Issues when running ROMS coupled with bio_UMAINE15 model

[master]

varinfo.dat

(179.58 KiB) Downloaded 497 times

Hi, I got puzzled when running ROMS with UMAINE15 (CoSiNE) model. I can run ROMS successfully without CoSiNE. However, when I running with the CoSiNE model, there are some issues.
I know there is someone running it successfully, and I only got one FAQ about the CoSiNE

(viewtopic.php?p=13904#p13904)

, while my error is different from that one.
Besides, I have checked the mod_ncparam.f90，while I can't check out the errors. I have put the varinfo.dat at the end of this post. Could anyone can help me?

Code: Select all

mpirun -np 4 ./UPWELLING ../input/roms_upwelling.in

Code: Select all

--------------------------------------------------------------------------
--------------------------------------------------------------------------------
 Model Input Parameters:  ROMS/TOMS version 3.8
                          Thursday - December 24, 2020 - 10:34:23 PM
--------------------------------------------------------------------------------
forrtl: severe (66): output statement overflows record, unit -5, file Internal Formatted Write
Image              PC                Routine            Line        Source
UPWELLING          00000000023683E3  Unknown               Unknown  Unknown
UPWELLING          000000000239CBE2  Unknown               Unknown  Unknown
UPWELLING          00000000020AEA6D  mod_ncparam_mp_in        2002  mod_ncparam.f90
UPWELLING          0000000001BC693C  read_phypar_              222  read_phypar.f90
UPWELLING          0000000001584426  inp_par_                   93  inp_par.f90
UPWELLING          000000000040B0A6  ocean_control_mod          86  ocean_control.f90
UPWELLING          000000000040A8FA  MAIN__                     95  master.f90
UPWELLING          000000000040A61E  Unknown               Unknown  Unknown
libc-2.17.so       00002B917811BC05  __libc_start_main     Unknown  Unknown
UPWELLING          000000000040A529  Unknown               Unknown  Unknown
forrtl: severe (66): output statement overflows record, unit -5, file Internal Formatted Write
Image              PC                Routine            Line        Source
UPWELLING          00000000023683E3  Unknown               Unknown  Unknown
UPWELLING          000000000239CBE2  Unknown               Unknown  Unknown
UPWELLING          00000000020AEA6D  mod_ncparam_mp_in        2002  mod_ncparam.f90
UPWELLING          0000000001BC693C  read_phypar_              222  read_phypar.f90
UPWELLING          0000000001584426  inp_par_                   93  inp_par.f90
UPWELLING          000000000040B0A6  ocean_control_mod          86  ocean_control.f90
UPWELLING          000000000040A8FA  MAIN__                     95  master.f90
UPWELLING          000000000040A61E  Unknown               Unknown  Unknown
libc-2.17.so       00002B43714F9C05  __libc_start_main     Unknown  Unknown
UPWELLING          000000000040A529  Unknown               Unknown  Unknown
forrtl: severe (66): output statement overflows record, unit -5, file Internal Formatted Write
Image              PC                Routine            Line        Source
UPWELLING          00000000023683E3  Unknown               Unknown  Unknown
UPWELLING          000000000239CBE2  Unknown               Unknown  Unknown
UPWELLING          00000000020AEA6D  mod_ncparam_mp_in        2002  mod_ncparam.f90
UPWELLING          0000000001BC693C  read_phypar_              222  read_phypar.f90
UPWELLING          0000000001584426  inp_par_                   93  inp_par.f90
UPWELLING          000000000040B0A6  ocean_control_mod          86  ocean_control.f90
UPWELLING          000000000040A8FA  MAIN__                     95  master.f90
UPWELLING          000000000040A61E  Unknown               Unknown  Unknown
libc-2.17.so       00002B60B980BC05  __libc_start_main     Unknown  Unknown
UPWELLING          000000000040A529  Unknown               Unknown  Unknown
forrtl: severe (66): output statement overflows record, unit -5, file Internal Formatted Write
Image              PC                Routine            Line        Source
UPWELLING          00000000023683E3  Unknown               Unknown  Unknown
UPWELLING          000000000239CBE2  Unknown               Unknown  Unknown
UPWELLING          00000000020AEA6D  mod_ncparam_mp_in        2002  mod_ncparam.f90
UPWELLING          0000000001BC693C  read_phypar_              222  read_phypar.f90
UPWELLING          0000000001584426  inp_par_                   93  inp_par.f90
UPWELLING          000000000040B0A6  ocean_control_mod          86  ocean_control.f90
UPWELLING          000000000040A8FA  MAIN__                     95  master.f90
UPWELLING          000000000040A61E  Unknown               Unknown  Unknown
libc-2.17.so       00002B2B3DDA9C05  __libc_start_main     Unknown  Unknown
UPWELLING          000000000040A529  Unknown               Unknown  Unknown
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[63988,1],0]
  Exit code:    66
--------------------------------------------------------------------------
[admin:215584] 4 more processes have sent help message help-oob-ud.txt / create-qp-failed
[admin:215584] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[admin:215584] 4 more processes have sent help message help-oob-ud.txt / no-ports-usable
[admin:215584] 7 more processes have sent help message help-mpi-btl-openib.txt / no device params found
[admin:215584] 7 more processes have sent help message help-mpi-btl-openib-cpc-base.txt / no cpcs for port

