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revision 1.1489 by dimitri, Sun Aug 7 07:08:14 2011 UTC revision 1.1541 by mlosch, Fri Dec 2 15:29:07 2011 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/obcs (Stevens BCs):
8      - fix various problems in the phase speed computations of the Stevens
9        boundary conditions:
10        - sign error for western and southern boundaries,
11        - time tendencies were underestimated by factor of dTracerLev and some just
12          zero (for multidim advection schemes) -> now estimate time tendencies
13          from difference between previous (n) time level and the one before (n-1);
14          this requires storing a field per tracer per boundary, also in the pickup
15          files.
16        - replace deltaTmom in cflMer/Zon computation with dTracerLev
17        - set default phase velocity to cflMer/Zon
18      - update verification experiment exp4.stevens
19    o pkg/generic_advdiff (implicit_r):
20      - fix implicit vertical advection conservation with AB and/or NonLin-FreeSurf
21        (remove Tr*d/dz(w) in gad_implicit_r.F and add it in gad_calc_rhs.F);
22      - fix implicit vertical diffusion or advection with NonLin FreeSurf
23        (was using current recip_hFacC instead of future recip_hFacC): set future
24        recip_hFac in thermodynamics.F and pass & use it in all vertical implicit
25        solver S/R ;
26      - fill diagnostics of vertical advective fluxes (computed from tendency)
27        when using implicit vert. advection;
28      - update output of exp that uses NonLin-FreeSurf & implicit vertical diffusion:
29         global_ocean.90x40x15 (fwd+AD), global_ocean.cs32x15 (4 fwd +4 AD),
30         tutorial_global_oce_in_p (fwd), tutorial_tracer_adjsens (AD)
31         and cpl_aim+ocn (used in ocean); to be fixed: bottom_ctrl_5x5.
32    o pkg/diagnostics:
33      - add diags for T & S tendency which goes through Adams-Bashforth.
34    
35    checkpoint63f (2011/11/30)
36    o pkg/obcs/obcs_calc_stevens.F:
37      - join some loops to reduce number of if-statements
38      - fix a bug in code for northern and southern boundaries.
39    o pkg/seaice/seaice_init_varia.F
40      - undo resetting UVM=0 that has slipped in unnoticed in r1.49 and
41        caused zero ice-velocities for the B-grid code
42    o pkg/seaice/seaice_init_fixed.F
43      - fix a bug in the initialisation of the second metric terms
44        k2AtC and k2AtZ: k2AtC was set to the value of k2AtZ and k2AtZ was 0.
45      - this affects all seaice configurations with useCurviLinearGrid = .true.
46        and SEAICEuseDynamics = .true. (default) and SEAICEuseMetricTerms
47        = .true. (default)
48      - the only verification experiment affected is global_ocean.cs32x15:
49        icedyn, seaice, and seaice_dynmix (AD)
50    o pkg/thsice/thsice_diagnostics_state.F
51      - only for TARGET_NEC_SX: initialise all of tmpFld, so that overlap does
52        not contain garbage that can lead to surprises in diagstats_calc.F
53    o model/src:
54      - move bi,bj loops inside INTEGR_CONTINUITY ;
55      - call INTEGR_CONTINUITY directly from forward_step.F
56        (previously called from momentum_correction_step.F)
57      - call UPDATE_ETAH from integr_continuity.F and update initialise_varia.F,
58        forward_step.F and pkg/ecco/the_main_loop.F
59    o model/src/do_oceanic_phys.F:
60      - reset addMass to zero only if useICEFRONT ;
61      - separated k-loop for rhoInSitu calculation ;
62      - add 2 diagnostics for wVel*delta^k(Rho) at constant pressure (= WdRHO_P)
63        and at constant T,S (= WdRHOdP);
64      NOTE: change diagnostics WRHOMASS : this is now simply the Vertical transport
65        of In-Situ Density (Anomaly) (=wVel*rho^bar-k) (previously was Vertical
66        transport of locally-referenced potential density);
67        to recover old diag: (WRHOMASS)_old = (WRHOMASS)_new -1/2 * (WdRHOdP)
68    o gluemnc:
69      - replace ncrcat with ncks when adding variables to *.glob.nc
70      - change the way variables without record dimensions are handled so that
71        files that have variables with and without record variables can be glued:
72        add a record dimension with a new unique name to be able to differentiate
73        between variable with and without a-prior record dimensions. Remove
74        this record dimension before adding the variable to the *.glob.nc file.
