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-revision 1.1714 by jmc,
Mon Aug 13 13:14:49 2012 UTC
+revision 1.1794 by jmc,
Thu Dec 27 20:09:11 2012 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o pkg/cheapaml:
+   - use standard routine (S/R GET_PERIODIC_INTERVAL) to decide when it is time
+     to load new forcing fields.
+   - add missing "_d 0" where it's needed; + some editing (improve indentation).
+   - remove switch to "-r8" compiler option (no longer needed) in verification
+     cheapAML_box, keep same output (small trucation error differences).
+ o verification/offline_exf_seaice:
+   - add thermodynamics only test.
+ o verification/cheapAML_box:
+   - split the domain in 8 (2x4) tiles; add MPI and multi-threaded test;
+     keep same output (same 14 digits for cg2d).
+   - switch on "-r8" compiler option (some numerical values are missing
+     the "_d 0") and update output (only 6 digits for cg2d were preserved).
+ checkpoint64b (2012/12/24)
+ o pkg/cheapaml:
+   - remove un-used variables (Qnet,EmPmR) from pickup files.
+   - store tendency of advected variables into cheapaml pickup file
+     and fix the AB-2 restart.
+ o verification/offline_exf_seaice and lab_sea adjoint:
+   - switch to new code (#undef SEAICE_GROWTH_LEGACY).
+   - switch to 4 time steps in offline, consistent with lab_sea.
+   - match parameters from SEAICE_GROWTH_LEGACY branch in data.seaice.
+   - update results after change of experiment seaice.
+ o pkg/seaice:
+   - remove option SEAICE_MULTICATEGORY; has been replaced with run-time
+     parameter SEAICE_multDim. Issue a warning if SEAICE_MULTICATEGORY is
+     still defined since SEAICE_multDim needs to be set to MULTDIM value (from
+     SEAICE_SIZE.h) to recover previous #define SEAICE_MULTICATEGORY default.
+ o model/src:
+   - add run-time parameter to select CG2D solver minimum-residual solution
+     (in case of a poor convergence).
+ o pkg/seaice/seaice_lsr.F
+   - move calculation of matrix coefficients into new
+     S/R SEAICE_CALC_LSR_COEFFS; for now this routine remains in the same
+     file; the main purpose of this change is to be able to reuse the code
+     in S/R SEAICE_PRECONDITIONER
+   - modify the computation of the residual so that the mass of sea-ice
+     is not used twice; this simplifies the calculations, but since
+     the residual is never used except when LSR_mixIniGuess.ge.4---and this is
+     not tested in testreport---this does not affect the testreport results.
+ o verification/seaice_obcs:
+   - disable SEAICE_GROWTH_LEGACY; reset input files to match those of
+     verification/lab_sea/input.salt_plume; changes results/output.txt*
+ o model/src:
+   - adapt quasi-hydrostatic formulation to work with p or p* coordinate.
+ o pkg/seaice:
+   - improve description of parameters in seaice_fgmres.F and start
+     cleaning up the code
+   - change name of SCALPROD to SEAICE_SCALPROD and modify meaning of
+     second argument
+   - add a metric based on grid cell area to SEAICE_SCALPROD; update
+     results of offline_exf_seaice.dyn_jfnk
+   - compute initial residual norm in seaice_jfnk based on SEAICE_SCALPROD
+ o pkg/aim_v23:
+   - fix an other bug in dissipation heating (grid-cell area was missing).
+ o model/src + pkg/seaice:
+   - add global (multi-tile) linear solver for pair of tri-diagonal system
+     along X and Y lines, respectively for U and V component.
+     Note: 1) MPI and cube-exchange not yet coded.
+) probably not accurate for poorly conditioned / large size problem.
+   - add option for SEAICE_LSR to use global (multi-tile) tri-diagonal solver;
+     default: not compiled and not used.
