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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/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 |
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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) |
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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 |
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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 |
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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). |
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o toolm/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. |
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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/incCPP_OPTIONS.h). |
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o model/src: |
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- remove parameter "useOldFreezing" from PARAMS.h and push it to the |
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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). |
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o pkg/gmredi: |
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- add option (GM_CALC_TRANSP_FROM_VEL) to compute transport directly from |
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velocity (same scheme but affects machine truncation) for GM_AdvForm. |
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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. |
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checkpoint64q (2013/11/17) |
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o verification: |
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- generate new output on baudelaire (gfortran, -ieee) for OpenAD experiments |
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tutorial_global_oce_biogeo and global_ocean.90x40x15. |
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- generate new output (growth & melt) for seaice_itd experiment after |
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updating the input pickup_seaice files (previously wrong). |
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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 |
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(instead of _GLOBAL_SUM_RL) to get the final cost from all procs & threads: |
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o this fixes global-sum value if multi-threads (since GLOBAL_SUM_TILE_RL |
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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, |
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thsice_cost_final.F and ecco_cost_final.F (this one affects lab_sea |
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forward gradients: update output). |
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- update */code_oad/externalDummies.F by adding dummy GLOBAL_SUM_TILE_RL |
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S/R and, for most exp., also comment out GLOBAL_SUM_R8. |
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o pkg/mom_common: |
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- move to pkg/mom_common and model/src (previously in tutorial_deep_convection |
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code) 2nd version of isotropic 3-D Smagorinsky code interface: strain and |
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viscosity are locally declared in dynmics.F and pass as argument to CALC_GW; |
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ensure that all field value that are used are set. |
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o tutorial_deep_convection (smag3d): |
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- add missing scaling in mom_calc_smag_3d.F; |
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- set smag3D_coeff in input.smag3d such that results do not change. |
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o pkg/dic: |
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- change dic_cost.F to compute cost on each tile first and then apply |
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GLOBAL_SUM_TILE_RL: this affects forward gradient of AD experiments |
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tutorial_dic_adjoffline & tutorial_global_oce_biogeo; update output. |
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- remove kLev argument and use GLOBAL_SUM_TILE_RL in tracer_meanarea. |
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o eesupp/src & pkg/mdsio: |
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- remove gather/scatter_vector.F (from eesupp) and mdsio_read/writevector.F |
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(from pkg/mdsio) since they are no longer used for tape IO. |
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- move simple C subroutine "setdir.c" from pkg/compon_communic to eesupp/src |
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(+ keep a copy in pkg/atm_ocn_coupler). |
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o verification/isomip: |
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- split domain in 8 squared tiles (instead of just 2) for FWD, AD & OAD tests. |
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o tools/build_options: |
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- optfile linux_amd64_ifort11, fast (no ieee) case: |
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to get a working restart for all experiments, add "-fp-model source" |
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to FOPTIM (also remove "-opt-streaming-stores auto" <- this is the default). |
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checkpoint64p (2013/10/20) |
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o pkg/autodiff: |
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- adread_adwrite.F: when type and length do not match ALLOW_AUTODIFF_WHTAPEIO |
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criteria, return to simple (default) tape IO format. |
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o pkg/mdsio (+ eesupp/src): |
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- rewrite/simplify tape-IO S/R (new S/R MDS_READ/WRITE_TAPE replace |
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previous MDSREAD/WRITEVECTOR) with 2 array argument from each type (R4/R8); |
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- fix globalFile and singleCpuIO options using simpler global mapping. |
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- new pairs of scatter/gather vector S/R (one for each type, generated from |
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template) corresponding to simpler global mapping. |
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- adread_write.F: switch to new S/R (but leave old calls commented) and write |
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to globalFile when parameter globalFiles is set to True. |
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- switch on useSingleCpuIO in AD experiments: global_ocean.90x40x15 & isomip. |
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o pkg/autodiff: |
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- adread_adwrite.F: add a hack for RS arrays (when RS=real*4); |
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with ALLOW_AUTODIFF_WHTAPEIO defined, since corresponding (real*4) is |
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missing, just add a STOP if array type do not match. |
