croco issueshttps://gitlab.inria.fr/croco-ocean/croco/-/issues2024-03-25T16:25:07+01:00https://gitlab.inria.fr/croco-ocean/croco/-/issues/176Compilation : transition from ifort to ifx2024-03-25T16:25:07+01:00Solene Le GacCompilation : transition from ifort to ifxSee warning during compilation :
`ifort: remark #10448: Intel(R) Fortran Compiler Classic (ifort) is now deprecated and will be discontinued late 2024. Intel recommends that customers transition now to using the LLVM-based Intel(R) For...See warning during compilation :
`ifort: remark #10448: Intel(R) Fortran Compiler Classic (ifort) is now deprecated and will be discontinued late 2024. Intel recommends that customers transition now to using the LLVM-based Intel(R) Fortran Compiler (ifx) for continued Windows* and Linux* support, new language support, new language features, and optimizations. Use '-diag-disable=10448' to disable this message. mv a.out croco`2024-12-31https://gitlab.inria.fr/croco-ocean/croco/-/issues/100Sediment USGS improvement2023-01-27T17:04:04+01:00Morvan guillaumeSediment USGS improvementSome improvements needed for USGS model test case :
* [ ] Some bugs appears with ifort compilation on Sandbar / Rip / Sed_toy floc 0d
* [ ] Check TidalFlat test case
* [ ] Use of USGS with Estuary / Vilaine
* [ ] Need matlab example scri...Some improvements needed for USGS model test case :
* [ ] Some bugs appears with ifort compilation on Sandbar / Rip / Sed_toy floc 0d
* [ ] Check TidalFlat test case
* [ ] Use of USGS with Estuary / Vilaine
* [ ] Need matlab example script for plotting sed toy floc / estuary / vilaine
* [ ] Clean some tipos
A need also appears to have a realistic test case included within CVTK routine like Benguela
* [ ] Vilaine test caseMorvan guillaumeMorvan guillaume2023-06-15https://gitlab.inria.fr/croco-ocean/croco/-/issues/35Mustang & Sediment - Conservation of mass if morphodynamic with sediment in s...2024-02-20T12:05:56+01:00Solene Le GacMustang & Sediment - Conservation of mass if morphodynamic with sediment in suspensionA SED_TOY 1DV configuration has been used with morphodyn and without it.
The results show a non conservation of mass if morphodyn is applied.
This appears to come from the position in the time loop of the call to set_depth_morphodyn whi...A SED_TOY 1DV configuration has been used with morphodyn and without it.
The results show a non conservation of mass if morphodyn is applied.
This appears to come from the position in the time loop of the call to set_depth_morphodyn which update the vertical grid using the variation dh compute by MUSTANG.MustangSolene Le GacSolene Le Gac2022-06-01https://gitlab.inria.fr/croco-ocean/croco/-/issues/28Mass source point2022-05-30T19:02:36+02:00Matthieu CaillaudMass source pointPossibility to add a source point as a volume vertical influx. With this feature there is no need to take care of the position of the source with the mask and a source can be added anywhere on the grid. The outflow is applied at rho point.Possibility to add a source point as a volume vertical influx. With this feature there is no need to take care of the position of the source with the mask and a source can be added anywhere on the grid. The outflow is applied at rho point.new branchMatthieu CaillaudMatthieu Caillaud2022-04-01https://gitlab.inria.fr/croco-ocean/croco/-/issues/14bug at compilation with options AGRIF+WET_DRY+FRC_BRY2022-03-31T19:02:37+02:00Laurent ROBLOUbug at compilation with options AGRIF+WET_DRY+FRC_BRYThere is a missing piece of code to handle boundary conditions at compilation for the case AGRIF+WET_DRY+FRC_BRY (code compilation fails and complains about variables ubclm, vbclm).There is a missing piece of code to handle