| 4 |
Notes on tags used in MITgcmUV |
Notes on tags used in MITgcmUV |
| 5 |
============================== |
============================== |
| 6 |
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|
| 7 |
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o pkg/exch2: |
| 8 |
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- in exch2*_get_rx[1,2]: use new list "W2_tileIndex" to replace search |
| 9 |
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through list of all tiles my proc owns. |
| 10 |
|
o model/src: |
| 11 |
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- AUTODIFF only: in calc_adv_flow.F, recompute rTransKp (instead of copying |
| 12 |
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from rTrans) to simplify dependencies (no need to store rTrans anymore in |
| 13 |
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calling S/R); this affects AD results at machine truncation level: |
| 14 |
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update AD-output (TAF) of experiments: 1D_ocean_ice_column, |
| 15 |
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bottom_ctrl_5x5 & obcs_ctrl (12 digits for AD grad, same FWD grad). |
| 16 |
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o tools/build_options: |
| 17 |
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- simplify Warnings options (-ieee & -devel cases) in linux_amd64_gfortran |
| 18 |
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o coupling interface pkgs: |
| 19 |
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[compon_communic, atm_compon_interf & ocn_compon_interf] |
| 20 |
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- move declaration of local array "ibuf" out of header file "CPLR_SIG.h" |
| 21 |
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to each S/R that needs it; remove un-used variables. |
| 22 |
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- change component tile registration (cpl_register.F in both compon_interf |
| 23 |
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and mitcomponent_tile_register.F) to pass the full list of tiles |
| 24 |
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information (including bi,bj) in 1 vector (instead of in a bi,bj matrix). |
| 25 |
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- with pkg/exch2: adopt the same convention used for I/O to define mapping |
| 26 |
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towards coupler global array (unless W2_useE2ioLayOut=F): |
| 27 |
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a) can now use different tiling between atm & ocn comp. |
| 28 |
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b) no needs to modify the run-Off map when changing tiling (was needed |
| 29 |
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even if using the same tiling between atm & ocn). |
| 30 |
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c) will allow to run with blank-tiles in 1 component (e.g., for ocean |
| 31 |
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full land tiles); not yet tested. |
| 32 |
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- check for valid mapping from comp. tile to coupler global array |
| 33 |
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- improve report of tile registration results to log file. |
| 34 |
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o pkg/exch2: |
| 35 |
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- in eesupp/src/eeboot.F: move call to W2_EEBOOT before Coupler |
| 36 |
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tile-registration (CPL_REGISTER); |
| 37 |
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- activate (un-comment) definition and setting of "W2_tileIndex" list to |
| 38 |
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store the local bi,bj indices of each tile; |
| 39 |
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- also print bi,bj in local report to log file; |
| 40 |
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- fix pkg/debug/debug_cs_corner_uv.F for the case nSy > 1 (left from |
| 41 |
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Jun 2009 modif of pkg/exch2). |
| 42 |
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o testing on baudelaire: |
| 43 |
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- run 2 tests at a time: no significant slow down (since enough cpu) and |
| 44 |
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get the full set of test done earlier |
| 45 |
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- switch the ifort test to "-devel" ; run the OpenAD test everyday. |
| 46 |
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o model/src/thermodynamics.F and routines called from it: |
| 47 |
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- pkg/gmredi: gmredi_residual_flow.F (replacing gmredi_calc_uvflow.F & |
| 48 |
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gmredi_calc_wflow.F) to update eulerian velocity (input) into residual |
| 49 |
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velocity (outp) by adding bolus velocity. |
| 50 |
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- model/src: calc_adv_flow.F (replacing calc_common_factors.F) to compute |
| 51 |
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mass transport from velocity + lateral grid cell area |
| 52 |
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- rename calc_gt.F to temp_integrate.F (includes call to TIMESTEP_TRACER) |
| 53 |
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- rename calc_gs.F to salt_integrate.F (includes call to TIMESTEP_TRACER) |
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in thermodynamics.F |
| 55 |
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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 |
| 57 |
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loop). |
| 58 |
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- compute locally (in thermodynamics.F) 3-D velocity field that is used to |
| 59 |
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advect tracers; pass it as argument to GAD_ADVECTION, GAD_SOM_ADVECT, |
| 60 |
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PTRACERS_ADVECTION, TEMP_INTEGRATE, SALT_INTEGRATE, PTRACERS_INTEGRATE, |
| 61 |
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GAD_IMPLICIT_R and PTRACERS_IMPLICIT |
| 62 |
