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revision 1.1068 by mlosch, Mon Feb 16 09:13:18 2009 UTC revision 1.1140 by jmc, Sat Jul 11 23:19:11 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 cg2d:
8       use simple EXCH (overlap size = 1 and ignore corners), like in cg3d.F :
9       this reduces number of EXCH calls by 2 when using exch2.
10       For now, keep previous size array for gc2d_nsa.F to avoid Pb with store
11       directives and missing simple EXCH (exch_s3d_rx) adjoint code.
12    o pkg/thsice:
13       add code for Near Infra-Red albedo (from Jeff)
14       (turned on with run-time flag: thSIce_calc_albNIR, in data.ice).
15    o ini_model_io:
16       move (from packages_readparms.F & initialise_fixed.F) to ini_model_io.F
17       MNC & MONITOR initialisation calls; move MNC calls from {pkg}_readparms.F
18       to {pkg}_init_fixed.F for {pkg}= kpp, seaice & shelfice.
19    
20    checkpoint61s
21    o pkg/exch2 (exch2_rxN_cube*):
22       remove last BARRIER (no need to synchronise after getting data from shared
23       buffer (get) as long as any change to buffer (put,recv) is between BARRIER)
24    o change tiling of natl_box (from 2 to 4 tiles) to get it tested with MPI+MTH
25      and generate new output (for the 2 tests) using default rotationPeriod.
26    o pkg/exch2:
27      - always call exch2_*_cube, not exch-1 anymore, if useCubedSphereExchange=F
28        (was already the case with AUTODIFF_EXCH2 defined)
29      - add bj in exch2 arrays and S/R.
30      - can now use pkg/exch2 for regular (non CS) set-up; switch test experiment
31        MLAdjust to exch2 (identical results except with MPI -> truncation diff);
32    o add pkg/longstep for ptracer timestep a multiple of U/V/T/S timestep
33      - adds deltaT argument to the subroutines TIMESTEP_TRACER DWNSLP_APPLY
34        GAD_ADVECTION GAD_CALC_RHS GAD_IMPLICIT_R GAD_SOM_ADVECT
35      - verification experiment natl_box.longstep
36    o build_options: ifort+mpi_aces optfile (following Constantinos advise):
37      allow different versions of ifort (8 or 9) and different versions
38       of mpi (mpich or mpich2) to be used with the same optfile.
39      requires to load a netcdf module and set MPI_INC_DIR (see comments inside
40       optfile). Change testing scripts (example_scripts/ACESgrid) accordingly.
41    o pkg/seaice:
42      fix previous modif (3-level field removed) for old-pickup reading
43    
44    checkpoint61r
45    o pkg/seaice:
46     - clean up the 3-time levels of UICE,VICE,HEFF,AREA in three steps:
47      1. introduce fields for time step (N-1)
48      2. do not use levels 2 and 3 anymore (but keep them)
49      3. replace 3D versions of UICE,VICE,HEFF,AREA by 2D versions. This
50         includes changes to pkg/thsice/thsice_get_velocity.F,
51         model/src/external_forcing_surf.F, pkg/obcs/obcs_apply_seaice.F, and
52         pkg/obcs/obcs_apply_uvice.F.
53     - completely remove code for leap-frog time stepping for second order
54       advection
55     - adjusted adjoint accordingly;
56       gradient checks have improved by an order of magnitude!
57    
58    checkpoint61q
59    o pkg/seaice: fix bug in free slip boundary conditons for LSOR solver
60     - the boundary conditions along open boundaries are unclear, because the
61       associated masks are set to zero and are thus treated as closed when
62       applying the slip-boundary conditions.
63     - move initialisation of grid variables from seaice_init_varia to _fixed
64    o adding doc/diags_changes.txt
65    o model/src:
66      do_the_model_io: rename few pkg S/R which are called from do_the_model_io,
67       to avoid "_diags" naming if no relation to pkg/diagnostics.
68      ini_theta,ini_salt: fix (at least compile the code) reading from NetCDF
69       file and only call PLOT_FIELD_XYZ if debugMode=T.
70      remove few PLOT_FIELD_XY calls outside initialisation.
71      remove few unnecessary BARRIER.
72    o pkg/salt_plume: add SaltPlumeSouthernOcean to allow disabling
73      of salt_plume package in Southern Ocean
74    o pkg/thsice:
75     - fix hOceMxL in overlap (needed for sea-ice advection);
76       update output of experiment global_ocean.cs32x15.icedyn.
