/[MITgcm]/MITgcm/doc/tag-index
ViewVC logotype

Diff of /MITgcm/doc/tag-index

Parent Directory Parent Directory | Revision Log Revision Log | View Revision Graph Revision Graph | View Patch Patch

revision 1.1901 by jmc, Thu Jul 25 01:12:45 2013 UTC revision 1.1953 by jmc, Fri Jan 3 17:28:19 2014 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o tools/adjoint_options:
8      - switch to fastopt.net TAF server (instead of default fastopt.de) for
9        AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default).
10    o model/src:
11      - remove some unnecessary TAF storage directives in forward_step.F and
12        in dynamics.F (note: not always removed by TAF, e.g., double storage
13        of kappaRU,kappaRV in former version of dynamics.F).
14    o model/src & pkg/ptracers:
15      - call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F
16        salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F)
17        and remove ptracers_dwnslp_apply.F & ptracers_implicit.F
18      - call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F)
19      - add fZon & fMer as output argument of S/R GAD_CALC_RHS.
20      - update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad).
21    o useSingleCpuInput separates single-CPU input from single-CPU output;
22        for now only implemented for in exf_interp_read.F
23    o verification/advect_xy:
24      - fix missing EXCH call in local version of ini_salt.F and update output.
25    o momentum diagnostics:
26      - fix which deltaT is used in Total-Tendency diagnostics.
27      - fix typo in diagnostics for momentum tendency from AB.
28    o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the
29        SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8
30    
31    checkpoint64r (2013/12/08)
32    o verification/*/results:
33      - Update reference output of experiments that were passing with just 13 digits
34         (make it easier to detect future changes in results)
35    o model/src & pkg/ptracers:
36      - move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to
37        inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F
38        to inside ptracers_integrate.F ; remove ptracers_advection.F
39    o coupling interface pkgs:
40        [atm_compon_interf, ocn_compon_interf & atm_ocn_coupler]
41      - change the config check to test the agreement of Ocean Depth
42        with ATM land/sea mask (instead of ATM orography);
43      - send to coupler the number of coupler time-steps to do for this run:
44        this allows to check for consistency and don't need anymore to be
45        specified in parameter file "data";
46      in coupler:
47      - check consistency of RunOff map versus Ocean Depth and ATM land/sea mask.
48      - improve report to log-file of config setting (pass log-file unit to few S/R)
49    o pkg/compon_communic:
50      - add coupling send/receive for non-tiled integer vector;
51      - add S/R to check and stop if any proc has an error (similar to
52        eesupp/src/stop_if_error.F but single thread and across Comm_World).
53    o pkg/exch2:
54      - in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search
55        through list of all tiles my proc owns.
56    o model/src:
57      - AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying
58        from rTrans) to simplify dependencies (no need to store rTrans anymore in
59        calling S/R); this affects AD results at machine truncation level:
60        update AD-output (TAF) of experiments: 1D_ocean_ice_column,
61        bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad).
62    o tools/build_options:
63      - simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran
64    o coupling interface pkgs:
65        [compon_communic, atm_compon_interf & ocn_compon_interf]
66      - move declaration of local array "ibuf" out of header file "CPLR_SIG.h"
67        to each S/R that needs it; remove un-used variables.
68      - change component tile registration (cpl_register.F in both compon_interf
69        and mitcomponent_tile_register.F) to pass the full list of tiles
70        information (including bi,bj) in 1 vector (instead of in a bi,bj matrix).
71      - with pkg/exch2: adopt the same convention used for I/O to define mapping
72        towards coupler global array (unless W2_useE2ioLayOut=F):
73         a) can now use different tiling between atm & ocn comp.
74         b) no needs to modify the run-Off map when changing tiling (was needed
75            even if using the same tiling between atm & ocn).
76         c) will allow to run with blank-tiles in 1 component (e.g., for ocean
77            full land tiles); not yet tested.
78      - check for valid mapping from comp. tile to coupler global array
79      - improve report of tile registration results to log file.
