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revision 1.1074 by mlosch, Tue Mar 3 10:01:40 2009 UTC revision 1.1152 by jmc, Tue Aug 25 16:34:35 2009 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7    checkpoint61u
8    o pkg/obcs:
9      - change OB?eta from _RS to _RL and put them into a separate commen block
10      - add code to read OB?eta from a file via obcs_prescribe_read: the code
11        compiles and does not destroy any other experiments, the data is read
12        properly, but the code is not tested in actual applications
13    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
14      create a meaningful unit attribute for the time coordinate variable
15    o pkg/ebm: add plenty of missing "_d 0" ;
16       update results of experiment global_ocean_ebm (fwd + adjoint tests)
17      Notes: several pieces of code only works for (very) specific set up
18       (domain size, lat range, etc ...); should be documented & stop if one
19       of those assumptions is not meet.
20    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
21       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
22          and offline_exf_seaice (seaicetd + adjoint).
23    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
24       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
25        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
26    o few changes to pass when compiling with strick checking of arguments
27       across S/R (allow to find few bugs in S/R calls).
28    o pkg/seaice:
29     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
30       2d-fields, for slightly better performance
31    
32    checkpoint61t
33    o pkg/seaice:
34     - remove unused variables in seaice_evp
35     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
36    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
37       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
38       each processor opens a different file (a fix from Matt).
39    o cg2d:
40       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
41       this reduces number of EXCH calls by 2 when using exch2.
42       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
43       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
44    o pkg/thsice:
45       add code for Near Infra-Red albedo (from Jeff)
46       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
47    o ini_model_io:
48       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
49       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
50       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
51    
52    checkpoint61s
53    o pkg/exch2 (exch2_rxN_cube*):
54       remove last BARRIER (no need to synchronise after getting data from shared
55       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
56    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
57      and generate new output (for the 2 tests) using default rotationPeriod.
58    o pkg/exch2:
59      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
60        (was already the case with AUTODIFF_EXCH2 defined)
61      - add bj in exch2 arrays and S/R.
62      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
63        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
64    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
65      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
66        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
67      - verification experiment natl_box.longstep
68    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
69      allow different versions of ifort (8 or 9) and different versions
70       of mpi (mpich or mpich2) to be used with the same optfile.
71      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
72       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
73    o pkg/seaice:
74      fix previous modif (3-level field removed) for old-pickup reading
75    
76    checkpoint61r
77    o pkg/seaice:
78     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
79      1. introduce fields for time step (N-1)
80      2. do not use levels 2 and 3 anymore (but keep them)
81      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
82         includes changes to pkg/thsice/thsice_get_velocity.F,
83         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
84         pkg/obcs/obcs_apply_uvice.F.
85     - completely remove code for leap-frog time stepping for second order
86       advection
87     - adjusted adjoint accordingly;
88       gradient checks have improved by an order of magnitude!
89    
90    checkpoint61q
91    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
92     - the boundary conditions along open boundaries are unclear, because the
93       associated masks are set to zero and are thus treated as closed when
94       applying the slip-boundary conditions.
95     - move initialisation of grid variables from seaice_init_varia to _fixed
96    o adding doc/diags_changes.txt
97    o model/src:
98      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
99       to avoid "_diags" naming if no relation to pkg/diagnostics.
100      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
101       file and only call PLOT_FIELD_XYZ if debugMode=T.
102      remove few PLOT_FIELD_XY calls outside initialisation.
103      remove few unnecessary BARRIER.
104    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
105      of salt_plume package in Southern Ocean
106    o pkg/thsice:
107     - fix hOceMxL in overlap (needed for sea-ice advection);
108       update output of experiment global_ocean.cs32x15.icedyn.
