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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 model/src: |
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- re-arrange extrapolation calculation in Adams-Bashforth S/R (affects machine |
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truncation) and add diagnostics for Adams-Bashforth tendency increment. |
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- update test-exp. AD output: |
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1D_ocean_ice_column, bottom_ctrl_5x5, lab_sea.noseaicedyn, obcs_ctrl; |
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and FWD output: exp4 (x3), fizhi-cs-32x32x40, fizhi-cs-aqualev20, |
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front_relax (x3), global_ocean.90x40x15 (x2), global_ocean.cs32x15 (x5), |
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global_ocean_ebm, ideal_2D_oce, internal_wave, isomip (x3), lab_sea (x4), |
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matrix_example, MLAdjust (x5), natl_box (x2), tutorial_advection_in_gyre, |
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tutorial_global_oce_in_p, tutorial_global_oce_latlon and |
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tutorial_plume_on_slope. |
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o pkg/diagnostics/diagstats_calc.F: add special code for TARGET_NEC_SX |
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that vectorises. This code uses 3 extra 2D fields, F90 array assignments |
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and F90 intrinsic routines SUM, MINVAL, MAXVAL, but since TARGET_NEC_SX |
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does not even come with an F77 compiler anymore, this should not be |
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a limitation |
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|
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checkpoint63e (2011/11/06) |
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o pkg/seaice adjoint of LSR: |
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- substantially rework STORE dirs. |
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- add new flag SEAICE_LSR_ADJOINT_ITER and parameter SOLV_MAX_FIXED |
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this flag will do SOLV_MAX_ITERS but only store SOLV_MAX_FIXED fields |
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and only perform SOLV_MAX_FIXED adjoint iters. |
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If flag SEAICE_LSR_ADJOINT_ITER is undef-ined, the store in the iteration |
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always goes to same record, meaning that the last forward field will be |
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the one used in the adjoint - an approximation. |
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- now produces non-zero LSR-related gradients, and acceptable gradients for |
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An's zonal (x-z) test case (to be checked in) |
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- lab_sea: produces acceptable gradients for lab_sea with forward/backward LSR |
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(but these are screwed up by the thermodynamics in the first place); |
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reduce from 4 to 3 timesteps to avoid t.d. issue as temporary solution; |
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output_adm.txt also reflects changes to seaice_lsr |
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- global_ocean.cs32x15: |
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* the "default" input_ad.seaice has been re-defined to always exclude dynamics |
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(output_adm.seaice.txt was updated) |
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* new input_ad.seaice_dynmix tests a forward LSR / backward free-drift |
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(output_adm.seaice_dynmix.txt) |
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o test-exp. exp4+stevens: |
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- switch off pTracers and nonHydrostatic (restart problems with NH); update output |
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o pkg/seaice (lsr solver): |
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- put coriolis term into FORCEX,Y (as in seaice_evp.F; previously in rhsU,V only); |
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update output (change truncation) of FWD test exp lab_sea & global_ocean.cs32x15 |
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- fix SEAICEuseFREEDRIFT for new OBCS version (ndef OBCS_UVICE_OLD) |
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- new parameter "LSR_mixIniGuess" allows (if=2,4) to mix free-drift solution |
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into initial guess for linearised solver; use weight ~ (1/err)^2,4. |
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- compute (with new S/R) and print initial (+ free-driff sol. if available) |
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and final residual of linearised system. |
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o pkg/pp81: add diagnostics for vertical eddy viscosity and diffusivity |
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(requires new subroutines pp81_init_fixed.F/pp81_diagnostics_init.F) |
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o pkg/obcs: Stevens BCs (still only for east and west) |
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- fix Stevens BCs by using intermediate velocities of previous |
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time step as "baroclinic" contribution rather velocity of one grid cell |
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inside the boundaries; more consistent but makes the entire treatment |
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more complicated, requires new pickup files and two new S/Rs: |
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obcs_copy_uv_n and obcs_save_uv_n |
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keep old version with flag OBCS_STEVENS_USE_INTERIOR_VELOCITY |
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(undefined by default) |
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- silently move computation of some grid factors into separate loops to |
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save some recomputations |
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- add a hack for non-linear free surface |
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- add a verification experiment to exp4 that tests this code |
