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revision 1.1036 by jmc, Mon Oct 27 20:15:21 2008 UTC revision 1.1114 by jmc, Mon Jun 1 14:22:57 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 pkg/mdsio:
8      - read/write tiled (local) files: read/write 1-level tile chunk at a time
9        (instead of segment of length sNx); expected to speed up tiled IO.
10    o pkg/exch2:
11      - take buffer copy from/to array out of S/R exch2_send/recv into new
12        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
13        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
14      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
15      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
16        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
17        including Topology header file (and common blocks).
18      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
19        remove 2nd exch call in exch2_s3d_rx (no longer needed).
20      - document S/R arg. list (+ update some comments)
21    o pkg/seaice:
22      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
23        of LSR (this change is expected to change the results slightly because now
24        it uses slightly difference moduli from the second last LSR solution, but
25        that is more consistent with the stress computations; this part of the code
26        is not tested in the verification experiments)
27      - fix diagnostics for flux of ice in case of B-grid
28      - turn strain rates eij and press into global fields within global
29        common block in SEAICE.h for more straighforward diagnostics
30      - fix diagnostics for principal stress components, press, zeta, eta
31        to give something meaning full
32    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
33      new output (all 4 tests) using default rotationPeriod.
34    o pkg KPP:
35      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
36      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
37        and normal grid from 1 to Nr)
38    o Fix computations of L4rdt in mom_calc_visc.F
39    o eesupp:
40      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
41      should be called before a "stop" if we know that all process are going
42      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
43    
44    checkpoint61o
45    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
46    o model/src/ini_curvilinear_grid.F:
47       compute angleSin/CosC when they are not read from a file
48    o pkg/seaice:
49       add pseudo time stepping for LSOR
50    o pkg/exch2:
51       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
52    o pkg/seaice:
53       Adding separate sea ice albedo, drag coefficients, and HO in Southern
54       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
55    o SingleCpuIO:
56       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
57    o pkg/seaice:
58       put exchanged variable in (local) common block for MPI+Multi-Threads
59       to work (necessary with exch1, and for now with exch2 too).
60    o verification: to get more experiments tested with mpi, mth and mpi+mth,
61      change tiling of:
62       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
63       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
64      update output of exp:
65       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
66       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
67      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
68                       (note: output.txt generated on faulks using only 1 tile)
69    o eesupp & mdsio (SingleCpuIO):
70     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
71       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
72       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
73     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
74     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
75       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
76    o pkg/exch2:
77     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
78       read parameter file "data.exch2" if it exists; otherwise try default regular
79       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
80     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
81       with new code (not to be used, just as a backup solution).
82     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
83       in utils/exch2/input.
84    
85    checkpoint61n
86    o eesupp & mdsio (SingleCpuIO):
87      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
88        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
89        receive real*4 array (instead of real*8) to read/write 32.bit files.
90        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
91         and remove new mapping S/R)
92    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
93      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
94        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
95        when using exch2. Add S/R to map global io-buffer to global model array.
96      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
97    
98    checkpoint61m
99    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
100      and add 3 other S/R for other types (R4,R8,RS).
101      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
102    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
103     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
104     - reduce number of macro definitions (keep only those which are used);
105       can always call directly the corrresponding S/R if needed.
106     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
107       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
108     Fixed wrong type of arg in:
109       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
110       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
111     To fix: global_sum of var in common block is wrong (multi-threaded) in:
112       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
113     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
114    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
115      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
116    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
117    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
118      edges are closed (zero depth); might happen with "blank tiles";
119      for now, disabled if using OBCS.
120    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
121      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
122    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
123      to reduce length of 1.D array print in STDOUT.
124    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
125      + use 48 tiles (16x8): this will allow to test "blank tiles".
126    o start to test MPI + multi-threaded (change testreport to skip tests
127      where number of tiles do not match).
128    o genmake2: add option "-omp" to turn on Open-MP ;
129      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
130    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
131      and keep the original tile numbering. Note: compatible with old
132      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
133    
134    checkpoint61l
135    o Overlaps had been forgotten in calculating ijk keys : fixed
136    o fix cyrus makedepend for gcc 4.4
137    o experiment fizhi-cs-aqualev20:
138      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
139      and generate new output. Note: new output is much closer to the old
140      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
141      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
142    o pkg/fizhi:
143     - change to avoid indices going deliberately over array-bounds
144     - remove unnecessary MPI stuff
145     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
146     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
147       does not go over array-bounds and therefore returns reliable output.
148     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
149       this S/R has 4 output arguments, which are used inside "get_alarm";
150       when it is called with the same variable "ndum" in place of several
151       output arguments, this produces weird side effect inside "get_alarm"
152      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
153       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
154       address) and produces error.
155    o tools/gemake2: (March 27-29 2009)
156      with option "-mpi": link *_mpi files from "MODS" dir (this is what
157      testreport does).
158    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
159    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
160       update lab_sea.lsr & lab_sea.salt_plume results
161    o pkg/seaice:
162      Major overhaul of the LSOR solver: change discretization from original
163      finite differences to finite volume. The old routine is still in the
164      file seaice_lsr.F and can be turned on with the CPP-flag
165      SEAICE_OLD_AND_BAD_DISCRETIZATION
166      Along with this change, the discretization of the strain rates is changed.
167      The same flag turns on the old discretization in seaice_calc_strainrates.F
168      All verification experiments with seaice are affected (except for
169      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
170      results by setting the above flag.
