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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/seaice: |
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- make deltaC a global variable, so that it can be used in ridging code |
| 9 |
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- first step towards ridging: introduce new routines that compute |
| 10 |
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ice strength based on ridging parameters |
| 11 |
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o verification/hs94.1x64x5: |
| 12 |
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- leave ALLOW_AUTODIFF_TAMC undefined in code_oad/AUTODIFF_OPTIONS.h |
| 13 |
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- do not use ECCO_CPPOPTIONS.h anymore for TAF & OpenAD Adjoint tests. |
| 14 |
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o autodiff: |
| 15 |
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- Start to include explicitly AUTODIFF_OPTIONS.h, COST_OPTIONS.h, |
| 16 |
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and CTRL_OPTIONS.h in src files (to enable to skip the ECCO_CPPOPTIONS.h) |
| 17 |
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For now, only in pkgs used in verification/hs94.1x64x5. |
| 18 |
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- Replace ALLOW_AUTODIFF_TAMC by ALLOW_AUTODIFF (except for tape/storage |
| 19 |
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which are specific to TAF/TAMC). |
| 20 |
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- Replace ALLOW_AUTODIFF_OPENAD by ALLOW_OPENAD: |
| 21 |
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since ALLOW_OPENAD is defined in PACKAGES_CONFIG.h (any time pkg/openad |
| 22 |
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is compiled), this simplifies/reduces which *_OPTIONS.h file to include. |
| 23 |
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- OpenAD: change Makefile to generate the appropriate AD_CONFIG.h when |
| 24 |
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building mitgcmuv_ad (make adAll). |
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o pkg/ecco: |
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- cost_gencost_seaicev4.F: |
| 27 |
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reformulate proxy cost as function of sst and local param SEAICE_freeze |
| 28 |
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change cost names from siv4-[sst,vol] to siv4-[deconc,exconc] |
| 29 |
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- add stop statement if old names siv4-[sst,vol] are used |
| 30 |
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- add snapshots + cost reports for atmospheric longwave |
| 31 |
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- remove factor 0.1 in front of wtau[u,v] |
| 32 |
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- replace never used flag ALLOW_TMI_COST_CONTRIBUTION with |
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ALLOW_TMI_SST_COST_CONTRIBUTION |
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o pkg/atm_phys: |
| 35 |
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- add some diagnostics for Short-wave and for convection S/R. |
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o pkg/seaice/seaice_growth: |
| 37 |
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- fix a bug in the lateral melt parameterization for SEAICE_ITD |
| 38 |
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in seaice_growth; tempFrz needs to be computed inside the i/j-loop |
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- rearrange loop order for better vector code in the same code block |
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- rewrite the floeDiameter formula to have fewer divisions |
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- (miraculously) none of this changes the results of seaice_itd |
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o pkg/smooth: |
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- move param smooth2Ddiffnbt to pkg/ecco |
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o pkg/salt_plume: |
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- salt_plume_frac.F: |
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clean up local param names |
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reformulate (1-frac) to frac; original 1-frac was based on swfrac code |
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o pkg/rw: |
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- add RS version of S/R READ_MFLDS_LEV. |
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o pkg/streamice: |
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- fix the restart test by writing/reading pickup_streamice files. |
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o pkg/seaice: |
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- refine checks for jfnk-related parameters |
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- comment out if statement with SEAICEuseIMEX parameter as long as there |
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is no IMEX code to avoid confusion and surprises |
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|
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checkpoint64u (2014/03/07) |
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o verification/MLAdjust: |
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- rename secondary test suffix: |
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1.leith -> A4FlxF + switch to flux-form & add side-drag |
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0.leithD -> AhFlxF + switch to flux-form |
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0.smag -> AhVrDv (use Vorticity-Div. visc form) + add side-drag |
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0.leith -> AhStTn (use Strain-Tension visc form) + add side-drag |
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o pkg/mom_vecinv: |
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- remove unused arguments from S/R MOM_VI_HDISSIP & MOM_HDISSIP (as it used |
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to be before mom_calc_visc.F) |
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- skip the call to MOM_CALC_TENSION & MOM_CALC_STRAIN if not needed. |
| 68 |
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- add 2nd copy of vort3 & strain that knows about lateral BC (free/no slip): |
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this is simpler for the adjoint and for diagnostics. |
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o model/src + pkg/momentum: |
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- add input files for 2-D additional Western and Southern cell-edge wall |
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(e.g., to add "thin-wall" where it is =1). |
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- fix sideDrag option for thin-walls with Non-Lin Free-Surf |
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using 2nd hFacZ that is computed from initial (fix domain) hFac |
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- known limitations of thin wall implementation: not yet coded for sigma |
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coords; not working with CD-scheme neither. |
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o pkg/seaice: |
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- rename recently introduced parameters from (wrong name) AB to |
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BDF (backward difference time discretisation) |
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- retire runtime parameters SEAICEuseAB2, SEAICE_abEps |
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o tools/adjoint_options: |
| 82 |
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- remove setting of "OPENAD=true" (now set by command line "genmake2 -oad") |
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|
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checkpoint64t (2014/02/01) |
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o pkg/ecco |
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- add compile flag ALLOW_GENCOST_TIMEVARY_WEIGHT in ECCO_OPTIONS.h and |
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runtime logical flag gencost_timevaryweight to read daily sea-ice sigma |
| 88 |
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- replace hard-coded record number and period which only work for monthly |
| 89 |