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o make gluemnc/xplodemnc work with (moron) non-GNU shell tools |
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checkpoint63d (2011/10/25) |
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o pkg/obcs + seaice-dynamics: |
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- new implementation calls OBCS_APPLY_UVICE (in seaice_dynsolver.F) before |
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solving for uIce,vIce and prevent SEAICE_LSR or SEAICE_EVP to modify OB |
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values (consistent with an implicit method). |
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- add option OBCS_UVICE_OLD (in OBCS_OPTIONS.h, defined by default) to |
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return to older implementation (same results as before); note that none of |
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the "experimental" OBCS_SEAICE options are implemented in the new version. |
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- switch test exp. seaice_obcs to use new version (update output). |
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o pkg/seaice: |
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- add few stop (B-grid & CS-exch, B-grid & obcs, AUTODIFF & SEAICE_maskRHS) |
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- add parenthesis in Water-Ice drag calculations (evp & lsr); |
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- in seaice_lsr.F, simplify and fix AA3 setting in case sNx or sNy=1; |
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and fix case SEAICE_waterDrag=0 (but unstable if no or little seaice) |
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- update output of test exp lab_sea that uses evp or lsr (fwd+ad) |
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and global_ocean.cs32x15 (icedyn & seaice fwd+ad). |
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o pkg/layers: |
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- Include potential density as new coordinate (Thanks to David Munday) |
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o pkg/dic: |
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- Remove subroutine CALC_PCO2_APPROX_CO3 from carbon_chem.F and add |
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carbonate computation/output to CALC_PCO2_APPROX |
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o pkg/generic_advdiff |
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- make TAF generate code that vectorizes: |
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gad_dst3fl_adv_*.F, gad_u3c4_impl_r.F |
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o model/src: |
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- improve vectorization also for adjoint code of |
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solve_tridiagonal and solve_pentadiagonal. As this requires up to |
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5 new 3D-fields, this code is only turned on for the combination of |
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ALLOW_AUTODIFF_TAMC and TARGET_NEC_SX. Also remove error message |
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for singular matrix check (only for TARGET_NEC_SX). |
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- remove hard-wiring of CPP-flag ALLOW_SOLVERS_KLOOPINSIDE to |
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ALLOW_AUTODIFF. This flag now needs to be set outside of |
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solve_tri/pentadiagonal.F |
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o pkg/exf: |
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- fix previous modif in exf_readparms.F (revision 1.66: treatment of |
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optional namelist EXF_NML_OBCS). |
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- add many debug-print (to trace down where pkg/cal error msg comes from) |
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o pkg/mom_vecinv/mom_vi_hdissip.F |
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- rearrange loops so that vectorization is improved and in particular |
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the adjoint routine vectorizes. The code is a little longer now, but I |
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think easier to read. |
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Note: CPP-flag MOM_VI_ORIGINAL_VISCA4 is not tested. |
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o pkg/seaice: |
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- allow to specify initial seaice velocity from files (uIceFile,vIceFile) |
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o pkg/exch2: |
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- alternative code (without tile x tile matrix) for cumulated (global) sum; |
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used as default; keep using matrix version in adjustment.cs-32x32x1. |
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o tools/build_options: |
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- after merging some MPI and/or multi-threads specific optfiles so that |
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the modified default optfile support both built (using genmake2 -mpi |
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for the MPI built, using genmake2 -omp for OpenMP built), |
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move now obsolete optfiles to tools/build_options/unsupported/ |
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(add copy of email sent to support list in doc/optfiles_changes.txt) |
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|
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checkpoint63c (2011/09/28) |
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o pkg/ebm: |
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- fix ebm_zonalmean.F for several procs in Ydir (nPy > 1); update output of |
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test exp. global_ocean_ebm (affects machine truncation, 12 digits for cg2d) |
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o pkg/seaice (SItracer pickup) |
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* Simple code for pickup of SItracer fields (#define ALLOW_SITRACER) |
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To be done: |
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- thorough testing of missing fields in S/R seaice_read_pickup |
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- thorough matching between generic tracers and specific fields used |