77    o pkg/seaice:
78     - make the (placeholder-)tracer IceAge a little more meaningful
79      by avoiding ridging of age due to convergent ice flow
80     - add diagnostics for surface temperature, atmospheric and oceanic
81       heat flux, and atmospheric and oceanic ice growth
82    
83    checkpoint61p
84    o eesupp (global_max & global_sum):
85     - add one more element to buffer (start at index 0) for GL_MAX/SUM output;
86     - remove starting & endding barrier (no longer needed)
87    o pkg/mdsio, writelocal:
88       works also in multi-threaded when LOCBIN_IO_THREAD_SAFE is undefined
89       (remove the STOP): uses shared buffer IO to store data from all threads
90       and then let master-thread write nThreads tiles.
91    o pkg/mdsio (read/write field):
92     - tiled IO done in 1 piece (all levels at a time);
93     - new header file "MDSIO_BUFF_3D.h" with 3-D buffers.
94     - multi-threaded: allow to read/write local (non-shared) array
95       (was already working with singleCpuIO ; now works also without);
96       => no longer needs barrier call after reading a file (added inside
97       mds_read/write field).
98     - move barrier calls outside gather/scatter_2d to mds_read/write_field
99    o pkg/obcs/exf
100      - exf_getffieldrec.F: add a few ". _d 0" and
101                            add code to catch the case fldperiod = 0.  
102      - obcs_precribe_read.F: change if statements so that they match
103                              the variable type (_RL)
104      - add a separate exf_iprec_obcs to exf_set_obcs (by default equal to
105        exf_iprec) as part of namelist EXF_NML_01
106    o pkg/mdsio:
107      - read/write tiled (local) files: read/write 1-level tile chunk at a time
108        (instead of segment of length sNx); expected to speed up tiled IO.
109    o pkg/exch2:
110      - take buffer copy from/to array out of S/R exch2_send/recv into new
111        S/R exch2_put/get ; Exch of local variable now works with MPI+MTH
112        (tested by removing commom block statement in SOLVE_FOR_PRESSURE.h).
113      - ad version of send/recv no longer needed (but needs exch2_ad_put/ad_get)
114      - simplify argument list of S/R exch2_get_uv_bounds and exch2_get_scal_bounds
115        (which replaces exch2_get_recv_bounds & exch2_get_send_bounds) by
116        including Topology header file (and common blocks).
117      - implement EXCH_IGNORE_CORNERS in scalar exchange (rx1);
118        remove 2nd exch call in exch2_s3d_rx (no longer needed).
119      - document S/R arg. list (+ update some comments)
120    o pkg/seaice:
121      - added SEAICE_CLIM_AIR code, which permits modulation of surface air
122        temperature and humidity over sea ice based on climatological values.
123      - clean up computation of Hibler+Bryan (1987) stress coupling for the case
124        of LSR (this change is expected to change the results slightly because now
125        it uses slightly difference moduli from the second last LSR solution, but
126        that is more consistent with the stress computations; this part of the code
127        is not tested in the verification experiments)
128      - fix diagnostics for flux of ice in case of B-grid
129      - turn strain rates eij and press into global fields within global
130        common block in SEAICE.h for more straighforward diagnostics
131      - fix diagnostics for principal stress components, press, zeta, eta
132        to give something meaning full
133    o change tiling of global_ocean.cs32x15 (12 tiles, 32x16) and generate
134      new output (all 4 tests) using default rotationPeriod.
135    o pkg KPP:
136      - add flag (LimitHblStable) to avoid limiting BL depth under stable conditions
137      - fix vertical indices in RI_IWMIX (match between KPP grid from 0 to Nr+1
138        and normal grid from 1 to Nr)
139    o Fix computations of L4rdt in mom_calc_visc.F
140    o eesupp:
141      new S/R ALL_PROC_DIE (like EEDIE, without irrelevant threads err msg):
142      should be called before a "stop" if we know that all process are going
143      to stop; if one Proc does call this S/R, will hang in MPI_FINALISE.