80    o pkg/exch2:
81      - in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler
82        tile-registration (CPL_REGISTER);
83      - activate (un-comment) definition and setting of "W2_tileIndex" list to
84        store the local bi,bj indices of each tile;
85      - also print bi,bj in local report to log file;
86      - fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from
87        Jun 2009 modif of pkg/exch2).
88    o testing on baudelaire:
89      - run 2 tests at a time: no significant slow down (since enough cpu) and
90        get the full set of test done earlier
91      - switch the ifort test to "-devel" ; run the OpenAD test everyday.
92    o model/src/thermodynamics.F and routines called from it:
93      - pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F &
94        gmredi_calc_wflow.F) to update eulerian velocity (input) into residual
95        velocity (outp) by adding bolus velocity.
96      - model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute
97        mass transport from velocity + lateral grid cell area
98      - rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER)
99      - rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER)
100     in thermodynamics.F
101      - remove k from thermodynamics.F and move it to temp_integrate.F
102        salt_integrate.F and ptracers_integrate.F (now done inside the tracer
103        loop).
104      - compute locally (in thermodynamics.F) 3-D velocity field that is used to
105        advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT,
106        PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE,
107        GAD_IMPLICIT_R and PTRACERS_IMPLICIT
108      - update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column,
109        global_ocean.90x40x15, tutorial_global_oce_biogeo and
110        tutorial_tracer_adjsens (+ TLM output).
111    o tools/OAD_support and (verification/*/) code_oad:
112      - OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to
113        module conversion ; remove unneeded CPP_EEOPTIONS.h.
114      - code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard
115        version (closer to model/inc/CPP_OPTIONS.h).
116    o model/src:
117      - remove parameter "useOldFreezing" from PARAMS.h and push it to the
118        retired list of parameters (routine FREEZE has been replace by surface
119        freezing (10.yrs ago) and by pkg/frazil (interior freezing).
120    o pkg/gmredi:
121      - add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from
122        velocity (same scheme but affects machine truncation) for GM_AdvForm.
123      - update output of FWD experiments: front_relax.bvp,
124        global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce.
125    
126    checkpoint64q (2013/11/17)
127    o verification:
128      - generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments
129        tutorial_global_oce_biogeo and global_ocean.90x40x15.
130      - generate new output (growth & melt) for seaice_itd experiment after
131        updating the input pickup_seaice files (previously wrong).
132    o pkg/cost:
133      - define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL
134        (instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads:
135        o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL
136          cannot be applied to var in common block).
137        o allows to get results independent of tile-per-proc setting (if using
138          slower GLOBAL_SUM_SEND_RECV option).
139      - update accordingly: seaice_cost_final.F, shelfice_cost_final.F,
140        thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea
141        forward gradients: update output).
142      - update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL
143        S/R and, for most exp., also comment out GLOBAL_SUM_R8.
144    o pkg/mom_common:
145      - move to pkg/mom_common and model/src (previously in tutorial_deep_convection
146        code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and
147        viscosity are locally declared in dynmics.F and pass as argument to CALC_GW;
148        ensure that all field value that are used are set.
149    o tutorial_deep_convection (smag3d):
150      - add missing scaling in mom_calc_smag_3d.F;
151      - set smag3D_coeff in input.smag3d such that results do not change.
152    o pkg/dic:
153      - change dic_cost.F to compute cost on each tile first and then apply
154        GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments
155        tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output.
156      - remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea.
157    o eesupp/src & pkg/mdsio:
158      - remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F
159        (from pkg/mdsio) since they are no longer used for tape IO.
160      - move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src
161        (+ keep a copy in pkg/atm_ocn_coupler).
162    o verification/isomip:
163      - split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests.
164    o tools/build_options:
165      - optfile linux_amd64_ifort11, fast (no ieee) case:
166        to get a working restart for all experiments, add "-fp-model source"
167        to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default).