varinfo.dat

(179.58 KiB) Downloaded 497 times

[kate]

2002 mod_ncparam.f90

What is on line 2002 of your mod_ncparam.f90? Mine has:

CASE ('idRtrc(icadet_calc)')

You then need to see if your equivalent to idRtrc(icadet_calc) is in your varinfo.dat.

The only varinfo.dat I have that might contain the CoSine stuff is this one: https://github.com/kshedstrom/Apps_mast ... arinfo.dat

[master]

What I used is the UMAINE15 model, the ROMS version is 3.8. The ROMS code is download from www.myroms.org, not your Github account. I don't know whether is the reason for the ROMS version. Because the UMAINE15 code is from Professor Xiu Peng, while what he gives to me is the whole ROMS 3.6 code containing UMAINE15. I choose the file related to UMAINE15, and then put it to my ROMS 3.8 version.
Besides, the ROMS code in your Github account contains the UMAINE31 (CoSiNE) model. Do you have debugged it? If you can run the UMAINE31 successfully, I can also use your code to try it again.

In my mod_ncparam.f90, the line 2002 is as follows:

Code: Select all

1989 !
1990 !  Determine metadata for quadratic tracer averages.
1991 !
1992             SELECT CASE (Vinfo(1))
1993               CASE ('tracer2')
1994                 varid=varid-1
1995                 DO i=1,MT
1996                   varid=varid+1
1997                   idTTav(i)=varid
1998                   DO ng=1,Ngrids
1999                     Fscale(varid,ng)=scale
2000                     Iinfo(1,varid,ng)=gtype
2001                   END DO
2002                   WRITE (Vname(1,varid),'(a,a)')                        &
2003      &                  TRIM(ADJUSTL(Vname(1,idTvar(i)))), '_2'
2004                   WRITE (Vname(2,varid),'(a,1x,a)')                     &
2005      &                  'time-averaged squared',                        &
2006      &                  TRIM(ADJUSTL(Vname(2,idTvar(i))))
2007                   IF (TRIM(ADJUSTL(Vname(3,idTvar(i)))).eq.             &
2008      &                'nondimensional') THEN
2009                     WRITE (Vname(3,varid),'(a)')                        &
2010      &                    TRIM(ADJUSTL(Vname(3,idTvar(i))))
2011                   ELSE
2012                     WRITE (Vname(3,varid),'(a,a)')                      &
2013      &                    TRIM(ADJUSTL(Vname(3,idTvar(i)))), '2'
2014                   END IF
2015                   WRITE (Vname(4,varid),'(a,a)')                        &

[kate]

I did run CoSine successfully, but it has been some years since I've tried. Claudine Hauri and I added an iron limitation to it.

As for your line 2002, you still need to make sure your varinfo.dat has everything you need in it. Did professor Peng give you a working one?

[master]

Hi, Mrs Kate.
I have checked out the varinfo.dat many times in last two days, while I can't find the errors. Nowadays I guess the errors are maybe in the varinfo.dat. Could you please tell me how to find where is inconsistent between my varinfo.dat and CoSiNE. Is there all the variable name used in CoSiNE model is in the file bio_UMAINE15_var.h? Shall it the same variable name between varinfo.dat, input nc file and bio_UMAINE15_var.h? Other than the CoSiNE model, where should I find the variable name used in ROMS, Is it also should be consistent with varinfo.dat file?

