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revision 1.1028 by dfer, Tue Oct 7 22:40:55 2008 UTC revision 1.1109 by jmc, Thu May 28 23:38:58 2009 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
8      new output (all 4 tests) using default rotationPeriod.
9    o Fix computations of L4rdt in mom_calc_visc.F
10    o eesupp:
11      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
12      should be called before a "stop" if we know that all process are going
13      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
14    
15    checkpoint61o
16    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
17    o model/src/ini_curvilinear_grid.F:
18       compute angleSin/CosC when they are not read from a file
19    o pkg/seaice:
20       add pseudo time stepping for LSOR
21    o pkg/exch2:
22       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
23    o pkg/seaice:
24       Adding separate sea ice albedo, drag coefficients, and HO in Southern
25       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
26    o SingleCpuIO:
27       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
28    o pkg/seaice:
29       put exchanged variable in (local) common block for MPI+Multi-Threads
30       to work (necessary with exch1, and for now with exch2 too).
31    o verification: to get more experiments tested with mpi, mth and mpi+mth,
32      change tiling of:
33       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
34       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
35      update output of exp:
36       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
37       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
38      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
39                       (note: output.txt generated on faulks using only 1 tile)
40    o eesupp & mdsio (SingleCpuIO):
41     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
42       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
43       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
44     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
45     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
46       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
47    o pkg/exch2:
48     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
49       read parameter file "data.exch2" if it exists; otherwise try default regular
50       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
51     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
52       with new code (not to be used, just as a backup solution).
53     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
54       in utils/exch2/input.
55    
56    checkpoint61n
57    o eesupp & mdsio (SingleCpuIO):
58      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
59        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
60        receive real*4 array (instead of real*8) to read/write 32.bit files.
61        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
62         and remove new mapping S/R)
63    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
64      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
65        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
66        when using exch2. Add S/R to map global io-buffer to global model array.
67      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
68    
69    checkpoint61m
70    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
71      and add 3 other S/R for other types (R4,R8,RS).
72      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
73    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
74     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
75     - reduce number of macro definitions (keep only those which are used);
76       can always call directly the corrresponding S/R if needed.
77     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
78       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
79     Fixed wrong type of arg in:
80       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
81       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
82     To fix: global_sum of var in common block is wrong (multi-threaded) in:
83       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
84     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
85    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
86      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
87    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
88    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
89      edges are closed (zero depth); might happen with "blank tiles";
90      for now, disabled if using OBCS.
91    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
92      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
93    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
94      to reduce length of 1.D array print in STDOUT.
95    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
96      + use 48 tiles (16x8): this will allow to test "blank tiles".
97    o start to test MPI + multi-threaded (change testreport to skip tests
98      where number of tiles do not match).
99    o genmake2: add option "-omp" to turn on Open-MP ;
100      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
101    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
102      and keep the original tile numbering. Note: compatible with old
103      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
104    
105    checkpoint61l
106    o Overlaps had been forgotten in calculating ijk keys : fixed
107    o fix cyrus makedepend for gcc 4.4
108    o experiment fizhi-cs-aqualev20:
109      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
110      and generate new output. Note: new output is much closer to the old
111      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
112      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
113    o pkg/fizhi:
114     - change to avoid indices going deliberately over array-bounds
115     - remove unnecessary MPI stuff
116     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
117     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
118       does not go over array-bounds and therefore returns reliable output.
119     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
120       this S/R has 4 output arguments, which are used inside "get_alarm";
121       when it is called with the same variable "ndum" in place of several
122       output arguments, this produces weird side effect inside "get_alarm"
123      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
124       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
125       address) and produces error.
126    o tools/gemake2: (March 27-29 2009)
127      with option "-mpi": link *_mpi files from "MODS" dir (this is what
128      testreport does).
129    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
130    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
131       update lab_sea.lsr & lab_sea.salt_plume results
132    o pkg/seaice:
133      Major overhaul of the LSOR solver: change discretization from original
134      finite differences to finite volume. The old routine is still in the
135      file seaice_lsr.F and can be turned on with the CPP-flag
136      SEAICE_OLD_AND_BAD_DISCRETIZATION
137      Along with this change, the discretization of the strain rates is changed.
138      The same flag turns on the old discretization in seaice_calc_strainrates.F
139      All verification experiments with seaice are affected (except for
140      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
141      results by setting the above flag.
