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revision 1.1726 by jmc, Tue Aug 28 21:13:08 2012 UTC revision 1.1749 by mlosch, Tue Oct 16 07:08:56 2012 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: add Jacobian-free Newton Krylov solver for ice dynamics
8      (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
9      and SEAICEuseJFNK=.true. A few things to note:
10      - involves a FGMRES, that is parallel but very inefficient,
11        because of many scalar products (global sums) in the Gram-Schmidt
12        orthogonalization method. Needs to be replaced. Original code
13        from J.-F. Lemieux
14      - preconditioner for FGMRES is a stripped down version of LSOR
15      - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
16        preconditioner. For the preconditioner, the default is set to 10.
17      - Jacobian times vector is computed with finite differences
18      - marginally related to JFNK-solver: add a smooth regularization for
19        zeta with tanh that will improve convergence (Lemieux and Tremblay,
20        2009) for any implicit solver (not implemented for EVP because EVP
21        does not need this regularization in the first place). Define
22        SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
23    o eesupp/src:
24      - check in genmake2 that intrinsic S/R flush is available.
25      - add S/R to flush IO unit (if intrinsic S/R flush is available)
26      - flush standard & error msg unit before MPI termination
27      - if debugMode, flush IO unit after printing msg
28    o pkg/ctrl:
29      - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
30        to ctrl_set_unpack_xyz.
31    
32    checkpoint64 (2012/10/09)
33    o pkg/shelfice
34      - in mom_fluxform.F, mom_vecinv.F:
35        CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
36        Bug fix KappaRU -> KappaRV
37        does not change verification/isomip but may change other setups
38        (presumably constant KappaRU=KappaRV)
39      - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
40    o pkg/obcs:
41      - fixed some indexing bugs in obcs_seaice_sponge.F
42      - added obcs relaxation subroutines for HSALT and HSNOW
43      - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
44    o pkg/seaice:
45      - add "multicategory" parameterization for snow in analogy to ice,
46        default is off for now.
47    o pkg/obcs:
48      - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
49        see verification/seaice_obcs/input.seaiceSponge for example application.
50      - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
51        index setting by master-thread. This fix multi-threads Pb in previous modifs.
52    o pkg/layers :
53      - add diagnostics to pkg/layers
54      - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
55        (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
56    o pkg/generic_advdiff/gad_implicit_r.F :
57      - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
58    o pkg/seaice/seaice_growth.F:
59      - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
60    o pkg/obcs:
61      - change default setting of OBCS_UVICE_OLD from defined to undef;
62      - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
63        in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
64      - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
65      - change OB null index value (OB_indexNone) to -99 ; this fix the problem
66        with Southern & Western OB at a tile edge (at least in a simple set-up).
67    o pkg/obcs:
68      - change settings of OB index in case OB coincides with tile edge (shared by
69        2 tiles), so that common OB location is registered by both tiles (instead of
70        only 1). However, for Southern and Western OB, index value = 0 is not
71        recognized as valid OB index (=default null value) and needs to be fixed.
72      - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
73      - new parameter "OB_indexNone" for null index value (for now, still zero)
74        to replace hard-coded null index value of zero.
75    o pkg/exch2:
76      - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
77        always check buffer-size (but outside the loop); move checking for valid
78        index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
79        print each tile and point connection only if |W2_printMsg|>= 2 and 3.
80    o pkg/ctrl (pack & unpack):
81      - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
82        (locally defined) for different variables (+ remove the variable-specific
83        file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
84        (to be extended to other local file names in ctrl.h).
85    o pkg/flt:
86      - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
87    o pkg/mdsio:
88      - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
89    o tools/genmake2:
90      - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
91        (added by Alistair in version 1.51 for building without make depend);
92      - remove Header files list (H_SRC_FILES) from the dependence of targets
93         ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
94        place in version 1.23): this save going through staf when unrelated header
95        file has been modified.
96       Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
97        "make depend" step, still need to do "make links" before "make adtaf".
98    o eesupp/src (+ few pkg src files) & genmake2:
99      - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
100      - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
101      - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
102         upper/lower case ; account for space between "#" and undef/define)
103    o pkg/flt (with exch2):
104      - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
105      - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
106    
107    checkpoint63s (2012/09/05)
108    o pkg/ecco:
109      - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
110      - add more relevant #ifdef ALLOW_SMOOTH ones.
111      - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
112    o pkg/ctrl:
113      - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
114        ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
115      - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
116        doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
117        ctrlSmoothCorrel3D (new).
118        The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
119      - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
120      - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
121        controls when useAtmWind, and vice versa.
122      - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
123      - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
124          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
125      - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
126          #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
127      - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
128        replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
129    o pkg/smooth:
130      - remove un-necessary includes.
131      - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
132        Those CPP options were never defined, and not necessary.
133    o model/src:
134      - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
135      - standard treatment of useSMOOTH.
136    o pkg/autodiff:
137      - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
138        useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
139    o pkg/exch2:
140      - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
141        + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
142      - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
143        and tiles to process mapping.
144      - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
145        moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
146        rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
147        from w2_eeboot.F to w2_readparms.F.
148    o eesupp/src:
149      - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
150        ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
151        also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
152      - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
153        is defined (remove condition on usingMPI) to match cases where MPI_INIT
154        has been called.
155      - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
156      - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
157        (so that on 1 proc, get same myPid independently of usingMPI)
158      - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
159        useCubedSphereExchange with EXCH-1 (safer).
160      - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
161    o pkg/ggl90:
162      - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
163        used in ALLOW_GGL90_SMOOTH code.
164    o pkg/flt:
165      - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
166        floats at the Southern end of the domain).
167    o eesupp/inc:
168      - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
169        but not used (and not to be used) anywhere, just for documentation.
170    o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
171      - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
172        a) can damage previously written records in any other multi-record files.
173        b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
174  o tools/genmake2:  o tools/genmake2:
175    - define variable MAKE within Makefile and use it in place of 'make';    - define variable MAKE within Makefile and use it in place of 'make';
176    - update AD_CONFIG.h (if needed) before building any of the executable    - update AD_CONFIG.h (if needed) before building any of the executable
# Line 11  o tools/genmake2: Line 178  o tools/genmake2:
178      and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;      and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
179    - always print usual warning comment 'this file is automatically generated'    - always print usual warning comment 'this file is automatically generated'
180      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).      from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
181    o pkg/cheapaml:
182      - updated to correspond to the code used in accepted paper (Nico Wienders).
183  o pkg/exf:  o pkg/exf:
184      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.      added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
185      ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)      ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
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