boundary conditions at compilation for the case AGRIF+WET_DRY+FRC_BRY (code compilation fails and complains about variables ubclm, vbclm).Bug fixLaurent ROBLOULaurent ROBLOU2019-03-13https://gitlab.inria.fr/croco-ocean/croco/-/issues/13debug2022-03-31T19:02:37+02:00DEBREU LaurentdebugGeneralize debug to compare 2 parallel runs (or 2 sequential runs)Generalize debug to compare 2 parallel runs (or 2 sequential runs)DEBREU LaurentDEBREU Laurent2019-03-11https://gitlab.inria.fr/croco-ocean/croco/-/issues/177check run_run_forecast2024-03-25T17:36:23+01:00Gildas Camboncheck run_run_forecastCheck the run_croco_foracast with updated Forecast_tools/
@marchesielloCheck the run_croco_foracast with updated Forecast_tools/
@marchesielloRELEASE_2024_MARCHMorvan guillaumeMorvan guillaumehttps://gitlab.inria.fr/croco-ocean/croco/-/issues/175AGRIF - warnings temp array2024-03-26T14:08:30+01:00Solene Le GacAGRIF - warnings temp arrayWhen using `-check all` option with ifort, a lot of warnings are raised about temporary arrays:
`forrtl: warning (406): fort: (1): In call to AGRIF_SET_BC, an array temporary was created for argument #2$`
Is it something to improve ? O...When using `-check all` option with ifort, a lot of warnings are raised about temporary arrays:
`forrtl: warning (406): fort: (1): In call to AGRIF_SET_BC, an array temporary was created for argument #2$`
Is it something to improve ? Or is it something intrinsic to Agrif?https://gitlab.inria.fr/croco-ocean/croco/-/issues/173Files to clean2024-03-20T12:06:34+01:00Solene Le GacFiles to cleanSome files still refer to ROMS and not CROCO.
Are they still functional?
Are they in the right place? (some could be better placed in the tool repository).
Example : `OCEAN/initfloats.m` and `TEST_CASES/make_clim_IGW.m`Some files still refer to ROMS and not CROCO.
Are they still functional?
Are they in the right place? (some could be better placed in the tool repository).
Example : `OCEAN/initfloats.m` and `TEST_CASES/make_clim_IGW.m`https://gitlab.inria.fr/croco-ocean/croco/-/issues/172Issue with files numbering2024-03-18T18:34:25+01:00Jonathan GulaIssue with files numberingBug for the initial wrt_his if nrpfhis = 1
"ERROR in def_his/avg: Cannot create netCDF file: OUT/croco_his.0000/.nc"
This happens when nrechis=0 and nrpfhis=1, it gives lvar=-1 and insert_time_index fails (in def_his.F)
One solution i...Bug for the initial wrt_his if nrpfhis = 1
"ERROR in def_his/avg: Cannot create netCDF file: OUT/croco_his.0000/.nc"
This happens when nrechis=0 and nrpfhis=1, it gives lvar=-1 and insert_time_index fails (in def_his.F)
One solution is to move up the line "nrechis=max(1,nrechis)" (in wrt_his.F) before calling def_his.Jonathan GulaJonathan Gulahttps://gitlab.inria.fr/croco-ocean/croco/-/issues/171XIOS32024-03-15T13:45:43+01:00Rachid BenshilaXIOS3A reminder to switch to XIOS3 (one day). Lionel tried it some time ago, his comments below :
> suite au passage RedHat d’Irene qui m’a tout foutu en l’air, je suis passé à XIOS3 dans WRF et CROCO. ll y a quelques modifs à faire dans les...A reminder to switch to XIOS3 (one day). Lionel tried it some time ago, his comments below :
> suite au passage RedHat d’Irene qui m’a tout foutu en l’air, je suis passé à XIOS3 dans WRF et CROCO. ll y a quelques modifs à faire dans les 2 codes ainsi que dans iodef.xml. Après des tests sur mes configs en cours, je pense que ça vaut le coup de dégager xios2.5 et de passer à xios3, ça marche beaucoup mieux. Des problèmes que j’avais avec une grille \~2000x1500x100 avec XIOS2.5 :
>
> - lenteur du code
> - temps d’attente d’ecriture assez long qui bloque les codes malgré des processeurs dédiés
> - comportement imprévisible selon le nombre de procs utilisés.
