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revision 1.1083 by jmc, Fri Mar 27 00:09:17 2009 UTC revision 1.1158 by mlosch, Fri Sep 18 12:36:12 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/kpp:
8     -add double diffusive contributions as a hack, turned off by default
9      for now, and the code can be excluded with a CPP-flag
10      EXCLUDE_KPP_DOUBLEDIFF just as EXCLUDE_KPP_SHEAR_MIX
11     -add a verification experiments to "vermix" to test this code
12    o pkg/mom_common:
13      Move computation of length scales to mom_init_fixed.F (avoid recomputation
14      at each time-steps*levels).
15    o pkg/layers:
16      Created a new package for computing volume fluxes in temperature or
17      [not yet implemented] density layers, e.g. for calculating residual
18      overturning circulations.
19    o pkg/diagnostics:
20      implement a RS type version for the set of DIAGNOSTICS-FILL subroutines
21    o fix few RS/RL type mismatch (check with ifort 11.1 "-warn all" option)
22    o pkg/mdsio (& pkg/rw): rework high level S/R interface:
23      To avoid mixing type (RS/RL) of input/output array argument,
24      replace single mixed-type array with a pair from each type (RS/RL).
25    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
26      is now implemented for all pkgs (previously only done for the main pickup)
27    
28    checkpoint61u
29    o pkg/obcs:
30      - change OB?eta from _RS to _RL and put them into a separate commen block
31      - add code to read OB?eta from a file via obcs_prescribe_read: the code
32        compiles and does not destroy any other experiments, the data is read
33        properly, but the code is not tested in actual applications
34    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
35      create a meaningful unit attribute for the time coordinate variable
36    o pkg/ebm: add plenty of missing "_d 0" ;
37       update results of experiment global_ocean_ebm (fwd + adjoint tests)
38      Notes: several pieces of code only works for (very) specific set up
39       (domain size, lat range, etc ...); should be documented & stop if one
40       of those assumptions is not meet.
41    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
42       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
43          and offline_exf_seaice (seaicetd + adjoint).
44    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
45       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
46        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
47    o few changes to pass when compiling with strick checking of arguments
48       across S/R (allow to find few bugs in S/R calls).
49    o pkg/seaice:
50     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
51       2d-fields, for slightly better performance
52    
53    checkpoint61t
54    o pkg/seaice:
55     - remove unused variables in seaice_evp
56     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
57    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
58       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
59       each processor opens a different file (a fix from Matt).
60    o cg2d:
61       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
62       this reduces number of EXCH calls by 2 when using exch2.
63       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
64       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
65    o pkg/thsice:
66       add code for Near Infra-Red albedo (from Jeff)
67       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
68    o ini_model_io:
69       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
70       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
71       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
72    
73    checkpoint61s
74    o pkg/exch2 (exch2_rxN_cube*):
75       remove last BARRIER (no need to synchronise after getting data from shared
76       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
77    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
78      and generate new output (for the 2 tests) using default rotationPeriod.
79    o pkg/exch2:
80      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
81        (was already the case with AUTODIFF_EXCH2 defined)
82      - add bj in exch2 arrays and S/R.
83      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
84        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
85    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
86      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
87        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
88      - verification experiment natl_box.longstep
89    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
90      allow different versions of ifort (8 or 9) and different versions
91       of mpi (mpich or mpich2) to be used with the same optfile.
92      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
93       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
94    o pkg/seaice:
95      fix previous modif (3-level field removed) for old-pickup reading
96    
97    checkpoint61r
98    o pkg/seaice:
99     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
100      1. introduce fields for time step (N-1)
101      2. do not use levels 2 and 3 anymore (but keep them)
102      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
103         includes changes to pkg/thsice/thsice_get_velocity.F,
104         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
105         pkg/obcs/obcs_apply_uvice.F.
106     - completely remove code for leap-frog time stepping for second order
107       advection
108     - adjusted adjoint accordingly;
109       gradient checks have improved by an order of magnitude!
