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adding ecco1x1 verification/global_with_CFC11 experiment
preparing verification/coupled_ucla for columbia
modifications of verification/coupled_ucla to run on lomax
o added the [#include "AD_CONFIG.h"] statement to all files that need it for adjoint/tl #defines o re-worked the build logic in genmake2 to support AD_CONFIG.h o removed tools/genmake since it no longer works
changes to pkg/cal and pkg/exf that allow and speed-up long integrations
disable pkg/cfc
remove admlm package
Modified ocean_inversion_project/input/data and tools/genmake
provide ARPACK interface
added "preliminary" support for SGI Altix in tools/genmake
o Added case gfdl-sgi-o3k o added option '-arpack' with default lib dir for arpack
extended DISABLE list
disable dic, gchem by default.
adding platform=itrda-linux-cluster
Adding platform=SP4 for bluesky.ucar.edu plus interactive run script
Added removal of fort.* files.
Changed initialization of variables so that defaults can be set in the users environment. e.g. setenv platform="myblessedmachine.com" in .cshrc
dding platform aer-linux-cluster+mpi
NB: Need to merge genmake between MAIN branch and ecco-branch
they've diverged a lot
Adding platform aer-linux-cluster+mpi
o add a new platform SunFire+mpi (SunFire 15000) to genmake
release1_p14 o Added interpolation routine pkg/exf/new_interp.F for on-the-fly interpolation. Enable with USE_EXF_INTERPOLATION and specify input grids in data.exf o Added direct pressure solver pkg/solver. See pkg/solver/README.directSolver for instructions.
NOOPTFILES & NOOPTFLAGS not reset if already defined (.e.g in .genmakerc)
o Reduced derivative singularities in pkg/seaice.
Adding -platform=SP4 Modif. for DEC Alpha (many dont have makedepend; use mkdep instead).
Merging from release1_p12: o Modifications for using pkg/exf with pkg/seaice - improved description of the various forcing configurations - added basic radiation bulk formulae to pkg/exf - units/sign fix for evap computation in exf_getffields.F - updated verification/global_with_exf/results/output.txt o Added pkg/sbo for computing IERS Special Bureau for the Oceans (SBO) core products, including oceanic mass, center-of-mass, angular, and bottom pressure (see pkg/sbo/README.sbo). o Lower bound for viscosity/diffusivity in pkg/kpp/kpp_routines.F to avoid negative values in shallow regions. - updated verification/natl_box/results/output.txt - updated verification/lab_sea/results/output.txt o MPI gather, scatter: eesupp/src/gather_2d.F and scatter_2d.F o Added useSingleCpuIO option (see PARAMS.h). o Updated useSingleCpuIO option in mdsio_writefield.F to work with multi-field files, e.g., for single-file pickup. o pkg/seaice: - bug fix in growth.F: QNET for no shortwave case - added HeffFile for specifying initial sea-ice thickness - changed SEAICE_EXTERNAL_FLUXES wind stress implementation o Added missing /* */ to CPP comments in pkg/seaice, pkg/exf, kpp_transport_t.F, forward_step.F, and the_main_loop.F o pkg/seaice: - adjoint-friendly modifications - added a SEAICE_WRITE_PICKUP at end of the_model_main.F
Modified File tools/genmake
Branch release1_coupled contains code for coupling
to UCLA atmospheric model:
cvs tag ucla1
Branched off tag release1_beta1
Modified eesupp/src/eeboot_minimal.F, eedie.F, exch_jam.F,
global_max.F, global_sum.F, gsum_jam.F, ini_procs.F, and main.F
model/src/dynamics.F, forward_step.F, freeze.F, ini_parms.F,
set_defaults.F, the_main_loop.F, the_model_main.F, timestep.F,
write_state.F, and mdsio_writefield.F
pkg/timeave/TIMEAVE_STATV.h, timeave_statv_write.F,
timeave_statvars.F, and model/inc/PARAMS.h,
Added model/src/do_coupled_ucla.F and verification/coupled_ucla
NOTES:
MPI_COMM_WORLD -> MPI_COMM_MODEL in
exch_jam.F, global_max.F global_sum.F, and gsum_jam.F
Added useSingleCpuIO: ini_procs.F, PARAMS.h, ini_parms.F,
set_defaults.F, mdsio_writefield.F, and subroutine
GATHER_2D in do_coupled_ucla.F
checkpoint47b_post
Merging from release1_p9:
o pkg/seaice
- removed GOTO's and added taf directives
- double precision constants to reduce the g77 (Linux)
to F77 (SGI) differences reported in release1_p8
o tools/genmake
- added SGI options
o verification/testscript
- updated to that of checkpoint47a_post
o verification/global_ocean.90x40x15/input/eedata
- modified for SGI f77 compatibility
o verification/lab_sea
- added description of sea-ice model
- added missing matlab routines
- added test of thermodynamics parallelization
Modified Files:
doc/tag-index pkg/seaice/SEAICE_FFIELDS.h
pkg/seaice/SEAICE_PARAMS.h pkg/seaice/adi.F
pkg/seaice/advect.F pkg/seaice/budget.F pkg/seaice/diffus.F
pkg/seaice/dynsolver.F pkg/seaice/groatb.F pkg/seaice/growth.F
pkg/seaice/lsr.F pkg/seaice/ostres.F
pkg/seaice/seaice_do_diags.F pkg/seaice/seaice_get_forcing.F
pkg/seaice/seaice_init.F pkg/seaice/seaice_model.F
pkg/seaice/seaice_readparms.F tools/genmake
verification/global_ocean.90x40x15/input/eedata
verification/lab_sea/README
verification/lab_sea/matlab/lookat_exp1.m
verification/lab_sea/matlab/lookat_exp2.m
verification/lab_sea/matlab/lookat_exp3.m
verification/lab_sea/matlab/lookat_exp4.m
verification/lab_sea/matlab/lookat_exp5.m
verification/lab_sea/matlab/lookat_exp6.m
verification/lab_sea/results/AREAtave.0000000010.data
verification/lab_sea/results/HEFFtave.0000000010.data
verification/lab_sea/results/UICEtave.0000000010.data
verification/lab_sea/results/VICEtave.0000000010.data
verification/lab_sea/results/output.txt
Added Files:
verification/lab_sea/seaice.ps
verification/lab_sea/matlab/lookat_exp7.m
verification/lab_sea/matlab/mmax.m
verification/lab_sea/matlab/mypcolor.m
verification/lab_sea/matlab/myquiver.m
verification/lab_sea/matlab/readbin.m
verification/lab_sea/matlab/wysiwyg.m
Removed Files:
verification/lab_sea/code/KPP_OPTIONS.h
release1_p9
o pkg/seaice
- removed GOTO's and added taf directives
- double precision constants to reduce the g77 (Linux)
to F77 (SGI) differences reported in release1_p8
o tools/genmake
- added SGI options
o verification/testscript
- updated to that of checkpoint47a_post
o verification/global_ocean.90x40x15/input/eedata
- modified for SGI f77 compatibility
o verification/lab_sea
- added description of sea-ice model
- added missing matlab routines
- added test of thermodynamics parallelization
Modified Files:
Tag: release1
doc/tag-index pkg/seaice/SEAICE_FFIELDS.h
pkg/seaice/SEAICE_PARAMS.h pkg/seaice/adi.F
pkg/seaice/advect.F pkg/seaice/budget.F pkg/seaice/diffus.F
pkg/seaice/dynsolver.F pkg/seaice/groatb.F pkg/seaice/growth.F
pkg/seaice/lsr.F pkg/seaice/ostres.F
pkg/seaice/seaice_do_diags.F pkg/seaice/seaice_get_forcing.F
pkg/seaice/seaice_init.F pkg/seaice/seaice_model.F
pkg/seaice/seaice_readparms.F tools/genmake
verification/testscript
verification/global_ocean.90x40x15/input/eedata
verification/lab_sea/README
verification/lab_sea/code/CPP_EEOPTIONS.h
verification/lab_sea/code/CPP_EEOPTIONS_MPI.h
verification/lab_sea/code/CPP_OPTIONS.h
verification/lab_sea/code/SIZE.h
verification/lab_sea/code/SIZE_2x1.h
verification/lab_sea/input/data
verification/lab_sea/matlab/lookat_exp1.m
verification/lab_sea/matlab/lookat_exp2.m
verification/lab_sea/matlab/lookat_exp3.m
verification/lab_sea/matlab/lookat_exp4.m
verification/lab_sea/matlab/lookat_exp5.m
verification/lab_sea/matlab/lookat_exp6.m
verification/lab_sea/results/AREAtave.0000000010.data
verification/lab_sea/results/HEFFtave.0000000010.data
verification/lab_sea/results/UICEtave.0000000010.data
verification/lab_sea/results/VICEtave.0000000010.data
verification/lab_sea/results/output.txt
Added Files:
Tag: release1
verification/lab_sea/seaice.ps
verification/lab_sea/matlab/lookat_exp7.m
verification/lab_sea/matlab/mmax.m
verification/lab_sea/matlab/mypcolor.m
verification/lab_sea/matlab/myquiver.m
verification/lab_sea/matlab/readbin.m
verification/lab_sea/matlab/wysiwyg.m
Removed Files:
Tag: release1
verification/lab_sea/code/KPP_OPTIONS.h
Turning off bulk_force and therm_seaice by default.