+ o pkg/seaice:
+   - first attempt at a multi-threaded fgmres solver for the JFNK solver:
+     introduce bi/bj loops and use global_sum_tile_rl instead of
+     mpi_allreduce in seaice_fgmres.F
+   - improve diagnostics output for fgmres solver (seaice_fgmres.F)
+   - replace a few unnecessary goto statements by if-blocks  (seaice_fgmres.F)
+   - add a verification experiment for JFNK in offline_exf_seaice
+ o verification:
+   - change (for now, only fwd test) offline_exf_seaice experiment:
+     use a re-entrant channel with idealized coastline (trapezoidal shape)
+     at southern boundary to explore seaice dynamics and thermodynamics
+     with simple forcing. Main set-up has dynamics+thermo and SST relaxation;
+     secondary test (input.thsice) use thermodynamics only with SST relaxation.
+   - add seaice-dynamics only secondary test using LSR and pkg/thsice advection.
+ o pkg/exf:
+   - disable "sstExtrapol" when Nr=1
+ o verification:
+   - add new experiment "cheapAML_box" (simple 1 layer set-up from Bruno Deremble)
+     to test pkg/cheapaml.
+ o pkg/aim_v23 & pkg/shap_filt:
+   - fix dissipation heating (erroneous gravity multiplication factor).
+ o pkg/seaice:
+   - remove unused field pressPre from jfnk solver
+   - rename two subroutines in seaice_preconditioner.F
+ o eesupp/src:
+    - S/R MDSFINDUNIT avoids reserved unit numbers (scrUnit1, eeDataUnit ...)
+ o pkg/seaice/seaice_preconditioner.F: fix preconditioner once again
+    - remove wrong parts of the rhs and the lhs (were in there
+      because I did not understand the concept of this preconditioner)
+    - add an exchange between u- and v-sweep. This increases communication
+      by a factor of two but improves the convergence of jfnk. Ideally,
+      one would like the u- and v-sweep to be independent. So far within
+      undocumented ifdefs
+    - reorganize the extra computations for printing the residuals
+ o tools/genmake2:
+   - comment out the "mpif.h" include in NetCDF test programm (for MPI built)
+     since it's not necessary (and was preventing to use MNC in some cases).
+ checkpoint64a (2012/11/16)
+ o pkg/autodiff:
+   - improve pkg-internal logical parameter switch (inAd/inFwd mode) so that
+     autodiff_readparms.F no longer depends on calling order (within
+     packages_readparms.F) and no longer requires to include ${PKG}_PARMS.h):
+     rename param turnFreeDriftInAdMode to SEAICEuseFREEDRIFTswitchInAd
+     and change param SEAICEuseDYNAMICSinAdMode to SEAICEuseDYNAMICSswitchInAd.
+ o pkg/obcs:
+   - adding tidal velocity forcing capability to obcs
+     for usage example, see verification/seaice_obcs/input.tides
+ o pkg/seaice:
+   - turn the LSR-relaxation parameters WFAU/V into runtime parameters
+     SEAICE_LSRrelaxU/V
+   - introduce runtime parameter SEAICEetaZmethod (=0 by default)
+ o pkg/aim_v23:
+   - implement heating from friction (bottom friction and stratospheric drag).
+ o pkg/shap_filt:
+   - fix diagnostic "SHAP_dKE" (was 2 time smaller); implement heating from
+     dissipation but only for Shap_funct=2, active when addFrictionHeating=T.
+ o model/src:
+   - move AddMass common block from DYNVARS.h to FFIELDS.h; allow to read-in
+     time-constant addMass field from file (addMassFile);
+   - support for heating due to friction (and Kinetic Energy dissipation):
+     add option, run-time switch and 3-D field array + support code ; each pkg
+     or S/R can add heating contribution (if there is a sink of KE); the sum is
+     accounted for as a Temperature tendency term (EXTERNAL_FORCING_T).
+ o pkg/seaice:
+   - complete merge of ITD code into seaice_growth.F
+     from MITgcm_contrib/torge/itd/code/
+     no verification so far, but Torge Martin tested
+     "1-D test case and Beaufort set up;
+     deliver okay results after 1 model year."