110    
111    checkpoint61q
112    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
113     - the boundary conditions along open boundaries are unclear, because the
114       associated masks are set to zero and are thus treated as closed when
115       applying the slip-boundary conditions.
116     - move initialisation of grid variables from seaice_init_varia to _fixed
117    o adding doc/diags_changes.txt
118    o model/src:
119      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
120       to avoid "_diags" naming if no relation to pkg/diagnostics.
121      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
122       file and only call PLOT_FIELD_XYZ if debugMode=T.
123      remove few PLOT_FIELD_XY calls outside initialisation.
124      remove few unnecessary BARRIER.
125    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
126      of salt_plume package in Southern Ocean
127    o pkg/thsice:
128     - fix hOceMxL in overlap (needed for sea-ice advection);
129       update output of experiment global_ocean.cs32x15.icedyn.
130    o pkg/seaice:
131     - make the (placeholder-)tracer IceAge a little more meaningful
132      by avoiding ridging of age due to convergent ice flow
133     - add diagnostics for surface temperature, atmospheric and oceanic
134       heat flux, and atmospheric and oceanic ice growth
135    
136    checkpoint61p
137    o eesupp (global_max & global_sum):
138     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
139     - remove starting & endding barrier (no longer needed)
140    o pkg/mdsio, writelocal:
141       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
142       (remove the STOP): uses shared buffer IO to store data from all threads
143       and then let master-thread write nThreads tiles.
144    o pkg/mdsio (read/write field):
145     - tiled IO done in 1 piece (all levels at a time);
146     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
147     - multi-threaded: allow to read/write local (non-shared) array
148       (was already working with singleCpuIO ; now works also without);
149       => no longer needs barrier call after reading a file (added inside
150       mds_read/write field).
151     - move barrier calls outside gather/scatter_2d to mds_read/write_field
152    o pkg/obcs/exf
153      - exf_getffieldrec.F: add a few ". _d 0" and
154                            add code to catch the case fldperiod = 0.  
155      - obcs_precribe_read.F: change if statements so that they match
156                              the variable type (_RL)
157      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
158        exf_iprec) as part of namelist EXF_NML_01
159    o pkg/mdsio:
160      - read/write tiled (local) files: read/write 1-level tile chunk at a time
161        (instead of segment of length sNx); expected to speed up tiled IO.
162    o pkg/exch2:
163      - take buffer copy from/to array out of S/R exch2_send/recv into new
164        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
165        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
166      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
167      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
168        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
169        including Topology header file (and common blocks).
170      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
171        remove 2nd exch call in exch2_s3d_rx (no longer needed).
172      - document S/R arg. list (+ update some comments)
173    o pkg/seaice:
174      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
175        temperature and humidity over sea ice based on climatological values.
176      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
177        of LSR (this change is expected to change the results slightly because now
178        it uses slightly difference moduli from the second last LSR solution, but
179        that is more consistent with the stress computations; this part of the code
180        is not tested in the verification experiments)
181      - fix diagnostics for flux of ice in case of B-grid
182      - turn strain rates eij and press into global fields within global
183        common block in SEAICE.h for more straighforward diagnostics
184      - fix diagnostics for principal stress components, press, zeta, eta
185        to give something meaning full
186    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
187      new output (all 4 tests) using default rotationPeriod.
188    o pkg KPP:
189      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
190      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
191        and normal grid from 1 to Nr)
192    o Fix computations of L4rdt in mom_calc_visc.F
193    o eesupp:
194      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
195      should be called before a "stop" if we know that all process are going
196      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
197    
198    checkpoint61o
199    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
200    o model/src/ini_curvilinear_grid.F:
201       compute angleSin/CosC when they are not read from a file
202    o pkg/seaice:
203       add pseudo time stepping for LSOR
204    o pkg/exch2:
205       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
206    o pkg/seaice:
207       Adding separate sea ice albedo, drag coefficients, and HO in Southern
208       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
209    o SingleCpuIO:
210       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
211    o pkg/seaice:
212       put exchanged variable in (local) common block for MPI+Multi-Threads
213       to work (necessary with exch1, and for now with exch2 too).
