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revision 1.1048 by jmc, Tue Dec 30 18:00:09 2008 UTC revision 1.1122 by mlosch, Thu Jun 11 09:04:13 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/seaice: make the (placeholder-)tracer IceAge a little more meaningful
8      by avoiding ridging of age due to convergent ice flow
9    
10    checkpoint61p
11    o eesupp (global_max & global_sum):
12     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
13     - remove starting & endding barrier (no longer needed)
14    o pkg/mdsio, writelocal:
15       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
16       (remove the STOP): uses shared buffer IO to store data from all threads
17       and then let master-thread write nThreads tiles.
18    o pkg/mdsio (read/write field):
19     - tiled IO done in 1 piece (all levels at a time);
20     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
21     - multi-threaded: allow to read/write local (non-shared) array
22       (was already working with singleCpuIO ; now works also without);
23       => no longer needs barrier call after reading a file (added inside
24       mds_read/write field).
25     - move barrier calls outside gather/scatter_2d to mds_read/write_field
26    o pkg/obcs/exf
27      - exf_getffieldrec.F: add a few ". _d 0" and
28                            add code to catch the case fldperiod = 0.  
29      - obcs_precribe_read.F: change if statements so that they match
30                              the variable type (_RL)
31      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
32        exf_iprec) as part of namelist EXF_NML_01
33    o pkg/mdsio:
34      - read/write tiled (local) files: read/write 1-level tile chunk at a time
35        (instead of segment of length sNx); expected to speed up tiled IO.
36    o pkg/exch2:
37      - take buffer copy from/to array out of S/R exch2_send/recv into new
38        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
39        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
40      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
41      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
42        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
43        including Topology header file (and common blocks).
44      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
45        remove 2nd exch call in exch2_s3d_rx (no longer needed).
46      - document S/R arg. list (+ update some comments)
47    o pkg/seaice:
48      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
49        temperature and humidity over sea ice based on climatological values.
50      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
51        of LSR (this change is expected to change the results slightly because now
52        it uses slightly difference moduli from the second last LSR solution, but
53        that is more consistent with the stress computations; this part of the code
54        is not tested in the verification experiments)
55      - fix diagnostics for flux of ice in case of B-grid
56      - turn strain rates eij and press into global fields within global
57        common block in SEAICE.h for more straighforward diagnostics
58      - fix diagnostics for principal stress components, press, zeta, eta
59        to give something meaning full
60    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
61      new output (all 4 tests) using default rotationPeriod.
62    o pkg KPP:
63      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
64      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
65        and normal grid from 1 to Nr)
66    o Fix computations of L4rdt in mom_calc_visc.F
67    o eesupp:
68      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
69      should be called before a "stop" if we know that all process are going
70      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
71    
72    checkpoint61o
73    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
74    o model/src/ini_curvilinear_grid.F:
75       compute angleSin/CosC when they are not read from a file
76    o pkg/seaice:
77       add pseudo time stepping for LSOR
78    o pkg/exch2:
79       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
80    o pkg/seaice:
81       Adding separate sea ice albedo, drag coefficients, and HO in Southern
82       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
83    o SingleCpuIO:
84       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
85    o pkg/seaice:
86       put exchanged variable in (local) common block for MPI+Multi-Threads
87       to work (necessary with exch1, and for now with exch2 too).
88    o verification: to get more experiments tested with mpi, mth and mpi+mth,
89      change tiling of:
90       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
91       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
92      update output of exp:
93       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
94       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
95      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
96                       (note: output.txt generated on faulks using only 1 tile)
97    o eesupp & mdsio (SingleCpuIO):
98     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
99       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
100       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
101     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
102     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
103       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
104    o pkg/exch2:
105     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
106       read parameter file "data.exch2" if it exists; otherwise try default regular
107       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
108     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
109       with new code (not to be used, just as a backup solution).
110     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
111       in utils/exch2/input.
112    
113    checkpoint61n
114    o eesupp & mdsio (SingleCpuIO):
115      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
116        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
117        receive real*4 array (instead of real*8) to read/write 32.bit files.
118        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
119         and remove new mapping S/R)
120    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
121      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
122        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
123        when using exch2. Add S/R to map global io-buffer to global model array.
124      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
125    
126    checkpoint61m
127    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
128      and add 3 other S/R for other types (R4,R8,RS).
129      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
130    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
131     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
132     - reduce number of macro definitions (keep only those which are used);
133       can always call directly the corrresponding S/R if needed.