Yeah, he gives me an upwelling example, while I can't run it correctly with CoSiNE. I can only run it without CoSiNE.

In these two days, I also deleted the last files which are edited by myself. I recompile and rerun the model using the application files given by Professor Peng. There is another error. I can know that this error is related to the varinfo.dat. Could you please help me again?

Code: Select all

mpirun -np 4 ./UPWELLING ../input/ocean_upwelling.in

Code: Select all

--------------------------------------------------------------------------
--------------------------------------------------------------------------------
 Model Input Parameters:  ROMS/TOMS version 3.8
                          Sunday - December 27, 2020 - 11:34:30 PM
--------------------------------------------------------------------------------

 Wind-Driven Upwelling/Downwelling over a Periodic Channel

 Operating system : Linux
 CPU/hardware     : x86_64
 Compiler system  : ifort
 Compiler command : /public/home/rengz/software/mpi_intel/bin/mpif90
 Compiler flags   : -fp-model precise -heap-arrays -g -check all -check bounds -traceback -check uninit -warn interfaces,nouncalled -gen-interfaces
 MPI Communicator : 0  PET size = 4

 Input Script     : ../input/ocean_upwelling.in

 SVN Root URL     : https://www.myroms.org/svn/src/trunk
 SVN Revision     : 990

 Local Root       : /public/home/rengz/ROMS/src
 Header Dir       : /public/home/rengz/ROMS/Apps/ECS_test/header
 Header file      : upwelling.h
 Analytical Dir   : /public/home/rengz/ROMS/Apps/ECS_test