Turning off thermodynamic_seaice and bulk_forcing by default.
Added platform custom option "c01+pgi" for using Portland f90 compiler on the myrinet-3 cluster.
Merging from release1_p8 branch: Adding package parameters and hooks for new seaice package.
Adding new package: pkg/seaice Sea ice model by D. Menemenlis (JPL) and Jinlun Zhang (Seattle). The sea-ice code is based on Hibler (1979-1980). Two sea-ice dynamic solvers, ADI and LSR, are included.
I finally give in: g77 is now the first compiler in the list of compilers to search for. The only way to get the others is to specify -fc on the genmake command line. It's a shame since ifc is better but now that ifc is in /usr/local it is impossible to use testscript meaningfully...
Fix for Fujitsu suggested by Naoki Hirose. - added "-print" to "find" when searching packages.
Missing CPP define for pkg/debug
Damn, I hate SUNs.
Well, who'd have guessed that SUN ship g77 by default! I'm restricting the automatic search of compilers to Linux platforms until we do a general tidy up of genmake.
o added new option -cpp=... which defines a CPP macro on the cpp command line o added -fc=... which specifies the $FC variable o made the platform target "Linux*" now searches for ifc, g77, pgf77, f77 etc in the $PATH and select the appropriate options. This should be done for all platforms but I can't remember my passwords on anything except Linux boxes....
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
genmake with MAKEDEPEND variable was still missing in ecco-branch
Added PTRACERS package
This allows an arbitrary number of passive tracers to be integrated
forward simultaneously with the dynamicaly model.
+ Implemented so far:
- basic forward algorithm (time-stepping, advection, diffusion, convection)
- I/O and checkpointing
- GM/Redi *but* using the GM/Redi coefficient of Salt
+ Not implemented so far:
- KPP
- OBCS
+ No specific example supplied (yet) but global_ocean.90x40x15 has the
necessary data.ptracer file. Simply use -enable=ptracers and uncomment
line in data.pkg. PTRACER01 then reproduces Salt exactly.
+ This package is disabled by default since it increases storage.
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.
Added variable MAKEDEPEND. Is modified for case SunOS, uses ../tools/xmakedepend
o added tools/xmakedepend to circumvene shortcoming of SUN's makedepend (size too small) o in tools/genmake * invoking ../tools/xmakedepend instead of makedepend * changed compiler flags for case SunOS
o added tools/xmakedepend to circumvene shortcoming of SUN's makedepend (size too small) o in tools/genmake * invoking ../tools/xmakedepend instead of makedepend * changed compiler flags for case SunOS
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
Removed $S64 overwrite ('cat') for case SunOS.
Updating ecco-branch-mod1 to checkpoint44. Will be tagged ecco-branch-mod2.
Added "flt" to the default DISABLE list.
Adding TARGET_PWR3 for IBM SP3 platform.
Broke +pgi mode with last change. Swapped order so that PGI is checked for before g77.
Added entry to handle RH on alpha
Re-arranged sequence of operations for Adams-Bashforth o this does not change numbers o this makes it very easy to extract forcing/diffusion out of ABII by changing calling sequence in calc_gt, calc_gs,... Key modifications: o new s/r: ADAMS_BASHFORTH2 gT=3/2*gT-1/2*gTnm1 o changed TIMESTEP_TRACER from gTnm1=t+dt*(3/2*gT-1/2*gTnm1) to gT=T+dt*gT o changed CALC_GT,CALC_GS & CALC_GTR1 to calcuate "gT" defined by new timestep_tracer (ie. including forcing, ABII, N-L F-S, etc...) now calls ADAMS_BASHFORTH2 and FREESURF_RESCALE_G o changed CYCLE_TRACER appropriately T=gT only Other associated mods: o new s/r: FREESURF_RESCALE_G applies non-linear free-surface term this used to be in TIMESTEP_TRACER o added myIter as argument to CALC_GS,CALC_GT,CALC_GTR1
Fix script to be compatible with tcsh on Digital UNIX
Fix compiler options for backwards compatibility with Sun Workshop 5.0 compilers
New compiler options for SunOS: o faster o actually allows AIM pkg to compile
Typo in DEFINES.