109    o pkg/seaice:
110     - make the (placeholder-)tracer IceAge a little more meaningful
111      by avoiding ridging of age due to convergent ice flow
112     - add diagnostics for surface temperature, atmospheric and oceanic
113       heat flux, and atmospheric and oceanic ice growth
114    
115    checkpoint61p
116    o eesupp (global_max & global_sum):
117     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
118     - remove starting & endding barrier (no longer needed)
119    o pkg/mdsio, writelocal:
120       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
121       (remove the STOP): uses shared buffer IO to store data from all threads
122       and then let master-thread write nThreads tiles.
123    o pkg/mdsio (read/write field):
124     - tiled IO done in 1 piece (all levels at a time);
125     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
126     - multi-threaded: allow to read/write local (non-shared) array
127       (was already working with singleCpuIO ; now works also without);
128       => no longer needs barrier call after reading a file (added inside
129       mds_read/write field).
130     - move barrier calls outside gather/scatter_2d to mds_read/write_field
131    o pkg/obcs/exf
132      - exf_getffieldrec.F: add a few ". _d 0" and
133                            add code to catch the case fldperiod = 0.  
134      - obcs_precribe_read.F: change if statements so that they match
135                              the variable type (_RL)
136      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
137        exf_iprec) as part of namelist EXF_NML_01
138    o pkg/mdsio:
139      - read/write tiled (local) files: read/write 1-level tile chunk at a time
140        (instead of segment of length sNx); expected to speed up tiled IO.
141    o pkg/exch2:
142      - take buffer copy from/to array out of S/R exch2_send/recv into new
143        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
144        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
145      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
146      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
147        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
148        including Topology header file (and common blocks).
149      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
150        remove 2nd exch call in exch2_s3d_rx (no longer needed).
151      - document S/R arg. list (+ update some comments)
152    o pkg/seaice:
153      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
154        temperature and humidity over sea ice based on climatological values.
155      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
156        of LSR (this change is expected to change the results slightly because now
157        it uses slightly difference moduli from the second last LSR solution, but
158        that is more consistent with the stress computations; this part of the code
159        is not tested in the verification experiments)
160      - fix diagnostics for flux of ice in case of B-grid
161      - turn strain rates eij and press into global fields within global
162        common block in SEAICE.h for more straighforward diagnostics
163      - fix diagnostics for principal stress components, press, zeta, eta
164        to give something meaning full
165    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
166      new output (all 4 tests) using default rotationPeriod.
167    o pkg KPP:
168      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
169      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
170        and normal grid from 1 to Nr)
171    o Fix computations of L4rdt in mom_calc_visc.F
172    o eesupp:
173      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
174      should be called before a "stop" if we know that all process are going
175      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
176    
177    checkpoint61o
178    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
179    o model/src/ini_curvilinear_grid.F:
180       compute angleSin/CosC when they are not read from a file
181    o pkg/seaice:
182       add pseudo time stepping for LSOR
183    o pkg/exch2:
184       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
185    o pkg/seaice:
186       Adding separate sea ice albedo, drag coefficients, and HO in Southern
187       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
188    o SingleCpuIO:
189       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
190    o pkg/seaice:
191       put exchanged variable in (local) common block for MPI+Multi-Threads
192       to work (necessary with exch1, and for now with exch2 too).
193    o verification: to get more experiments tested with mpi, mth and mpi+mth,
194      change tiling of:
195       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
196       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
197      update output of exp:
198       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
199       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
200      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
201                       (note: output.txt generated on faulks using only 1 tile)
202    o eesupp & mdsio (SingleCpuIO):
203     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
204       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
205       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
206     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
207     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
208       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
209    o pkg/exch2:
210     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
211       read parameter file "data.exch2" if it exists; otherwise try default regular
212       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
213     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
214       with new code (not to be used, just as a backup solution).
215     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
216       in utils/exch2/input.
217    
218    checkpoint61n
219    o eesupp & mdsio (SingleCpuIO):
220      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
221        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
222        receive real*4 array (instead of real*8) to read/write 32.bit files.
223        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
224         and remove new mapping S/R)
225    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
226      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
227        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
228        when using exch2. Add S/R to map global io-buffer to global model array.