+   - complete merge of SEAICE_SIZE.h into all relevant routines
+   - move computation of eta at Z-points into calc_viscosities
+     + introduce global field etaZ
+     + add different methods for computing etaZ, for now the old
+       method (simple averages of eta to Z-points) is hardwired
+     + replace etaMeanZ by etaZ in seaice_lsr, seaice_calc_residual,
+       seaice_preconditioner
+   - simplify computations for SEAICE_ZETA_SMOOTHREG
+   - seaice_preconditioner:
+     + replace one remaining press by pressLoc (mistake)
+     + adjust printing of residuals
+   - improve I/O of diagnostics of JFNK in seaice_jfnk.F:
+     + add (SEAICE.h) and rename some counters (initiliased in
+       seaice_init_fixed.F)
+     + add _BEGIN/END_MASTER (myThid)  around print statements
+     + print total number of iterations and failures over SEAICE_monFreq
+       interval to STDOUT
+   - move control over output-messages by fgmres to seaice_jfnk to save
+     some operations
+   - move resetting initial guess for fgmres outside of seaice_fgmres_driver
+     in order to make restarts with sol .ne. zero (fgmres with restarts)
+     (seaice_jfnk.F, seaice_fgmres.F)
+   - seaice_calc_l/rhs.F: replace maskW/S by maskInW/S; this fixes
+     a serious convergence problem when open boundaries are involved
+ o pkg/ggl90: fix computation of control volumes for the case of
+   ALLOW_GGL90_HORIZDIFF (probably not used very often): move control volumes
+   up half a grid cell from C-centered to W-centered (pointed out by C. Eden)
+ o pkg/seaice: simplify seaice_evp by avoiding use of extra fields u/vIceC
+ o pkg/autodiff
+   - Add inAdMode switch for SEAICEuseDYNAMICS:
+     SEAICEuseDYNAMICSinAdMode
+     (extend logic in ADAUTODIFF_INADMODE_SET)
+ o pkg/seaice
+   - Step 1 of merging ice-thickness distribution (ITD) code from
+     MITgcm_contrib/torge/itd/ (author: Torge Martin)
+     The code implements concept laid out in Thorndike et al. (1975);
+     code is enabled via CPP flag SEAICE_ITD
+     nITD (in SEAICE_SIZE.h) defines number of ice thickness categories;
+     code is not complete yet!!
+   - SEAICE_SIZE.h now included in almost all seaice routines
+ o verification (using seaice):
+   - switch back seaice-dynamics (+ lower SOLV_MAX_ITERS) in ADM exp.
+     global_ocean.cs32x15.seaice ; update results.
+   - compile B-grid dynamics in FW test exp 1D_ocean_ice_column ;
+   - compile C-grid dynamics with #define SEAICE_ALLOW_JFNK in FW test exp
+     offline_exf_seaice (previously compiling B-grid).
+ o pkg/exf:
+   - fix some STOP conditions in exf_check.F (from Aug 28, modifs did not allow
+     to specify neither just 1 comp of wind or wind-stress, nor no surface momentum
+     forcing): just replace CPP option ALLOW_ATM_WIND with run-time param useAtmWind.
+ o pkg/layers (adjust changes from Sept 19):
+   - do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F)
+     this allows to remove "layers_maxNum" dimension from all layers arrays.
+ o pkg/layers (adjust changes from Sept 19):
+   - remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ;
+   - snap-shot extended to all type of layers (not just the 1rst type);
+   - remove layers variables when corresponding CPP option is undef.
+ o pkg/layers:
+   - rename pkg/layers variable and add new output (layer exist & un-weighted
+     velocity in layer)
+ o pkg/seaice:
+   - simplify (?) ocean-drag coefficent computations by using
+     the same routine in all three solvers (saves some code lines)
+   - remove global fields DRAGA and DRAGS from C-grid code and
+     declare them locally in lsr.F (the only place where they are
+     still used)
+   - update AD output of lab_sea.evp (very sensitive anyway).
+ o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics
+   (Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK
+   and SEAICEuseJFNK=.true. A few things to note:
+   - involves a FGMRES, that is parallel but very inefficient,
+     because of many scalar products (global sums) in the Gram-Schmidt
+     orthogonalization method. Needs to be replaced. Original code
+     from J.-F. Lemieux
+   - preconditioner for FGMRES is a stripped down version of LSOR
+   - SOLV_MAX_ITERS is now used for LSOR as a solver and as a
+     preconditioner. For the preconditioner, the default is set to 10.