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- update AD-output (TAF & OAD) of experiments: 1D_ocean_ice_column, |
| 63 |
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global_ocean.90x40x15, tutorial_global_oce_biogeo and |
| 64 |
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tutorial_tracer_adjsens (+ TLM output). |
| 65 |
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o tools/OAD_support and (verification/*/) code_oad: |
| 66 |
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- OAD_support/cb2mGetModules.csh: add PACKAGES_CONFIG.h in header file to |
| 67 |
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module conversion ; remove unneeded CPP_EEOPTIONS.h. |
| 68 |
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- code_oad/CPP_OPTIONS.h: remove PACKAGES_CONFIG.h and use a more standard |
| 69 |
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version (closer to model/inc/CPP_OPTIONS.h). |
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o model/src: |
| 71 |
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- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
| 72 |
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retired list of parameters (routine FREEZE has been replace by surface |
| 73 |
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freezing (10.yrs ago) and by pkg/frazil (interior freezing). |
| 74 |
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o pkg/gmredi: |
| 75 |
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- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
| 76 |
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velocity (same scheme but affects machine truncation) for GM_AdvForm. |
| 77 |
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- update output of FWD experiments: front_relax.bvp, |
| 78 |
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global_ocean.90x40x15.dwnslp, global_ocean.cs32x15 and ideal_2D_oce. |
| 79 |
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|
| 80 |
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checkpoint64q (2013/11/17) |
| 81 |
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o verification: |
| 82 |
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- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
| 83 |
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tutorial_global_oce_biogeo and global_ocean.90x40x15. |
| 84 |
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- generate new output (growth & melt) for seaice_itd experiment after |
| 85 |
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updating the input pickup_seaice files (previously wrong). |
| 86 |
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o pkg/cost: |
| 87 |
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- define a "final cost function" for each tile, and use GLOBAL_SUM_TILE_RL |
| 88 |
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(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
| 89 |
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o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL |
| 90 |
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cannot be applied to var in common block). |
| 91 |
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o allows to get results independent of tile-per-proc setting (if using |
| 92 |
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slower GLOBAL_SUM_SEND_RECV option). |
| 93 |
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- update accordingly: seaice_cost_final.F, shelfice_cost_final.F, |
| 94 |
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thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
| 95 |
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forward gradients: update output). |
| 96 |
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- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
| 97 |
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S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
| 98 |
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o pkg/mom_common: |
| 99 |
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- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
| 100 |
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code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
| 101 |
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viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
| 102 |
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ensure that all field value that are used are set. |
| 103 |
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o tutorial_deep_convection (smag3d): |
| 104 |
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- add missing scaling in mom_calc_smag_3d.F; |
| 105 |
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- set smag3D_coeff in input.smag3d such that results do not change. |
| 106 |
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o pkg/dic: |
| 107 |
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- change dic_cost.F to compute cost on each tile first and then apply |
| 108 |
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GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
| 109 |
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tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
| 110 |
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- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
| 111 |
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o eesupp/src & pkg/mdsio: |
| 112 |
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- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
| 113 |
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(from pkg/mdsio) since they are no longer used for tape IO. |
| 114 |
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- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
| 115 |
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(+ keep a copy in pkg/atm_ocn_coupler). |
| 116 |
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o verification/isomip: |
| 117 |
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- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
| 118 |
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o tools/build_options: |
| 119 |
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- optfile linux_amd64_ifort11, fast (no ieee) case: |
| 120 |
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to get a working restart for all experiments, add "-fp-model source" |
