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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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- 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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|
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checkpoint64t (2014/02/01) |
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o pkg/thsice |
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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 |
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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 |
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seaice_model in the adjoint that is problematic when seaice_model is |
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turned off in the adjoint. The resolved issue dated back to July when |
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EXTERNAL_FORCING_SURF call was moved. |
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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). |
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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) |
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and remove ptracers_dwnslp_apply.F & ptracers_implicit.F |
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- call MATRIX_STORE_TENDENCY_EXP for each tracer (in ptracers_integrate.F) |
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- add fZon & fMer as output argument of S/R GAD_CALC_RHS. |
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- update TAF AD-output of experiments global_ocean.90x40x15 (13 for AD-grad). |
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o useSingleCpuInput separates single-CPU input from single-CPU output; |
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for now only implemented for in exf_interp_read.F |
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o verification/advect_xy: |
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- fix missing EXCH call in local version of ini_salt.F and update output. |
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o momentum diagnostics: |
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- fix which deltaT is used in Total-Tendency diagnostics. |
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- fix typo in diagnostics for momentum tendency from AB. |
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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) |
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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] |
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- change the config check to test the agreement of Ocean Depth |
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with ATM land/sea mask (instead of ATM orography); |
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- send to coupler the number of coupler time-steps to do for this run: |
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this allows to check for consistency and don't need anymore to be |
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specified in parameter file "data"; |
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in coupler: |
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- check consistency of RunOff map versus Ocean Depth and ATM land/sea mask. |
| 85 |
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- improve report to log-file of config setting (pass log-file unit to few S/R) |
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o pkg/compon_communic: |
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- add coupling send/receive for non-tiled integer vector; |
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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). |
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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 |
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through list of all tiles my proc owns. |
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o model/src: |
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- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
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from rTrans) to simplify dependencies (no need to store rTrans anymore in |
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calling S/R); this affects AD results at machine truncation level: |
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update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
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bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
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o tools/build_options: |
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- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
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o coupling interface pkgs: |
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[compon_communic, atm_compon_interf & ocn_compon_interf] |
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- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
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to each S/R that needs it; remove un-used variables. |
| 105 |
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- change component tile registration (cpl_register.F in both compon_interf |
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and mitcomponent_tile_register.F) to pass the full list of tiles |
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information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
| 108 |
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- with pkg/exch2: adopt the same convention used for I/O to define mapping |
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towards coupler global array (unless W2_useE2ioLayOut=F): |
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a) can now use different tiling between atm & ocn comp. |
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b) no needs to modify the run-Off map when changing tiling (was needed |
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even if using the same tiling between atm & ocn). |
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c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
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full land tiles); not yet tested. |
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- check for valid mapping from comp. tile to coupler global array |
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- improve report of tile registration results to log file. |
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o pkg/exch2: |
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- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
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tile-registration (CPL_REGISTER); |
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- activate (un-comment) definition and setting of "W2_tileIndex" list to |
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store the local bi,bj indices of each tile; |
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- also print bi,bj in local report to log file; |
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- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
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Jun 2009 modif of pkg/exch2). |
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o testing on baudelaire: |
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- run 2 tests at a time: no significant slow down (since enough cpu) and |
| 127 |
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get the full set of test done earlier |
| 128 |
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- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
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o model/src/thermodynamics.F and routines called from it: |
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- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
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gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
| 132 |
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velocity (outp) by adding bolus velocity. |
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- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
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mass transport from velocity + lateral grid cell area |
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- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
| 136 |
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- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
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in thermodynamics.F |
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- remove k from thermodynamics.F and move it to temp_integrate.F |
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salt_integrate.F and ptracers_integrate.F (now done inside the tracer |
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loop). |
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- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
| 142 |
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advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