>
> Au point que j’avais laissé XIOS pour certaines configs au profit de NC4PAR ou que j’avais accepté un temps d’écriture asses long aussi bien en NC4PAR qu’en XIOS, //\_FILES était alors la meilleure option, mais ça peut etre rédhibitoire en fonction du nombre de fichiers, découpage, etc
>
> Tout semble réglé avec XIOS3.https://gitlab.inria.fr/croco-ocean/croco/-/issues/170pb compil with AGRIF + BULK2024-03-14T11:37:39+01:00Swen Jullienpb compil with AGRIF + BULKCompilation with AGRIF and BULK gives an error (tested with intel)Compilation with AGRIF and BULK gives an error (tested with intel)RELEASE_2024_MARCHhttps://gitlab.inria.fr/croco-ocean/croco/-/issues/169ocean2pisces.F90 compatibility issues with new air-sea2024-03-14T06:13:49+01:00Subhadeep Maishalsubhadeepmaishal@kgpian.iitkgp.ac.inocean2pisces.F90 compatibility issues with new air-seaHi,
Respected sir/madam
I tried to compile croco-dev_2024_CPL_before_release branch
CPL+PISCES
without CPL keys it's able to compile.
almost all branches have this ocean2pisces.F90 file. except 141-new-pisces-version.
**And find th...Hi,
Respected sir/madam
I tried to compile croco-dev_2024_CPL_before_release branch
CPL+PISCES
without CPL keys it's able to compile.
almost all branches have this ocean2pisces.F90 file. except 141-new-pisces-version.
**And find this error **
mpiifort -c -O2 -mcmodel=medium -fno-alias -i4 -r8 -fp-model precise -I/home/20cl91p02/NEXTGEN/LIB_INSTALL/NETCDF4_HDF5/include -I/scratch/20cl91p02/NEXTGEN/CONFIG/load_balance/oasis3_mct_install/build/lib/psmile.MPI1 -I/scratch/20cl91p02/NEXTGEN/CONFIG/load_balance/oasis3_mct_install/build/lib/mct -I/home/20cl91p02/NEXTGEN/LIB_INSTALL/NETCDF4_HDF5/include ocean2pisces_.f90 -o ocean2pisces.o
ocean2pisces_.f90(769): error #5082: Syntax error, found END-OF-STATEMENT when expecting one of: <IDENTIFIER> / //
common /exchange_fields_oasis3/ srcv_clname,ssnd_clname,
--------------------------------------------------------------^
ocean2pisces_.f90(770): error #5082: Syntax error, found '&' when expecting one of: <LABEL> <END-OF-STATEMENT> ; <IDENTIFIER> TYPE MODULE ELEMENTAL IMPURE NON_RECURSIVE ...
& srcv_nid ,ssnd_nid
--------------------------------------^
ocean2pisces_.f90(770): error #6274: This statement must not appear in the specification part of a module.
& srcv_nid ,ssnd_nid
--------------------------------------^
ocean2pisces_.f90(772): error #6236: A specification statement cannot appear in the executable section.
INTEGER :: oasis_time, oasis_runtime
**and more**
ocean2pisces_.f90(827): error #6404: This name does not have a type, and must have an explicit type. [ISTRP]
Istrp = Istr
------^
ocean2pisces_.f90(828): error #6404: This name does not have a type, and must have an explicit type. [IENDP]
Iendp = Iend
------^
ocean2pisces_.f90(829): error #6404: This name does not have a type, and must have an explicit type. [JSTRP]
Jstrp = Jstr
------^
ocean2pisces_.f90(830): error #6404: This name does not have a type, and must have an explicit type. [JENDP]
Jendp = Jend
------^
ocean2pisces_.f90(836): error #6410: This name has not been declared as an array or a function. [GDEPW_N]
gdepw_n(i,j,N+2-k) = -(z_w(i,j,k-1)-z_w(i,j,N))
---------------^
ocean2pisces_.f90(1752): catastrophic error: Too many errors, exiting
**compilation aborted for ocean2pisces_.f90 (code 1)
gmake: *** [ocean2pisces.o] Error 1**
Thank you
Have a good day!https://gitlab.inria.fr/croco-ocean/croco/-/issues/167COUPLING : problem job not killed when error in croco when opening input files2024-03-14T16:38:02+01:00Swen JullienCOUPLING : problem job not killed when error in croco when opening input filesIn coupled mode, the job is not killed by CROCO when CROCO faces an error in reading netcdf files: "ERROR: Abnormal termination: netCDF INPUT"
Example :
GET_SMFLUX - unable to open forcing netCDF file: ^@^@^
GET_SMFLUX - ERROR: reques...In coupled mode, the job is not killed by CROCO when CROCO faces an error in reading netcdf files: "ERROR: Abnormal termination: netCDF INPUT"
Example :
GET_SMFLUX - unable to open forcing netCDF file: ^@^@^
GET_SMFLUX - ERROR: requested time record 0 exeeds the last available
record 0 in forcing netCDF file: ^@^@^
TDAYS = 1827. last available SMS_TIME = 0.000
MAIN - number of records written into history file(s): 0
number of records written into restart file(s): 0
number of records written into averages file(s): 0
ERROR: Abnormal termination: netCDF INPUT
We need to force CROCO to send a killing command (probably to oasis) to correctly kill the run.https://gitlab.inria.fr/croco-ocean/croco/-/issues/163MUSTANG - review of output2024-03-07T11:59:37+01:00Solene Le GacMUSTANG - review of outputDelete cppkey #key_MUSTANG_specif_outputs and add booleans in namelist to manage which variables to output.
