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2009WP/Release_v3.2 – NEMO
wiki:2009WP/Release_v3.2

Version 39 (modified by ctlod, 15 years ago) (diff)

--

Release v3.2


content

  • New Physics : tidal mixing ; RGB light penetration + ocean color ;
  • Cleaning of lib_mpp
  • IOM for the output
  • achievement of the coupled interface
  • VVL reactivation
  • Improved time-stepping achitecture

...


Minor bug fixes / enhancements

Ticket in bold includes some severe BUGs that have to be corrected in the release v3.2.

  • AGRIF
#443 Coordinates cannot be read under AGRIF
#415 runtime array allocation error with AGRIF
#341 Interpolation on the fly with AGRIFRachid ?
#261 AGRIF syntax problem with allocation of FLD arrays
#108 AGRIF with ice
#107 AGRIF with time-splitting
#106 AGRIF with time-splitting
#73 tradmp.F90 never called when using AGRIF ...
  • ENVironment
#409 ins_make [ -t "target host" ] ???
#407 alias and csh ???
#396 Add a first guess of ORCA2_LIM_PISCES configuration in libIGCM
#240 setting up and running NVTK on new target Claude action. Some point already solved. To be achieved in v3.2 ??? NVTK
  • LIM2
#194 LIM-2 damping option true identified bug. No real pressure to solve it urgently limdmp_2.F90 ==> v3.3 or later
#364 wrong sign in lbc_lnk for gradients in limadv.F90 True identified bug, easy to fix. To be done in v3.2 (cf. limadv_2.F90 in attachment and with style correction limadv_2_gm. NB 1: to be convinced, just plot the 1st moments of any fields in the ice restart file, they change sign at the north fold boundary. NB 2: in the _gm there is !!gm comments associated to optimisation modification that would change the results if there are wrong ) limadv_2.F90
  • LIM3
#464 Hard coded number of ice categories true identified bug. No simple solution. limdia.F90 ==> v3.3 or later
#439 Array index out of bounds in limsbc.F90 true identified bug. easy to fix. To be done in v3.2 (cf. limsbc.F90 in attachment and with style correction limsbc_gm.F90. Note that in the _gm there is !!gm comments associated to optimisation modification that would change the results if there are wrong ) limsbc.F90
#400 LIM3 : useless akappa and alambd arrays ?We agree, a cleaning of useless array is required. Should be done latter, when introducing EVP rheology in LIM2. ==> v3.3
#364 wrong sign in lbc_lnk for gradients in limadv.F90 We agree, to be done in v3.2 (cf. limadv.F90 in attachment and with style correction limadv_gm.F90. NB 1: to be convinced, just plot the 1st moments of any fields in the ice restart file, they change sign at the north fold boundary. . Note 2: in the _gm there is !!gm comments associated to optimisation modification that would change the results if there are wrong ) limadv.F90
#354 ORCA-LIM3 MPI problem? Apparently, it was a user error. The ticket can be closed. Rachid, do you agree? invalid
#243 simplification of computation of snow-ice energy in limthd_ent I (Gurvan) don't understand this ticket. Ask Martin for further info. postponed form v3.3
#195 LIM-3 a damping option should be added for regional configurations pending issue, can be included in Brice timetable ==> v3.3 or later
  • OFF
#320 update modules of the off-line Christian, off-line should be OK for v3.2, no? OFF
  • OPA

Physics

#462 Bug in zdftmx when using zdfddm change the order of the call in step. Done step.F90
#459 RGB light penetration + ocean color: paper documentationGurvan DOC
#458 tidal mixing: paper documentationGurvan DOC
#457 tidal mixing: optimisation Detail and code provided by Gurvan in attachment of the ticket. Done zdftmx.F90
#435 wrong index in ldfslp.F90 Done ldfslp.F90
#371 Mixed laplacian and bilaplacian operators Lap-bilap option, code provided and checked through the NVTK. Gurvan for code review: as provided it does not work, waiting for a reply from ed.blockley. probably not in v3.2 dynldf.F90 , ldfdyn.F90 , ldfdyn_oce.F90
#361 Proposal for diaptr Required for IPPC runs, routines provided. Claude + Gurvan ? diaptr.F90 + namelist
#239 diaptr code duplication / deficiencies clearly a problem to be solved... who? Claude/Sebastian?? diaptr.F90
#356 eosbn2: should we update the equation of state ? This should be added in the roadmap 2010 together with an option for P instead of z in eos ==> v3.4 or later
#331 No bottom friction if mbathy=2 to be solved together with #233. See Andrew work
#233 bottom friction issue... true identified bug. A clean solution is under development by Andrew. To be done in v3.2

Vertical coordinate

#434 mesh_zgr inconsistency when using zps I (Gurvan) think that JMM is right, we should return back to 3D arrays and recompute the e3tp etc after the check of the bathymetry ! Sebastian+Gurvan ? domain, domzgr.F90, domwri.F90
#381 bugs in "subroutine zgr_sco" to be checked domzgr.F90
#366 sbot_min not properly used in hybrid coordinate option (zgr_sco module in domzgr) small true identified bug. easy to fix. To be done in v3.2 (Gurvan) domzgr.F90