75        This procedure automatically works also for grid.*.nc files that do not
76        have any record dimension.
77    o verification/cpl_aim+ocn:
78      - generate new reference output on baudelaire (gfortran, mpich2) (previously
79        from old aces-grid cluster, ao + ifort) and update 'run_cpl_test' script.
80    o pkg/obcs/obcs_calc_stevens.F:
81      - add code for northern and southern boundaries.
82      - reorder some loops to save some operations and so that drFBar can be scalar
83    o model/src:
84      - re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine
85        truncation) and add diagnostics for Adams-Bashforth tendency increment.
86      - update test-exp. AD output:
87        1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl;
88      and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20,
89        front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5),
90        global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4),
91        matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre,
92        tutorial_global_oce_in_p, tutorial_global_oce_latlon and
93        tutorial_plume_on_slope.
94    o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX
95      that vectorises. This code uses 3 extra 2D fields, F90 array assignments
96      and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX
97      does not even come with an F77 compiler anymore, this should not be
98      a limitation
99    
100    checkpoint63e (2011/11/06)
101    o pkg/seaice adjoint of LSR:
102      - substantially rework STORE dirs.
103      - add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED
104        this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields
105        and only perform SOLV_MAX_FIXED adjoint iters.
106        If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration
107        always goes to same record, meaning that the last forward field will be
108        the one used in the adjoint - an approximation.
109      - now produces non-zero LSR-related gradients, and acceptable gradients for
110        An's zonal (x-z) test case (to be checked in)
111      - lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR
112        (but these are screwed up by the thermodynamics in the first place);
113        reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution;
114        output_adm.txt also reflects changes to seaice_lsr
115      - global_ocean.cs32x15:
116        * the "default" input_ad.seaice has been re-defined to always exclude dynamics
117          (output_adm.seaice.txt was updated)
118        * new input_ad.seaice_dynmix tests a forward LSR / backward free-drift
119          (output_adm.seaice_dynmix.txt)
120    o test-exp. exp4+stevens:
121      - switch off pTracers and nonHydrostatic (restart problems with NH); update output
122    o pkg/seaice (lsr solver):
123      - put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only);
124        update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15
125      - fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD)
126      - new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution
127        into initial guess for linearised solver; use weight ~ (1/err)^2,4.
128      - compute (with new S/R) and print initial (+ free-driff sol. if available)
129        and final residual of linearised system.
130    o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity
131      (requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F)
132    o pkg/obcs: Stevens BCs (still only for east and west)
133      - fix Stevens BCs by using intermediate velocities of previous
134        time step as "baroclinic" contribution rather velocity of one grid cell
135        inside the boundaries; more consistent but makes the entire treatment
136        more complicated, requires new pickup files and two new S/Rs:
137        obcs_copy_uv_n and obcs_save_uv_n
138        keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY
139        (undefined by default)
140      - silently move computation of some grid factors into separate loops to
141        save some recomputations
142      - add a hack for non-linear free surface
143      - add a verification experiment to exp4 that tests this code
144    o make gluemnc/xplodemnc work with (moron) non-GNU shell tools
145    
146    checkpoint63d (2011/10/25)
147    o pkg/obcs + seaice-dynamics:
148      - new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before
149        solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB
150        values (consistent with an implicit method).
151      - add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to
152        return to older implementation (same results as before); note that none of
153        the "experimental" OBCS_SEAICE options are implemented in the new version.
154      - switch test exp. seaice_obcs to use new version (update output).
155    o pkg/seaice:
156      - add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS)
157      - add parenthesis in Water-Ice drag calculations (evp & lsr);
158      - in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1;
159        and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice)
160      - update output of test exp lab_sea that uses evp or lsr (fwd+ad)
161        and global_ocean.cs32x15 (icedyn & seaice fwd+ad).
