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revision 1.1074 by mlosch, Tue Mar 3 10:01:40 2009 UTC revision 1.1147 by jmc, Wed Aug 5 22:58:06 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: add missing "_d 0" in HSNOW initialisation
8       update results of experiments: lab_sea (3 fwd tests + 2 adjoint tests)
9          and offline_exf_seaice (seaicetd + adjoint).
10    o add missing "_d 0" in ShortWave flux penetration (S/R SWFRAC):
11       update results of experiments: lab_sea (4 fwd tests + 3 adjoint),
12        seaice_obcs, global_ocean.cs32x15 (icedyn & thsice) and natl_box (x2).
13    o few changes to pass when compiling with strick checking of arguments
14       across S/R (allow to find few bugs in S/R calls).
15    o pkg/seaice:
16     - seaice_evp: move if-statement out of loop (TEM) at the cost of 11 new
17       2d-fields, for slightly better performance
18    
19    checkpoint61t
20    o pkg/seaice:
21     - remove unused variables in seaice_evp
22     - reduce number of SQRT in seaice_evp and seaice_calc_viscosities
23    o eeset_parms.F, open_copy_data_file.F & ini_parms.F:
24       named file replacing SCRATCH files (for TARGET_BGL & TARGET_CRAYXT):
25       each processor opens a different file (a fix from Matt).
26    o cg2d:
27       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
28       this reduces number of EXCH calls by 2 when using exch2.
29       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
30       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
31    o pkg/thsice:
32       add code for Near Infra-Red albedo (from Jeff)
33       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
34    o ini_model_io:
35       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
36       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
37       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
38    
39    checkpoint61s
40    o pkg/exch2 (exch2_rxN_cube*):
41       remove last BARRIER (no need to synchronise after getting data from shared
42       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
43    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
44      and generate new output (for the 2 tests) using default rotationPeriod.
45    o pkg/exch2:
46      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
47        (was already the case with AUTODIFF_EXCH2 defined)
48      - add bj in exch2 arrays and S/R.
49      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
50        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
51    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
52      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
53        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
54      - verification experiment natl_box.longstep
55    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
56      allow different versions of ifort (8 or 9) and different versions
57       of mpi (mpich or mpich2) to be used with the same optfile.
58      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
59       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
60    o pkg/seaice:
61      fix previous modif (3-level field removed) for old-pickup reading
62    
63    checkpoint61r
64    o pkg/seaice:
65     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
66      1. introduce fields for time step (N-1)
67      2. do not use levels 2 and 3 anymore (but keep them)
68      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
69         includes changes to pkg/thsice/thsice_get_velocity.F,
70         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
71         pkg/obcs/obcs_apply_uvice.F.
72     - completely remove code for leap-frog time stepping for second order
73       advection
74     - adjusted adjoint accordingly;
75       gradient checks have improved by an order of magnitude!
76    
77    checkpoint61q
78    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
79     - the boundary conditions along open boundaries are unclear, because the
80       associated masks are set to zero and are thus treated as closed when
81       applying the slip-boundary conditions.
82     - move initialisation of grid variables from seaice_init_varia to _fixed
83    o adding doc/diags_changes.txt
84    o model/src:
85      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
86       to avoid "_diags" naming if no relation to pkg/diagnostics.
87      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
88       file and only call PLOT_FIELD_XYZ if debugMode=T.
89      remove few PLOT_FIELD_XY calls outside initialisation.
90      remove few unnecessary BARRIER.
91    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
92      of salt_plume package in Southern Ocean
93    o pkg/thsice:
94     - fix hOceMxL in overlap (needed for sea-ice advection);
95       update output of experiment global_ocean.cs32x15.icedyn.