229      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
230    
231    checkpoint61m
232    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
233      and add 3 other S/R for other types (R4,R8,RS).
234      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
235    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
236     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
237     - reduce number of macro definitions (keep only those which are used);
238       can always call directly the corrresponding S/R if needed.
239     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
240       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
241     Fixed wrong type of arg in:
242       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
243       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
244     To fix: global_sum of var in common block is wrong (multi-threaded) in:
245       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
246     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
247    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
248      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
249    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
250    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
251      edges are closed (zero depth); might happen with "blank tiles";
252      for now, disabled if using OBCS.
253    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
254      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
255    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
256      to reduce length of 1.D array print in STDOUT.
257    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
258      + use 48 tiles (16x8): this will allow to test "blank tiles".
259    o start to test MPI + multi-threaded (change testreport to skip tests
260      where number of tiles do not match).
261    o genmake2: add option "-omp" to turn on Open-MP ;
262      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
263    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
264      and keep the original tile numbering. Note: compatible with old
265      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
266    
267    checkpoint61l
268    o Overlaps had been forgotten in calculating ijk keys : fixed
269    o fix cyrus makedepend for gcc 4.4
270    o experiment fizhi-cs-aqualev20:
271      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
272      and generate new output. Note: new output is much closer to the old
273      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
274      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
275    o pkg/fizhi:
276     - change to avoid indices going deliberately over array-bounds
277     - remove unnecessary MPI stuff
278     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
279     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
280       does not go over array-bounds and therefore returns reliable output.
281     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
282       this S/R has 4 output arguments, which are used inside "get_alarm";
283       when it is called with the same variable "ndum" in place of several
284       output arguments, this produces weird side effect inside "get_alarm"
285      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
286       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
287       address) and produces error.
288    o tools/gemake2: (March 27-29 2009)
289      with option "-mpi": link *_mpi files from "MODS" dir (this is what
290      testreport does).
291    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
292    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
293       update lab_sea.lsr & lab_sea.salt_plume results
294    o pkg/seaice:
295      Major overhaul of the LSOR solver: change discretization from original
296      finite differences to finite volume. The old routine is still in the
297      file seaice_lsr.F and can be turned on with the CPP-flag
298      SEAICE_OLD_AND_BAD_DISCRETIZATION
299      Along with this change, the discretization of the strain rates is changed.
300      The same flag turns on the old discretization in seaice_calc_strainrates.F
301      All verification experiments with seaice are affected (except for
302      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
303      results by setting the above flag.
304      Further changes involve changes in defaults:
305      - ALLOW_FLOODING is defined and turned on by default
306      - SEAICEadvSnow = .true. is now the default
307      - SEAICEadvSalt = .true. is now the default
308      - SEAICEadvAge  = .true. is now the default
309      - SEAICE_clipVelocities  = .false. is now the default
310                                         (as per J. Zhang's recommendation)
311      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
312        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
313      - seaice_growth: replace computation of UG by a simple copy from wspeed
314    
315    checkpoint61k
316    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
317      seaice_lsr: fixed a few metric terms,
318                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
319                  add more debugging diagnostics
320      seaice_evp: removed superfluous many metric terms of FV discretization
321                  of stress divergence
322                  affects lab_sea, lab_sea.hb87
323      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
324                  of stress divergence for non-evp solver
325                  (this part is not tested anywhere)
326      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
327                  they were effectively only half slip
328                  affects lab_sea.hb87
329      updated all relevant verification experiments (except lab_sea//output_adm.txt
330        which was left over, but fails at level 7 & 6)
331    
332    checkpoint61j
333    o pkg/seaice: turn a few hard wired parameters into run time parameters
334    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
335      time in seconds as promised by the usints in seaice_monitor and exf_monitor
336  o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids  o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
337    that are not cubed-sphere grids    that are not cubed-sphere grids
338  o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR  o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR

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