VVL re-activation

#382 bugs in "subroutine dom_vvl" fse3w computation Already corrected see domzgr_substitute.h90 ticket to be closed
#337 partial cells and vvl This contains an improvement to the hydrostatic pressure gradient correction in vvl case. To be checked by Rachid + Gurvan. In the trunk, we are currently using the sco correction which works ==> v3.2 or v3.3
#232 Optimization of dynspg_ts with key_vvl Already included in the trunk (see dynspg_ts). ticket to be closed
#329 vvl and time splitting 2 points here: (1) correct thickness timestep : should be OK in Rachid's latest version of dynspg_ts ; to be checked in v3.2. (2) removal of asselin filter on the barotropic part in dynnxt.F90 : I (Gurvan) don't think it is a good idea. dynspg_ts.F90
#328 vertical velocity and key_vvl We agree. In the current trunk, the call to wzv (now ssh_wzv) is done at the begining of step. The vertical velocity has to be removed from the restart file To be done in v3.2 Rachid + Gurvan restart.F90
#209 Bug in domvvl : wrong e3u e3v and e3f scale factors + change name of mut to ee_t partly solved in the trunk (see domvvl). The suppression of 3D arrays (mut, muu, muv, muf) does not work, we don't understand why (it will not be done in v3.2). The change in trazdf_imp and exp are still a pending issue to be solved in v3.2 (Rachid + Gurvan) trazdf_imp.F90 , trazdf_exp.F90

Surface module (SBC)

#436 Implementation of CICE and UM coupling code as part of S0.1 and S0.3 On-going work. Waiting for Exeter input ==> v3.3 or later
#406 optimize sbcssr.F90 routine We agree. Done sbcssr.F90

Bugs

#433 #363 potential non initialized value in trazdf_imp same minor bugs. To be solved in v3.2. Done trazdf_imp.F90
#424 missing lbc_lnk in sbcmod Sebastian answer properly to this ticket. Don't think we need to do something invalid ?
#419 Bug in dynvor_een when flux form is activated small true identified bug. easy to fix: add to CALL lbc_lnk( zwz, 'F', 1. ), Done dynvor.F90
#403 Calculation of avmb in zdf_tke_init true identified bug. To be done in v3.2. The idea is to add the background profile of avt and avm in the restart when tradv_cen2 is used (see zdfini.F90 and traadv_cen2.F90 in attachement and zdfini_gm & traadv_cen2 for further style modifications) zdfini.F90 , traadv_cen2.F90
#377 SBC fldread additions Improvment to SBC, code provided and checked through the NVTK. Sebastian for code review? fldread.F90 , iom.F90 , bdydta.F90 , sbcblk_clio.F90 , sbcflx.F90 , sbcice_if.F90 , sbcrnf.F90 , sbc_ssr.F90 , domain.F90 , in_out_manager.F90
#375 fldread and Interpolation on the FlySeem easy to do, Sebastian do you agree? seb response: No idea!!! we should ask to Steve fldread.F90
#365 wrong scale factors used in bdyvol small true identified bug. easy to fix. To be done in v3.2 (cf. bdyvol.F90 in attachment) bdyvol.F90
#368 bug in calendar of lim and top outputs done for lim. status of top? Christian? to be closed if Christian is ok
#342 #468 wrong computation of the heat contain almost done + should be associated with a full review for mld diag... must be done for IPCC
#332 Mistake in comment in nam_dynvor easy to fix. To be done in v3.2 Claude + Gurvan namelist
#244 tradmp A priori, this was done intentionally by Gurvan. Gurvan check it again! no action?
#129 Use of F95 signed zero causes incorrect results True identified problem. Specific compiler option added to circumvent it. A cleaner solution is to remove all SIGN instruction from the code, especially in sea-ice. ==> v3.3 or later
#127 Arrays go out of bounds true identified bug. rather easy to fix but using a other technique than the one proposed in the ticket. To be done in v3.2 (for diafwb.F90, see gm's comments and routines attached to the ticket. There is 2 other bug corrected in diafwb. For cla.F90, there is several other bugs, so at the end I completely re-wrote the module, merging cla, cla_div and cla_dynspg. See gm's comments and routines attached to the ticket. ) cla.F90 , diafwb.F90 suppress cla_div, cla_dynspg

IO issues

#437Distribution of "CALL iom_put" in NEMO-TOP Brice, Christian. On going work in the trunk. To be achieved in v3.2 whole NEMO
#410 PGF90-F-0004-Unable to open MODULE file netcdf.mod (fliocom.f90: 5) ???
#405 bug in diawri_dimg.h90 small true identified bug. easy to fix. To be done in v3.2 (cf. diawri_dimg.h90 in attachment) diawri_dimg.h90
#374 Addition of clobber and chunksize when opening NetCDF files Done. Wait for ioipsl improvement to extent modifications to all NetCDF files created in the code, and really close the ticket wait for ioipsl
#372 problem with netcdf syncing Invalid bug report Closed closed
#359 cleaning of calendar variables Sebastian + Gurvan action? phycst.F90 and others...
#343 no more runoff in outputs... keep runoff in the output only with IOM outputs, no more with standard one. Done done in changeset:1482
#314 wrong name of trends output file : key_trdmld, key_trmld_trc Christian should fix this problem trdmld
#296 obcdta_bt out of date To be solved together with major rewriting of OBC by MERCATOR. Rachid, you agree? ==> v3.3 or later
#237 Undefined behaviour writing to ocean.output from multiple pes Sebastian + Rachid do you agree? Seb: Yes, but this concerns only the first 10 lines of ocean.output, no? It cannot be bad... we should check the same kind of things with solver.stat and time (Yann reported problems with these files wrtitten by all cpus, I don't remember if we corrected it or not.
#201 simplified definition of the model time step Minor improvement. in v3.2 only if we have enough time ==> v3.2 or later

Misc. staff

#447 IOF and cutting along latitude ??? I (Gurvan) don't understand the nature of the problem. Rachid some idea?
#445 Performance of NEMO 3.1 idem as for #447
#200 dtatem & dtasal : cleaning - move the call from step to tradmp - merge in 1 module This should be added in the roadmap 2010 together with the system consolidation / simplification ==> v3.4 or later
#379 clean lib_mpp Done lib_mpp.F90, lbcnfd .F90 , lbclnk.F90