 Resolution, Grid 01: 40x80x16,  Parallel Nodes: 4,  Tiling: 2x2


 Physical Parameters, Grid: 01
 =============================

       1440  ntimes            Number of timesteps for 3-D equations.
     30.000  dt                Timestep size (s) for 3-D equations.
         30  ndtfast           Number of timesteps for 2-D equations between
                                 each 3D timestep.
          1  ERstr             Starting ensemble/perturbation run number.
          1  ERend             Ending ensemble/perturbation run number.
          0  nrrec             Number of restart records to read from disk.
          T  LcycleRST         Switch to recycle time-records in restart file.
        288  nRST              Number of timesteps between the writing of data
                                 into restart fields.
          1  ninfo             Number of timesteps between print of information
                                 to standard output.
          T  ldefout           Switch to create a new output NetCDF file(s).
         72  nHIS              Number of timesteps between the writing fields
                                 into history file.
          0  nQCK              Number of timesteps between the writing fields
                                 into quicksave file.
          1  ntsAVG            Starting timestep for the accumulation of output
                                 time-averaged data.
         72  nAVG              Number of timesteps between the writing of
                                 time-averaged data into averages file.
          1  ntsDIA            Starting timestep for the accumulation of output
                                 time-averaged diagnostics data.
         72  nDIA              Number of timesteps between the writing of
                                 time-averaged data into diagnostics file.
 0.0000E+00  nl_tnu2(01)       NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for tracer 01: temp
 0.0000E+00  nl_tnu2(02)       NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for tracer 02: salt
 5.0000E+00  nl_visc2          NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for momentum.
          F  LuvSponge         Turning OFF sponge on horizontal momentum.
          F  LtracerSponge(01) Turning OFF sponge on tracer 01: temp
          F  LtracerSponge(02) Turning OFF sponge on tracer 02: salt
 1.0000E-06  Akt_bak(01)       Background vertical mixing coefficient (m2/s)
                                 for tracer 01: temp
 1.0000E-06  Akt_bak(02)       Background vertical mixing coefficient (m2/s)
                                 for tracer 02: salt
 1.0000E-05  Akv_bak           Background vertical mixing coefficient (m2/s)
                                 for momentum.
 3.0000E-04  rdrg              Linear bottom drag coefficient (m/s).
 3.0000E-03  rdrg2             Quadratic bottom drag coefficient.
 2.0000E-02  Zob               Bottom roughness (m).
          2  Vtransform        S-coordinate transformation equation.
          4  Vstretching       S-coordinate stretching function.
 3.0000E+00  theta_s           S-coordinate surface control parameter.
 0.0000E+00  theta_b           S-coordinate bottom  control parameter.
     25.000  Tcline            S-coordinate surface/bottom layer width (m) used
                                 in vertical coordinate stretching.
   1025.000  rho0              Mean density (kg/m3) for Boussinesq approximation.
      0.000  dstart            Time-stamp assigned to model initialization (days).
       0.00  time_ref          Reference time for units attribute (yyyymmdd.dd)
 0.0000E+00  Tnudg(01)         Nudging/relaxation time scale (days)
                                 for tracer 01: temp
 0.0000E+00  Tnudg(02)         Nudging/relaxation time scale (days)
                                 for tracer 02: salt
 0.0000E+00  Znudg             Nudging/relaxation time scale (days)
                                 for free-surface.
 0.0000E+00  M2nudg            Nudging/relaxation time scale (days)
                                 for 2D momentum.
 0.0000E+00  M3nudg            Nudging/relaxation time scale (days)
                                 for 3D momentum.
 0.0000E+00  obcfac            Factor between passive and active
                                 open boundary conditions.
          F  VolCons(1)        NLM western  edge boundary volume conservation.
          F  VolCons(2)        NLM southern edge boundary volume conservation.
          F  VolCons(3)        NLM eastern  edge boundary volume conservation.
          F  VolCons(4)        NLM northern edge boundary volume conservation.
     14.000  T0                Background potential temperature (C) constant.
     35.000  S0                Background salinity (PSU) constant.
   1027.000  R0                Background density (kg/m3) used in linear Equation
                                 of State.
 1.7000E-04  Tcoef             Thermal expansion coefficient (1/Celsius).
 0.0000E+00  Scoef             Saline contraction coefficient (1/PSU).
      1.000  gamma2            Slipperiness variable: free-slip (1.0) or
                                                      no-slip (-1.0).
          F  LuvSrc            Turning OFF momentum point Sources/Sinks.
          F  LwSrc             Turning OFF volume influx point Sources/Sinks.
          F  LtracerSrc(01)    Turning OFF point Sources/Sinks on tracer 01: temp
          F  LtracerSrc(02)    Turning OFF point Sources/Sinks on tracer 02: salt
          F  LsshCLM           Turning OFF processing of SSH climatology.
          F  Lm2CLM            Turning OFF processing of 2D momentum climatology.
          F  Lm3CLM            Turning OFF processing of 3D momentum climatology.
          T  LtracerCLM(01)    Turning ON  processing of climatology tracer 01: temp
          T  LtracerCLM(02)    Turning ON  processing of climatology tracer 02: salt
          F  LnudgeM2CLM       Turning OFF nudging of 2D momentum climatology.
          F  LnudgeM3CLM       Turning OFF nudging of 3D momentum climatology.
          F  LnudgeTCLM(01)    Turning OFF nudging of climatology tracer 01: temp
          F  LnudgeTCLM(02)    Turning OFF nudging of climatology tracer 02: salt

          T  Hout(idFsur)      Write out free-surface.
          T  Hout(idUbar)      Write out 2D U-momentum component.
          T  Hout(idVbar)      Write out 2D V-momentum component.
          T  Hout(idUvel)      Write out 3D U-momentum component.
          T  Hout(idVvel)      Write out 3D V-momentum component.
          T  Hout(idWvel)      Write out W-momentum component.
          T  Hout(idOvel)      Write out omega vertical velocity.
          T  Hout(idTvar)      Write out tracer 01: temp
          T  Hout(idTvar)      Write out tracer 02: salt
forrtl: severe (408): fort: (3): Subscript #1 of the array HOUT has value 0 which is less than the lower bound of 1