144    
145    checkpoint61o
146    o pkg/exch2: change check_depths to issue just a warning (instead of error+stop)
147    o model/src/ini_curvilinear_grid.F:
148       compute angleSin/CosC when they are not read from a file
149    o pkg/seaice:
150       add pseudo time stepping for LSOR
151    o pkg/exch2:
152       temporary fix for exch2_s3d_rx; update results of exp. hs94.cs-32x32x5.impIGW
153    o pkg/seaice:
154       Adding separate sea ice albedo, drag coefficients, and HO in Southern
155       Ocean from those in Arctic Ocean.  See *_south in SEAICE_PARAMS.h
156    o SingleCpuIO:
157       fix bug put before chkp61n (May 11), when more than 2 MPI cpu are used.
158    o pkg/seaice:
159       put exchanged variable in (local) common block for MPI+Multi-Threads
160       to work (necessary with exch1, and for now with exch2 too).
161    o verification: to get more experiments tested with mpi, mth and mpi+mth,
162      change tiling of:
163       aim.5l_Equatorial_Channel, aim.5l_LatLon, dome, exp4, global_ocean.90x40x15,
164       hs94.cs-32x32x5, MLAdjust, offline_exf_seaice & tutorial_plume_on_slope
165      update output of exp:
166       exp4, global_ocean.90x40x15(+.dwslp), MLAdjust(all 5),
167       tutorial_plume_on_slope and hs94.cs-32x32x5 (use default rotationPeriod)
168      + ideal_2D_ocean: use default rotation period + test Global_Sum_SINGLECPU
169                       (note: output.txt generated on faulks using only 1 tile)
170    o eesupp & mdsio (SingleCpuIO):
171     - remove MISSING_TILE_IO (from MDSIO_OPTIONS.h), replaced by run-time
172       parameter "W2_useE2ioLayOut" (read from file "data.exch2").
173       Note: was not effective for globalFile & useSingleCpuIO=F; now fixed.
174     - move MDSIO_SCPU.h (pkg/mdsio) to EEBUFF_SCPU.h (eesupp/inc).
175     - fix GLOBAL_SUM_SINGLECPU when using Exch2; re-use same buffers and same
176       gather/scatter S/R as with SingleCpuIO (=> 1 less 2D global RL array).
177    o pkg/exch2:
178     - new code to set-up W2-Exch2 topology (replace matlab-topology-generator):
179       read parameter file "data.exch2" if it exists; otherwise try default regular
180       cube without blank-tile; new header file "W2_EXCH2_SIZE.h";
181     - update matlab-topology-generator (exch2_setup_cs6_print.m) to be compatible
182       with new code (not to be used, just as a backup solution).
183     - add examples (e.g., for lat-lon-cap_120) of parameter file "data.exch2"
184       in utils/exch2/input.
185    
186    checkpoint61n
187    o eesupp & mdsio (SingleCpuIO):
188      - move mapping to global io-buffer inside gather_2d/scater_2d: this save
189        memory (1 less 2D global RL array); skip 1 buffer copy; and only send/
190        receive real*4 array (instead of real*8) to read/write 32.bit files.
191        (new template for gather_2d/scater_2d, new set of S/R MDS_PASS_R4,8toRL,S
192         and remove new mapping S/R)
193    o pkg/mdsio: in preparation for topology-generator within pkg/exch2:
194      - Change declaration of SingleCpuIO buffer, reduced to only 1 dim.:
195        xyBuffer_size, which is set to W2_ioBufferSize from W2_EXCH2_PARAMS.h
196        when using exch2. Add S/R to map global io-buffer to global model array.
197      - uses exch2_global_Nx,y instead of exch2_domain_nxt,nyt.
198    
199    checkpoint61m
200    o write_utils : change WRITE_1D_R8 to WRITE_1D_RL
201      and add 3 other S/R for other types (R4,R8,RS).
202      Change calls to WRITE_0D/1D_R[4,8,S,L] to match the type of argument.
203    o eesupp/inc/CPP_EEMACROS.h (EXCH & GLOBAL_SUM/MAX macros):
204     - ensure suffix (_R4,_R8,_RS,_RL) correspondance between macro and S/R ;
205     - reduce number of macro definitions (keep only those which are used);
206       can always call directly the corrresponding S/R if needed.
207     - everywhere in the code: change macros (EXCH & GLOBAL_SUM/MAX) suffix
208       _R4/_R8 to _RS/_RL when applied to _RS/_RL variable.