142      Further changes involve changes in defaults:
143      - ALLOW_FLOODING is defined and turned on by default
144      - SEAICEadvSnow = .true. is now the default
145      - SEAICEadvSalt = .true. is now the default
146      - SEAICEadvAge  = .true. is now the default
147      - SEAICE_clipVelocities  = .false. is now the default
148                                         (as per J. Zhang's recommendation)
149      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
150        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
151      - seaice_growth: replace computation of UG by a simple copy from wspeed
152    
153    checkpoint61k
154    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
155      seaice_lsr: fixed a few metric terms,
156                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
157                  add more debugging diagnostics
158      seaice_evp: removed superfluous many metric terms of FV discretization
159                  of stress divergence
160                  affects lab_sea, lab_sea.hb87
161      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
162                  of stress divergence for non-evp solver
163                  (this part is not tested anywhere)
164      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
165                  they were effectively only half slip
166                  affects lab_sea.hb87
167      updated all relevant verification experiments (except lab_sea//output_adm.txt
168        which was left over, but fails at level 7 & 6)
169    
170    checkpoint61j
171    o pkg/seaice: turn a few hard wired parameters into run time parameters
172    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
173      time in seconds as promised by the usints in seaice_monitor and exf_monitor
174    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
175      that are not cubed-sphere grids
176    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
177    o pkg/ctrl:
178      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
179    o non-hydrostatic (calc_gw.F):
180      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
181      update output of exp. global_ocean.cs32x15.viscA4
182    o remove backward compatibility for thetaMin,phiMin
183      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
184    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
185      interpolated wind field not only for curvilineargrid=.true., but also
186      for a rotated grid (rotateGrid=.true.)
187    o pkg/exf: add capability to bypass interpolation for runoff
188      by setting yet another CPP-flag
189    o eesupp/src, B-grid exchange:
190      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
191    o autodiff
192      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
193      allows to switch to single-prec common blocks;
194      corresponding switch occurs in tamc.h, integer isbyte
195      TAF store directivs "byte" and "kind" seem equivalent;
196      Most tamc.h have been updated correspondingly.
197    
198    checkpoint61i
199    o autodiff:
200      fix autodiff_sore/_restore indices for obcs
201      (spotted by I. Hoteit, M. Mazloff)
202    o pkg/autodiff, pkg/ctrl:
203      Add flag to reduce all tapelev I/O to single-prec.
204      In data.ctrl set
205        doSinglePrecTapelev = .TRUE.
206    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
207      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
208    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
209      real fresh water flux (not yet)
210    o pkg/mdsio & rw:
211     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
212     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
213    o pkg/flt:
214     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
215       init_fixed & ini_varia.
216     - clean-up & simplify linear interpolation S/R:
217       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
218     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
219     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
220     - add vert. coordinate & horiz. indices to output files.
221     - change vertical position in initial condition, from index to depth [m].
222     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
223       (easier to get to a curvilinear grid) ; delX,delY no longer used.
224    o pkg/ggl90: a few modifications:
225     - fix bottom boundary condition, and interpolation of KappaE
226       near top and bottom
227     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
228     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
229     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
230    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
231      (maintain temporary backward compatibility, until next checkpoint)
232    
233    checkpoint61h
234    o pkg/diagnostics with "periodic averaging diagnostics":
235      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
236    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
237    o pkg/obcs: fix loop ranges for balancing code
238    o pkg/flt:
239     - improve criteria for finding which tile owns a float.
240     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
241    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
242      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
243      with ocean biogeo)
244    o pkg/flt:
245     - do some cleaning and fix the restart ;
246     - add output.txt in flt_example/results to get this pkg tested.
247    o genmake2: add an EXTENDED_SRC option and flag.