Image              PC                Routine            Line        Source
UPWELLING          00000000022F2216  Unknown               Unknown  Unknown
UPWELLING          0000000001C349C3  read_phypar_             2611  read_phypar.f90
UPWELLING          00000000015411D6  inp_par_                   93  inp_par.f90
UPWELLING          000000000040C466  ocean_control_mod          86  ocean_control.f90
UPWELLING          000000000040BCBA  MAIN__                     95  master.f90
UPWELLING          000000000040B9DE  Unknown               Unknown  Unknown
libc-2.17.so       00002ABD15FE4C05  __libc_start_main     Unknown  Unknown
UPWELLING          000000000040B8E9  Unknown               Unknown  Unknown
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
forrtl: error (78): process killed (SIGTERM)
Image              PC                Routine            Line        Source
UPWELLING          00000000022F578A  Unknown               Unknown  Unknown
libpthread-2.17.s  00002AF2FA0495E0  Unknown               Unknown  Unknown
libpsmx2-fi.so     00002AF310247079  Unknown               Unknown  Unknown
mca_mtl_ofi.so     00002AF31156E935  ompi_mtl_ofi_prog     Unknown  Unknown
libopen-pal.so.40  00002AF2FD6CEB24  opal_progress         Unknown  Unknown
libmpi.so.40.10.3  00002AF2F9A60FB8  ompi_request_defa     Unknown  Unknown
libmpi.so.40.10.3  00002AF2F9AB48EB  ompi_coll_base_bc     Unknown  Unknown
libmpi.so.40.10.3  00002AF2F9AB4A8E  ompi_coll_base_bc     Unknown  Unknown
mca_coll_tuned.so  00002AF311D85DB6  ompi_coll_tuned_b     Unknown  Unknown
libmpi.so.40.10.3  00002AF2F9A780D7  MPI_Bcast             Unknown  Unknown
libmpi_mpifh.so.4  00002AF2F97F4D94  pmpi_bcast            Unknown  Unknown
UPWELLING          00000000017E16FB  distribute_mod_mp         549  distribute.f90
UPWELLING          0000000001541294  inp_par_                   94  inp_par.f90
UPWELLING          000000000040C466  ocean_control_mod          86  ocean_control.f90
UPWELLING          000000000040BCBA  MAIN__                     95  master.f90
UPWELLING          000000000040B9DE  Unknown               Unknown  Unknown
libc-2.17.so       00002AF2FA47BC05  __libc_start_main     Unknown  Unknown
UPWELLING          000000000040B8E9  Unknown               Unknown  Unknown
forrtl: error (78): process killed (SIGTERM)
Image              PC                Routine            Line        Source
UPWELLING          00000000022F578A  Unknown               Unknown  Unknown
libpthread-2.17.s  00002B87274385E0  Unknown               Unknown  Unknown
libpsmx2-fi.so     00002B873D58B230  Unknown               Unknown  Unknown
libpsmx2-fi.so     00002B873D58F683  psmx2_cq_poll_mq      Unknown  Unknown
libpsmx2-fi.so     00002B873D59028E  Unknown               Unknown  Unknown
mca_mtl_ofi.so     00002B873E8B7935  ompi_mtl_ofi_prog     Unknown  Unknown
libopen-pal.so.40  00002B872AABDB24  opal_progress         Unknown  Unknown
libmpi.so.40.10.3  00002B8726E4FFB8  ompi_request_defa     Unknown  Unknown
libmpi.so.40.10.3  00002B8726EA3600  ompi_coll_base_bc     Unknown  Unknown
libmpi.so.40.10.3  00002B8726EA3A8E  ompi_coll_base_bc     Unknown  Unknown
mca_coll_tuned.so  00002B873F0CEDB6  ompi_coll_tuned_b     Unknown  Unknown
libmpi.so.40.10.3  00002B8726E670D7  MPI_Bcast             Unknown  Unknown
libmpi_mpifh.so.4  00002B8726BE3D94  pmpi_bcast            Unknown  Unknown
UPWELLING          00000000017E16FB  distribute_mod_mp         549  distribute.f90
UPWELLING          0000000001541294  inp_par_                   94  inp_par.f90
UPWELLING          000000000040C466  ocean_control_mod          86  ocean_control.f90
UPWELLING          000000000040BCBA  MAIN__                     95  master.f90
UPWELLING          000000000040B9DE  Unknown               Unknown  Unknown
libc-2.17.so       00002B872786AC05  __libc_start_main     Unknown  Unknown
UPWELLING          000000000040B8E9  Unknown               Unknown  Unknown
forrtl: error (78): process killed (SIGTERM)
Image              PC                Routine            Line        Source
UPWELLING          00000000022F578A  Unknown               Unknown  Unknown
libpthread-2.17.s  00002B6B935E25E0  Unknown               Unknown  Unknown
libpsm2.so.2.1     00002B6B9ABB19B6  psm2_mq_ipeek         Unknown  Unknown
libpsmx2-fi.so     00002B6BA9796683  psmx2_cq_poll_mq      Unknown  Unknown
libpsmx2-fi.so     00002B6BA979728E  Unknown               Unknown  Unknown
mca_mtl_ofi.so     00002B6BAAABE935  ompi_mtl_ofi_prog     Unknown  Unknown
libopen-pal.so.40  00002B6B96C67B24  opal_progress         Unknown  Unknown
libmpi.so.40.10.3  00002B6B92FF9FB8  ompi_request_defa     Unknown  Unknown
libmpi.so.40.10.3  00002B6B9304D8EB  ompi_coll_base_bc     Unknown  Unknown
libmpi.so.40.10.3  00002B6B9304DA8E  ompi_coll_base_bc     Unknown  Unknown
mca_coll_tuned.so  00002B6BAB2D5DB6  ompi_coll_tuned_b     Unknown  Unknown
libmpi.so.40.10.3  00002B6B930110D7  MPI_Bcast             Unknown  Unknown
libmpi_mpifh.so.4  00002B6B92D8DD94  pmpi_bcast            Unknown  Unknown
UPWELLING          00000000017E16FB  distribute_mod_mp         549  distribute.f90
UPWELLING          0000000001541294  inp_par_                   94  inp_par.f90
UPWELLING          000000000040C466  ocean_control_mod          86  ocean_control.f90
UPWELLING          000000000040BCBA  MAIN__                     95  master.f90
UPWELLING          000000000040B9DE  Unknown               Unknown  Unknown
libc-2.17.so       00002B6B93A14C05  __libc_start_main     Unknown  Unknown
UPWELLING          000000000040B8E9  Unknown               Unknown  Unknown
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[54484,1],0]
  Exit code:    152
--------------------------------------------------------------------------
[admin:157441] 4 more processes have sent help message help-oob-ud.txt / create-qp-failed
[admin:157441] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[admin:157441] 4 more processes have sent help message help-oob-ud.txt / no-ports-usable
[admin:157441] 7 more processes have sent help message help-mpi-btl-openib.txt / no device params found
[admin:157441] 7 more processes have sent help message help-mpi-btl-openib-cpc-base.txt / no cpcs for port
[rengz@admin output]$

