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Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
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============================== |
============================== |
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o pkg/layers (adjust changes from Sept 19): |
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- do snap-shot output and fill diagnostics from inside iLa loop (layers_calc.F) |
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this allows to remove "layers_maxNum" dimension from all layers arrays. |
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o pkg/layers (adjust changes from Sept 19): |
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- remove ALLOW_LAYERS_OUTPUT ; fix snap-shot and time-ave output ; |
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- snap-shot extended to all type of layers (not just the 1rst type); |
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- remove layers variables when corresponding CPP option is undef. |
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o pkg/layers: |
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- rename pkg/layers variable and add new output (layer exist & un-weighted |
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velocity in layer) |
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o pkg/seaice: |
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- simplify (?) ocean-drag coefficent computations by using |
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the same routine in all three solvers (saves some code lines) |
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- remove global fields DRAGA and DRAGS from C-grid code and |
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declare them locally in lsr.F (the only place where they are |
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still used) |
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o pkg/seaice: add Jacobian-free Newton Krylov solver for ice dynamics |
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(Lemieux et al. 2010, 2012). Turn on with the usual SEAICE_ALLOW_JFNK |
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and SEAICEuseJFNK=.true. A few things to note: |
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- involves a FGMRES, that is parallel but very inefficient, |
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because of many scalar products (global sums) in the Gram-Schmidt |
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orthogonalization method. Needs to be replaced. Original code |
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from J.-F. Lemieux |
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- preconditioner for FGMRES is a stripped down version of LSOR |
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- SOLV_MAX_ITERS is now used for LSOR as a solver and as a |
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preconditioner. For the preconditioner, the default is set to 10. |
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- Jacobian times vector is computed with finite differences |
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- marginally related to JFNK-solver: add a smooth regularization for |
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zeta with tanh that will improve convergence (Lemieux and Tremblay, |
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2009) for any implicit solver (not implemented for EVP because EVP |
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does not need this regularization in the first place). Define |
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SEAICE_ZETA_SMOOTHREG in SEAICE_OPTIONS.h to use. |
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o eesupp/src: |
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- check in genmake2 that intrinsic S/R flush is available. |
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- add S/R to flush IO unit (if intrinsic S/R flush is available) |
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- flush standard & error msg unit before MPI termination |
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- if debugMode, flush IO unit after printing msg |
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o pkg/ctrl: |
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- ctrl_unpack.F, ALLOW_GENARR3D_CONTROL code: fix missing argument in call |
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to ctrl_set_unpack_xyz. |
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checkpoint64 (2012/10/09) |
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o pkg/shelfice |
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- in mom_fluxform.F, mom_vecinv.F: |
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CALL SHELFICE_V_DRAG(bi,bj,k,vFld,KE,KappaRU,vF,myThid) |
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Bug fix KappaRU -> KappaRV |
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does not change verification/isomip but may change other setups |
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(presumably constant KappaRU=KappaRV) |
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- fix diagnostics SHIU/Vdrag (thanks to Tom Millgate) |
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o pkg/obcs: |
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- fixed some indexing bugs in obcs_seaice_sponge.F |
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- added obcs relaxation subroutines for HSALT and HSNOW |
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- changes verification/seaice_obcs/results/obcs_seaice_sponge.F |
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o pkg/seaice: |
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- add "multicategory" parameterization for snow in analogy to ice, |
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default is off for now. |
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o pkg/obcs: |
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- added obcs_seaice_sponge.F for obcs relaxation of seaice variables; |
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see verification/seaice_obcs/input.seaiceSponge for example application. |
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- remove local commom bloc "OBCS_GLOBAL" in obcs_readparms.F and do all the OB |
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index setting by master-thread. This fix multi-threads Pb in previous modifs. |
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o pkg/layers : |
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- add diagnostics to pkg/layers |
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- move the meat of pkg/layers from layers_calc.F to layers_fluxcalc.F |
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(from R.Tulloch). Layers_calc.F now calls layers_fluxcalc.F accordingly. |
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o pkg/generic_advdiff/gad_implicit_r.F : |
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- fix ADVr diagnostics in case of both implicit vertical advection and diffusion. |
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o pkg/seaice/seaice_growth.F: |
