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revision 1.1045 by mlosch, Wed Nov 26 15:27:02 2008 UTC revision 1.1118 by jmc, Mon Jun 8 04:33:33 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 (read/write field):
8     - tiled IO done in 1 piece (all levels at a time);
9     - multi-threaded: allow to read/write local (non-shared) array
10       (was already working with singleCpuIO ; now works also without);
11       => no longer needs barrier call after reading a file (added inside
12       mds_read/write field).
13     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
14     - move barrier calls outside gather/scatter_2d to mds_read/write_field
15    o pkg/obcs/exf
16      - exf_getffieldrec.F: add a few ". _d 0" and
17                            add code to catch the case fldperiod = 0.  
18      - obcs_precribe_read.F: change if statements so that they match
19                              the variable type (_RL)
20      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
21        exf_iprec) as part of namelist EXF_NML_01
22    o pkg/mdsio:
23      - read/write tiled (local) files: read/write 1-level tile chunk at a time
24        (instead of segment of length sNx); expected to speed up tiled IO.
25    o pkg/exch2:
26      - take buffer copy from/to array out of S/R exch2_send/recv into new
27        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
28        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
29      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
30      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
31        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
32        including Topology header file (and common blocks).
33      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
34        remove 2nd exch call in exch2_s3d_rx (no longer needed).
35      - document S/R arg. list (+ update some comments)
36    o pkg/seaice:
37      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
38        temperature and humidity over sea ice based on climatological values.
39      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
40        of LSR (this change is expected to change the results slightly because now
41        it uses slightly difference moduli from the second last LSR solution, but
42        that is more consistent with the stress computations; this part of the code
43        is not tested in the verification experiments)
44      - fix diagnostics for flux of ice in case of B-grid
45      - turn strain rates eij and press into global fields within global
46        common block in SEAICE.h for more straighforward diagnostics
47      - fix diagnostics for principal stress components, press, zeta, eta
48        to give something meaning full
49    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
50      new output (all 4 tests) using default rotationPeriod.
51    o pkg KPP:
52      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
53      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
54        and normal grid from 1 to Nr)
55    o Fix computations of L4rdt in mom_calc_visc.F
56    o eesupp:
57      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
58      should be called before a "stop" if we know that all process are going
59      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
60    
61    checkpoint61o
62    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
63    o model/src/ini_curvilinear_grid.F:
64       compute angleSin/CosC when they are not read from a file
65    o pkg/seaice:
66       add pseudo time stepping for LSOR
67    o pkg/exch2:
68       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
69    o pkg/seaice:
70       Adding separate sea ice albedo, drag coefficients, and HO in Southern
71       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
72    o SingleCpuIO:
73       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
74    o pkg/seaice:
75       put exchanged variable in (local) common block for MPI+Multi-Threads
76       to work (necessary with exch1, and for now with exch2 too).
77    o verification: to get more experiments tested with mpi, mth and mpi+mth,
78      change tiling of:
79       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
80       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
81      update output of exp:
82       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
83       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
84      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
85                       (note: output.txt generated on faulks using only 1 tile)
86    o eesupp & mdsio (SingleCpuIO):
87     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
88       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
89       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
90     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
91     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
92       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
93    o pkg/exch2:
94     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
95       read parameter file "data.exch2" if it exists; otherwise try default regular
96       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
97     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
98       with new code (not to be used, just as a backup solution).
99     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
100       in utils/exch2/input.
101    
102    checkpoint61n
103    o eesupp & mdsio (SingleCpuIO):
104      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
105        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
106        receive real*4 array (instead of real*8) to read/write 32.bit files.
107        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
108         and remove new mapping S/R)
109    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
110      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
111        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
112        when using exch2. Add S/R to map global io-buffer to global model array.
113      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
114    
115    checkpoint61m
116    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
117      and add 3 other S/R for other types (R4,R8,RS).
118      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
119    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
120     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
121     - reduce number of macro definitions (keep only those which are used);
122       can always call directly the corrresponding S/R if needed.
123     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
124       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
125     Fixed wrong type of arg in:
126       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
127       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
128     To fix: global_sum of var in common block is wrong (multi-threaded) in:
129       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
130     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
131    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
132      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
133    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
134    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
135      edges are closed (zero depth); might happen with "blank tiles";
136      for now, disabled if using OBCS.
137    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
138      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
139    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
140      to reduce length of 1.D array print in STDOUT.
141    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
142      + use 48 tiles (16x8): this will allow to test "blank tiles".
143    o start to test MPI + multi-threaded (change testreport to skip tests
144      where number of tiles do not match).
145    o genmake2: add option "-omp" to turn on Open-MP ;
146      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
147    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
148      and keep the original tile numbering. Note: compatible with old
149      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
150    
151    checkpoint61l
152    o Overlaps had been forgotten in calculating ijk keys : fixed
153    o fix cyrus makedepend for gcc 4.4
154    o experiment fizhi-cs-aqualev20:
155      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
156      and generate new output. Note: new output is much closer to the old
157      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
158      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
159    o pkg/fizhi:
160     - change to avoid indices going deliberately over array-bounds
161     - remove unnecessary MPI stuff
162     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
163     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
164       does not go over array-bounds and therefore returns reliable output.
165     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
166       this S/R has 4 output arguments, which are used inside "get_alarm";
167       when it is called with the same variable "ndum" in place of several
168       output arguments, this produces weird side effect inside "get_alarm"
169      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
170       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
171       address) and produces error.
172    o tools/gemake2: (March 27-29 2009)
173      with option "-mpi": link *_mpi files from "MODS" dir (this is what
174      testreport does).
