not used).
168    o model/src:
169      initialise dPhiHydX,dPhiHydY inside calc_grad_phi_hyd.F (so that TAF does
170      not drop it in S/R mddynamics, producing NaN in hs94.1x64x5 AD-test exp).
171    o utils/matlab/rdmnc.m: adapt to be able to use the generic matlab netcdf API
172    o pkg/ctrl: require a specific set of control variables and exf-flags for
173      adjoint of seaice (stop in ctrl_check.F if conditions are not satisfied)
174    o model/src:
175     a) 1rst version of a new driver S/R to turn-off output freq and flags after the
176       1rst forward sweep, to avoid over-writing output files during recomputations
177       recomputations (& grdchk); called from cost_final.F (& ctrl_init_ctrlvar.F ?)
178     b) 2nd version:
179      - add specific pkg S/R for seaice & ptracers (called from S/R TURNOFF_MODEL_IO);
180      - switch-off more output flags (exf_monFreq, chkPtFreq, dumpInitAndLast,
181         writePickupAtEnd) + seaice & ptracers output;
182      - do not switch off MNC flags (otherwise, won't get admonitor netcdf file)
183    o model/src:
184      - new S/R rotate_uv2en_rl (..._rs) that rotates vector fields.
185    o pkg/exch2:
186      - remove "simulationMode" from arg. list of S/R EXCH2_RX1,2_CUBE ;
187      - add argument "signOption" to EXCH2_RX1_CUBE (will be needed for SM exch).
188    o pkg/autodiff & exch2:
189      process exch_uv_agrid_3d_rx.f & exch2_uv_agrid_3d_rx.f through TAF
190      (for now, only if ALLOW_EXCH2 is defined).
191    o pkg/autodiff:
192      - include PACKAGES_CONFIG.h in exch*ad.flow & exch*ad.F
193        (not supposed to be in CPP_OPTIONS.h) to get ALLOW_EXCH2 defined correctly.
194       + clean-up comments (_RS is not always real*4)
195      - fix bug in ADEXCH_UV_3D_RX (without EXCH2, was calling the forward exch S/R)
196      - add a stop in ADEXCH_UV_AGRID_3D_RX if trying to use it with EXCH2:
197        was calling a forward exch2, which is wrong ; used in SEAICE & EXF pkgs.
198    o testreport (AD-tests):
199      no longer link files from dir "../input" (1rst link files from
200      "../input_ad.[xx]" if secondary test "xx" and then from "../input_ad")
201    
202    checkpoint62f (2010/04/29)
203    o model/src/the_main_loop.F:
204      adjust store directives for seaice evp and multicategory according to
205      pkg/ecco/the_main_loop.F
206    o adjoint:
207      global_sum_ad was incomplete (noted many times by many people ;)
208      nice description by Jean U. as follows:
209      * allreduce(var) in global_sum.F can be interpreted as
210        reduce(sum) followed by broadcast of sum.
211      * The adjoint of that is
212        sum(adjoint) followed by broadcast(summed adjoint value)
213        or in other words, allreduce(sum, adjoint vars)
214      We were missing the sum(adjoint)!
215      Benign, except(!) for "global" scalars appearing in tile loops (bi,bj)
216      (noted by J.M. Campin, e.g., in cost_ssh_mean, variable offset).
217      The fix should produce 16-digit accuracy between
218      single-CPU multi-tile (e.g. nSx=2, nPx=1) and
219      multi-CPU single-tile (e.g. nSx=1, nPx-2)
220      We'll probably change this yet again shortly
221    o eesupp/src:
222      - fix global_sum_r4 (wrong from previous modif in Jun 2009; ever used ?)
223    o pkg/icefront
224      - ALLOW_SUBGLACIAL_RUNOFF option adds capability for time-evolving
225        specification of addmass array based on a 2D field, which is added
226        at bottommost wet level at each horizontal location.
227    o model/src:
228     horizontal grid initialisation (other than curvilinear): add code for Exch2 IO
229     layout; (not always compatible with delX,delY setting; commented out for now).
230    o pkg/exch2:
231     change tile to processor setting (case nSy*nPy > 1): allows default model mapping
232     (myX and myYGlobalLow) to be used for simple (1 facet, no blank tile) config.
233    
234    checkpoint62e (2010/04/15)
235    o pkg/obcs:
236      - fix wrong index in OBCS_SPONGE_V for Eastern-OB (reported by David Hebert).
237    o pkg/dic:
238      -fix bug in fe_chem.F for multi-tile (nSx*nSy > 1) set-up;
239        (note: not presently tested in any forward verification exp.)
240       update tutorial_global_oce_biogeo AD output file.
241    o pkg/exf:
242      - account for the variation of albedo as a function of zenith angle
243        by defining ALLOW_ZENITHANGLE in EXF_OPTIONS.h
244  o build_options:  o build_options:
245   - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"   - rename "linux_ia64_ifort+mpi_ice_nas" to "linux_amd64_ifort+mpi_ice_nas"
246  o pkg/dic:  o pkg/dic:

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