| 121 |
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to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
| 122 |
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|
| 123 |
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checkpoint64p (2013/10/20) |
| 124 |
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o pkg/autodiff: |
| 125 |
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- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
| 126 |
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criteria, return to simple (default) tape IO format. |
| 127 |
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o pkg/mdsio (+ eesupp/src): |
| 128 |
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- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
| 129 |
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previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
| 130 |
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- fix globalFile and singleCpuIO options using simpler global mapping. |
| 131 |
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- new pairs of scatter/gather vector S/R (one for each type, generated from |
| 132 |
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template) corresponding to simpler global mapping. |
| 133 |
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- adread_write.F: switch to new S/R (but leave old calls commented) and write |
| 134 |
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to globalFile when parameter globalFiles is set to True. |
| 135 |
|
- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
| 136 |
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o pkg/autodiff: |
| 137 |
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- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
| 138 |
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with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
| 139 |
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missing, just add a STOP if array type do not match. |
| 140 |
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o pkg/exf: |
| 141 |
|
- to allow to use seaice-fraction from pkg/exf in other pkgs than pkg/seaice: |
| 142 |
|
rename CPP option EXF_ALLOW_SEAICE_RELAX to EXF_SEAICE_FRACTION |
| 143 |
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and rename array obsSIce to exf_iceFraction. |
| 144 |
|
o tutorial_deep_convection: |
| 145 |
|
- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
| 146 |
|
for now all in this exp. code dir. |
| 147 |
|
- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
| 148 |
|
testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
| 149 |
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o eesupp/src: |
| 150 |
|
- added SINGLE_DISK_IO option because reading of parameter files on |
| 151 |
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very large number of processors did not work with existing set-up |
| 152 |
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|
| 153 |
|
checkpoint64o (2013/09/25) |
| 154 |
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o pkg/atm_phys & atm_compon_interf: |
| 155 |
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- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
| 156 |
|
o tools/build_options: |
| 157 |
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- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
| 158 |
|
& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
| 159 |
|
remove CPP setting (was identical to genmake2 default). |
| 160 |
|
o pkg/gmredi & model/src: Some updating and work done on the residual model. |
| 161 |
|
- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
| 162 |
|
- fixed up the calculation of the eddy stress and how it is added to the |
| 163 |
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external forcing via taueddy_external_forcing.F |
| 164 |
|
- at the moment, it is very experimental and only works with the variable eddy |
| 165 |
|
diffusivity calculated in gmredi_k3d.F |
| 166 |
|
o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
| 167 |
|
lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
| 168 |
|
o testreport (& tools/do_tst_2+2): |
| 169 |
|
- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
| 170 |
|
o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
| 171 |
|
- remove CPP='cpp -traditional -P' (this is genmake2 default) |
| 172 |
|
- add switch (for big setups) to use 'medium' memory-model (but leave it |
| 173 |
|
commented out for now). Note: needed with FC 19 to compile big setups. |
| 174 |
|
o pkg/atm_compon_interf: |
| 175 |
|
- regroup per field origin (model & pkgs) the coupling storage routines |
| 176 |
|
(which accumalate in time each coupling field) |
| 177 |
|
- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
| 178 |
|
update accordingly + simplify aim_do_physics.F |
| 179 |
|
|
| 180 |
|
checkpoint64n (2013/08/26) |
| 181 |
|
o pkg/bbl: |
| 182 |
|
- update formulation to reduce dispersion of tracer properties in bbl |
| 183 |
|
- replaced horizontal and vertical transport parameters with velocities |
| 184 |
|
- changes results for verification/global_with_exf.yearly |
| 185 |
|
o verification/halfpipe_streamice: |
| 186 |
|
- change to matrix construction; update both Fwd & AD output. |
| 187 |
|
o verification/tutorial_tracer_adjsens: |
| 188 |
|
- OpenAD test: switch to vector-invariant momentum since fluxform with |
| 189 |
|
rStar causes problems with OpenAD; update output. |
| 190 |
|
o tools: |
| 191 |
|
- genmake2: define a common prefix for all temp-file names ; move them |
| 192 |
|
to local /tmp disk (but would be easy to move them back); |
| 193 |
|
- xmakedepend: apply the same switch for temp-files. |
| 194 |
|
o pkg/offline: |
| 195 |
|
- changes for use with rStar (NLFS): assume that we continue to provide |
| 196 |
|
UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
| 197 |
|
output files) and apply r* scaling at each time-step (function of the time |
| 198 |
|
varying Eta field); use normal pickup files (needed for restart with NLFS). |
| 199 |
|
o adjoint with OpenAD: |
| 200 |
|
- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
| 201 |
|
package openad. This package has to be compiled for all runs with OpenAD |
| 202 |
|
instead of specifying code_oad_all as a modification directory. |
| 203 |
|