[kate]

So now what's on this line?

read_phypar_ 2611 read_phypar.f90

If you're getting your code from Professor Peng, shouldn't you be asking him how to get it to run?

[master]

Now, line 2611 are as follows:
In my ocean_roms.in file, there actually isn't

Code: Select all

Hout(idpthR,ng)

, while it's "if" judegment code in read_phypar.f90. In my opinion, it doesn't matter whether

Code: Select all

Hout(idpthR,ng)

in my ocean_roms.in file or not.

Code: Select all

2600             IF (Hout(idWvel,ng)) WRITE (out,170) Hout(idWvel,ng),       &
2601      &         'Hout(idWvel)',                                          &
2602      &         'Write out W-momentum component.'
2603             IF (Hout(idOvel,ng)) WRITE (out,170) Hout(idOvel,ng),       &
2604      &         'Hout(idOvel)',                                          &
2605      &         'Write out omega vertical velocity.'
2606             DO itrc=1,NAT
2607               IF (Hout(idTvar(itrc),ng)) WRITE (out,180)                &
2608      &            Hout(idTvar(itrc),ng), 'Hout(idTvar)',                &
2609      &            'Write out tracer ', itrc, TRIM(Vname(1,idTvar(itrc)))
2610             END DO
2611             IF (Hout(idpthR,ng)) WRITE (out,170) Hout(idpthR,ng),       &
2612      &         'Hout(idpthR)',                                          &
2613      &         'Write out time-varying dephts of RHO-points.'
2614             IF (Hout(idpthU,ng)) WRITE (out,170) Hout(idpthU,ng),       &
2615      &         'Hout(idpthU)',                                          &
2616      &         'Write out time-varying dephts of U-points.'
2617             IF (Hout(idpthV,ng)) WRITE (out,170) Hout(idpthV,ng),       &
2618      &         'Hout(idpthV)',                                          &
2619      &         'Write out time-varying dephts of V-points.'
2620             IF (Hout(idpthW,ng)) WRITE (out,170) Hout(idpthW,ng),       &
2621      &         'Hout(idpthW)',                                          &
2622      &         'Write out time-varying dephts of W-points.'
2623             IF (Hout(idUsms,ng)) WRITE (out,170) Hout(idUsms,ng),       &
2624      &         'Hout(idUsms)',                                          &
2625      &         'Write out surface U-momentum stress.'

