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revision 1.1075 by mlosch, Tue Mar 3 14:07:45 2009 UTC revision 1.1151 by mlosch, Tue Aug 11 15:47:16 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/obcs:
8      - change OB?eta from _RS to _RL and put them into a separate commen block
9      - add code to read OB?eta from a file via obcs_prescribe_read: the code
10        compiles and does not destroy any other experiments, the data is read
11        properly, but the code is not tested in actual applications
12    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
13      create a meaningful unit attribute for the time coordinate variable
14    o pkg/ebm: add plenty of missing "_d 0" ;
15       update results of experiment global_ocean_ebm (fwd + adjoint tests)
16      Notes: several pieces of code only works for (very) specific set up
17       (domain size, lat range, etc ...); should be documented & stop if one
18       of those assumptions is not meet.
19    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
20       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
21          and offline_exf_seaice (seaicetd + adjoint).
22    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
23       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
24        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
25    o few changes to pass when compiling with strick checking of arguments
26       across S/R (allow to find few bugs in S/R calls).
27    o pkg/seaice:
28     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
29       2d-fields, for slightly better performance
30    
31    checkpoint61t
32    o pkg/seaice:
33     - remove unused variables in seaice_evp
34     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
35    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
36       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
37       each processor opens a different file (a fix from Matt).
38    o cg2d:
39       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
40       this reduces number of EXCH calls by 2 when using exch2.
41       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
42       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
43    o pkg/thsice:
44       add code for Near Infra-Red albedo (from Jeff)
45       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
46    o ini_model_io:
47       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
48       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
49       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
50    
51    checkpoint61s
52    o pkg/exch2 (exch2_rxN_cube*):
53       remove last BARRIER (no need to synchronise after getting data from shared
54       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
55    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
56      and generate new output (for the 2 tests) using default rotationPeriod.
57    o pkg/exch2:
58      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
59        (was already the case with AUTODIFF_EXCH2 defined)
60      - add bj in exch2 arrays and S/R.
61      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
62        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
63    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
64      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
65        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
66      - verification experiment natl_box.longstep
67    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
68      allow different versions of ifort (8 or 9) and different versions
69       of mpi (mpich or mpich2) to be used with the same optfile.
70      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
71       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
72    o pkg/seaice:
73      fix previous modif (3-level field removed) for old-pickup reading
74    
75    checkpoint61r
76    o pkg/seaice:
77     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
78      1. introduce fields for time step (N-1)
79      2. do not use levels 2 and 3 anymore (but keep them)
80      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
81         includes changes to pkg/thsice/thsice_get_velocity.F,
82         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
83         pkg/obcs/obcs_apply_uvice.F.
84     - completely remove code for leap-frog time stepping for second order
85       advection
86     - adjusted adjoint accordingly;
87       gradient checks have improved by an order of magnitude!
88    
89    checkpoint61q
90    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
91     - the boundary conditions along open boundaries are unclear, because the
92       associated masks are set to zero and are thus treated as closed when
93       applying the slip-boundary conditions.
94     - move initialisation of grid variables from seaice_init_varia to _fixed
95    o adding doc/diags_changes.txt
96    o model/src:
97      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
98       to avoid "_diags" naming if no relation to pkg/diagnostics.
99      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
100       file and only call PLOT_FIELD_XYZ if debugMode=T.
101      remove few PLOT_FIELD_XY calls outside initialisation.
102      remove few unnecessary BARRIER.
103    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
104      of salt_plume package in Southern Ocean
105    o pkg/thsice:
106     - fix hOceMxL in overlap (needed for sea-ice advection);
107       update output of experiment global_ocean.cs32x15.icedyn.
