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-revision 1.1093 by jmc,
Wed Apr 29 18:10:27 2009 UTC
+revision 1.1139 by jmc,
Wed Jul  8 23:38:05 2009 UTC
 Line 4 
 $Name$
      Notes on tags used in MITgcmUV
      ==============================
+ o pkg/thsice: add code for Near Infra-Red albedo (from Jeff)
+    (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
+ o move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
+   MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
+   to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
+ checkpoint61s
+ o pkg/exch2 (exch2_rxN_cube*):
+    remove last BARRIER (no need to synchronise after getting data from shared
+    buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
+ o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
+   and generate new output (for the 2 tests) using default rotationPeriod.
+ o pkg/exch2:
+   - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
+     (was already the case with AUTODIFF_EXCH2 defined)
+   - add bj in exch2 arrays and S/R.
+   - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
+     MLAdjust to exch2 (identical results except with MPI -> truncation diff);
+ o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
+   - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
+     GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
+   - verification experiment natl_box.longstep
+ o build_options: ifort+mpi_aces optfile (following Constantinos advise):
+   allow different versions of ifort (8 or 9) and different versions
+    of mpi (mpich or mpich2) to be used with the same optfile.
+   requires to load a netcdf module and set MPI_INC_DIR (see comments inside
+    optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
+ o pkg/seaice:
+   fix previous modif (3-level field removed) for old-pickup reading
+ checkpoint61r
+ o pkg/seaice:
+  - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
+. introduce fields for time step (N-1)
+. do not use levels 2 and 3 anymore (but keep them)
+. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
+      includes changes to pkg/thsice/thsice_get_velocity.F,
+      model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
+      pkg/obcs/obcs_apply_uvice.F.
+  - completely remove code for leap-frog time stepping for second order
+    advection
+  - adjusted adjoint accordingly;
+    gradient checks have improved by an order of magnitude!
+ checkpoint61q
+ o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
+  - the boundary conditions along open boundaries are unclear, because the
+    associated masks are set to zero and are thus treated as closed when
+    applying the slip-boundary conditions.
+  - move initialisation of grid variables from seaice_init_varia to _fixed
+ o adding doc/diags_changes.txt
+ o model/src:
+   do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
+    to avoid "_diags" naming if no relation to pkg/diagnostics.
+   ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
+    file and only call PLOT_FIELD_XYZ if debugMode=T.
+   remove few PLOT_FIELD_XY calls outside initialisation.
+   remove few unnecessary BARRIER.
+ o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
+   of salt_plume package in Southern Ocean
+ o pkg/thsice:
+  - fix hOceMxL in overlap (needed for sea-ice advection);
+    update output of experiment global_ocean.cs32x15.icedyn.
+ o pkg/seaice:
+  - make the (placeholder-)tracer IceAge a little more meaningful
+   by avoiding ridging of age due to convergent ice flow
+  - add diagnostics for surface temperature, atmospheric and oceanic
+    heat flux, and atmospheric and oceanic ice growth
+ checkpoint61p
+ o eesupp (global_max & global_sum):
+  - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
+  - remove starting & endding barrier (no longer needed)
+ o pkg/mdsio, writelocal:
+    works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
+    (remove the STOP): uses shared buffer IO to store data from all threads
+    and then let master-thread write nThreads tiles.
+ o pkg/mdsio (read/write field):
+  - tiled IO done in 1 piece (all levels at a time);
+  - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
+  - multi-threaded: allow to read/write local (non-shared) array
+    (was already working with singleCpuIO ; now works also without);
+    => no longer needs barrier call after reading a file (added inside
+    mds_read/write field).
+  - move barrier calls outside gather/scatter_2d to mds_read/write_field
+ o pkg/obcs/exf
+   - exf_getffieldrec.F: add a few ". _d 0" and
+                         add code to catch the case fldperiod = 0.