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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: |
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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: |
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- add 1rst version of isotropic 3-D Smagorinsky code (from Louis-Philippe), |
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for now all in this exp. code dir. |
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- add secondary test using Smag-3D viscosity (keep very low backgroud visc for |
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testing) and flux-limter advection scheme for Temp. (no explicit diffusion). |
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o eesupp/src: |
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- added SINGLE_DISK_IO option because reading of parameter files on |
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very large number of processors did not work with existing set-up |
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checkpoint64o (2013/09/25) |
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o pkg/atm_phys & atm_compon_interf: |
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- allows for coupling of gray-atmosphere (atm_phys) with ocean. |
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o tools/build_options: |
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- switch from "-fPIC" to "-mcmodel=medium" in optfiles: linux_amd64_gfortran |
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& linux_amd64_ifort11 and in linux_amd64_g77 & linux_amd64_open64 also |
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remove CPP setting (was identical to genmake2 default). |
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o pkg/gmredi & model/src: Some updating and work done on the residual model. |
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- created new file model/src/calc_eddy_stress.F to calculate the eddy stress. |
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- fixed up the calculation of the eddy stress and how it is added to the |
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external forcing via taueddy_external_forcing.F |
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- at the moment, it is very experimental and only works with the variable eddy |
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diffusivity calculated in gmredi_k3d.F |
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o pkg/seaice/seaice_check.F: add a check to catch the case of specifying |
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lw/swfluxfile instead of lw/swdownfile in data.exf together with pkg/seaice |
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o testreport (& tools/do_tst_2+2): |
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- for MPI test, set default COMMAND to 'mpirun -v -np TR_NPROC ./{executable}' |
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o tools/build_options: linux_amd64_gfortran & linux_amd64_ifort11: |
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- remove CPP='cpp -traditional -P' (this is genmake2 default) |
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- add switch (for big setups) to use 'medium' memory-model (but leave it |
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commented out for now). Note: needed with FC 19 to compile big setups. |
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o pkg/atm_compon_interf: |
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- regroup per field origin (model & pkgs) the coupling storage routines |
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(which accumalate in time each coupling field) |
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- move bi,bj loops inside atm_store_my_data.F and store also wind-stress; |
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update accordingly + simplify aim_do_physics.F |
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checkpoint64n (2013/08/26) |
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o pkg/bbl: |
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- update formulation to reduce dispersion of tracer properties in bbl |
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- replaced horizontal and vertical transport parameters with velocities |
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- changes results for verification/global_with_exf.yearly |
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o verification/halfpipe_streamice: |
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- change to matrix construction; update both Fwd & AD output. |
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o verification/tutorial_tracer_adjsens: |
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- OpenAD test: switch to vector-invariant momentum since fluxform with |
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rStar causes problems with OpenAD; update output. |
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o tools: |
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- genmake2: define a common prefix for all temp-file names ; move them |
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to local /tmp disk (but would be easy to move them back); |
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- xmakedepend: apply the same switch for temp-files. |
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o pkg/offline: |
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- changes for use with rStar (NLFS): assume that we continue to provide |
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UVELMASS/hFacW_ini & VVELMASS/hFacS_ini (hFacWi,S_ini as written in grid |
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output files) and apply r* scaling at each time-step (function of the time |
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varying Eta field); use normal pickup files (needed for restart with NLFS). |
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o adjoint with OpenAD: |
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- move OpenAD-specific files from verification/OpenAD/code_oad_all to a new |
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package openad. This package has to be compiled for all runs with OpenAD |
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instead of specifying code_oad_all as a modification directory. |
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- link the fortran templates from tools/OAD_support to the build directory |
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for preprocessing to avoid conflicts between different setups compiled |
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simultaneously and simplify cleanup. |
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o pkg/exf: |
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- in exf_getforcing.F: comment out most of the EXCH calls (fields used by |
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main model or other pkgs are exchanged in EXF_MAPFIELDS). |
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o model/src: |
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- do_stagger_fields_exchanges.F: skip EXCH calls when using pkg/offline |
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(similar to do_fields_blocking_exchanges.F). |
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o tools/genmake2: |
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- remove TAF output src code just before calling staf (when not doing a fresh |
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built, will stop if things go wrong with staf). |