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PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
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GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
| 145 |
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- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
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global_ocean.90x40x15, tutorial_global_oce_biogeo and |
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tutorial_tracer_adjsens (+ TLM output). |
| 148 |
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o tools/OAD_support and (verification/*/) code_oad: |
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- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
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module conversion ; remove unneeded CPP_EEOPTIONS.h. |
| 151 |
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- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
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version (closer to model/inc/CPP_OPTIONS.h). |
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o model/src: |
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- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
| 155 |
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retired list of parameters (routine FREEZE has been replace by surface |
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freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
| 157 |
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o pkg/gmredi: |
| 158 |
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- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
| 159 |
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velocity (same scheme but affects machine truncation) for GM_AdvForm. |
| 160 |
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- update output of FWD experiments: front_relax.bvp, |
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global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
| 162 |
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|
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checkpoint64q (2013/11/17) |
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o verification: |
| 165 |
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- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
| 166 |
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tutorial_global_oce_biogeo and global_ocean.90x40x15. |
| 167 |
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- generate new output (growth & melt) for seaice_itd experiment after |
| 168 |
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updating the input pickup_seaice files (previously wrong). |
| 169 |
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o pkg/cost: |
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- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
| 171 |
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(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
| 172 |
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o this fixes global-sum value if multi-threads (since GLOBAL_SUM_RL |
| 173 |
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cannot be applied to var in common block). |
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o allows to get results independent of tile-per-proc setting (if using |
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slower GLOBAL_SUM_SEND_RECV option). |
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- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
| 177 |
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thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
| 178 |
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forward gradients: update output). |
| 179 |
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- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
| 180 |
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S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
| 181 |
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o pkg/mom_common: |
| 182 |
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- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
| 183 |
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code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
| 184 |
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viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
| 185 |
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ensure that all field value that are used are set. |
| 186 |
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o tutorial_deep_convection (smag3d): |
| 187 |
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- add missing scaling in mom_calc_smag_3d.F; |
| 188 |
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- set smag3D_coeff in input.smag3d such that results do not change. |
| 189 |
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o pkg/dic: |
| 190 |
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- change dic_cost.F to compute cost on each tile first and then apply |
| 191 |
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GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
| 192 |
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tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
| 193 |
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- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
| 194 |
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o eesupp/src & pkg/mdsio: |
| 195 |
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- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
| 196 |
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(from pkg/mdsio) since they are no longer used for tape IO. |
| 197 |
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- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
| 198 |
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(+ keep a copy in pkg/atm_ocn_coupler). |
| 199 |
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o verification/isomip: |
| 200 |
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- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
| 201 |
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o tools/build_options: |
| 202 |
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- optfile linux_amd64_ifort11, fast (no ieee) case: |
| 203 |
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to get a working restart for all experiments, add "-fp-model source" |
| 204 |
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to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
| 205 |
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|
| 206 |
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checkpoint64p (2013/10/20) |
| 207 |
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o pkg/autodiff: |
| 208 |
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- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
| 209 |
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criteria, return to simple (default) tape IO format. |
| 210 |
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o pkg/mdsio (+ eesupp/src): |
| 211 |
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- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
| 212 |
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previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
| 213 |
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- fix globalFile and singleCpuIO options using simpler global mapping. |
| 214 |
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- new pairs of scatter/gather vector S/R (one for each type, generated from |
| 215 |
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template) corresponding to simpler global mapping. |
| 216 |
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- adread_write.F: switch to new S/R (but leave old calls commented) and write |
| 217 |
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to globalFile when parameter globalFiles is set to True. |
| 218 |
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- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
| 219 |
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o pkg/autodiff: |
| 220 |
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- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
| 221 |
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with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
| 222 |
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missing, just add a STOP if array type do not match. |
| 223 |
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o pkg/exf: |
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- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
| 225 |
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rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
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and rename array obsSIce to exf_iceFraction. |
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o tutorial_deep_convection: |
o tutorial_deep_convection: |
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- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
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for now all in this exp. code dir. |
for now all in this exp. code dir. |
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