+   - obcs_precribe_read.F: change if statements so that they match
+                           the variable type (_RL)
+   - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
+     exf_iprec) as part of namelist EXF_NML_01
+ o pkg/mdsio:
+   - read/write tiled (local) files: read/write 1-level tile chunk at a time
+     (instead of segment of length sNx); expected to speed up tiled IO.
+ o pkg/exch2:
+   - take buffer copy from/to array out of S/R exch2_send/recv into new
+     S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
+     (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
+   - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
+   - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
+     (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
+     including Topology header file (and common blocks).
+   - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
+     remove 2nd exch call in exch2_s3d_rx (no longer needed).
+   - document S/R arg. list (+ update some comments)
+ o pkg/seaice:
+   - added SEAICE_CLIM_AIR code, which permits modulation of surface air
+     temperature and humidity over sea ice based on climatological values.
+   - clean up computation of Hibler+Bryan (1987) stress coupling for the case
+     of LSR (this change is expected to change the results slightly because now
+     it uses slightly difference moduli from the second last LSR solution, but
+     that is more consistent with the stress computations; this part of the code
+     is not tested in the verification experiments)
+   - fix diagnostics for flux of ice in case of B-grid
+   - turn strain rates eij and press into global fields within global
+     common block in SEAICE.h for more straighforward diagnostics
+   - fix diagnostics for principal stress components, press, zeta, eta
+     to give something meaning full
+ o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
+   new output (all 4 tests) using default rotationPeriod.
+ o pkg KPP:
+   - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
+   - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
+     and normal grid from 1 to Nr)
+ o Fix computations of L4rdt in mom_calc_visc.F
+ o eesupp:
+   new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
+   should be called before a "stop" if we know that all process are going
+   to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
+ checkpoint61o
+ o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
+ o model/src/ini_curvilinear_grid.F:
+    compute angleSin/CosC when they are not read from a file
+ o pkg/seaice:
+    add pseudo time stepping for LSOR
+ o pkg/exch2:
+    temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
+ o pkg/seaice:
+    Adding separate sea ice albedo, drag coefficients, and HO in Southern
+    Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
+ o SingleCpuIO:
+    fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
+ o pkg/seaice:
+    put exchanged variable in (local) common block for MPI+Multi-Threads
+    to work (necessary with exch1, and for now with exch2 too).
+ o verification: to get more experiments tested with mpi, mth and mpi+mth,
+   change tiling of:
+    aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
+    hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
+   update output of exp:
+    exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
+    tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
+   + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
+                    (note: output.txt generated on faulks using only 1 tile)
+ o eesupp & mdsio (SingleCpuIO):
+  - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
+    parameter "W2_useE2ioLayOut" (read from file "data.exch2").
+    Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
+  - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
+  - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
+    gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
+ o pkg/exch2:
+  - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
+    read parameter file "data.exch2" if it exists; otherwise try default regular
+    cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
+  - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
+    with new code (not to be used, just as a backup solution).
+  - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
+    in utils/exch2/input.
+ checkpoint61n
+ o eesupp & mdsio (SingleCpuIO):
+   - move mapping to global io-buffer inside gather_2d/scater_2d: this save
+     memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
+     receive real*4 array (instead of real*8) to read/write 32.bit files.
+     (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
+      and remove new mapping S/R)
+ o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
+   - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
+     xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
+     when using exch2. Add S/R to map global io-buffer to global model array.
+   - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
  checkpoint61m
  o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
    and add 3 other S/R for other types (R4,R8,RS).
    Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
  o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
   - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
   - reduce number of macro definitions (keep only those which are used);
     can always call directly the corrresponding S/R if needed.
   - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
     _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
   Fixed wrong type of arg in:
     atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
     ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
   To fix: global_sum of var in common block is wrong (multi-threaded) in:
     dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
   To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
- o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi
+ o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
+   "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
  o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
  o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
    edges are closed (zero depth); might happen with "blank tiles";
-   for now, disable if using OBCS.
+   for now, disabled if using OBCS.
  o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
    link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
  o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)

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