108    o pkg/seaice:
109     - make the (placeholder-)tracer IceAge a little more meaningful
110      by avoiding ridging of age due to convergent ice flow
111     - add diagnostics for surface temperature, atmospheric and oceanic
112       heat flux, and atmospheric and oceanic ice growth
113    
114    checkpoint61p
115    o eesupp (global_max & global_sum):
116     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
117     - remove starting & endding barrier (no longer needed)
118    o pkg/mdsio, writelocal:
119       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
120       (remove the STOP): uses shared buffer IO to store data from all threads
121       and then let master-thread write nThreads tiles.
122    o pkg/mdsio (read/write field):
123     - tiled IO done in 1 piece (all levels at a time);
124     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
125     - multi-threaded: allow to read/write local (non-shared) array
126       (was already working with singleCpuIO ; now works also without);
127       => no longer needs barrier call after reading a file (added inside
128       mds_read/write field).
129     - move barrier calls outside gather/scatter_2d to mds_read/write_field
130    o pkg/obcs/exf
131      - exf_getffieldrec.F: add a few ". _d 0" and
132                            add code to catch the case fldperiod = 0.  
133      - obcs_precribe_read.F: change if statements so that they match
134                              the variable type (_RL)
135      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
136        exf_iprec) as part of namelist EXF_NML_01
137    o pkg/mdsio:
138      - read/write tiled (local) files: read/write 1-level tile chunk at a time
139        (instead of segment of length sNx); expected to speed up tiled IO.
140    o pkg/exch2:
141      - take buffer copy from/to array out of S/R exch2_send/recv into new
142        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
143        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
144      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
145      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
146        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
147        including Topology header file (and common blocks).
148      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
149        remove 2nd exch call in exch2_s3d_rx (no longer needed).
150      - document S/R arg. list (+ update some comments)
151    o pkg/seaice:
152      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
153        temperature and humidity over sea ice based on climatological values.
154      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
155        of LSR (this change is expected to change the results slightly because now
156        it uses slightly difference moduli from the second last LSR solution, but
157        that is more consistent with the stress computations; this part of the code
158        is not tested in the verification experiments)
159      - fix diagnostics for flux of ice in case of B-grid
160      - turn strain rates eij and press into global fields within global
161        common block in SEAICE.h for more straighforward diagnostics
162      - fix diagnostics for principal stress components, press, zeta, eta
163        to give something meaning full
164    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
165      new output (all 4 tests) using default rotationPeriod.
166    o pkg KPP:
167      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
168      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
169        and normal grid from 1 to Nr)
170    o Fix computations of L4rdt in mom_calc_visc.F
171    o eesupp:
172      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
173      should be called before a "stop" if we know that all process are going
174      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
175    
176    checkpoint61o
177    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
178    o model/src/ini_curvilinear_grid.F:
179       compute angleSin/CosC when they are not read from a file
180    o pkg/seaice:
181       add pseudo time stepping for LSOR
182    o pkg/exch2:
183       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
184    o pkg/seaice:
185       Adding separate sea ice albedo, drag coefficients, and HO in Southern
186       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
187    o SingleCpuIO:
188       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
189    o pkg/seaice:
190       put exchanged variable in (local) common block for MPI+Multi-Threads
191       to work (necessary with exch1, and for now with exch2 too).
192    o verification: to get more experiments tested with mpi, mth and mpi+mth,
193      change tiling of:
194       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
195       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
196      update output of exp:
197       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
198       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
199      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
200                       (note: output.txt generated on faulks using only 1 tile)
201    o eesupp & mdsio (SingleCpuIO):
202     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
203       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
204       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
205     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
206     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
207       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
208    o pkg/exch2:
209     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
210       read parameter file "data.exch2" if it exists; otherwise try default regular
211       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
212     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
213       with new code (not to be used, just as a backup solution).
214     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
215       in utils/exch2/input.
216    
217    checkpoint61n
218    o eesupp & mdsio (SingleCpuIO):
219      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
220        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
221        receive real*4 array (instead of real*8) to read/write 32.bit files.
222        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
223         and remove new mapping S/R)
224    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
225      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
226        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
227        when using exch2. Add S/R to map global io-buffer to global model array.