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- fix SItflux diagnostics in virtual salt flux + balanceEmpmr case. |
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o pkg/obcs: |
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- change default setting of OBCS_UVICE_OLD from defined to undef; |
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- use new parameter OB_indexNone for null index value (instead of hard-coded 0) |
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in all pkg/obcs code and in other pkgs; remove k loop in obcs_check_depths.F; |
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- pass OB_indexNone as (new) argument to S/R CTRL_MASK_SET_[X,Y]Z; |
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- change OB null index value (OB_indexNone) to -99 ; this fix the problem |
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with Southern & Western OB at a tile edge (at least in a simple set-up). |
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o pkg/obcs: |
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- change settings of OB index in case OB coincides with tile edge (shared by |
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2 tiles), so that common OB location is registered by both tiles (instead of |
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only 1). However, for Southern and Western OB, index value = 0 is not |
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recognized as valid OB index (=default null value) and needs to be fixed. |
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- modify accordingly OBCS_BALANCE_FLOW and OBCS_MONITOR (avoid double counting) |
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- new parameter "OB_indexNone" for null index value (for now, still zero) |
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to replace hard-coded null index value of zero. |
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o pkg/exch2: |
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- improve W2_USE_E2_SAFEMODE (faster) and W2_E2_DEBUG_ON: |
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always check buffer-size (but outside the loop); move checking for valid |
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index from W2_USE_E2_SAFEMODE to W2_E2_DEBUG_ON; in W2_E2_DEBUG_ON, |
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print each tile and point connection only if |W2_printMsg|>= 2 and 3. |
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o pkg/ctrl (pack & unpack): |
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- in ctrl_pack.F & ctrl_unpack.F, use the same local file-name variable |
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(locally defined) for different variables (+ remove the variable-specific |
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file name in CTRL_GENARR.h). For now, only implemented for GENARR2/3D_CONTROL |
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(to be extended to other local file names in ctrl.h). |
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o pkg/flt: |
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- add a FLT_Iter0 option (similar to PTRACERS_Iter0). |
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o pkg/mdsio: |
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- fix missing STOP in mdsio_readvec_loc.F (case ioUnit=0) when file is missing |
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o tools/genmake2: |
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- add similar dependences for target EXE_AD & EXE_FTL as we have for EXECUTABLE |
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(added by Alistair in version 1.51 for building without make depend); |
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- remove Header files list (H_SRC_FILES) from the dependence of targets |
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ad_input_code.f & ftl_input_code.f (not clear why it was added in the first |
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place in version 1.23): this save going through staf when unrelated header |
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file has been modified. |
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Note: for an intermediate target (e.g., ad_input_code.f or adtaf) without |
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"make depend" step, still need to do "make links" before "make adtaf". |
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o eesupp/src (+ few pkg src files) & genmake2: |
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- finish to remove ALWAYS_USE_MPI in source code that TAF does not see; |
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- no longer set ALWAYS_USE_MPI in Makefile (was done by genmake2). |
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- improve genmake2 checking for ALLOW_${PKG} in CPP_OPTIONS.h files (distinguish |
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upper/lower case ; account for space between "#" and undef/define) |
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o pkg/flt (with exch2): |
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- cleaning: fix so that it compiles; move remaining MPI calls out of flt_exch2.F; |
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- simplify threads synchronisation; fix (many issues) multi-threaded with MPI. |
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checkpoint63s (2012/09/05) |
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o pkg/ecco: |
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- remove #ifdef ALLOW_SMOOTH_CORREL3D brackets. |
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- add more relevant #ifdef ALLOW_SMOOTH ones. |
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- sort out useAtmWind, useSMOOTH, ctrlSmoothCorrel2D. |
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o pkg/ctrl: |
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- CTRL_OPTIONS.h : document CPPs related to smoothing; ALLOW_SMOOTH_CORREL2D/3D, |
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ALLOW_CTRL_SMOOTH, ALLOW_SMOOTH_CTRL2D, ALLOW_SMOOTH_CTRL3D. |
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- ctrl.h : document run time params doInitXX, doMainPack, doMainUnpack, doPackDiag, |
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doSinglePrecTapelev (audodiff param!), ctrlSmoothCorrel2D (new) and |
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ctrlSmoothCorrel3D (new). |
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The added ctrlSmoothCorrel2D/3D replace the old ALLOW_SMOOTH_CORREL2D/3D CPP. |
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- ctrl_readparms.F : initialise ctrlSmoothCorrel2D/3D and read from namelist. |
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- ctrl_init.F ctrl_pack.F ctrl_unpack.F : switch off ustress/vstress |
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controls when useAtmWind, and vice versa. |
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- ctrl_map_ini_ecco.F : UVEL0, VVEL0, edtaux, edtauy cannot be smoothed as tracers. |