Fix for SUNs: changed -fast to -dalign in order to avoid adding more and more routines to NOPTIMFILES. This should be viewed as a temporary fix.
Silly thing on SUNs: echo -n Fred echo's "-n Fred". Duh.
Added files mon_printstats_rl.F mon_printstats_rs.F to NOOPTFILES list in genmake for SunOS, otherwise compilation would fail on SunOS 5.8 (e.g. slough.mit.edu).
The "small_f" target should not be removed from genmake. It is needed for creating the TAMC source code.
Added new target to help testscript deal with the -quick option.
Added run-time control of vector-invariant/flux-form momentum eqns.
Now remove temporary file hlist.inc which was being left behind.
Fixed problem which infinite links; header files ended up linked to themselves because the ./ directory was the first in the INCLUDEDIRS list. Now INCLUDES has -I. in it and ./ is at end of search path.
Added (uncommented) header links. Header files are now linked just like other source files.
Added -ieee flag to genmake (only affect Linux for now) to see if we can pin-down this rediculous sensitivity of model to small changes in code. Testscript uses -ieee by default.
Removed KAP stuff for DEC's since most people don't have it and we weren't using it anyway.
Added grdchk to default disable list.
Added ini_cori.F to NOOPTFILES on SUNs. It seems any trig. fns inside loops get vectorized incorrectly! Definitately a compiler bug.
Added ini_spherical_polar_grid.F to NOOPTFILES for new SUNs.
Merge from branch pre38: o essential mods for cubed sphere o debugged atmosphere, dynamcis + physics (aim) o new packages (mom_vecinv, mom_fluxform, ...)
Added the following packages to default disable: autodiff cal cost ctrl ecco exf. We might think of adding kpp iand gmredi as well.
Changed "look" of commentary on packages to make it clearer what is enabled and what is disabled.
Added options -r8 -static for case IRIX64 - "Configuring for SGI Mips"
Added method for generating eesupp source code if it is needed. Does not break anything if the old code is place.
Tentative changes of paths for MPI/JAM to work on cnodes.
Sorting packages alphabetically so that the behaviour is "predictable". - otherwise they come out sorted by inode number!
Brought -help up to date.
Added inheritence to the -disable=pkg option. sub-directories inherit the disabled option. The enabled option is not inherited since all packages are enabled by default.
Changed search algorithm for packages; properly handles structured packages.
Avoid error trying to scan a file in ./pkg as if it were a directory.
package "timeave" replacing "diags": remove dir "diags" from standard path
Added makefile and cleanlinks targets to help automated testing.
Fixed -disable=all. I previously added a test to make sure that -disable=pkg failed if pkg didn't exist.
Switched order of source code directories (pkg/* now infront of model/src, eesupp/src and diags/src). Added catch for diabling non-existent package.
Simplified setting of EXEDIR to fix bug in .genmakerc
Change "make CLEAN" to clean *.meta and *.data files from $EXEDIR rather than $ROOTDIR/verification/*/input . Safer this way.
Broke -rootdir=dir when adding auto scan feature.
Added autoscan feature to set ROOTDIR if not specified.
Changes to make c35 work on DEC. Refs. to unitialized array elements and compile options.
Fixed comma separated lists bug.
Merged changes from branch "branch-atmos-merge" into MAIN (checkpoint34) - substantial modifications to algorithm sequence (dynamics.F) - packaged OBCS, Shapiro filter, Zonal filter, Atmospheric Physics
Changed -mymods CLO and MYMODS variable to -mods and MODS to satisfy Chris's paranoia that we're influenced by MOM. Poor boy needs help.
Fixes for SunOS csh (it's great how unportable csh is!)
Missing "/" in EXECUTABLE
Added -enable=pkg1 -disable=pkg2 options. *** Need to test on other platforms
Adding AIM physics code as package along with simple
test.