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(e.g. volume-weighted age, area-weighted age, salinity, ...) |
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o pkg/grdchk: |
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- all procs calculate and print finite-difference gradient (for testreport) |
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- change description output used by testreport; |
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- AD testing: also compare and report Finite-difference gradient; |
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=> update all output_adm*.txt |
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o test exp. global_ocean_ebm: |
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- switch back useRealFreshWaterFlux (no problem anymore with run-off); |
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and turn on exactConserve; update (fwd) output. |
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o pkg/seaice (LSR): |
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- print to STDOUT number of solver iterations at SEAICE_monFreq interval. |
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- modify solver to deal cleanly with u/v switch at face edges (CS-grid): |
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* identical results with non-CS topology (but save up to half of EXCH calls) |
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* no much changes in cs-32 verification tests since no ice at face edges |
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(differences due to convergence criteria, since nb of iterations changed) |
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* expect some differences on lat-lon-cap grid. |
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update FWD results of global_ocean.cs32x15 test exp. (icedyn & seaice) |
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o pkg/exch2: |
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- add new CPP option to disable Cumul-Sum matrix (to save storage when using |
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many tiles); until alternative coding is added, just add a stop. |
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o pkg/kpp: |
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- move ptracer/salt correction to KPP diffusivity from calc_3d_diffusivity.F |
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to S/R KPP_CALC_DIFF_PTR (+ add tracer-index to argument list). |
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o optfiles: |
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- merged few MPI specific (*+mpi*) and multi-threads specific (*+mth) optfiles |
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into corresponding standard one, which now support different build: |
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(when using "genmake2 -mpi" for MPI built, "genmake2 -omp" for OpenMP built) |
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- add "darwin_amd64_gfortran" optfile (initially from Constantinos, tested by Gael) |
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o pkg/obcs (seaice): |
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- add missing EXCH for uIce,vIce after applying OBCS; |
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- remove S/R EXF_SWAPFFIELDS_X/Y , disable S/R EXF_SET_OBCS_X/Y by adding |
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argument = number of levels to S/R EXF_SWAPFFIELDS_XZ/YZ and S/R |
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EXF_SET_OBCS_XZ/YZ ; update obcs_exf_load.F; |
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- fix EXF_SET_OBCS_XZ/YZ for multi-threaded (assuming loaded arrays are shared) |
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- verification exp. seaice_obcs: split domain in 2 tiles ; add SIZE.h_mpi |
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and eedata.mth for MPI and mutlti-threaded testing. |
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o pkg/flt: |
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- make FLT EXCH working with multi-threads (and MPI + multi-threads); |
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- use buffer for floats IO (trajectories & profiles); size set in FLT_SIZE.h; |
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- fix pickup and trajectories + profiles output with multi-threads; |
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- add parameter to select group of fields to write along trajectory and |
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profile (default unchanged); |
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- only call PORT_RAND* function when flt_noise <> 0; |
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- add multi-threaded test for verification exp. flt_example. |
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o eesupp/src: |
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- fix S/R ALL_PROC_DIE for MPI+multi-threads. |
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- USE_OMP_THREADING: check that number of threads (from eedata) matches |
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actual number (from env.var. setting). |
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o pkg/ebm: |
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- fix multi-threading in ebm_area_t.F ; clean-up EBM.h header file. |
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- add multi-threaded test for verification exp. global_ocean_ebm |
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|
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checkpoint63b (2011/08/29) |
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o pkg/ebm: |
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- fix sign of runoff; |
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- update directly forcing fields (Qnet,EmPmR) to use standard |
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external_forcing_surf.F (remove ebm_forcing_surf.F); |
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- avoid loading forcing fields a 2nd time (1rst time from ini_forcing.F); |
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- set either tauThetaClimRelax (in data) or tauThetaZonRelax (in data.ebm) |
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and apply relaxation towards corresponding SST field (2-D map or ZonAver). |
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- update global_ocean_ebm parameters file data and update output (fwd+ad). |
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o verification/matrix_example: |
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- split domain in 8 tiles (2x4); add SIZE.h_mpi and eedata.mth for |