+   - Jacobian times vector is computed with finite differences
+   - marginally related to JFNK-solver: add a smooth regularization for
+     zeta with tanh that will improve convergence (Lemieux and Tremblay,
+) for any implicit solver (not implemented for EVP because EVP
+     does not need this regularization in the first place). Define
+     SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use.
+ o eesupp/src:
+   - check in genmake2 that intrinsic S/R flush is available.
+   - add S/R to flush IO unit (if intrinsic S/R flush is available)
+   - flush standard & error msg unit before MPI termination
+   - if debugMode, flush IO unit after printing msg
+ o pkg/ctrl:
+   - ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call
+     to ctrl_set_unpack_xyz.
+ checkpoint64 (2012/10/09)
+ o pkg/shelfice
+   - in mom_fluxform.F, mom_vecinv.F:
+     CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid)
+     Bug fix KappaRU -> KappaRV
+     does not change verification/isomip but may change other setups
+     (presumably constant KappaRU=KappaRV)
+   - fix diagnostics SHIU/Vdrag (thanks to Tom Millgate)
+ o pkg/obcs:
+   - fixed some indexing bugs in obcs_seaice_sponge.F
+   - added obcs relaxation subroutines for HSALT and HSNOW
+   - changes verification/seaice_obcs/results/obcs_seaice_sponge.F
+ o pkg/seaice:
+   - add "multicategory" parameterization for snow in analogy to ice,
+     default is off for now.
+ o pkg/obcs:
+   - added obcs_seaice_sponge.F for obcs relaxation of seaice variables;
+     see verification/seaice_obcs/input.seaiceSponge for example application.
+   - remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB
+     index setting by master-thread. This fix multi-threads Pb in previous modifs.
+ o pkg/layers :
+   - add diagnostics to pkg/layers
+   - move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F
+     (from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly.
+ o pkg/generic_advdiff/gad_implicit_r.F :
+   - fix ADVr diagnostics in case of both implicit vertical advection and diffusion.
+ o pkg/seaice/seaice_growth.F:
+   - fix SItflux diagnostics in virtual salt flux + balanceEmpmr case.
+ o pkg/obcs:
+   - change default setting of OBCS_UVICE_OLD from defined to undef;
+   - use new parameter OB_indexNone for null index value (instead of hard-coded 0)
+     in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F;
+   - pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z;
+   - change OB null index value (OB_indexNone) to -99 ; this fix the problem
+     with Southern & Western OB at a tile edge (at least in a simple set-up).
+ o pkg/obcs:
+   - change settings of OB index in case OB coincides with tile edge (shared by
+tiles), so that common OB location is registered by both tiles (instead of
+     only 1). However, for Southern and Western OB, index value = 0 is not
+     recognized as valid OB index (=default null value) and needs to be fixed.
+   - modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting)
+   - new parameter "OB_indexNone" for null index value (for now, still zero)
+     to replace hard-coded null index value of zero.
+ o pkg/exch2:
+   - improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON:
+     always check buffer-size (but outside the loop); move checking for valid
+     index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON,
+     print each tile and point connection only if |W2_printMsg|>= 2 and 3.
+ o pkg/ctrl (pack & unpack):
+   - in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable
+     (locally defined) for different variables (+ remove the variable-specific
+     file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL
+     (to be extended to other local file names in ctrl.h).
+ o pkg/flt:
+   - add a FLT_Iter0 option (similar to PTRACERS_Iter0).
+ o pkg/mdsio:
+   - fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing
+ o tools/genmake2:
+   - add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE
+     (added by Alistair in version 1.51 for building without make depend);
+   - remove Header files list (H_SRC_FILES) from the dependence of targets
+      ad_input_code.f & ftl_input_code.f (not clear why it was added in the first
+     place in version 1.23): this save going through staf when unrelated header
+     file has been modified.
+    Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without
+     "make depend" step, still need to do "make links" before "make adtaf".
+ o eesupp/src (+ few pkg src files) & genmake2:
+   - finish to remove ALWAYS_USE_MPI in source code that TAF does not see;
+   - no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2).
