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revision 1.1081 by mlosch, Fri Mar 20 16:04:38 2009 UTC revision 1.1154 by jmc, Tue Sep 1 20:45:26 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 (& pkg/rw): rework high level S/R interface:
8      To avoid mixing type (RS/RL) of input/output array argument,
9      replace single mixed-type array with a pair from each type (RS/RL).
10    o setting pickupSuff force to start from a pickup (even if nIter0=0): this
11      is now implemented for all pkgs (previously only done for the main pickup)
12    
13    checkpoint61u
14    o pkg/obcs:
15      - change OB?eta from _RS to _RL and put them into a separate commen block
16      - add code to read OB?eta from a file via obcs_prescribe_read: the code
17        compiles and does not destroy any other experiments, the data is read
18        properly, but the code is not tested in actual applications
19    o ini_mnc_vars.F: if available (ALLOW_CAL), use startTime_1 and 2 to
20      create a meaningful unit attribute for the time coordinate variable
21    o pkg/ebm: add plenty of missing "_d 0" ;
22       update results of experiment global_ocean_ebm (fwd + adjoint tests)
23      Notes: several pieces of code only works for (very) specific set up
24       (domain size, lat range, etc ...); should be documented & stop if one
25       of those assumptions is not meet.
26    o pkg/seaice: add missing "_d 0" in HSNOW initialisation
27       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
28          and offline_exf_seaice (seaicetd + adjoint).
29    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
30       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
31        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
32    o few changes to pass when compiling with strick checking of arguments
33       across S/R (allow to find few bugs in S/R calls).
34    o pkg/seaice:
35     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
36       2d-fields, for slightly better performance
37    
38    checkpoint61t
39    o pkg/seaice:
40     - remove unused variables in seaice_evp
41     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
42    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
43       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
44       each processor opens a different file (a fix from Matt).
45    o cg2d:
46       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
47       this reduces number of EXCH calls by 2 when using exch2.
48       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
49       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
50    o pkg/thsice:
51       add code for Near Infra-Red albedo (from Jeff)
52       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
53    o ini_model_io:
54       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
55       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
56       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
57    
58    checkpoint61s
59    o pkg/exch2 (exch2_rxN_cube*):
60       remove last BARRIER (no need to synchronise after getting data from shared
61       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
62    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
63      and generate new output (for the 2 tests) using default rotationPeriod.
64    o pkg/exch2:
65      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
66        (was already the case with AUTODIFF_EXCH2 defined)
67      - add bj in exch2 arrays and S/R.
68      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
69        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
70    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
71      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
72        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
73      - verification experiment natl_box.longstep
74    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
75      allow different versions of ifort (8 or 9) and different versions
76       of mpi (mpich or mpich2) to be used with the same optfile.
77      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
78       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
79    o pkg/seaice:
80      fix previous modif (3-level field removed) for old-pickup reading
81    
82    checkpoint61r
83    o pkg/seaice:
84     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
85      1. introduce fields for time step (N-1)
86      2. do not use levels 2 and 3 anymore (but keep them)
87      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
88         includes changes to pkg/thsice/thsice_get_velocity.F,
89         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
90         pkg/obcs/obcs_apply_uvice.F.
91     - completely remove code for leap-frog time stepping for second order
92       advection
93     - adjusted adjoint accordingly;
94       gradient checks have improved by an order of magnitude!
95    
96    checkpoint61q
97    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
98     - the boundary conditions along open boundaries are unclear, because the
99       associated masks are set to zero and are thus treated as closed when
100       applying the slip-boundary conditions.
101     - move initialisation of grid variables from seaice_init_varia to _fixed
102    o adding doc/diags_changes.txt
103    o model/src:
104      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
105       to avoid "_diags" naming if no relation to pkg/diagnostics.
106      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
107       file and only call PLOT_FIELD_XYZ if debugMode=T.
108      remove few PLOT_FIELD_XY calls outside initialisation.
109      remove few unnecessary BARRIER.