162    o pkg/layers:
163      - Include potential density as new coordinate (Thanks to David Munday)
164    o pkg/dic:
165      - Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add
166        carbonate computation/output to CALC_PCO2_APPROX
167    o pkg/generic_advdiff
168      - make TAF generate code that vectorizes:
169        gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F
170    o model/src:
171      - improve vectorization also for adjoint code of
172        solve_tridiagonal and solve_pentadiagonal. As this requires up to
173        5 new 3D-fields, this code is only turned on for the combination of
174        ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message
175        for singular matrix check (only for TARGET_NEC_SX).
176      - remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to
177        ALLOW_AUTODIFF. This flag now needs to be set outside of
178        solve_tri/pentadiagonal.F
179    o pkg/exf:
180      - fix previous modif in exf_readparms.F (revision 1.66: treatment of
181        optional namelist EXF_NML_OBCS).
182      - add many debug-print (to trace down where pkg/cal error msg comes from)
183    o pkg/mom_vecinv/mom_vi_hdissip.F
184      - rearrange loops so that vectorization is improved and in particular
185        the adjoint routine vectorizes. The code is a little longer now, but I
186        think easier to read.
187        Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested.
188    o pkg/seaice:
189      - allow to specify initial seaice velocity from files (uIceFile,vIceFile)
190    o pkg/exch2:
191      - alternative code (without tile x tile matrix) for cumulated (global) sum;
192        used as default; keep using matrix version in adjustment.cs-32x32x1.
193    o tools/build_options:
194      - after merging some MPI and/or multi-threads specific optfiles so that
195        the modified default optfile support both built (using genmake2 -mpi
196        for the MPI built, using genmake2 -omp for OpenMP built),
197        move now obsolete optfiles to tools/build_options/unsupported/
198       (add copy of email sent to support list in doc/optfiles_changes.txt)
199    
200    checkpoint63c (2011/09/28)
201    o pkg/ebm:
202      - fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of
203        test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d)
204    o pkg/seaice (SItracer pickup)
205    * Simple code for pickup of SItracer fields (#define ALLOW_SITRACER)
206      To be done:
207      - thorough testing of missing fields in S/R seaice_read_pickup
208      - thorough matching between generic tracers and specific fields used
209        (e.g. volume-weighted age, area-weighted age, salinity, ...)
210    o pkg/grdchk:
211      - all procs calculate and print finite-difference gradient (for testreport)
212      - change description output used by testreport;
213      - AD testing: also compare and report Finite-difference gradient;
214        => update all output_adm*.txt
215    o test exp. global_ocean_ebm:
216      - switch back useRealFreshWaterFlux (no problem anymore with run-off);
217        and turn on exactConserve; update (fwd) output.
218    o pkg/seaice (LSR):
219      - print to STDOUT number of solver iterations at SEAICE_monFreq interval.
220      - modify solver to deal cleanly with u/v switch at face edges (CS-grid):
221        * identical results with non-CS topology (but save up to half of EXCH calls)
222        * no much changes in cs-32 verification tests since no ice at face edges
223         (differences due to convergence criteria, since nb of iterations changed)
224        * expect some differences on lat-lon-cap grid.
225        update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice)
226    o pkg/exch2:
227      - add new CPP option to disable Cumul-Sum matrix (to save storage when using
228        many tiles); until alternative coding is added, just add a stop.
229    o pkg/kpp:
230      - move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F
231        to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list).
232    o optfiles:
233      - merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles
234        into corresponding standard one, which now support different build:
235        (when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built)
236      - add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael)
237    o pkg/obcs (seaice):
238      - add missing EXCH for uIce,vIce after applying OBCS;
239      - remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding
240        argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R
241        EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F;
242      - fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared)
243      - verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi
244        and eedata.mth for MPI and mutlti-threaded testing.