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with read-in runtime param that works for other periods (month,day,year) |
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o pkg/thsice |
| 91 |
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- corrected store directive fixes thsice adjoint gradient checks |
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o genmake2 & testreport: |
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- add genmake2 option "-oad" to generate a Makefile for OpenAD built and |
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in this case, use tools/adjoint_options/adjoint_oad as default AD optfile. |
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Update testreport accordingly. No need to set "export OPENAD=true" |
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in adjoint_options/adjoint_oad anymore (will be removed later). |
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o pkg/shelfice: |
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- put T & S shelfice forcing into model surfaceForcing_T,_S (for now, |
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only if SHELFICEboundaryLayer=F); Change model/src/external_forcing.F |
| 100 |
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so that surface forcing applies to k=kSurf if using pkg/shelfice. |
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o pkg/ctrl, pkg/grdchk, pkg/ecco: |
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- Changes to make GENARR more modular (i.e. invisible if not used) |
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o model/src/temp_integrate.F and salt_integrate.F |
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- re-include store directives that were removed on Dec 27th. |
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o model/src/external_forcing_surf.F |
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- add storage directives for EmPmR and PmEpR to avoid recomputation of |
| 107 |
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seaice_model in the adjoint that is problematic when seaice_model is |
| 108 |
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turned off in the adjoint. The resolved issue dated back to July when |
| 109 |
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EXTERNAL_FORCING_SURF call was moved. |
| 110 |
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Update global_ocean.cs32x15/*/output_adm.seaice_dynmix.txt accordingly. |
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o pkg/exf/exf_check.F |
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- fix a small bug again (originally found by Wentao Liu, now found again) |
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- streamline error output |
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o pkg/streamice and aim_v23: |
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- replace a few "_EXCH_XY_RL (" with "_EXCH_XY_RL(", so that |
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Apple's /usr/bin/cpp knows what to do: |
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Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) |
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Target: x86_64-apple-darwin13.0.0 |
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checkpoint64s (2014/01/05) |
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o tools/adjoint_options: |
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- switch to fastopt.net TAF server (instead of default fastopt.de) for |
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AD optfiles adjoint_diva & adjoint_f95 (similar to adjoint_default). |
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o model/src: |
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- remove some unnecessary TAF storage directives in forward_step.F and |
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in dynamics.F (note: not always removed by TAF, e.g., double storage |
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of kappaRU,kappaRV in former version of dynamics.F). |
| 128 |
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o model/src & pkg/ptracers: |
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- call directly GAD_IMPLICIT_R & IMPLDIFF + DWNSLP_APPLY from temp_integrate.F |
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salt_integrate.F and ptracers_integrate.F (instead of from thermodynamics.F) |
| 131 |
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and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
| 132 |
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- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
| 133 |
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- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
| 134 |
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- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
| 135 |
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o useSingleCpuInput separates single-CPU input from single-CPU output; |
| 136 |
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for now only implemented for in exf_interp_read.F |
| 137 |
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o verification/advect_xy: |
| 138 |
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- fix missing EXCH call in local version of ini_salt.F and update output. |
| 139 |
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o momentum diagnostics: |
| 140 |
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- fix which deltaT is used in Total-Tendency diagnostics. |
| 141 |
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- fix typo in diagnostics for momentum tendency from AB. |
| 142 |
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o pkg/seaice/seaice_lsr.F: fix an initialisation bug for the |
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SEAICE_VECTORIZE_LSR_ZEBRA option that lead to NaNs on a NEC-SX8 |
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checkpoint64r (2013/12/08) |
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o verification/*/results: |
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- Update reference output of experiments that were passing with just 13 digits |
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(make it easier to detect future changes in results) |
| 149 |
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o model/src & pkg/ptracers: |
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- move calls to GAD_ADVECTION (Multi-Dim advection) from thermodynamics.F to |
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inside temp_integrate.F and salt_integrate.F and from ptracers_advection.F |
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to inside ptracers_integrate.F ; remove ptracers_advection.F |
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o coupling interface pkgs: |
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[atm_compon_interf, ocn_compon_interf & atm_ocn_coupler] |
| 155 |
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- change the config check to test the agreement of Ocean Depth |
| 156 |
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with ATM land/sea mask (instead of ATM orography); |
| 157 |
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- send to coupler the number of coupler time-steps to do for this run: |
| 158 |
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this allows to check for consistency and don't need anymore to be |
| 159 |
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specified in parameter file "data"; |
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in coupler: |
| 161 |
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- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
| 162 |
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- improve report to log-file of config setting (pass log-file unit to few S/R) |
| 163 |
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o pkg/compon_communic: |
| 164 |
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- add coupling send/receive for non-tiled integer vector; |
| 165 |
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- add S/R to check and stop if any proc has an error (similar to |
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eesupp/src/stop_if_error.F but single thread and across Comm_World). |
| 167 |
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o pkg/exch2: |
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- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
| 169 |
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through list of all tiles my proc owns. |
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o model/src: |