214    o verification: to get more experiments tested with mpi, mth and mpi+mth,
215      change tiling of:
216       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
217       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
218      update output of exp:
219       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
220       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
221      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
222                       (note: output.txt generated on faulks using only 1 tile)
223    o eesupp & mdsio (SingleCpuIO):
224     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
225       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
226       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
227     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
228     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
229       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
230    o pkg/exch2:
231     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
232       read parameter file "data.exch2" if it exists; otherwise try default regular
233       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
234     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
235       with new code (not to be used, just as a backup solution).
236     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
237       in utils/exch2/input.
238    
239    checkpoint61n
240    o eesupp & mdsio (SingleCpuIO):
241      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
242        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
243        receive real*4 array (instead of real*8) to read/write 32.bit files.
244        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
245         and remove new mapping S/R)
246    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
247      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
248        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
249        when using exch2. Add S/R to map global io-buffer to global model array.
250      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
251    
252    checkpoint61m
253    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
254      and add 3 other S/R for other types (R4,R8,RS).
255      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
256    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
257     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
258     - reduce number of macro definitions (keep only those which are used);
259       can always call directly the corrresponding S/R if needed.
260     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
261       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
262     Fixed wrong type of arg in:
263       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
264       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
265     To fix: global_sum of var in common block is wrong (multi-threaded) in:
266       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
267     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
268    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
269      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
270    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
271    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
272      edges are closed (zero depth); might happen with "blank tiles";
273      for now, disabled if using OBCS.
274    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
275      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
276    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
277      to reduce length of 1.D array print in STDOUT.
278    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
279      + use 48 tiles (16x8): this will allow to test "blank tiles".
280    o start to test MPI + multi-threaded (change testreport to skip tests
281      where number of tiles do not match).
282    o genmake2: add option "-omp" to turn on Open-MP ;
283      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
284    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
285      and keep the original tile numbering. Note: compatible with old
286      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
287    
288    checkpoint61l
289    o Overlaps had been forgotten in calculating ijk keys : fixed
290    o fix cyrus makedepend for gcc 4.4
291    o experiment fizhi-cs-aqualev20:
292      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
293      and generate new output. Note: new output is much closer to the old
294      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
295      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
296    o pkg/fizhi:
297     - change to avoid indices going deliberately over array-bounds
298     - remove unnecessary MPI stuff
299     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
300     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
301       does not go over array-bounds and therefore returns reliable output.
302     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
303       this S/R has 4 output arguments, which are used inside "get_alarm";
304       when it is called with the same variable "ndum" in place of several
305       output arguments, this produces weird side effect inside "get_alarm"
306      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
307       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
308       address) and produces error.
309    o tools/gemake2: (March 27-29 2009)
310      with option "-mpi": link *_mpi files from "MODS" dir (this is what
311      testreport does).
312  o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output  o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
313  o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:  o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
314     update lab_sea.lsr & lab_sea.salt_plume results     update lab_sea.lsr & lab_sea.salt_plume results
315  o pkg/seaice:  o pkg/seaice:
316    Major overhaul of the LSOR solver: change discretization from original    Major overhaul of the LSOR solver: change discretization from original
# Line 19  o pkg/seaice: Line 324  o pkg/seaice:
324    results by setting the above flag.    results by setting the above flag.
325    Further changes involve changes in defaults:    Further changes involve changes in defaults:
326    - ALLOW_FLOODING is defined and turned on by default    - ALLOW_FLOODING is defined and turned on by default
327    - SEAICE_advSnow = .true. is now the default    - SEAICEadvSnow = .true. is now the default
328    - SEAICE_advSalt = .true. is now the default    - SEAICEadvSalt = .true. is now the default
329    - SEAICE_advAge  = .true. is now the default    - SEAICEadvAge  = .true. is now the default
330    - SEAICE_clipVelocities  = .false. is now the default    - SEAICE_clipVelocities  = .false. is now the default
331                                       (as per J. Zhang's recommendation)                                       (as per J. Zhang's recommendation)
332    - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE    - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE

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