209     Fixed wrong type of arg in:
210       atm2d/put_ocnvars.F cheapaml/cheapaml.F ocn_compon_interf/ocn_apply_import.F
211       ctrl/ctrl_map_ini_ecco.F seaice/seaice_do_diags.F seaice/seaice_model.F
212     To fix: global_sum of var in common block is wrong (multi-threaded) in:
213       dic/dic_atmos.F ebm/ebm_area_t.F ebm/ebm_zonalmean.F sbo/sbo_calc.F
214     To fix: aim_v23/aim_do_co2.F (BARRIER & GLOBAL_SUM within bi,bj loops)
215    o adjustment.cs-32x32x1: test "blank tiles" when compiling with mpi; 2nd
216      "nlfs" mpi test is going to stop when checking for unconnected tile egdes.
217    o eesupp/src: new S/R to stop everyone when 1 (or more) Proc. find an error
218    o pkg/exch2: new S/R EXCH2_CHECK_DEPTHS to check that unconnected tile
219      edges are closed (zero depth); might happen with "blank tiles";
220      for now, disabled if using OBCS.
221    o tools/gemake2: delete modifs from March 27-29 2009 (with option "-mpi":
222      link *_mpi files from "MODS" dir) to return to a strait-forward behavior.
223    o move read_write.F to write_utils.F ; new parameter (maxLengthPrt1D)
224      to reduce length of 1.D array print in STDOUT.
225    o adjustment.cs-32x32x1: changed to oceanic test with 1 continent
226      + use 48 tiles (16x8): this will allow to test "blank tiles".
227    o start to test MPI + multi-threaded (change testreport to skip tests
228      where number of tiles do not match).
229    o genmake2: add option "-omp" to turn on Open-MP ;
230      passed to testreport (if using -mth) ; merge few (*+mth) optfiles.
231    o pkg/exch2 (+ utils/exch2): ignore blank tiles (instead of removing them)
232      and keep the original tile numbering. Note: compatible with old
233      W2_EXCH2_TOPOLOGY.h & w2_e2setup.F topology files.
234    
235    checkpoint61l
236    o Overlaps had been forgotten in calculating ijk keys : fixed
237    o fix cyrus makedepend for gcc 4.4
238    o experiment fizhi-cs-aqualev20:
239      switching to new version of S/R GETPWHERE (#define TRY_NEW_GETPWHERE)
240      and generate new output. Note: new output is much closer to the old
241      one (v1.8) generated with pgf77 -O2 on Mar 14 2007 than it is from
242      the previous one (v1.9) generated with pgf77 -O0 on Jun 13 2007.
243    o pkg/fizhi:
244     - change to avoid indices going deliberately over array-bounds
245     - remove unnecessary MPI stuff
246     - perpetual spring equinox with "#define FIZHI_USE_FIXED_DAY"
247     - new version of S/R GETPWHERE available with #define TRY_NEW_GETPWHERE:
248       does not go over array-bounds and therefore returns reliable output.
249     - in fizhi_driver.F & fizhi_turb.F, fix "get_alarm" calls:
250       this S/R has 4 output arguments, which are used inside "get_alarm";
251       when it is called with the same variable "ndum" in place of several
252       output arguments, this produces weird side effect inside "get_alarm"
253      (e.g., datein=dates(n) is overwritten by timein=times(n) since both
254       datein & timein, resp. 2nd and 3rd arg., are pointed to the same "ndum"
255       address) and produces error.
256    o tools/gemake2: (March 27-29 2009)
257      with option "-mpi": link *_mpi files from "MODS" dir (this is what
258      testreport does).
259    o lab_sea experiment: change from 2x1 tiles to 2x2 tiles and regenerate output
260    o pkg/seaice: fix bug in new version of S/R SEAICE_LSR.F:
261       update lab_sea.lsr & lab_sea.salt_plume results
262    o pkg/seaice:
263      Major overhaul of the LSOR solver: change discretization from original
264      finite differences to finite volume. The old routine is still in the
265      file seaice_lsr.F and can be turned on with the CPP-flag
266      SEAICE_OLD_AND_BAD_DISCRETIZATION
267      Along with this change, the discretization of the strain rates is changed.
268      The same flag turns on the old discretization in seaice_calc_strainrates.F
269      All verification experiments with seaice are affected (except for
270      seaice_exf_offline); global_ocean.cs32x15/input.icedyn recovers the old
271      results by setting the above flag.