Okay, thank you very much. I have tried many times, while there are many wrongs when I run this model. I would ask Professor Peng directly for some help. Thank you very much.

[kate]

Now you need to make sure idpthR is in your varinfo.dat.

[master]

Yeah, idpthR isn't in my varinfo.dat file, besides, there are time-averaging variables that aren't in my varinfo.dat. I have added them to my varinfo.dat. Now the Upwelling test case without bio_UMAINE15 can run successfully. If I activate the bio_UMAINE15, there is another problem. For more information there is the log and error file.

I have read mp_exchange.f90 file according to the error information.
Line 812 in mp_exchange.f90 are as follows:

Code: Select all

797       IF (Sexchange) THEN
 798         CALL mpi_wait (Srequest, status(1,2), Serror)
 799         IF (Serror.ne.MPI_SUCCESS) THEN
 800           CALL mpi_error_string (Serror, string, Lstr, Ierror)
 801           Lstr=LEN_TRIM(string)
 802           WRITE (stdout,20) 'MPI_SEND/MPI_IRECV (Southern Edge)',       &
 803      &                      MyRank, Serror, string(1:Lstr)
 804           exit_flag=2
 805           RETURN
 806         END IF
 807         DO m=GrecvS,1,-1
 808           mc=(GrecvS-m)*Ilen
 809           j=Jstr-m
 810           DO i=Imin,Imax
 811             icS=1+(i-Imin)+mc
 812             A(i,j)=recvS(icS)
 813           END DO
 814         END DO
 815         IF (PRESENT(B)) THEN
 816           ioff=icS
 817           DO m=GrecvS,1,-1
 818             mc=(GrecvS-m)*Ilen
 819             j=Jstr-m
 820             DO i=Imin,Imax
 821               icS=ioff+1+(i-Imin)+mc
 822               B(i,j)=recvS(icS)
 823             END DO
 824           END DO
 825         END IF

What does this error information mean in line 812?

couple_3.8_error.log

(20.33 KiB) Downloaded 425 times

couple_3.8.log

(48.79 KiB) Downloaded 431 times

[kate]

It means it's trying to pass a bad value in an MPI call. You need to look up a level to:

758 analytical.f90

[master]

The code of line 758 in analytical.f90 is as follows:

Code: Select all

714 !-----------------------------------------------------------------------
 715 ! Compute coordinate transformation metrics at RHO-points "pm" and
 716 ! "pn"  (1/m) associated with the differential distances in XI and
 717 ! ETA, respectively.
 718 !-----------------------------------------------------------------------
 719 !
 720       DO j=MIN(JstrT,Jstr-1),MAX(Jend+1,JendT)
 721         DO i=MIN(IstrT,Istr-1),MAX(Iend+1,IendT)
 722           wrkX(i,j)=1.0_r8/dx
 723           wrkY(i,j)=1.0_r8/dy
 724         END DO
 725       END DO
 726       DO j=JstrT,JendT
 727         DO i=IstrT,IendT
 728           pm(i,j)=wrkX(i,j)
 729           pn(i,j)=wrkY(i,j)
 730         END DO
 731       END DO
 732 !
 733 !  Report statistics.
 734 !
 735       CALL stats_2dfld (ng, tile, iNLM, r2dvar, Stats(9),               &
 736      &                  LBi, UBi, LBj, UBj, pm)
 737       IF (DOMAIN(ng)%NorthEast_Corner(tile)) THEN
 738         WRITE (stdout,10) 'reciprocal XI-grid spacing: pm',             &
 739      &                     ng, Stats(9)%min, Stats(9)%max
 740       END IF
 741       CALL stats_2dfld (ng, tile, iNLM, r2dvar, Stats(10),              &
 742      &                  LBi, UBi, LBj, UBj, pn)
 743       IF (DOMAIN(ng)%NorthEast_Corner(tile)) THEN
 744         WRITE (stdout,10) 'reciprocal ETA-grid spacing: pn',            &
 745      &                     ng, Stats(10)%min, Stats(10)%max
 746       END IF
 747 !
 748 !  Exchange boundary data.
 749 !
 750       IF (EWperiodic(ng).or.NSperiodic(ng)) THEN
 751         CALL exchange_r2d_tile (ng, tile,                               &
 752      &                          LBi, UBi, LBj, UBj,                     &
 753      &                          pm)
 754         CALL exchange_r2d_tile (ng, tile,                               &
 755      &                          LBi, UBi, LBj, UBj,                     &
 756      &                          pn)
 757       END IF
 758       CALL mp_exchange2d (ng, tile, model, 2,                           &
 759      &                    LBi, UBi, LBj, UBj,                           &
 760      &                    NghostPoints,                                 &
 761      &                    EWperiodic(ng), NSperiodic(ng),               &
 762      &                    pm, pn)
 763 !