168    
169    checkpoint64p (2013/10/20)
170    o pkg/autodiff:
171      - adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO
172        criteria, return to simple (default) tape IO format.
173    o pkg/mdsio (+ eesupp/src):
174      - rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace
175        previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8);
176      - fix globalFile and singleCpuIO options using simpler global mapping.
177      - new pairs of scatter/gather vector S/R (one for each type, generated from
178        template) corresponding to simpler global mapping.
179      - adread_write.F: switch to new S/R (but leave old calls commented) and write
180        to globalFile when parameter globalFiles is set to True.
181      - switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip.
182    o pkg/autodiff:
183      - adread_adwrite.F: add a hack for RS arrays (when RS=real*4);
184        with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is
185        missing, just add a STOP if array type do not match.
186    o pkg/exf:
187      - to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice:
188         rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION
189         and rename array obsSIce to exf_iceFraction.
190    o tutorial_deep_convection:
191      - add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe),
192        for now all in this exp. code dir.
193      - add secondary test using Smag-3D viscosity (keep very low backgroud visc for
194        testing) and flux-limter advection scheme for Temp. (no explicit diffusion).
195    o eesupp/src:
196      - added SINGLE_DISK_IO option because reading of parameter files on
197        very large number of processors did not work with existing set-up
198    
199    checkpoint64o (2013/09/25)
200    o pkg/atm_phys & atm_compon_interf:
201      - allows for coupling of gray-atmosphere (atm_phys) with ocean.
202    o tools/build_options:
203      - switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran
204        & linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also
205        remove CPP setting (was identical to genmake2 default).
206    o pkg/gmredi & model/src: Some updating and work done on the residual model.
207      - created new file model/src/calc_eddy_stress.F to calculate the eddy stress.
208      - fixed up the calculation of the eddy stress and how it is added to the
209        external forcing via taueddy_external_forcing.F
210      - at the moment, it is very experimental and only works with the variable eddy
211        diffusivity calculated in gmredi_k3d.F
212    o pkg/seaice/seaice_check.F: add a check to catch the case of specifying
213        lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice
214    o testreport (& tools/do_tst_2+2):
215      - for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}'
216    o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11:
217      - remove CPP='cpp -traditional -P' (this is genmake2 default)
218      - add switch (for big setups) to use 'medium' memory-model (but leave it
219        commented out for now). Note: needed with FC 19 to compile big setups.
220    o pkg/atm_compon_interf:
221      - regroup per field origin (model & pkgs) the coupling storage routines
222         (which accumalate in time each coupling field)
223      - move bi,bj loops inside atm_store_my_data.F and store also wind-stress;
224        update accordingly + simplify aim_do_physics.F
225    
226    checkpoint64n (2013/08/26)
227    o pkg/bbl:
228      - update formulation to reduce dispersion of tracer properties in bbl
229      - replaced horizontal and vertical transport parameters with velocities
230      - changes results for verification/global_with_exf.yearly
231    o verification/halfpipe_streamice:
232      - change to matrix construction; update both Fwd & AD output.
233    o verification/tutorial_tracer_adjsens:
234      - OpenAD test: switch to vector-invariant momentum since fluxform with
235        rStar causes problems with OpenAD; update output.
236    o tools:
237      - genmake2: define a common prefix for all temp-file names ; move them
238        to local /tmp disk (but would be easy to move them back);
239      - xmakedepend: apply the same switch for temp-files.
240    o pkg/offline:
241      - changes for use with rStar (NLFS): assume that we continue to provide
242        UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid
243        output files) and apply r* scaling at each time-step (function of the time
244        varying Eta field); use normal pickup files (needed for restart with NLFS).
245    o adjoint with OpenAD:
246      - move OpenAD-specific files from verification/OpenAD/code_oad_all to a new
247        package openad.  This package has to be compiled for all runs with OpenAD
248        instead of specifying code_oad_all as a modification directory.