134     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
135       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
136     Fixed wrong type of arg in:
137       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
138       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
139     To fix: global_sum of var in common block is wrong (multi-threaded) in:
140       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
141     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
142    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
143      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
144    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
145    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
146      edges are closed (zero depth); might happen with "blank tiles";
147      for now, disabled if using OBCS.
148    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
149      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
150    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
151      to reduce length of 1.D array print in STDOUT.
152    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
153      + use 48 tiles (16x8): this will allow to test "blank tiles".
154    o start to test MPI + multi-threaded (change testreport to skip tests
155      where number of tiles do not match).
156    o genmake2: add option "-omp" to turn on Open-MP ;
157      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
158    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
159      and keep the original tile numbering. Note: compatible with old
160      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
161    
162    checkpoint61l
163    o Overlaps had been forgotten in calculating ijk keys : fixed
164    o fix cyrus makedepend for gcc 4.4
165    o experiment fizhi-cs-aqualev20:
166      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
167      and generate new output. Note: new output is much closer to the old
168      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
169      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
170    o pkg/fizhi:
171     - change to avoid indices going deliberately over array-bounds
172     - remove unnecessary MPI stuff
173     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
174     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
175       does not go over array-bounds and therefore returns reliable output.
176     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
177       this S/R has 4 output arguments, which are used inside "get_alarm";
178       when it is called with the same variable "ndum" in place of several
179       output arguments, this produces weird side effect inside "get_alarm"
180      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
181       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
182       address) and produces error.
183    o tools/gemake2: (March 27-29 2009)
184      with option "-mpi": link *_mpi files from "MODS" dir (this is what
185      testreport does).
186    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
187    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
188       update lab_sea.lsr & lab_sea.salt_plume results
189    o pkg/seaice:
190      Major overhaul of the LSOR solver: change discretization from original
191      finite differences to finite volume. The old routine is still in the
192      file seaice_lsr.F and can be turned on with the CPP-flag
193      SEAICE_OLD_AND_BAD_DISCRETIZATION
194      Along with this change, the discretization of the strain rates is changed.
195      The same flag turns on the old discretization in seaice_calc_strainrates.F
196      All verification experiments with seaice are affected (except for
197      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
198      results by setting the above flag.
199      Further changes involve changes in defaults:
200      - ALLOW_FLOODING is defined and turned on by default
201      - SEAICEadvSnow = .true. is now the default
202      - SEAICEadvSalt = .true. is now the default
203      - SEAICEadvAge  = .true. is now the default
204      - SEAICE_clipVelocities  = .false. is now the default
205                                         (as per J. Zhang's recommendation)
206      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
207        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
208      - seaice_growth: replace computation of UG by a simple copy from wspeed
209    
210    checkpoint61k
211    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
212      seaice_lsr: fixed a few metric terms,
213                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
214                  add more debugging diagnostics
215      seaice_evp: removed superfluous many metric terms of FV discretization
216                  of stress divergence
217                  affects lab_sea, lab_sea.hb87
218      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
219                  of stress divergence for non-evp solver
220                  (this part is not tested anywhere)
221      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
222                  they were effectively only half slip
223                  affects lab_sea.hb87
224      updated all relevant verification experiments (except lab_sea//output_adm.txt
225        which was left over, but fails at level 7 & 6)
226    
227    checkpoint61j
228    o pkg/seaice: turn a few hard wired parameters into run time parameters
229    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
230      time in seconds as promised by the usints in seaice_monitor and exf_monitor
231    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
232      that are not cubed-sphere grids
233    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
234    o pkg/ctrl:
235      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
236    o non-hydrostatic (calc_gw.F):
237      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
238      update output of exp. global_ocean.cs32x15.viscA4
239    o remove backward compatibility for thetaMin,phiMin
240      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
241    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
242      interpolated wind field not only for curvilineargrid=.true., but also
243      for a rotated grid (rotateGrid=.true.)
244    o pkg/exf: add capability to bypass interpolation for runoff
245      by setting yet another CPP-flag
246    o eesupp/src, B-grid exchange:
247      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
248    o autodiff
249      new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
250      allows to switch to single-prec common blocks;
251      corresponding switch occurs in tamc.h, integer isbyte
252      TAF store directivs "byte" and "kind" seem equivalent;
253      Most tamc.h have been updated correspondingly.
254    
255    checkpoint61i
256    o autodiff:
257      fix autodiff_sore/_restore indices for obcs
258      (spotted by I. Hoteit, M. Mazloff)
259    o pkg/autodiff, pkg/ctrl:
260      Add flag to reduce all tapelev I/O to single-prec.
261      In data.ctrl set
262        doSinglePrecTapelev = .TRUE.