So far only checked that code still compiles with
#undef ALLOW_AIM
Next step is to test the code in action!
Two things to note
1. Modified genmake to have pgf77 defaults of
r8, line longer than 72 and declaration checking off
for files without IMPLCIT NONE. This is required
to get Francos code to compile.
2. Otherwise no changes to main code. Just package +
verification test.
Spelling correctino (pn -> on)
OK - so I didn't test it before commiting... ...now seems to work perfectly from any location. Fingers crossed.
Added .h files to scan of source directories to avoid errors due to directories with only .h files and no .F files.
o No longer use -f option for links. This was dangerous in the hands of the incompetent o Now use rules to create links. o Added -rootdir= and -mymods= options.o This allows multiple experiments to be concurrently compiled from the same source code which greatly reduces testing/debuggin time. The original mode of oepration: cd bin; ../tools/genmake make depend make is as before except the default action is to make Makefile rather than Makefile.$platform From the experiments location: cd verification/myexp/code (or location of additional/modified code) ../../../tools/genmake -rootdir=../../.. (or absolute path) make depend make Or if you are really sick: cd verification/myexp/inputs (or location where executable will be run) ../../../tools/genmake -rootdir=../../.. -mymods=../code (or absolute paths) make depend make Still to be done: Implement this under autoconf/make!?
Fix so that "make CLEAN" doesn't delete files in natl_box/output
Added csrclist.inc to the remove list after Makefile generation
Adopted to new routine external_fields_load.F.
Added target small_f to create source code for TAMC before compiling.
Added cases for Cray T90 (sn7113) and SV1 (sn3002): TARGET_CRAY_VECTOR. (P.H.)
Added paths to ../pkg/ directory.
Added yet another Hyades only path for the two-proc libraries
Set LIBS properly for JAM libaries. (affects Hyades only)
Tidied up the options for the Linux platform.
Minor mods for compiling on T3E.
Added "JAM" routines for use with Artic network (Hyades cluster).
Set value for WORDLENGTH on all platforms in genmake.
Implemented new I/O package (mdsio.F). This package does parallel
I/O in much the same way as dfile.F used to except it uses "direct
access" rather than (f77) unformatted sequential access.
Problems with dfile.F package included:
o unnecessary memory use (each process had two global sized buffers)
o inability to read the files it had written without post-processing
o "tiled" files were tiled by process/thread rather than actual tiles
o created huge numbers of files with no alternatives
Features of the mdsio.F package:
o direct-access binary writes
o no excessive memory use
o ability to read/write from multiple record files
o "tiled" files are based on "WRAPPER" tiles so that the number
and content of files is independent of the number of threads
and/or processes
o option to create single "global" files rather than "tiled" files
o ability to read both "global" and "tiled" files
[Caveat: the tiling of files must match the model tiles]
o checkpoints now use a single file per model section
ie. one file for the hydrostatic model core, one file
for the non-hydrostatic extensions and one file for the C-D
extensions
o the mid-level I/O routines now is broken into more source files
read_write_fld.F supplies basic I/O routines with the same interface
as the original I/O package
read_write_rec.F supplies I/O routines which allow multiple records
write_state.F writes the model state
checkpoint.F supplies the read/write checkpoint routines
All the example input data has had to be modified to be direct-access.
Otherwise only routines that used I/O have been affected and not
all of those have been due to the continuity of arguments in
the read_write_fld.F routines.
What needs to be done? We have to create a suite of conversion
utilities for users with old-style data. Also supply the option
for using old-style I/O, not just for die-hards but for reading
data too extensive to be converted. And more...
Changes for linux and command line operation.
Change of rule "Clean". Clean used to remove *.[Fc] but this might be dangerous. So now it removes only links.
Changes to allow for atmospheric integration builds of the code
Changes to support - g77 compilation under Linux - LR(1) form of 64-bit is D or E for constants - Modified adjoint of exch with adjoint variables acuumulated.
Correction to missing file tim.c and genmake for checkpoint15
Changes for new exchange routines which do general tile <-> tile connectivity, variable width overlap regions and provide hooks for shared memory and DMA protocols like Arctic, Memory Channel etc..
Added changes for SGI onyx support HP Exemplar support from Dimitri
We decided to skip the KAP preprocessor stage on the DEC Alpha's by default. (KAP isn't always available, even on our own well maintained platforms...)
Tidy up configure (now genmake!) and doc/README for release of checkpoint12.
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