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- fix target "adobj" (left from TAF version-2 transition) |
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o pkg/diagnostics: |
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- add a parameter to track the status of pkg/diagnostics activation; |
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this replace/extend the use of logical param "settingDiags" (to check |
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when adding diag to the list) to also check any DIAGNOSTICS_[]FILL* call. |
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New S/R to print error message and stop when pkgStatus is not right. |
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- to try: add a warning when "data.diagnostics" exist but useDiagnostics=F. |
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|
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checkpoint64m (2013/08/13) |
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o model/inc: |
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- move FCORI_MACROS.h from PARAMS(_MACROS).h to GRID_MACROS.h (left from |
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8 yrs ago modif when Coriolis arrays were moved from PARAMS.h to GRID.h) |
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o pkg/kpp & aim_v23: |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
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o pkg/seaice: |
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- restore (last time on 2011/12/24) ability to compile pkg/seaice with |
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undefined pkg/exf ALLOW_ATM_TEMP or ALLOW_RUNOFF CPP-options. |
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- only call DIAGNOSTICS_FILL when useDiagnostics=TRUE. |
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o eesupp/src: |
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- fix check for overlap-size argument (myOLn.GT.MAX_OLY_EXCH) |
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in exch1_rx[_ad].template (thanks to Francois Lefeuvre report). |
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o switch to TAF version-2: |
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- add flow directives to "freeze" naming convention for ad-routines that |
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are used in I/O routines of adjoint state and associated common blocks |
| 200 |
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that are used in adcommon.h (backward compatible with version-1) |
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- update all ad-optfiles (in tools/adjoint_options + few local to some |
| 202 |
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verification exp) to switch to latest TAF version (currently 2.5.5); |
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merge "*_mpi" adoptfiles into the corresponding non-mpi (but commented |
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out except for diva). |
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- the major change with TAF version-2 is that both the differentiated |
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routines and the forward routines (new) are returned as part of the TAF |
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output source code. Update genmake2 accordingly. |
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- new output for AD experiment tutorial_global_oce_biogeo (better AD gradient |
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with version-2 when compared to TLM or FWD gradient); other experiments |
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output show minor changes (machine truncation level); update the few AD & |
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TLM output with 12 matching digits only (some prior to version-2 switch). |
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|
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checkpoint64l (2013/08/05) |
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o model/src: |
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- in dynamics.F, skip the call to CALC_VISCOSITY if momViscosity=F |
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- main_do_loop.F: no longer includes additional (AUTODIFF) header files |
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when using TAF but only if using OpenAD. |
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o pkg/mom_common+fluxform+vecinv: |
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- always set horiz. viscosity arrays to background value before calling |
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MOM_CALC_VISC (in MOM_FLUXFORM & MOM_VECINV) and call S/R MOM_CALC_VISC |
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only when using variable horiz. viscosity (useVariableVisc=T); |
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- simplify mom_vecinv.F (only 1 block for momViscosity). |
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o pkg/mom_common: variable horiz. viscosity in NH code |
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- move horiz-viscosity 3-D arrays viscAh_W & viscA4_W (used in calc_gw.F) |
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from model/inc/NH_VARS.h to pkg/mom_common/MOM_VISC.h |
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- store in common block (in MOM_VISC.h) logical parameters: useHarmonicVisc, |
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useBiharmonicVisc & useVariableVisc. |
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- fix old bug (already in 1rst implementation of variable horizontal viscosity |
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in calc_gw.F, version 1.27, 2006/06/20): |
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horizontal bi-harmonic viscosity in gW was missing when wiscA4W=0 |
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even if variable bi-harmonic viscosity (e.g., viscA4Grid) was non-zero. |
| 232 |
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- change background horiz viscosity in vertical momentum (gW) to always be |
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viscAhW,viscA4W (instead of switching to viscAhD, viscA4D when using |
| 234 |
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any type of variable viscosity, e.g., viscAh/4Grid) |
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- change default value of viscAhW,viscA4W to viscAhD,viscA4D (instead of |
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viscAh,viscA4) which default to viscAh,viscA4 : this avoid missing |
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horiz. viscosity in W eq when just setting viscAhD/Z,viscA4D/Z (since |
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default viscAh,viscA4 is zero). |
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o model/src: |
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- extend length of drC & recip_drC from Nr to Nr+1. |
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o Divided Adjoint (DIVA) with MPI: |
o Divided Adjoint (DIVA) with MPI: |
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- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
- genmake2: do not create local ./mpi_headers dir when no file to copy into. |
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- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
- remove option ALLOW_DIVIDED_ADJOINT_MPI (replaced by ALLOW_DIVIDED_ADJOINT |
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