110    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
111      of salt_plume package in Southern Ocean
112    o pkg/thsice:
113     - fix hOceMxL in overlap (needed for sea-ice advection);
114       update output of experiment global_ocean.cs32x15.icedyn.
115    o pkg/seaice:
116     - make the (placeholder-)tracer IceAge a little more meaningful
117      by avoiding ridging of age due to convergent ice flow
118     - add diagnostics for surface temperature, atmospheric and oceanic
119       heat flux, and atmospheric and oceanic ice growth
120    
121    checkpoint61p
122    o eesupp (global_max & global_sum):
123     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
124     - remove starting & endding barrier (no longer needed)
125    o pkg/mdsio, writelocal:
126       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
127       (remove the STOP): uses shared buffer IO to store data from all threads
128       and then let master-thread write nThreads tiles.
129    o pkg/mdsio (read/write field):
130     - tiled IO done in 1 piece (all levels at a time);
131     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
132     - multi-threaded: allow to read/write local (non-shared) array
133       (was already working with singleCpuIO ; now works also without);
134       => no longer needs barrier call after reading a file (added inside
135       mds_read/write field).
136     - move barrier calls outside gather/scatter_2d to mds_read/write_field
137    o pkg/obcs/exf
138      - exf_getffieldrec.F: add a few ". _d 0" and
139                            add code to catch the case fldperiod = 0.  
140      - obcs_precribe_read.F: change if statements so that they match
141                              the variable type (_RL)
142      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
143        exf_iprec) as part of namelist EXF_NML_01
144    o pkg/mdsio:
145      - read/write tiled (local) files: read/write 1-level tile chunk at a time
146        (instead of segment of length sNx); expected to speed up tiled IO.
147    o pkg/exch2:
148      - take buffer copy from/to array out of S/R exch2_send/recv into new
149        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
150        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
151      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
152      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
153        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
154        including Topology header file (and common blocks).
155      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
156        remove 2nd exch call in exch2_s3d_rx (no longer needed).
157      - document S/R arg. list (+ update some comments)
158    o pkg/seaice:
159      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
160        temperature and humidity over sea ice based on climatological values.
161      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
162        of LSR (this change is expected to change the results slightly because now
163        it uses slightly difference moduli from the second last LSR solution, but
164        that is more consistent with the stress computations; this part of the code
165        is not tested in the verification experiments)
166      - fix diagnostics for flux of ice in case of B-grid
167      - turn strain rates eij and press into global fields within global
168        common block in SEAICE.h for more straighforward diagnostics
169      - fix diagnostics for principal stress components, press, zeta, eta
170        to give something meaning full
171    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
172      new output (all 4 tests) using default rotationPeriod.
173    o pkg KPP:
174      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
175      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
176        and normal grid from 1 to Nr)
177    o Fix computations of L4rdt in mom_calc_visc.F
178    o eesupp:
179      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
180      should be called before a "stop" if we know that all process are going
181      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
182    
183    checkpoint61o
184    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
185    o model/src/ini_curvilinear_grid.F:
186       compute angleSin/CosC when they are not read from a file
187    o pkg/seaice:
188       add pseudo time stepping for LSOR
189    o pkg/exch2:
190       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
191    o pkg/seaice:
192       Adding separate sea ice albedo, drag coefficients, and HO in Southern
193       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
194    o SingleCpuIO:
195       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
196    o pkg/seaice:
197       put exchanged variable in (local) common block for MPI+Multi-Threads
198       to work (necessary with exch1, and for now with exch2 too).
199    o verification: to get more experiments tested with mpi, mth and mpi+mth,
200      change tiling of:
201       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
202       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
203      update output of exp:
204       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
205       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
206      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
207                       (note: output.txt generated on faulks using only 1 tile)
208    o eesupp & mdsio (SingleCpuIO):
209     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
210       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
211       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
212     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
213     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
214       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
215    o pkg/exch2:
216     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
217       read parameter file "data.exch2" if it exists; otherwise try default regular
218       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
219     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
220       with new code (not to be used, just as a backup solution).
221     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
222       in utils/exch2/input.
