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start big merge by removing stuff
move pkg-specific flow directives from pkg/autodiff to corresponding pkg
Bringing autodiff/ up to date with code
Very prelim. preparations for forward dump&restart during adjoint calculation.
Merging from ecco-branch: Use cluster local disks for purely local I/O vs. globally visible disks needed for ctrl stuff.
Use cluster local disks for purely local I/O vs. globally visible disks needed for ctrl stuff.
Small adjustments to global2x2_tot setup
o Modifications of obcs - bug fixes in cost package - bug fixes in grdchk package
Preparing next differentiable checkpoint and sync of MAIN vs. ecco-branch
Preparing next differentiable checkpoint and sync of MAIN vs. ecco-branch
Modifications, corrections and additions to obcs code.
Updating all adjoint-related makefiles
Modif's to enable tangent linear run in ECCO environment o main problem is missing call mdsreadfield out of exf_set_gen o incorrect g_active_write_... o (re-) init of bar files and g_bar files
Updating makefile to sync SRC list with cost/ ctrl/ exf/ obcs/
Modified adjoint/makefile and pkg/exf/exf_bulkformulae.F
updating
o exf totally restructured
- replaced all exf_set_ routines by one generic exf_set_gen.F
and made sure it's still differentiable
- split exf_getffields.F into new exf_bulkformulae.F
- exf_inscal_/exf_outscal_ suffixes consistent with field names
- updated adjoint/makefile and relevant verif. accordingly
Updating SOURCE list
makefile totally updated: o file list up to date with c49 o new target for tangent linear o old targets modified
Changes to restore differentiability of code w.r.t. previous tag (mostly adding new routines to make list and replacing pressure by totPhiHyd).
o Added cost_ice for sea-ice volume sensitivity experiment.
o added verification/lab_sea as per release1_p12_pre
o adjoint-friendly modifications to pkg/seaice
- adjoint-friendly modifications
seaice adjoint test case
Modified Files: adjoint/makefile verification/natl_box_adjoint/README
Modifications to correctly handle evap field for adjoint.
o Merging pkg/exf and pkg/seaice from cvs tag ecco_ice2
02/11/03 cvs tag ecco_ice1 Updated verification/natl_box_forward and natl_box_adjoint
Generate separate TAF std output for ftl and ad. Add target bothtaf.
o few modif.'s to get latest version adjointed (mainly kick out code in ini_linear_phisurf) o modif's to run adjoint with exactConserv o case GM_BOLUS_ADVEC should be cleaned S/R gmredi_slope_psi should be cleaned o verification/carbon now has exactConserv=.TRUE.
Updating makefile
Updating makefile list.
Bringing differentiability up to date.
Merging from release1_p8 branch:
o external_fields_load:
- added this routine to TAF list
- needed to make some common blocks global and additional storing
along the same lines as exf package (checkpoint_lev?_directives.h)
Added external_fields_load routine to TAF list. Update corresponding checkpointing lists (analog to exf handling of swapping).
Merging adjoint makefile from release1.
makefile up to date with new flow directive
Merging patches between release1_p1 and release1_p2: o fixed array boundary problem for adjoint (related to partial recomputation within subroutine related to dynamics -> calc_viscosity -> mom_... o fixed recomputation in thermodynamics o prepare (but not complete) recomputation problem in impldiff o fixed problem for adjoint of global_max o switched off sponge layer code in external_forcing Bug fix in ctrl_mask_set_yz (spotted by G. Gebbie)
Added dependency to .F -> .f
These changes constitute a patch to release1. They were made on a development branch called "release1_final" and are on the main trunk between chkpt44d_post and checkpoint44h_post along with other changes. This code is equivalent to chkpt44d_post with the following patches: - AD-related changes for GMRedi - fixes i KPP (delZ -> drF) - hook to OBCS songe layer code in external_forcing - errorMessageUnit non-zero in eeboot.F - modified test cost function and carbon verif.
Changes encapsulated by checkpoint43a-release1mods and chkpt44d_post
on the main trunk.
These are:
o added missing EXCLUDE_MONITOR flags
o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
(incompatible typ in MIN/MAX expressions caused problems
on IBM SP3)
o in genmake added variable MAKEDEPEND
plus resetting for case SunOS
o added timer_stats.c routine for IBM SP3
o removed variables in dynamics
o real fresh water flux implemented with non-linear free-surface.
o few fix (mask in shap_s2, EmPmR in external_field_load,
USE_NATURAL_BCS in solve_for_P);
o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
o merge of relevant stuff from the ecco-branch:
- genmake: removed $S64 overwrite for case SunOS
- pkg/exf: update and corrections for field swapping and obcs
- pkg/ecco: parameter lists for the_model_main, the_main_loop
harmonized between ECCO and MITgcm
- pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
updated checkpointing_lev... lists for obcs
- model/src: minor changes in forward_step, plot_field
added directive for divided adjoint in the_main_loop
- pkg/mdsio: added mdsio_gl_slice
o check parameters & config (chkpt44a_pre,post)
o OBC and NonLin_FrSurf.
o fix bug in mom_vi_del2uv
o select when filters are applied ; add options to zonal_filter (data.zonfilt)
o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
o update AIM experiments (NCEP input files)
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
o added some stuff for AD
These were merged with
cvs co -r release1 -P MITgcm
cd MITgcm
cvs update -kk
cvs update -j checkpoint43a-release1mods -j chkpt44d_post -d -P -kk
o added new cost routines to diff. list. o removed comm_stats, ini_communication_patterns from diff. list (no more need to "keep" MPI headers for adjoint generation)
Enable I/O swapping of surface flux control vector for adjoint.