171      Further changes involve changes in defaults:
172      - ALLOW_FLOODING is defined and turned on by default
173      - SEAICEadvSnow = .true. is now the default
174      - SEAICEadvSalt = .true. is now the default
175      - SEAICEadvAge  = .true. is now the default
176      - SEAICE_clipVelocities  = .false. is now the default
177                                         (as per J. Zhang's recommendation)
178      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
179        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
180      - seaice_growth: replace computation of UG by a simple copy from wspeed
181    
182    checkpoint61k
183    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
184      seaice_lsr: fixed a few metric terms,
185                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
186                  add more debugging diagnostics
187      seaice_evp: removed superfluous many metric terms of FV discretization
188                  of stress divergence
189                  affects lab_sea, lab_sea.hb87
190      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
191                  of stress divergence for non-evp solver
192                  (this part is not tested anywhere)
193      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
194                  they were effectively only half slip
195                  affects lab_sea.hb87
196      updated all relevant verification experiments (except lab_sea//output_adm.txt
197        which was left over, but fails at level 7 & 6)
198    
199    checkpoint61j
200    o pkg/seaice: turn a few hard wired parameters into run time parameters
201    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
202      time in seconds as promised by the usints in seaice_monitor and exf_monitor
203    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
204      that are not cubed-sphere grids
205    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
206    o pkg/ctrl:
207      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
208    o non-hydrostatic (calc_gw.F):
209      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
210      update output of exp. global_ocean.cs32x15.viscA4
211    o remove backward compatibility for thetaMin,phiMin
212      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
213    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
214      interpolated wind field not only for curvilineargrid=.true., but also
215      for a rotated grid (rotateGrid=.true.)
216    o pkg/exf: add capability to bypass interpolation for runoff
217      by setting yet another CPP-flag
218    o eesupp/src, B-grid exchange:
219      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
220    o autodiff
221      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
222      allows to switch to single-prec common blocks;
223      corresponding switch occurs in tamc.h, integer isbyte
224      TAF store directivs "byte" and "kind" seem equivalent;
225      Most tamc.h have been updated correspondingly.
226    
227    checkpoint61i
228    o autodiff:
229      fix autodiff_sore/_restore indices for obcs
230      (spotted by I. Hoteit, M. Mazloff)
231    o pkg/autodiff, pkg/ctrl:
232      Add flag to reduce all tapelev I/O to single-prec.
233      In data.ctrl set
234        doSinglePrecTapelev = .TRUE.
235    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
236      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
237    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
238      real fresh water flux (not yet)
239    o pkg/mdsio & rw:
240     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
241     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
242    o pkg/flt:
243     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
244       init_fixed & ini_varia.
245     - clean-up & simplify linear interpolation S/R:
246       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
247     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
248     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
249     - add vert. coordinate & horiz. indices to output files.
250     - change vertical position in initial condition, from index to depth [m].
251     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
252       (easier to get to a curvilinear grid) ; delX,delY no longer used.
253    o pkg/ggl90: a few modifications:
254     - fix bottom boundary condition, and interpolation of KappaE
255       near top and bottom
256     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
257     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
258     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
259    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
260      (maintain temporary backward compatibility, until next checkpoint)
261    
262    checkpoint61h
263    o pkg/diagnostics with "periodic averaging diagnostics":
264      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
265    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
266    o pkg/obcs: fix loop ranges for balancing code
267    o pkg/flt:
268     - improve criteria for finding which tile owns a float.
269     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
270    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
271      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
272      with ocean biogeo)
273    o pkg/flt:
274     - do some cleaning and fix the restart ;
275     - add output.txt in flt_example/results to get this pkg tested.
276    o genmake2: add an EXTENDED_SRC option and flag.
277       for now, cannot be turned on on command line (only through genmake_local)
278    o pkg/mdsio: read/write vector:
279     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
280     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
281       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
282     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
283      (drop to 4 digits matching for grad). But this test does not look very
284      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
285    
286    checkpoint61g
287    o pkg/flt:
288      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
289       + make OPTIONS file more standard.
290      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
291      - fix _BYTESWAPIO CPP-Flag
292      - standard reading of file-parameter "data.flt"
293      - fix argument list of S/R FLT_RESTART
294      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
295    o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
296    o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
297      a still unfixed compiler/optimization bug
298    
299    checkpoint61f
300    o pkg/seaice, LSR solver: fix bug in GLOBAL_MAX calls ;
301      update results of global_ocean.cs32x15.icedyn test.
302    o move getcon.F from model/src to pkg/fizhi.
303    o pkg/exf: add parameter for extrapolation of temp up to the surface
304       and option to prevent negative evap (in bulk_largeyeager04 only).
305    o Prather Advection scheme: fix tracer conservation for divergent flow
306      (e.g., when using NonLin Free-Surface).
307    o kpp: retire KPPmld diagnostics --> use MXLDEPTH instead
308    o gmredi (Visbeck-variable-K):
309     - add more parameters to Visbeck-variable-K.
310     - use a 5 points average for dSigmaR in Visbeck-K calculation
311       (more "homogenous": same stencil and same weights as in dSigmaH)
312     - update output of ideal_2D_oce experiment.
313  o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4  o fix CPP-flag REAL4_IS_SLOW, when _RS expands into real*4
314    (#undef REAL4_IS_SLOW)    (#undef REAL4_IS_SLOW)
315   - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4   - pkg/mnc/mnc_cw_cvars.F: write _RS-grid variable as netcdf-real*4
# Line 2273  o add two new packages Line 2579  o add two new packages
2579    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2580    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2581      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2582      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2583  o add offline package  o add offline package
2584  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2585    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

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