272      Further changes involve changes in defaults:
273      - ALLOW_FLOODING is defined and turned on by default
274      - SEAICEadvSnow = .true. is now the default
275      - SEAICEadvSalt = .true. is now the default
276      - SEAICEadvAge  = .true. is now the default
277      - SEAICE_clipVelocities  = .false. is now the default
278                                         (as per J. Zhang's recommendation)
279      - B-grid, and thus not tested: SEAICE_TEST_ICE_STRESS_1/EXPLICIT_SSH_SLOPE
280        is defined, SEAICE_TEST_ICE_STRESS_1 is renamed into SEAICE_BICE_STRESS
281      - seaice_growth: replace computation of UG by a simple copy from wspeed
282    
283    checkpoint61k
284    o pkg/seaice: a few bug fixes mostly concerning the metric terms:
285      seaice_lsr: fixed a few metric terms,
286                  affects lab_sea.lsr, lab_sea.salt_plume, seaice_obcs
287                  add more debugging diagnostics
288      seaice_evp: removed superfluous many metric terms of FV discretization
289                  of stress divergence
290                  affects lab_sea, lab_sea.hb87
291      seaice_ocean_stress: removed superfluous many metric terms of FV discretization
292                  of stress divergence for non-evp solver
293                  (this part is not tested anywhere)
294      seaice_calc_strainrates: fixed a bug in no-slip boundary conditions,
295                  they were effectively only half slip
296                  affects lab_sea.hb87
297      updated all relevant verification experiments (except lab_sea//output_adm.txt
298        which was left over, but fails at level 7 & 6)
299    
300    checkpoint61j
301    o pkg/seaice: turn a few hard wired parameters into run time parameters
302    o pkg/seaice/exf/monitor: turn netcdf coordinate variable T into model
303      time in seconds as promised by the usints in seaice_monitor and exf_monitor
304    o pkg/mnc: fix the coordinate variables for multi-tile curvi-linear grids
305      that are not cubed-sphere grids
306    o pkg/seaice: fix a bug for the rare case of SEAICE_VECTORIZE_LSR
307    o pkg/ctrl:
308      fix bug in ctrl_depth_ini.F (EXCH_XYZ was applied to 2-D field xx_r_low)
309    o non-hydrostatic (calc_gw.F):
310      fix viscA4 on CS-grid + fix diagnostics: Wm_Diss & Wm_Advec
311      update output of exp. global_ocean.cs32x15.viscA4
312    o remove backward compatibility for thetaMin,phiMin
313      (replaced by xgOrigin,ygOrigin on Jan 27, 2009)
314    o pkg/exf: fix a serious bug in exf_set_uv.F: do a rotation of the
315      interpolated wind field not only for curvilineargrid=.true., but also
316      for a rotated grid (rotateGrid=.true.)
317  o pkg/exf: add capability to bypass interpolation for runoff  o pkg/exf: add capability to bypass interpolation for runoff
318    by setting yet another CPP-flag    by setting yet another CPP-flag
319    o eesupp/src, B-grid exchange:
320      add simple (6 tiles, non MPI) CS exch + standard interface S/R.
321  o autodiff  o autodiff
322    new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV    new CPP option ALLOW_TAMC_SINGLEPREC_COMLEV
323    allows to switch to single-prec common blocks;    allows to switch to single-prec common blocks;
# Line 21  o pkg/autodiff, pkg/ctrl: Line 333  o pkg/autodiff, pkg/ctrl:
333    Add flag to reduce all tapelev I/O to single-prec.    Add flag to reduce all tapelev I/O to single-prec.
334    In data.ctrl set    In data.ctrl set
335      doSinglePrecTapelev = .TRUE.      doSinglePrecTapelev = .TRUE.
336  o model/src/ini_curvilinear_grid.F: check in hack for SX8 compiler  o model/src/ini_curvilinear_grid.F, new grid-file format without EXCH2:
337    to make sure that recip_dxV and recip_dyU are never zero, until we    check in hack for SX8 compiler (for dxV, dyU); remove it afterwards.
   have a proper exchange for them. Most compilers do not seem  
   to mind divisions by zero in the overlaps, as long as the results are  
   not used anywhere, but sxf90 does.  
338  o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for  o pkg/shelfice: fix bug with SHELFICEconserve flag, prepare for
339    real fresh water flux (not yet)    real fresh water flux (not yet)
340  o pkg/mdsio & rw:  o pkg/mdsio & rw:

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