Merged updates into release1_final.
Updated list for new routines.
Merging changes on MAIN between checkpoint43 and checkpoint43a-release1mods
Command: cvs -q update -jcheckpoint43 -jcheckpoint43a-release1mods -d -P
These changes are most of the changes between c43 and c44 except those
that occured after "12:45 11 Jan 2002". As far as I can tell it is
checkpoint43 with the following mods:
o fix bug in mom_vi_del2uv
o select when filters are applied ; add options to zonal_filter (data.zonfilt) o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
o update AIM experiments (NCEP input files)
o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
o added some stuff for AD
o Jamar wet-points
This update does not contain the following mods that are in checkpoint44
o bug fix in pkg/generic_advdiff/
- thread related bug, bi,bj arguments in vertical advection routines
o some changes to pkg/autodiff, pkg/cost, pkg/exf, pkg/ecco,
verification/carbon and model/src/ related to adjoint
o some new Matlab scripts for diagnosing model density
- utils/matlab/dens_poly3.m and ini_poly3.m
The list of exclusions is accurate based on a "cvs diff". The list of
inclusions is based on the record in doc/tag-index which may not be complete.
Small fix for SUN.
ssuming path for TAF and TAMC are known (e.g. in $path) -> $TAF and $TAMC are default.
Assuming path for TAF and TAMC are known (e.g. in $path) -> $TAF and $TAMC are default.
Removed src file from list.
o Updating adjoint/makefile to ECCO code o Adding optim and lsopt for line search optimization. o Adding verif. experiments for ECCO Code will be tagged ecco-branch-mod1.
* Updated adjoint/makefile
o removed "_ecco" from names
o added/modified forward mode options
o added dependent vector option
o tried SVD matrix computation (doesn't work;
too much memory use by TAF)
* Updated flow directives related to FTL
* removed global_sum__g.F (not necessary)
* initialise forward mode anomalies in ctrl_unpack.F
(so far "crude" initialization only).
* Added flag ALLOW_TANGENTLINEAR_RUN complememting
ALLOW_ADJOINT_RUN
* driver routine the_model_main.F needs separate call
to FTL routine G_THE_MAIN_LOOP with parameter list
identical to THE_MAIN_LOOP (TAF doesn't remove arguments).
* added template file tangentlinear_model.F
for forward mode.
Added option -nonew_arg to TAFFLAGS to retain consistency between TAF 1.3... and previous versions.
Removing ini_procs.f from AD list (doesn't have to and must not be differentiated).
Preparing adjoint of Held-Suarez: - bugfix for storing in absence of CD code - adding EXACT_CONSERV to AD list - new routine ini_autodiff to add TAMC-specific initialisations - adding Shapiro filter to AD list
Fixed AD-related problems: o Store directives up-to-date with re-arranged Adams-Bashforth (mainly thermodynamics.F) o New store directives for multi-dim. advection schemes * new CPP flag ALLOW_MULTI_DIM_ADVECTION * new common block and key passkey (mainly gad_advection.F) o Modified store directives for split of dynamics/thermodynamics for the case ALLOW_KPP o Cleaned argument list for timestep_tracer.F
Updated to rearranged Adams-Bashforth.
Target "adrestore" added to targets "adtaf" and "adtamc".
Updating to new gad_... mom_... routines.
Updated to code in c40pre8.
o New package pkg/rw/ needed new flow directives for TAMC. o Replacement of calc_mom_rhs by mom_fluxform and mom_vecinv needed update of adjoint/makefile and additional store directives in the_main_loop.F to cover all cases.
Updates to generate tangent linear code.
Extended list of code to be differentiated: o added routines related to diffkr, kapgm o added routines related to split into dynamics/thermodynamics.
Missing routine in SRC list added.
Added a flow directive file for ecco_check_exp.
Added S/R forward_step.F
Added more routines to be differentiated.
o Updated makefile to incorporate new routines and flow directives o Added "make adtaf" for usage of TAF instead of TAMC. o Bug fix in adjoint_ecco_sed.com o Removed some adjoint prototype code
Updated reference adjoint code and TAMC protocol for test case verification/vero/.
See doc/tag-index and doc/notes_c37_adj.txt Preparation for stand-alone autodifferentiability.
Modifications and additions to enable automatic differentiation. Detailed info's in doc/notes_c37_adj.txt
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