- link the fortran templates from tools/OAD_support to the build directory |
| 204 |
|
for preprocessing to avoid conflicts between different setups compiled |
| 205 |
|
simultaneously and simplify cleanup. |
| 206 |
|
o pkg/exf: |
| 207 |
|
- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
| 208 |
|
main model or other pkgs are exchanged in EXF_MAPFIELDS). |
| 209 |
|
o model/src: |
| 210 |
|
- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
| 211 |
|
(similar to do_fields_blocking_exchanges.F). |
| 212 |
|
o tools/genmake2: |
| 213 |
|
- remove TAF output src code just before calling staf (when not doing a fresh |
| 214 |
|
built, will stop if things go wrong with staf). |
| 215 |
|
- fix target "adobj" (left from TAF version-2 transition) |
| 216 |
|
o pkg/diagnostics: |
| 217 |
|
- add a parameter to track the status of pkg/diagnostics activation; |
| 218 |
|
this replace/extend the use of logical param "settingDiags" (to check |
| 219 |
|
when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
| 220 |
|
New S/R to print error message and stop when pkgStatus is not right. |
| 221 |
|
- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
| 222 |
|
|
| 223 |
|
checkpoint64m (2013/08/13) |
| 224 |
|
o model/inc: |
| 225 |
|
- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
| 226 |
|
8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
| 227 |
|
o pkg/kpp & aim_v23: |
| 228 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 229 |
|
o pkg/seaice: |
| 230 |
|
- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
| 231 |
|
undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
| 232 |
|
- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
| 233 |
|
o eesupp/src: |
| 234 |
|
- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
| 235 |
|
in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
| 236 |
|
o switch to TAF version-2: |
| 237 |
|
- add flow directives to "freeze" naming convention for ad-routines that |
| 238 |
|
are used in I/O routines of adjoint state and associated common blocks |
| 239 |
|
that are used in adcommon.h (backward compatible with version-1) |
| 240 |
|
- update all ad-optfiles (in tools/adjoint_options + few local to some |
| 241 |
|
verification exp) to switch to latest TAF version (currently 2.5.5); |
| 242 |
|
merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
| 243 |
|
out except for diva). |
| 244 |
|
- the major change with TAF version-2 is that both the differentiated |
| 245 |
|
routines and the forward routines (new) are returned as part of the TAF |
| 246 |
|
output source code. Update genmake2 accordingly. |
| 247 |
|
- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
| 248 |
|
with version-2 when compared to TLM or FWD gradient); other experiments |
| 249 |
|
output show minor changes (machine truncation level); update the few AD & |
| 250 |
|
TLM output with 12 matching digits only (some prior to version-2 switch). |
| 251 |
|
|
| 252 |
|
checkpoint64l (2013/08/05) |
| 253 |
|
o model/src: |
| 254 |
|
- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
| 255 |
|
- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
| 256 |
|
when using TAF but only if using OpenAD. |
| 257 |
|
o pkg/mom_common+fluxform+vecinv: |
| 258 |
|
- always set horiz. viscosity arrays to background value before calling |
| 259 |
|
MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
| 260 |
|
only when using variable horiz. viscosity (useVariableVisc=T); |
| 261 |
|
- simplify mom_vecinv.F (only 1 block for momViscosity). |
| 262 |
|
o pkg/mom_common: variable horiz. viscosity in NH code |
| 263 |
|
- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
| 264 |
|
from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
| 265 |
|
- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
| 266 |
|
useBiharmonicVisc & useVariableVisc. |
| 267 |
|
- fix old bug (already in 1rst implementation of variable horizontal viscosity |
| 268 |
|
in calc_gw.F, version 1.27, 2006/06/20): |
| 269 |
|
horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
| 270 |
|
even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
| 271 |
|
- change background horiz viscosity in vertical momentum (gW) to always be |
| 272 |
|
viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
| 273 |
|
any type of variable viscosity, e.g., viscAh/4Grid) |
| 274 |
|
- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
| 275 |
|
viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
| 276 |
|
horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
| 277 |
|
default viscAh,viscA4 is zero). |
| 278 |
|
o model/src: |
| 279 |
|
- extend length of drC & recip_drC from Nr to Nr+1. |
| 280 |
|
o Divided Adjoint (DIVA) with MPI: |
| 281 |
|
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
| 282 |
|
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
| 283 |
|
and ALLOW_USE_MPI) from model/src code and from ECCO_CPPOPTIONS.h. |
| 284 |
|
|
| 285 |
|
checkpoint64k (2013/07/23) |
| 286 |
|
o tools/OAD_support: |
| 287 |
|
- avoid the need for file "oadtempflile" in insertTemplateDir.bash |
| 288 |
|
and remove it from genmake2. |
| 289 |
|
o tools/build_options: |
| 290 |
|
- remove MPI_HEADER_FILES_INC setting (no longer used) and comment out |
| 291 |
|
MPI_HEADER_FILES list (let genmake2 find the missing headers) |
| 292 |
o verification/halfpipe_streamice: |
o verification/halfpipe_streamice: |
| 293 |
-change to driving stress formulation, affects results |
- change to driving stress formulation; update both Fwd & AD output. |
| 294 |
|
o tools/genmake2 and Divided Adjoint with MPI: |
| 295 |
|
- remove default setting of MPIINCLUDEDIR from $MPIHOME (always been broken); |
| 296 |
|
- only create local ./mpi_headers dir if using MPI and MPIINCLUDEDIR is set; |
| 297 |
|
- add new variable (LOCAL_MPI_HEADERS, replace MPI_HEADER_FILES_INC) in |
| 298 |
|
Makefile, which is set by genmake2, and check which mpi-headers are needed. |
| 299 |
|
Note: need to update adjoint_options/adjoint_diva_mpi accordingly. |
| 300 |
|
- update target "CLEAN" (to also remove ./mpi_headers/ dir). |
| 301 |
o testreport: |
o testreport: |
| 302 |
- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
- changes for Divided Adjoint Run: when file "run_ADM_DIVA" is present, |
| 303 |
perform additional runs (number of additional runs is "add_DIVA_runs" taken |
perform additional runs (number of additional runs is "add_DIVA_runs" taken |
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