This is now possible thank to issue #133 which allow to separate vname vectors for each feature.Delete cppkey #key_MUSTANG_specif_outputs and add booleans in namelist to manage which variables to output.
This is now possible thank to issue #133 which allow to separate vname vectors for each feature.Solene Le GacSolene Le Gachttps://gitlab.inria.fr/croco-ocean/croco/-/issues/162Issues with AGRIF+PISCES (v2.)2024-02-16T14:34:01+01:00Subhadeep Maishalsubhadeepmaishal@kgpian.iitkgp.ac.inIssues with AGRIF+PISCES (v2.)Hi,
Issues with **p4zprod.F90** when **AGRIF+PISCES** (v2.) in check_master_vs_v1.3.1 (**without USE_CALENDAR**)
trc3d(ji,jj,K,jp_pphy2 ) = zprorcad(ji,jj,jk) * zmsk ! primary production by diatom
trc3d(ji,jj...Hi,
Issues with **p4zprod.F90** when **AGRIF+PISCES** (v2.) in check_master_vs_v1.3.1 (**without USE_CALENDAR**)
trc3d(ji,jj,K,jp_pphy2 ) = zprorcad(ji,jj,jk) * zmsk ! primary production by diatom
trc3d(ji,jj,K,jp_pnew ) = zpronewn(ji,jj,jk) * zmsk ! new primary production by nanophyto
trc3d(ji,jj,K,jp_pnew2 ) = zpronewd(ji,jj,jk) * zmsk ! new primary production by diatom
trc3d(ji,jj,K,jp_pbsi ) = zprorcad(ji,jj,jk) * zysopt(ji,jj,jk) * zmsk ! biogenic silica production
trc3d(ji,jj,K,jp_pfed ) = zprofed (ji,jj,jk) * zmsk ! biogenic iron production by diatom
trc3d(ji,jj,K,jp_pfen ) = zprofen (ji,jj,jk) * zmsk! biogenic iron production by nanophyto
trc3d(ji,jj,K,jp_pnewo2) = ( o2ut + o2nit ) & ! Oxygen production by the New Produc.
& * ( zpronewn(ji,jj,jk) + zpronewd(ji,jj,jk) ) * zmsk
trc3d(ji,jj,K,jp_prego2) = o2ut * & ! Oxygen production by the Regen Produc.
Thank youhttps://gitlab.inria.fr/croco-ocean/croco/-/issues/156croco_tools and also ONLINE : deal with dateline, 0-360 vs -180-1802024-02-03T20:18:47+01:00Swen Julliencroco_tools and also ONLINE : deal with dateline, 0-360 vs -180-180pb when passing the dateline and/or using make_croco_grd_from_wrf as the grid is 0-360 and ERA5 and mercator forcing files for CROCO are in -180-180.
- deal with this within the scripts (periodicity, detect if passing 180 or if passing ...pb when passing the dateline and/or using make_croco_grd_from_wrf as the grid is 0-360 and ERA5 and mercator forcing files for CROCO are in -180-180.