248       for now, cannot be turned on on command line (only through genmake_local)
249    o pkg/mdsio: read/write vector:
250     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
251     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
252       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
253     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
254      (drop to 4 digits matching for grad). But this test does not look very
255      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
256    
257    checkpoint61g
258    o pkg/flt:
259      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
260       + make OPTIONS file more standard.
261      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
262      - fix _BYTESWAPIO CPP-Flag
263      - standard reading of file-parameter "data.flt"
264      - fix argument list of S/R FLT_RESTART
265      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
266    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
267    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
268      a still unfixed compiler/optimization bug
269    
270    checkpoint61f
271    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
272      update results of global_ocean.cs32x15.icedyn test.
273    o move getcon.F from model/src to pkg/fizhi.
274    o pkg/exf: add parameter for extrapolation of temp up to the surface
275       and option to prevent negative evap (in bulk_largeyeager04 only).
276    o Prather Advection scheme: fix tracer conservation for divergent flow
277      (e.g., when using NonLin Free-Surface).
278    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
279    o gmredi (Visbeck-variable-K):
280     - add more parameters to Visbeck-variable-K.
281     - use a 5 points average for dSigmaR in Visbeck-K calculation
282       (more "homogenous": same stencil and same weights as in dSigmaH)
283     - update output of ideal_2D_oce experiment.
284    o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
285      (#undef REAL4_IS_SLOW)
286     - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
287       coordinate variable
288     - pkg/monitor/monitor.F: call mon_printstats_rs for _RS variables
289       (surface forcing fields), removes some of the functionality
290     - model/src/write_grid.F: write _RS variables as RS-netcdf variables
291     - model/src/diags_oceanic_surf_flux.F: fix a few diagnostics, but
292       probably not all: copy _RS surface flux fields to RL field before
293       calling DIAGNOSTICS_FILL
294     - model/inc/CPP_EEMACROS.h: make the _EXCH_*_RS macros expand into
295       real*4 (CALL EXCH_*_RS) versions.
296     - tested in 2 experiments: inverted_barometer & solid-body.cs-32x32x1
297       (generate new output).
298    
299    checkpoint61e
300    o gmredi (Visbeck-variable-K):
301      - fix the "OLD_VISBECK_CALC" option + move the #undef to GMREDI_OPTIONS.h
302      - change computation of Visbeck-K where Slope > Smax :        
303        now: N*min(Slope,Smax) (similar to OLD_VISBECK_CALC with gkw91 taperFct)
304        previously was: M*sqrt(min(Slope,Smax)) ; update ideal_2D_oce output.
305    o bottom-drag in P-coord.: change units of bottomDragLinear & bottomDragQuadratic
306      to be the same as with Z-coord. (i.e., m/s & no-units respectively).
307    o calc_viscosity: fix index range (was wrong for CD-Scheme & explicit Visc)
308    o pkg gmredi, linear & fm07 tapering: put an upper limit on Slope^2 so that Kwz
309      does not become too large (to avoid precision problems in implicit-diffusion
310      solver); update ideal_2D_oce output.
311  o pkg ggl90:  o pkg ggl90:
312    - in ggl90_cal.F: compute only one set of visc/diff, used to    - in ggl90_cal.F: compute only one set of visc/diff, used to
313      step forward TKE/T/S/momentum      step forward TKE/T/S/momentum
314    - default value of GGL90viscMax/GGL90diffMax larger and equal (to    - default value of GGL90viscMax/GGL90diffMax larger and equal (to
315      have Prandlt =1)      have Prandlt =1)
316  o gmredi(fm07):  o gmredi (fm07):
317    - add lower limit on Transition layer thickness D + lower limit on D/lambda    - add lower limit on Transition layer thickness + lower limit on 1/lambda
318    - allow to set few more params from data.gmredi    - allow to set few more params from data.gmredi
319  o pkg ggl90:  o pkg ggl90:
320        - add missing sqrt(2) factor in computation of mixing length        - add missing sqrt(2) factor in computation of mixing length
# Line 2246  o add two new packages Line 2550  o add two new packages
2550    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2551    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2552      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2553      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2554  o add offline package  o add offline package
2555  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2556    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

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