+   - improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish
+      upper/lower case ; account for space between "#" and undef/define)
+ o pkg/flt (with exch2):
+   - cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F;
+   - simplify threads synchronisation; fix (many issues) multi-threaded with MPI.
+ checkpoint63s (2012/09/05)
+ o pkg/ecco:
+   - remove #ifdef ALLOW_SMOOTH_CORREL3D brackets.
+   - add more relevant #ifdef ALLOW_SMOOTH ones.
+   - sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D.
+ o pkg/ctrl:
+   - CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D,
+     ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D.
+   - ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag,
+     doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and
+     ctrlSmoothCorrel3D (new).
+     The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP.
+   - ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist.
+   - ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress
+     controls when useAtmWind, and vice versa.
+   - ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers.
+   - ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with
+       #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH.
+   - ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with
+       #ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH.
+   - ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F:
+     replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D.
+ o pkg/smooth:
+   - remove un-necessary includes.
+   - remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets.
+     Those CPP options were never defined, and not necessary.
+ o model/src:
+   - fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi).
+   - standard treatment of useSMOOTH.
+ o pkg/autodiff:
+   - add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode,
+     useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint.
+ o pkg/exch2:
+   - add "if usingMPI" where it was missing (in exch2_rx?_cube*.template)
+     + start to remove ALWAYS_USE_MPI in source code that TAF does not see.
+   - make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag
+     and tiles to process mapping.
+   - re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h)
+     moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h;
+     rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX
+     from w2_eeboot.F to w2_readparms.F.
+ o eesupp/src:
+   - set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of
+     ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F;
+     also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F
+   - in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI
+     is defined (remove condition on usingMPI) to match cases where MPI_INIT
+     has been called.
+   - fix bug I put in previous modif of exch_sm_3d_rx.template (not much used);
+   - change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings
+     (so that on 1 proc, get same myPid independently of usingMPI)
+   - add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and
+     useCubedSphereExchange with EXCH-1 (safer).
+   - add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI).
+ o pkg/ggl90:
+   - fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call)
+     used in ALLOW_GGL90_SMOOTH code.
+ o pkg/flt:
+   - fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping
+     floats at the Southern end of the domain).
+ o eesupp/inc:
+   - add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h);
+     but not used (and not to be used) anywhere, just for documentation.
+ o pkg/autodiff, exf, ptracers & seaice (AD & TL output):
+   - comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since:
+     a) can damage previously written records in any other multi-record files.
+     b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S.
+ o tools/genmake2:
+   - define variable MAKE within Makefile and use it in place of 'make';
+   - update AD_CONFIG.h (if needed) before building any of the executable
+     (forward, adjoint or tangent-lin); this involves a 2nd invocation of make;
+     and add the usual #ifndef/#define AD_CONFIG_H in AD_CONFIG.h;
+   - always print usual warning comment 'this file is automatically generated'
+     from script convert_cpp_cmd2defines (+ remove this warning from genmake2).
+ o pkg/cheapaml:
+   - updated to correspond to the code used in accepted paper (Nico Wienders).
+ o pkg/exf:
+     added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch.
+     ALLOW_ATM_WIND now just sets the useAtmWind default (see exf_readparms.F)
+     and force defines ALLOW_BULKFORMULAE (EXF_OPTIONS.h).
+ o pkg/exf, autodiff, ctrl, ecco and seaice:
+     remove ALLOW_ATM_WIND brackets, or replace them with useAtmWind ones.
+ o pkg/ctrl, ecco:
+     allow to compile both ALLOW_U/VSTRESS_CONTROL and ALLOW_U/VWIND_CONTROL.
+     Depending on useAtmWind, one is inactive, and the other is active (see
+     exf_getffields.F/exf_getsurfacefluxes.F).
+ o tools/genmake2:
+   - improve error msg when failing in 2nd test of check_for_broken_Ff
+   - fix option '-makefile' short-name (-mf according to genmake2 -help)
+   - source local config file "genmake_local" just after processing the genmake2
+     command arguments (previously done before processing arg).
+ o pkg/grdchk:
+   - add a call to TURNOFF_MODEL_IO for Tangent-Linear run (in this case, call
+     to this routine from cost_final has been dropped in g_cost_final)
+   - improve printed information (more explicit msg, no longer using "print *,"
+      fix fcpertminus printed value).