96    o pkg/seaice:
97     - make the (placeholder-)tracer IceAge a little more meaningful
98      by avoiding ridging of age due to convergent ice flow
99     - add diagnostics for surface temperature, atmospheric and oceanic
100       heat flux, and atmospheric and oceanic ice growth
101    
102    checkpoint61p
103    o eesupp (global_max & global_sum):
104     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
105     - remove starting & endding barrier (no longer needed)
106    o pkg/mdsio, writelocal:
107       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
108       (remove the STOP): uses shared buffer IO to store data from all threads
109       and then let master-thread write nThreads tiles.
110    o pkg/mdsio (read/write field):
111     - tiled IO done in 1 piece (all levels at a time);
112     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
113     - multi-threaded: allow to read/write local (non-shared) array
114       (was already working with singleCpuIO ; now works also without);
115       => no longer needs barrier call after reading a file (added inside
116       mds_read/write field).
117     - move barrier calls outside gather/scatter_2d to mds_read/write_field
118    o pkg/obcs/exf
119      - exf_getffieldrec.F: add a few ". _d 0" and
120                            add code to catch the case fldperiod = 0.  
121      - obcs_precribe_read.F: change if statements so that they match
122                              the variable type (_RL)
123      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
124        exf_iprec) as part of namelist EXF_NML_01
125    o pkg/mdsio:
126      - read/write tiled (local) files: read/write 1-level tile chunk at a time
127        (instead of segment of length sNx); expected to speed up tiled IO.
128    o pkg/exch2:
129      - take buffer copy from/to array out of S/R exch2_send/recv into new
130        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
131        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
132      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
133      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
134        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
135        including Topology header file (and common blocks).
136      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
137        remove 2nd exch call in exch2_s3d_rx (no longer needed).
138      - document S/R arg. list (+ update some comments)
139    o pkg/seaice:
140      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
141        temperature and humidity over sea ice based on climatological values.
142      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
143        of LSR (this change is expected to change the results slightly because now
144        it uses slightly difference moduli from the second last LSR solution, but
145        that is more consistent with the stress computations; this part of the code
146        is not tested in the verification experiments)
147      - fix diagnostics for flux of ice in case of B-grid
148      - turn strain rates eij and press into global fields within global
149        common block in SEAICE.h for more straighforward diagnostics
150      - fix diagnostics for principal stress components, press, zeta, eta
151        to give something meaning full
152    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
153      new output (all 4 tests) using default rotationPeriod.
154    o pkg KPP:
155      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
156      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
157        and normal grid from 1 to Nr)
158    o Fix computations of L4rdt in mom_calc_visc.F
159    o eesupp:
160      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
161      should be called before a "stop" if we know that all process are going
162      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
163    
164    checkpoint61o
165    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
166    o model/src/ini_curvilinear_grid.F:
167       compute angleSin/CosC when they are not read from a file
168    o pkg/seaice:
169       add pseudo time stepping for LSOR
170    o pkg/exch2:
171       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
172    o pkg/seaice:
173       Adding separate sea ice albedo, drag coefficients, and HO in Southern
174       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
175    o SingleCpuIO:
176       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
177    o pkg/seaice:
178       put exchanged variable in (local) common block for MPI+Multi-Threads
179       to work (necessary with exch1, and for now with exch2 too).
180    o verification: to get more experiments tested with mpi, mth and mpi+mth,
181      change tiling of:
182       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
183       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
184      update output of exp:
185       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
186       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
187      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
188                       (note: output.txt generated on faulks using only 1 tile)
189    o eesupp & mdsio (SingleCpuIO):
190     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
191       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
192       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
193     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
194     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
195       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
196    o pkg/exch2:
197     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
198       read parameter file "data.exch2" if it exists; otherwise try default regular
199       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
200     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
201       with new code (not to be used, just as a backup solution).
202     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
203       in utils/exch2/input.
204    
205    checkpoint61n
206    o eesupp & mdsio (SingleCpuIO):
207      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
208        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
209        receive real*4 array (instead of real*8) to read/write 32.bit files.