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MPI and mutlti-threaded testing. |
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o pkg/matrix: |
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- change name of S/R MATRIX_INIT to S/R MATRIX_INIT_VARIA ; |
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- fix for multi-tiles (add bi,bj indices to exp/impMatrixCounter); |
| 200 |
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- fix for multi-threaded (remove DATA statement); |
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- use standard DIFFERENT_MULTIPLE function; |
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- add MATRIX_OPTIONS.h |
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o verification/matrix_example: |
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To allow to split the domain in several tiles, change the domain size |
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from 31x31 to 32x32 by adding 1 row (on Southern side) + 1 column (on |
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Western side) of land points. |
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o (*_)write_pickup: |
| 208 |
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- fix few bugs in mypackage_read/write_pickup.F |
| 209 |
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- in MDS_WR_METAFILES calls, replace "myTime" by a local copy into |
| 210 |
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array of length 1 (was caught by compiler syntax-check). |
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o pkg/diagnostics (velocity potential solver): |
| 212 |
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- fix initialisation of main diagonal matrix (for overlap values) |
| 213 |
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o tools/build_options: |
| 214 |
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- towards single optfile for MPI and non-MPI built: merge few +mpi optfile |
| 215 |
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into previously non MPI one (linux_am64 pgf77,open64,pathf90,ifort11) |
| 216 |
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- linux_amd64_gfortran: merge +mpi_generic version into standard optfile: |
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* move IEEE flags to DEVEL section; take IEEE flags from +mpi_generic ; |
| 218 |
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* FAST case: for now, keep -O3 with ini_masks_etc.F in NOOPTFILES list; |
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and use "-devel" testreport option for standard testing on baudelaire. |
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o pkg/grdchk: |
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- Assume that all gradient-check position are within the same tile |
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corresponding to global indices (iGloTile,jGloTile) and that |
| 223 |
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positions (i,j indices or nbeg) are local to this tile; |
| 224 |
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- set tile local-indices and proc. number according to tile global-indices; |
| 225 |
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- remove grdchkwhichproc from namelist (retired param); |
| 226 |
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- send adjoint gradient to all procs so that all procs print it to STDOUT; |
| 227 |
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- switch on MPI test for global_ocean.90x40x15 AD test experiment. |
| 228 |
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o adding package bbl (Bottom Boundary Layer) |
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description in MITgcm/pkg/bbl/bbl_description.tex |
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example/test experiment in MITgcm_contrib/bbl |
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o adjoint verifications |
| 232 |
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- changed 5 experiments to multi-tiles |
| 233 |
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* global_ocean.90x40x15 |
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* obcs_ctrl |
| 235 |
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* offline_exf_seaice |
| 236 |
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* tutorial_dic_adjoffline |
| 237 |
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* tutorial_tracer_adjsens |
| 238 |
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changed reference output for those that crossed tile boundaries |
| 239 |
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(changed choices of gradient check positions) |
| 240 |
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- with same tiling, switch on MPI test for the last 4 (add SIZE.h_mpi) |
| 241 |
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- temporary bug fix in grdchk_loc.F for obcs |
| 242 |
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o genmake2 & testreport |
| 243 |
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- add target "obj" (just for OBJFILES files) to Makefile; |
| 244 |
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- add option to specify FEXTRAFLAGS on command line. |
| 245 |
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o pkg/mypackage: |
| 246 |
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- remove bi,bj arguments from argument list of S/R MYPACKAGE_CALC_RHS |
| 247 |
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|
| 248 |
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checkpoint63a (2011/08/02) |
| 249 |
o pkg/diagnostics (velocity potential): |
o pkg/diagnostics (velocity potential): |
| 250 |
- fix velocity-potential calculation when using OBCS: balance net inflow |
- fix velocity-potential calculation when using OBCS: balance net inflow |
| 251 |
at each level (new S/R OBCS_DIAG_BALANCE). |
at each level (new S/R OBCS_DIAG_BALANCE). |
| 296 |
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
Add Sub-Meso Eddies parameterisation from Baylor (for now, disabled with TAF), |
| 297 |
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
and test it in verification exp. "front_relax.bvp" (update output.bvp.txt) |
| 298 |
|
|
| 299 |
checkpoint63 (2011/07/11) |
checkpoint63 (2011/07/11) |
| 300 |
o pkg/exch2: |
o pkg/exch2: |
| 301 |
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
- rename+move: nTiles in W2_EXCH2_PARAMS.h --> exch2_nTiles in W2_EXCH2_TOPOLOGY.h |
| 302 |
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
- exch2 version of Cumul-Sum routine: S/R W2_SET_MAP_CUMSUM set up the |
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