+ o model/src:
+   - move call to COST_INIT_VARIA out of packages_init_variables.F directly
+     into initialise_varia.F (just after calling PACKAGES_INIT_VARIABLES):
+     this prevents getting cost-funct reset in adinitialise_varia recomputations.
+ o pkg/dic:
+   - move initialisation of "freefe" array from from dic_biotic_forcing.F to
+     fe_chem.F: this prevents TAF from dropping this initialisation in TLM code.
+ o pkg/grdchk:
+   - grdchk_main.F : added CALL GLOBAL_SUM_INT( ierr , myThid )
+   - grdchk_getadxx.F etc. : omit I/O if ierr.EQ.0
+ o pkg/autodiff/ctrl/grdchk :
+   - attempt to sort out what works and what does not,
+     with regard to I/O, and to warn/stop accordingly.
+ o pkg/grdchk:
+   - attempt to fix grdchk in the case of useSingleCpuIO.
+   - "if ( myProcId .EQ. grdchkwhichproc .AND. ierr .EQ. 0 )"
+    statements were moved from grdchk_main.F and into
+    grdchk_getadxx.F grdchk_getxx.F grdchk_setxx.F.
+   - a global sum is applied to record numbers icvrec/layer
+    out of grdchk_loc so that they be passed to I/O routines.
+ o pkg/smooth:
+   - fix recomputation that appeared with nlfs : use smooth_recip_hFacC,
+     smooth_hFacW, smooth_hFacS (copied at init_fixed) in 3d case.
+ o verification/testreport:
+   - add option '-tlm' for Tangent-Linear test (-adm,-oad,-tlm are all exclusive);
+   - can also use compressed (gzip) reference output file;
+   - change format (in pkg/grdchk) of TLM output (+ add forward gradient)
+     to be easier to collect by testreport.
+   - update existing TLM output (half out-of-date by more than 3 yrs).
+   - report NETCDF & LAPACK settings (from genmake2) in output dir.
+   - report run-time in each individual summary (previously only for AD test);
+     for TLM test, add also TAF version.
+   - add daily TLM test on (old) aces cluster + weekly test on baudelaire.
+ checkpoint63r (2012/08/15)
+ o tools/genmake2:
+   - fix Makefile for target ftlall (+ update files to clean after make ftlall)
+ o pkg/ecco/ecco_cost_final.F :
+   - fix fc print statements (to stdout and costfunction0000) so
+     that the printed value is always after the global sum.
+ o pkg/seaice/seaice_dynsolver.F :
+   - fix ice strength assymptote at SEAICE_area_max<1
+     (no change for the standard case of SEAICE_area_max=1)
  o some cleaning:
    - pkg source files: ensure that all *.F files from each pkg included the
      corresponding ${PKG}_OPTIONS.h file (except stand-alone src file which
      only includes CPP_EEOPTIONS.h); fix S/R CTRL_SMOOTH ; update AD experiment
      code_ad/*.F src files; add new option-file in pkg/admtlm + corresponding
      includes;
    - model/src: add PACKAGES_CONFIG.h wherever ALLOW_AUTODIFF[_TAMC] is used.
    - ALLOW_DIFFKR_CONTROL: add a stop in S/R CTRL_CHECK in case ALLOW_3D_DIFFKR
      is undef; also define /DYNVARS_DIFFKR/ common block in DYNVARS.h when
      ALLOW_DIFFKR_CONTROL is defined, to allow to compile and reach this stop.
    - update option-file CPP_OPTIONS.h of all AD experiments:
      * no longer include PACKAGES_CONFIG.h ;
      * includes ECCO_CPPOPTIONS.h if PACKAGES_CONFIG.h has been included ;
      * def/undef ALLOW_3D_DIFFKR independently of ALLOW_DIFFKR_CONTROL (before
        including ECCO_CPPOPTIONS.h).
  o pkg/cost, pkg/ctrl, pkg/ecco option-file:
    - clean-up and split content of old pkg/ecco/ECCO_CPPOPTIONS.h file into

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