263    o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
264      check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
265    o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
266      real fresh water flux (not yet)
267    o pkg/mdsio & rw:
268     - add argument & option to S/R MDS_WRITEVEC_LOC (avoid Open/Close & write-meta)
269     - add simple interface S/R to MDS_WRITEVEC_LOC in pkg/rw: WRITE_GLVEC_RX.
270    o pkg/flt:
271     - replace FLT_INIT by 3-steps standard initialization S/R: readparms,
272       init_fixed & ini_varia.
273     - clean-up & simplify linear interpolation S/R:
274       move flt_bilinear.F -> flt_interp_linear.F ; add arg. myThid.
275     - fix some indices (mainly vertical index) ; add IMPLICIT NONE.
276     - more efficient I/O, using new options of MDS_WRITEVEC_LOC S/R.
277     - add vert. coordinate & horiz. indices to output files.
278     - change vertical position in initial condition, from index to depth [m].
279     - store horizontal (decimal) indices i,j in common block (instead of coord. x,y)
280       (easier to get to a curvilinear grid) ; delX,delY no longer used.
281    o pkg/ggl90: a few modifications:
282     - fix bottom boundary condition, and interpolation of KappaE
283       near top and bottom
284     - use same set of viscosity/diffusivity for TKE/momnetum/tracer
285     - add smoothing option as in Blanke and Delecluse (1993) (--> ALLOW_GGL90_SMOOTH)
286     - add a few options for mixing-length upper limit (--> mxlMaxFlag)  
287    o rename thetaMin,phiMin -> xgOrigin,ygOrigin
288      (maintain temporary backward compatibility, until next checkpoint)
289    
290    checkpoint61h
291    o pkg/diagnostics with "periodic averaging diagnostics":
292      fix S/R DIAGNOSTICS_COUNT ; hack diagnostics_out.F to get NetCDF output.
293    o pkg/my82: add missing "_d 0" ; update output of exp. vermix.my82
294    o pkg/obcs: fix loop ranges for balancing code
295    o pkg/flt:
296     - improve criteria for finding which tile owns a float.
297     - fix FLT_EXCH for case without MPI ; apply cyclic BC + fix also the MPI case.
298    o Add well-mixed CO2 box in aim_v23 (which includes changes in pkg
299      aim_compon_interf, ocn_compon_interf, gchem, and dic to get coupling
300      with ocean biogeo)
301    o pkg/flt:
302     - do some cleaning and fix the restart ;
303     - add output.txt in flt_example/results to get this pkg tested.
304    o genmake2: add an EXTENDED_SRC option and flag.
305       for now, cannot be turned on on command line (only through genmake_local)
306  o pkg/mdsio: read/write vector:  o pkg/mdsio: read/write vector:
307   - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS   - singleCpuIO: fix RL/RS in MDSWRITEVECTOR by calling new S/R MDS_BUFFERtoRL/RS
308   - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR   - singleCpuIO=F: fix arrType & filePrec & _BYTESWAPIO in both MDSREADVECTOR
309     & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.     & MDSWRITEVECTOR by calling new S/R MDS_RD/WR_VEC_RL/RS.
310   - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)   - affects gradient of test-exp "bottom_ctrl_5x5" (not due to _BYTESWAPIO)
311    (drop to 4 digits matching for grad). But this test does not look very    (drop to 4 digits matching for grad). But this test does not look very
# Line 2308  o add two new packages Line 2607  o add two new packages
2607    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme    - my82 (Mellor and Yamada, 1982) level 2 turbulence closure scheme
2608    - these scheme operate in a similar manner as KPP (without ghat, of    - these scheme operate in a similar manner as KPP (without ghat, of
2609      course), however there is only one diffusivity that is used for both      course), however there is only one diffusivity that is used for both
2610      temperature and salinity (and passive tracers)ç      temperature and salinity (and passive tracers)
2611  o add offline package  o add offline package
2612  o add "verification/dic_example" which contains a dic-gchem-ptracer setup  o add "verification/dic_example" which contains a dic-gchem-ptracer setup
2613    provided by Stephanie Dutkiewicz    provided by Stephanie Dutkiewicz

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