223    
224    checkpoint61n
225    o eesupp & mdsio (SingleCpuIO):
226      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
227        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
228        receive real*4 array (instead of real*8) to read/write 32.bit files.
229        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
230         and remove new mapping S/R)
231    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
232      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
233        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
234        when using exch2. Add S/R to map global io-buffer to global model array.
235      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
236    
237    checkpoint61m
238    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
239      and add 3 other S/R for other types (R4,R8,RS).
240      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
241    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
242     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
243     - reduce number of macro definitions (keep only those which are used);
244       can always call directly the corrresponding S/R if needed.
245     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
246       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
247     Fixed wrong type of arg in:
248       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
249       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
250     To fix: global_sum of var in common block is wrong (multi-threaded) in:
251       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
252     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
253    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
254      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
255    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
256    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
257      edges are closed (zero depth); might happen with "blank tiles";
258      for now, disabled if using OBCS.
259    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
260      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
261    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
262      to reduce length of 1.D array print in STDOUT.
263    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
264      + use 48 tiles (16x8): this will allow to test "blank tiles".
265    o start to test MPI + multi-threaded (change testreport to skip tests
266      where number of tiles do not match).
267    o genmake2: add option "-omp" to turn on Open-MP ;
268      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
269    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
270      and keep the original tile numbering. Note: compatible with old
271      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
272    
273    checkpoint61l
274    o Overlaps had been forgotten in calculating ijk keys : fixed
275    o fix cyrus makedepend for gcc 4.4
276    o experiment fizhi-cs-aqualev20:
277      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
278      and generate new output. Note: new output is much closer to the old
279      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
280      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
281    o pkg/fizhi:
282     - change to avoid indices going deliberately over array-bounds
283     - remove unnecessary MPI stuff
284     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
285     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
286       does not go over array-bounds and therefore returns reliable output.
287     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
288       this S/R has 4 output arguments, which are used inside "get_alarm";
289       when it is called with the same variable "ndum" in place of several
290       output arguments, this produces weird side effect inside "get_alarm"
291      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
292       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
293       address) and produces error.
294    o tools/gemake2: (March 27-29 2009)
295      with option "-mpi": link *_mpi files from "MODS" dir (this is what
296      testreport does).
297    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
298    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
299       update lab_sea.lsr & lab_sea.salt_plume results
300  o pkg/seaice:  o pkg/seaice:
301    Major overhaul of the LSOR solver: change discretization from original    Major overhaul of the LSOR solver: change discretization from original
302    finite differences to finite volume. The old routine is still in the    finite differences to finite volume. The old routine is still in the
# Line 16  o pkg/seaice: Line 309  o pkg/seaice:
309    results by setting the above flag.    results by setting the above flag.
310    Further changes involve changes in defaults:    Further changes involve changes in defaults:
311    - ALLOW_FLOODING is defined and turned on by default    - ALLOW_FLOODING is defined and turned on by default
312    - SEAICE_advSnow = .true. is now the default    - SEAICEadvSnow = .true. is now the default
313    - SEAICE_advSalt = .true. is now the default    - SEAICEadvSalt = .true. is now the default
314    - SEAICE_advAge  = .true. is now the default    - SEAICEadvAge  = .true. is now the default
315    - SEAICE_clipVelocities  = .false. is now the default    - SEAICE_clipVelocities  = .false. is now the default
316                                       (as per J. Zhang's recommendation)                                       (as per J. Zhang's recommendation)
317    - 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
# Line 39  o pkg/seaice: a few bug fixes mostly con Line 332  o pkg/seaice: a few bug fixes mostly con
332    seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,    seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
333                they were effectively only half slip                they were effectively only half slip
334                affects lab_sea.hb87                affects lab_sea.hb87
335    updated all relevant verification experiments    updated all relevant verification experiments (except lab_sea//output_adm.txt
336        which was left over, but fails at level 7 & 6)
337    
338  checkpoint61j  checkpoint61j
339  o pkg/seaice: turn a few hard wired parameters into run time parameters  o pkg/seaice: turn a few hard wired parameters into run time parameters

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