210        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
211         and remove new mapping S/R)
212    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
213      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
214        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
215        when using exch2. Add S/R to map global io-buffer to global model array.
216      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
217    
218    checkpoint61m
219    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
220      and add 3 other S/R for other types (R4,R8,RS).
221      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
222    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
223     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
224     - reduce number of macro definitions (keep only those which are used);
225       can always call directly the corrresponding S/R if needed.
226     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
227       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
228     Fixed wrong type of arg in:
229       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
230       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
231     To fix: global_sum of var in common block is wrong (multi-threaded) in:
232       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
233     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
234    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
235      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
236    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
237    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
238      edges are closed (zero depth); might happen with "blank tiles";
239      for now, disabled if using OBCS.
240    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
241      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
242    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
243      to reduce length of 1.D array print in STDOUT.
244    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
245      + use 48 tiles (16x8): this will allow to test "blank tiles".
246    o start to test MPI + multi-threaded (change testreport to skip tests
247      where number of tiles do not match).
248    o genmake2: add option "-omp" to turn on Open-MP ;
249      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
250    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
251      and keep the original tile numbering. Note: compatible with old
252      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
253    
254    checkpoint61l
255    o Overlaps had been forgotten in calculating ijk keys : fixed
256    o fix cyrus makedepend for gcc 4.4
257    o experiment fizhi-cs-aqualev20:
258      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
259      and generate new output. Note: new output is much closer to the old
260      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
261      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
262    o pkg/fizhi:
263     - change to avoid indices going deliberately over array-bounds
264     - remove unnecessary MPI stuff
265     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
266     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
267       does not go over array-bounds and therefore returns reliable output.
268     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
269       this S/R has 4 output arguments, which are used inside "get_alarm";
270       when it is called with the same variable "ndum" in place of several
271       output arguments, this produces weird side effect inside "get_alarm"
272      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
273       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
274       address) and produces error.
275    o tools/gemake2: (March 27-29 2009)
276      with option "-mpi": link *_mpi files from "MODS" dir (this is what
277      testreport does).
278    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
279    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
280       update lab_sea.lsr & lab_sea.salt_plume results
281    o pkg/seaice:
282      Major overhaul of the LSOR solver: change discretization from original
283      finite differences to finite volume. The old routine is still in the
284      file seaice_lsr.F and can be turned on with the CPP-flag
285      SEAICE_OLD_AND_BAD_DISCRETIZATION
286      Along with this change, the discretization of the strain rates is changed.
287      The same flag turns on the old discretization in seaice_calc_strainrates.F
288      All verification experiments with seaice are affected (except for
289      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
290      results by setting the above flag.
291      Further changes involve changes in defaults:
292      - ALLOW_FLOODING is defined and turned on by default
293      - SEAICEadvSnow = .true. is now the default
294      - SEAICEadvSalt = .true. is now the default
295      - SEAICEadvAge  = .true. is now the default
296      - SEAICE_clipVelocities  = .false. is now the default
297                                         (as per J. Zhang's recommendation)
298      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
299        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
300      - seaice_growth: replace computation of UG by a simple copy from wspeed
301    
302    checkpoint61k
303    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
304      seaice_lsr: fixed a few metric terms,
305                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
306                  add more debugging diagnostics
307      seaice_evp: removed superfluous many metric terms of FV discretization
308                  of stress divergence
309                  affects lab_sea, lab_sea.hb87
310      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
311                  of stress divergence for non-evp solver
312                  (this part is not tested anywhere)
313      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
314                  they were effectively only half slip
315                  affects lab_sea.hb87
316      updated all relevant verification experiments (except lab_sea//output_adm.txt
317        which was left over, but fails at level 7 & 6)
318    
319    checkpoint61j
320    o pkg/seaice: turn a few hard wired parameters into run time parameters
321    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
322      time in seconds as promised by the usints in seaice_monitor and exf_monitor
323  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
324    that are not cubed-sphere grids    that are not cubed-sphere grids
325  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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