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- ctrl_get_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL2D with |
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#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel2D, IF useSMOOTH. |
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- ctrl_map_ini_gen.F : replace #ifdef ALLOW_SMOOTH_CORREL3D with |
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#ifdef ALLOW_SMOOTH, IF ctrlSmoothCorrel3D, IF useSMOOTH. |
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- ctrl_set_pack_xy[z].F, ctrl_set_unpack_xy[z].F: |
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replace ALLOW_SMOOTH_CORREL2D/3D brackets with ctrlSmoothCorrel2D/3D. |
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o pkg/smooth: |
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- remove un-necessary includes. |
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- remove ALLOW_SMOOTH*D and ALLOW_SMOOTH_CORREL*D brakets. |
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Those CPP options were never defined, and not necessary. |
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o model/src: |
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- fix CPP brackets in ini_mixing.F (GM_background_K belongs to gmredi). |
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- standard treatment of useSMOOTH. |
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o pkg/autodiff: |
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- add LOGICAL useGGL90inAdMode, useGGL90inFwdMode, useSALT_PLUMEinAdMode, |
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useSALT_PLUMEInFwdMode allowing to switch off ggl90 and salt_plume adjoint. |
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o pkg/exch2: |
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- add "if usingMPI" where it was missing (in exch2_rx?_cube*.template) |
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+ start to remove ALWAYS_USE_MPI in source code that TAF does not see. |
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- make new S/R W2_MAP_PROCS out of w2_eeboot.F to setup exch2 CommonFlag |
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and tiles to process mapping. |
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- re-arrange 3 header files (W2_EXCH2_PARAMS.h, _BUFFER.h & _TOPOLOGY.h) |
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moving /EXCH2_FILLVAL_RX/ & /W2_EXCH2_COMMFLAG/ to W2_EXCH2_TOPOLOGY.h; |
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rename "exch2_tProc" to "W2_tileProc" and move seting of e2FillValue_RX |
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from w2_eeboot.F to w2_readparms.F. |
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o eesupp/src: |
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- set exchNeedsMemsync & exchUsesBarrier according to "usingMPI" (instead of |
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ALWAYS_USE_MPI) + moved from ini_communication_patterns.F to eeset_parms.F; |
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also move setting of exchCollectStatistics from exch_init.F to eeset_parms.F |
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- in eedie.F and all_proc_die.F, always call MPI_FINALIZE when ALLOW_USE_MPI |
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is defined (remove condition on usingMPI) to match cases where MPI_INIT |
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has been called. |
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- fix bug I put in previous modif of exch_sm_3d_rx.template (not much used); |
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- change default (non-MPI) value of myPid (from 1 to 0) to match MPI settings |
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(so that on 1 proc, get same myPid independently of usingMPI) |
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- add a stop if multi-procs but usingMPI=F ; stop also if usingMPI=T and |
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useCubedSphereExchange with EXCH-1 (safer). |
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- add "if usingMPI" where it was missing (+ start to remove ALWAYS_USE_MPI). |
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o pkg/ggl90: |
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- fix bug in filling corner mask array "mskCor" (FILL_CS_CORNER_TR_RL call) |
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used in ALLOW_GGL90_SMOOTH code. |
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o pkg/flt: |
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- fix typo in FLT_WITHOUT_Y_PERIODICITY (the effect was to ignore stopping |
| 182 |
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floats at the Southern end of the domain). |
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o eesupp/inc: |
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- add a list of CPP-options which can be set by Makefile (DEF_IN_MAKEFILE.h); |
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but not used (and not to be used) anywhere, just for documentation. |
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o pkg/autodiff, exf, ptracers & seaice (AD & TL output): |
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- comment out the very nasty "writeBinaryPrec = writeStatePrec" line, since: |
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a) can damage previously written records in any other multi-record files. |
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b) if needed, can easily do it cleanly, by calling S/R WRITE_REC_3D_RL/S. |
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o tools/genmake2: |
o tools/genmake2: |
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- define variable MAKE within Makefile and use it in place of 'make'; |
- define variable MAKE within Makefile and use it in place of 'make'; |
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- update AD_CONFIG.h (if needed) before building any of the executable |
- update AD_CONFIG.h (if needed) before building any of the executable |
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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; |
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- always print usual warning comment 'this file is automatically generated' |
- always print usual warning comment 'this file is automatically generated' |
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from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
from script convert_cpp_cmd2defines (+ remove this warning from genmake2). |
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o pkg/cheapaml: |
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- updated to correspond to the code used in accepted paper (Nico Wienders). |
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o pkg/exf: |
o pkg/exf: |
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added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
added run time switch useAtmWind to replace ALLOW_ATM_WIND cpp switch. |
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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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