| 171 |
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- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
| 172 |
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from rTrans) to simplify dependencies (no need to store rTrans anymore in |
| 173 |
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calling S/R); this affects AD results at machine truncation level: |
| 174 |
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update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
| 175 |
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bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
| 176 |
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o tools/build_options: |
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- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
| 178 |
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o coupling interface pkgs: |
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[compon_communic, atm_compon_interf & ocn_compon_interf] |
| 180 |
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- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
| 181 |
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to each S/R that needs it; remove un-used variables. |
| 182 |
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- change component tile registration (cpl_register.F in both compon_interf |
| 183 |
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and mitcomponent_tile_register.F) to pass the full list of tiles |
| 184 |
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information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
| 185 |
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- with pkg/exch2: adopt the same convention used for I/O to define mapping |
| 186 |
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towards coupler global array (unless W2_useE2ioLayOut=F): |
| 187 |
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a) can now use different tiling between atm & ocn comp. |
| 188 |
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b) no needs to modify the run-Off map when changing tiling (was needed |
| 189 |
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even if using the same tiling between atm & ocn). |
| 190 |
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c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
| 191 |
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full land tiles); not yet tested. |
| 192 |
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- check for valid mapping from comp. tile to coupler global array |
| 193 |
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- improve report of tile registration results to log file. |
| 194 |
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o pkg/exch2: |
| 195 |
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- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
| 196 |
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tile-registration (CPL_REGISTER); |
| 197 |
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- activate (un-comment) definition and setting of "W2_tileIndex" list to |
| 198 |
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store the local bi,bj indices of each tile; |
| 199 |
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- also print bi,bj in local report to log file; |
| 200 |
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- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
| 201 |
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Jun 2009 modif of pkg/exch2). |
| 202 |
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o testing on baudelaire: |
| 203 |
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- run 2 tests at a time: no significant slow down (since enough cpu) and |
| 204 |
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get the full set of test done earlier |
| 205 |
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- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
| 206 |
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o model/src/thermodynamics.F and routines called from it: |
| 207 |
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- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
| 208 |
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gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
| 209 |
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velocity (outp) by adding bolus velocity. |
| 210 |
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- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
| 211 |
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mass transport from velocity + lateral grid cell area |
| 212 |
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- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
| 213 |
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- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
| 214 |
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in thermodynamics.F |
| 215 |
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- remove k from thermodynamics.F and move it to temp_integrate.F |
| 216 |
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salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
| 217 |
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loop). |
| 218 |
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- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
| 219 |
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advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
| 220 |
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PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
| 221 |
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GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
| 222 |
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- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
| 223 |
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global_ocean.90x40x15, tutorial_global_oce_biogeo and |
| 224 |
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tutorial_tracer_adjsens (+ TLM output). |
| 225 |
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o tools/OAD_support and (verification/*/) code_oad: |
| 226 |
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- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
| 227 |
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module conversion ; remove unneeded CPP_EEOPTIONS.h. |
| 228 |
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- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
| 229 |
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version (closer to model/inc/CPP_OPTIONS.h). |
| 230 |
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o model/src: |
| 231 |
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- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
| 232 |
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retired list of parameters (routine FREEZE has been replace by surface |
| 233 |
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freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
| 234 |
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o pkg/gmredi: |
| 235 |
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- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
| 236 |
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velocity (same scheme but affects machine truncation) for GM_AdvForm. |
| 237 |
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- update output of FWD experiments: front_relax.bvp, |
| 238 |
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global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
| 239 |
|
|
| 240 |
|
checkpoint64q (2013/11/17) |
| 241 |
o verification: |
o verification: |
| 242 |
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
| 243 |
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
tutorial_global_oce_biogeo and global_ocean.90x40x15. |
| 246 |
o pkg/cost: |
o pkg/cost: |
| 247 |
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
| 248 |
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
| 249 |
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL |
o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
| 250 |
cannot be applied to var in common block). |
cannot be applied to var in common block). |
| 251 |
o allows to get results independent of tile-per-proc setting (if using |
o allows to get results independent of tile-per-proc setting (if using |
| 252 |
slower GLOBAL_SUM_SEND_RECV option). |
slower GLOBAL_SUM_SEND_RECV option). |
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