245    o pkg/flt:
246      - make FLT EXCH working with multi-threads (and MPI + multi-threads);
247      - use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h;
248      - fix pickup and trajectories + profiles output with multi-threads;
249      - add parameter to select group of fields to write along trajectory and
250        profile (default unchanged);
251      - only call PORT_RAND* function when flt_noise <> 0;
252      - add multi-threaded test for verification exp. flt_example.
253    o eesupp/src:
254      - fix S/R ALL_PROC_DIE for MPI+multi-threads.
255      - USE_OMP_THREADING: check that number of threads (from eedata) matches
256        actual number (from env.var. setting).
257    o pkg/ebm:
258      - fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file.
259      - add multi-threaded test for verification exp. global_ocean_ebm
260    
261    checkpoint63b (2011/08/29)
262    o pkg/ebm:
263      - fix sign of runoff;
264      - update directly forcing fields (Qnet,EmPmR) to use standard
265        external_forcing_surf.F (remove ebm_forcing_surf.F);
266      - avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F);
267      - set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm)
268        and apply relaxation towards corresponding SST field (2-D map or ZonAver).
269      - update global_ocean_ebm parameters file data and update output (fwd+ad).
270    o verification/matrix_example:
271      - split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for
272        MPI and mutlti-threaded testing.
273    o pkg/matrix:
274      - change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ;
275      - fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter);
276      - fix for multi-threaded (remove DATA statement);
277      - use standard DIFFERENT_MULTIPLE function;
278      - add MATRIX_OPTIONS.h
279    o verification/matrix_example:
280       To allow to split the domain in several tiles, change the domain size
281        from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on
282        Western side) of land points.
283    o (*_)write_pickup:
284      - fix few bugs in mypackage_read/write_pickup.F
285      - in MDS_WR_METAFILES calls, replace "myTime" by a local copy into
286        array of length 1 (was caught by compiler syntax-check).
287    o pkg/diagnostics (velocity potential solver):
288      - fix initialisation of main diagonal matrix (for overlap values)
289    o tools/build_options:
290      - towards single optfile for MPI and non-MPI built: merge few +mpi optfile
291        into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11)
292      - linux_amd64_gfortran: merge +mpi_generic version into standard optfile:
293        * move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ;
294        * FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list;
295        and use "-devel" testreport option for standard testing on baudelaire.
296    o pkg/grdchk:
297      - Assume that all gradient-check position are within the same tile
298        corresponding to global indices (iGloTile,jGloTile) and that
299        positions (i,j indices or nbeg) are local to this tile;
300      - set tile local-indices and proc. number according to tile global-indices;
301      - remove grdchkwhichproc from namelist (retired param);
302      - send adjoint gradient to all procs so that all procs print it to STDOUT;
303      - switch on MPI test for global_ocean.90x40x15 AD test experiment.
304  o adding package bbl (Bottom Boundary Layer)  o adding package bbl (Bottom Boundary Layer)
305    description in MITgcm/pkg/bbl/bbl_description.tex    description in MITgcm/pkg/bbl/bbl_description.tex
306    example/test experiment in MITgcm_contrib/bbl    example/test experiment in MITgcm_contrib/bbl
   
307  o adjoint verifications  o adjoint verifications
308    - changed 5 experiments to multi-threaded    - changed 5 experiments to multi-tiles
309      * global_ocean.90x40x15      * global_ocean.90x40x15
310      * obcs_ctrl      * obcs_ctrl
311      * offline_exf_seaice      * offline_exf_seaice
# Line 17  o adjoint verifications Line 313  o adjoint verifications
313      * tutorial_tracer_adjsens      * tutorial_tracer_adjsens
314      changed reference output for those that crossed tile boundaries      changed reference output for those that crossed tile boundaries
315      (changed choices of gradient check positions)      (changed choices of gradient check positions)
316      - with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi)
317    - temporary bug fix in grdchk_loc.F for obcs    - temporary bug fix in grdchk_loc.F for obcs
   
318  o genmake2 & testreport  o genmake2 & testreport
319    - add target "obj" (just for OBJFILES files) to Makefile;    - add target "obj" (just for OBJFILES files) to Makefile;
320    - add option to specify FEXTRAFLAGS on command line.    - add option to specify FEXTRAFLAGS on command line.

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