228      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
229    
230    checkpoint61m
231    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
232      and add 3 other S/R for other types (R4,R8,RS).
233      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
234    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
235     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
236     - reduce number of macro definitions (keep only those which are used);
237       can always call directly the corrresponding S/R if needed.
238     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
239       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
240     Fixed wrong type of arg in:
241       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
242       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
243     To fix: global_sum of var in common block is wrong (multi-threaded) in:
244       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
245     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
246    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
247      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
248    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
249    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
250      edges are closed (zero depth); might happen with "blank tiles";
251      for now, disabled if using OBCS.
252    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
253      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
254    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
255      to reduce length of 1.D array print in STDOUT.
256    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
257      + use 48 tiles (16x8): this will allow to test "blank tiles".
258    o start to test MPI + multi-threaded (change testreport to skip tests
259      where number of tiles do not match).
260    o genmake2: add option "-omp" to turn on Open-MP ;
261      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
262    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
263      and keep the original tile numbering. Note: compatible with old
264      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
265    
266    checkpoint61l
267    o Overlaps had been forgotten in calculating ijk keys : fixed
268    o fix cyrus makedepend for gcc 4.4
269    o experiment fizhi-cs-aqualev20:
270      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
271      and generate new output. Note: new output is much closer to the old
272      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
273      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
274    o pkg/fizhi:
275     - change to avoid indices going deliberately over array-bounds
276     - remove unnecessary MPI stuff
277     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
278     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
279       does not go over array-bounds and therefore returns reliable output.
280     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
281       this S/R has 4 output arguments, which are used inside "get_alarm";
282       when it is called with the same variable "ndum" in place of several
283       output arguments, this produces weird side effect inside "get_alarm"
284      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
285       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
286       address) and produces error.
287    o tools/gemake2: (March 27-29 2009)
288      with option "-mpi": link *_mpi files from "MODS" dir (this is what
289      testreport does).
290    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
291    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
292       update lab_sea.lsr & lab_sea.salt_plume results
293    o pkg/seaice:
294      Major overhaul of the LSOR solver: change discretization from original
295      finite differences to finite volume. The old routine is still in the
296      file seaice_lsr.F and can be turned on with the CPP-flag
297      SEAICE_OLD_AND_BAD_DISCRETIZATION
298      Along with this change, the discretization of the strain rates is changed.
299      The same flag turns on the old discretization in seaice_calc_strainrates.F
300      All verification experiments with seaice are affected (except for
301      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
302      results by setting the above flag.
303      Further changes involve changes in defaults:
304      - ALLOW_FLOODING is defined and turned on by default
305      - SEAICEadvSnow = .true. is now the default
306      - SEAICEadvSalt = .true. is now the default
307      - SEAICEadvAge  = .true. is now the default
308      - SEAICE_clipVelocities  = .false. is now the default
309                                         (as per J. Zhang's recommendation)
310      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
311        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
312      - seaice_growth: replace computation of UG by a simple copy from wspeed
313    
314    checkpoint61k
315    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
316      seaice_lsr: fixed a few metric terms,
317                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
318                  add more debugging diagnostics
319      seaice_evp: removed superfluous many metric terms of FV discretization
320                  of stress divergence
321                  affects lab_sea, lab_sea.hb87
322      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
323                  of stress divergence for non-evp solver
324                  (this part is not tested anywhere)
325      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
326                  they were effectively only half slip
327                  affects lab_sea.hb87
328      updated all relevant verification experiments (except lab_sea//output_adm.txt
329        which was left over, but fails at level 7 & 6)
330    
331    checkpoint61j
332    o pkg/seaice: turn a few hard wired parameters into run time parameters
333  o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model  o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
334    time in seconds as promised by the usints in seaice_monitor and exf_monitor    time in seconds as promised by the usints in seaice_monitor and exf_monitor
335  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

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