249      - link the fortran templates from tools/OAD_support to the build directory
250        for preprocessing to avoid conflicts between different setups compiled
251        simultaneously and simplify cleanup.
252    o pkg/exf:
253      - in exf_getforcing.F: comment out most of the EXCH calls (fields used by
254        main model or other pkgs are exchanged in EXF_MAPFIELDS).
255    o model/src:
256      - do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline
257        (similar to do_fields_blocking_exchanges.F).
258    o tools/genmake2:
259      - remove TAF output src code just before calling staf (when not doing a fresh
260        built, will stop if things go wrong with staf).
261      - fix target "adobj" (left from TAF version-2 transition)
262    o pkg/diagnostics:
263      - add a parameter to track the status of pkg/diagnostics activation;
264        this replace/extend the use of logical param "settingDiags" (to check
265        when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call.
266        New S/R to print error message and stop when pkgStatus is not right.
267      - to try: add a warning when "data.diagnostics" exist but useDiagnostics=F.
268    
269    checkpoint64m (2013/08/13)
270    o model/inc:
271      - move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from
272        8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h)
273    o pkg/kpp & aim_v23:
274      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
275    o pkg/seaice:
276      - restore (last time on 2011/12/24) ability to compile pkg/seaice with
277        undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options.
278      - only call DIAGNOSTICS_FILL when useDiagnostics=TRUE.
279    o eesupp/src:
280      - fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH)
281        in exch1_rx[_ad].template (thanks to Francois Lefeuvre report).
282    o switch to TAF version-2:
283      - add flow directives to "freeze" naming convention for ad-routines that
284        are used in I/O routines of adjoint state and associated common blocks
285        that are used in adcommon.h (backward compatible with version-1)
286      - update all ad-optfiles (in tools/adjoint_options + few local to some
287        verification exp) to switch to latest TAF version (currently 2.5.5);
288        merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented
289        out except for diva).
290      - the major change with TAF version-2 is that both the differentiated
291        routines and the forward routines (new) are returned as part of the TAF
292        output source code. Update genmake2 accordingly.
293      - new output for AD experiment tutorial_global_oce_biogeo (better AD gradient
294        with version-2 when compared to TLM or FWD gradient); other experiments
295        output show minor changes (machine truncation level); update the few AD &
296        TLM output with 12 matching digits only (some prior to version-2 switch).
297    
298    checkpoint64l (2013/08/05)
299    o model/src:
300      - in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F
301      - main_do_loop.F: no longer includes additional (AUTODIFF) header files
302        when using TAF but only if using OpenAD.
303    o pkg/mom_common+fluxform+vecinv:
304      - always set horiz. viscosity arrays to background value before calling
305        MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC
306        only when using variable horiz. viscosity (useVariableVisc=T);
307      - simplify mom_vecinv.F (only 1 block for momViscosity).
308    o pkg/mom_common: variable horiz. viscosity in NH code
309      - move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F)
310        from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h
311      - store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc,
312        useBiharmonicVisc & useVariableVisc.
313      - fix old bug (already in 1rst implementation of variable horizontal viscosity
314        in calc_gw.F, version 1.27, 2006/06/20):
315        horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0
316        even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero.
317      - change background horiz viscosity in vertical momentum (gW) to always be
318        viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using
319        any type of variable viscosity, e.g., viscAh/4Grid)
320      - change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of
321        viscAh,viscA4) which default to viscAh,viscA4 :  this avoid missing
322        horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since
323        default viscAh,viscA4 is zero).
324    o model/src:
325      - extend length of drC & recip_drC from Nr to Nr+1.
326  o Divided Adjoint (DIVA) with MPI:  o Divided Adjoint (DIVA) with MPI:
327    - genmake2: do not create local ./mpi_headers dir when no file to copy into.    - genmake2: do not create local ./mpi_headers dir when no file to copy into.
328    - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT    - remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT

Legend:
Removed from v.1.1901  
changed lines
  Added in v.1.1953

  ViewVC Help
Powered by ViewVC 1.1.22