175    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
176    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
177       update lab_sea.lsr & lab_sea.salt_plume results
178    o pkg/seaice:
179      Major overhaul of the LSOR solver: change discretization from original
180      finite differences to finite volume. The old routine is still in the
181      file seaice_lsr.F and can be turned on with the CPP-flag
182      SEAICE_OLD_AND_BAD_DISCRETIZATION
183      Along with this change, the discretization of the strain rates is changed.
184      The same flag turns on the old discretization in seaice_calc_strainrates.F
185      All verification experiments with seaice are affected (except for
186      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
187      results by setting the above flag.
188      Further changes involve changes in defaults:
189      - ALLOW_FLOODING is defined and turned on by default
190      - SEAICEadvSnow = .true. is now the default
191      - SEAICEadvSalt = .true. is now the default
192      - SEAICEadvAge  = .true. is now the default
193      - SEAICE_clipVelocities  = .false. is now the default
194                                         (as per J. Zhang's recommendation)
195      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
196        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
197      - seaice_growth: replace computation of UG by a simple copy from wspeed
198    
199    checkpoint61k
200    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
201      seaice_lsr: fixed a few metric terms,
202                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
203                  add more debugging diagnostics
204      seaice_evp: removed superfluous many metric terms of FV discretization
205                  of stress divergence
206                  affects lab_sea, lab_sea.hb87
207      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
208                  of stress divergence for non-evp solver
209                  (this part is not tested anywhere)
210      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
211                  they were effectively only half slip
212                  affects lab_sea.hb87
213      updated all relevant verification experiments (except lab_sea//output_adm.txt
214        which was left over, but fails at level 7 & 6)
215    
216    checkpoint61j
217    o pkg/seaice: turn a few hard wired parameters into run time parameters
218    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
219      time in seconds as promised by the usints in seaice_monitor and exf_monitor
220    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
221      that are not cubed-sphere grids
222    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
223    o pkg/ctrl:
224      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
225    o non-hydrostatic (calc_gw.F):
226      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
227      update output of exp. global_ocean.cs32x15.viscA4
228    o remove backward compatibility for thetaMin,phiMin
229      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
230    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
231      interpolated wind field not only for curvilineargrid=.true., but also
232      for a rotated grid (rotateGrid=.true.)
233    o pkg/exf: add capability to bypass interpolation for runoff
234      by setting yet another CPP-flag
235    o eesupp/src, B-grid exchange:
236      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
237    o autodiff
238      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
239      allows to switch to single-prec common blocks;
240      corresponding switch occurs in tamc.h, integer isbyte
241      TAF store directivs "byte" and "kind" seem equivalent;
242      Most tamc.h have been updated correspondingly.
243    
244    checkpoint61i
245    o autodiff:
246      fix autodiff_sore/_restore indices for obcs
247      (spotted by I. Hoteit, M. Mazloff)
248    o pkg/autodiff, pkg/ctrl:
249      Add flag to reduce all tapelev I/O to single-prec.
250      In data.ctrl set
251        doSinglePrecTapelev = .TRUE.
252    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
253      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
254    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
255      real fresh water flux (not yet)
256    o pkg/mdsio & rw:
257     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
258     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
259    o pkg/flt:
260     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
261       init_fixed & ini_varia.
262     - clean-up & simplify linear interpolation S/R:
263       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
264     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
265     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
266     - add vert. coordinate & horiz. indices to output files.
267     - change vertical position in initial condition, from index to depth [m].
268     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
269       (easier to get to a curvilinear grid) ; delX,delY no longer used.
270    o pkg/ggl90: a few modifications:
271     - fix bottom boundary condition, and interpolation of KappaE
272       near top and bottom
273     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
274     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
275     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
276    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
277      (maintain temporary backward compatibility, until next checkpoint)
278    
279    checkpoint61h
280    o pkg/diagnostics with "periodic averaging diagnostics":
281      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
282    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
283    o pkg/obcs: fix loop ranges for balancing code
284    o pkg/flt:
285     - improve criteria for finding which tile owns a float.
286     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
287    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
288      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
289      with ocean biogeo)
290    o pkg/flt:
291     - do some cleaning and fix the restart ;
292     - add output.txt in flt_example/results to get this pkg tested.
293    o genmake2: add an EXTENDED_SRC option and flag.
294       for now, cannot be turned on on command line (only through genmake_local)
295    o pkg/mdsio: read/write vector:
296     - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
297     - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
298       & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
299     - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
300      (drop to 4 digits matching for grad). But this test does not look very
301      reliable (was already failling on eddy, fc5, at 6.digits). Update output.
302    
303    checkpoint61g
304    o pkg/flt:
305      - move FLT_CPPOPTIONS.h to FLT_OPTIONS.h (standard name)
306       + make OPTIONS file more standard.
307      - rename S/R MDSREADVECTOR_FLT to FLT_MDSREADVECTOR (to mach src file name)
308      - fix _BYTESWAPIO CPP-Flag
309      - standard reading of file-parameter "data.flt"
310      - fix argument list of S/R FLT_RESTART
311      still need to fix _BYTESWAPIO in pkg/mdsio/mdsio_writevector.F
312  o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell  o pkg/obcs: fix a CPP-flag, bug reported by Jeff Blundell
313  o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to  o gather_2d.F/scatter_2d.F: suppress vectorisation on NEC SX in respond to
314    a still unfixed compiler/optimization bug    a still unfixed compiler/optimization bug
# Line 2291  o add two new packages Line 2596  o add two new packages
2596    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2597    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2598      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2599      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2600  o add offline package  o add offline package
2601  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2602    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

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