- deal with this within the scripts (periodicity, detect if passing 180 or if passing 0 and adjust the longitudes values accordingly) => best option
- provide mercator and ERA5 on the 0-360 grid also => quick fixhttps://gitlab.inria.fr/croco-ocean/croco/-/issues/154croco_tools/Coupling_tools : updates for machines, and improvements2024-02-03T20:11:21+01:00Swen Julliencroco_tools/Coupling_tools : updates for machines, and improvementsadd leftraru and wchpc in run_wps
better deal with MPI or serial launch
add projection in namelist.wpsadd leftraru and wchpc in run_wps
better deal with MPI or serial launch
add projection in namelist.wpshttps://gitlab.inria.fr/croco-ocean/croco/-/issues/153COUPLING scripts : cleaning / improvement2024-02-26T16:09:15+01:00Swen JullienCOUPLING scripts : cleaning / improvement* In SCRIPTS_TOOLBOX/cpl_getfile.sh there are these lines : should be changed or removed
< #${io_getfile} ${INPUTDIRC}/mozaic_o2a_pech12c_pech025w.nc mozaic_o_ad01.nc
< #${io_getfile} ${INPUTDIRC}/mozaic_a2o_pech025w_pech12c.nc mo...* In SCRIPTS_TOOLBOX/cpl_getfile.sh there are these lines : should be changed or removed
< #${io_getfile} ${INPUTDIRC}/mozaic_o2a_pech12c_pech025w.nc mozaic_o_ad01.nc
< #${io_getfile} ${INPUTDIRC}/mozaic_a2o_pech025w_pech12c.nc mozaic_ad01_o.nc
* a typo « CPL-ROMS: OASIS_TIME » still exists…
* In mynamelist : maybe the flag owa or Afrc or 2o2a should be more un the CPL section (but used at the moment also for WW3 exectuables), see what would be the most relevant…
* deal better with the copy of mynamelist and myjob + myenv_mypath in the jobs_ directory during the run
* check / add a flag to suppress automatic change of myjob -> see if TEST mode is the good solution…
* Add a flag or the possibility to answer « yes » to remove previous job existing when re-launching a submitjob
* Add a note / comment that cppdefs or namelist.input should be changed in advance by the user for parameterization options!
* make configure.namelist.real and configure.namelist..wps coherent, or distinct as they should… for the moment almost similar except for isftcflx, not very convenient
* Do we want job.real.slurm.LEFTRARU job.real.pbs.WCHPC, i.e. for each machine or we just keep examples, or we should make them from header…
* Add the possibility to easily create a cplmask that merge SST from the ocean model and SST_INPUT (there are some similar scripts to deal with multiple domains)
Check if what is done without that is extrapolation of SST out of the area covered by the ocean domain (it seemed not to be the case in one configuration from a student in Huinay…)
* add croco.in.base.1 in CROCO_IN
* atm_getrst: pb when computing cplmask, missing ncks of
ncks -A -C -v LANDMASK wrfinput_$dom tmp.nc
ncks -A -C -v LAKEMASK wrfinput_$dom tmp.nc
ncks -A -C -v XLAT wrfinput_$dom tmp.nc
ncks -A -C -v XLONG wrfinput_$dom tmp.nc
* namelist wrf : pb with maxcpldom, which is only in the moving nest version... manage this
* jobcomp : we should have $OCE $CPL instead of absolute paths
* AGRIF_fixed_grid should stay in CROCO_IN, or should be rather placed in CROCO_FILES ?
* in ww3_shel / and wav namelist add the possibility to have bdy, track output and point outputhttps://gitlab.inria.fr/croco-ocean/croco/-/issues/152COUPLING scripts : create steps for serial (pre-pro / post-pro) and MPI (run)2024-02-03T20:00:19+01:00Swen JullienCOUPLING scripts : create steps for serial (pre-pro / post-pro) and MPI (run)Change the scripts to have preprocessing of WW3, as well as creation of OASIS restart files in a separate step to avoid booling several procs when only 1 is needed…
Put SERIAL_LAUNCH_WAV and MPI_LAUNCH_CMD in myenv_mypath only and not ...Change the scripts to have preprocessing of WW3, as well as creation of OASIS restart files in a separate step to avoid booling several procs when only 1 is needed…
Put SERIAL_LAUNCH_WAV and MPI_LAUNCH_CMD in myenv_mypath only and not myjob…
Check and change the scripts for dealing better with concatenation of outputs files (pb in some cases on the way some the time ouptut were removed..., and also very long in some cases)