While I have changed all the boundary condition to Per or Clo in my ocean_upwelling.in or bio_UMAINE15.in, and the Per open boundary condition is symmetric in east-west or north-south direction.

Line 116 in initial.f90 is as follows:

Code: Select all

109 !-----------------------------------------------------------------------
110 !  Set horizontal grid, bathymetry, and Land/Sea masking (if any).
111 !  Use analytical functions or read in from a grid NetCDF.
112 !-----------------------------------------------------------------------
113 !
114         DO ng=1,Ngrids
115           DO tile=first_tile(ng),last_tile(ng),+1
116             CALL ana_grid (ng, tile, iNLM)
117           END DO
118         END DO
119 !$OMP BARRIER
120 !

[kate]

Code: Select all

 758       CALL mp_exchange2d (ng, tile, model, 2,                           &
 759      &                    LBi, UBi, LBj, UBj,                           &
 760      &                    NghostPoints,                                 &
 761      &                    EWperiodic(ng), NSperiodic(ng),               &
 762      &                    pm, pn)

It is unhappy with your pm, pn values.

[master]

In my ana_grid.f90, some codes related to the pm and pn value are as follows:

Code: Select all

 383 #elif defined UPWELLING
 384       Xsize=1000.0_r8*REAL(Lm(ng),r8)
 385       Esize=1000.0_r8*REAL(Mm(ng),r8)
 386       depth=150.0_r8
 387       f0=-8.26E-05_r8
 388       beta=0.0_r8

Code: Select all

 511 #else
 512       dx=Xsize/REAL(Lm(ng),r8)
 513       dy=Esize/REAL(Mm(ng),r8)

Code: Select all

 700 #else
 701       DO j=J_RANGE
 702         DO i=I_RANGE
 703 # ifdef BL_TEST
 704           dx=0.5_r8*(4000.0_r8/REAL(Lm(ng)+1,r8))*REAL(i,r8)+675.0_r8
 705 # endif
 706           wrkX(i,j)=1.0_r8/dx
 707           wrkY(i,j)=1.0_r8/dy
 708         END DO
 709       END DO
 710 #endif

Code: Select all

 713       DO j=JstrT,JendT
 714         DO i=IstrT,IendT
 715           pm(i,j)=wrkX(i,j)
 716           pn(i,j)=wrkY(i,j)
 717         END DO
 718       END DO

ana_grid.h.txt

(42.02 KiB) Downloaded 409 times

In my ocean_upwelling.in file, what I set are

Code: Select all

Lm == 40, Mm == 80, N == 16

[kate]

If you don't have a working debugger, I would add print statements in there to make sure everything is as you expect it to be. You can add a print of min(pm), max(pm), min(pn), max(pn). Whatever it takes.

[master]

Ok, I've solved it during this weekend. The problem is very tricky, which is the open boundary condition settings. I have the inconsistent open boundary condition between physical and biological parts. For example, I closed the boundary in the north-south direction, while my biological open boundary condition is periodic in the north-south direction. I realized this problem thanks to this one.

viewtopic.php?p=15427#p15427

It's my pleasure that you help me a lot. It helps me improve my debugging ability when talking with you.
Happy new year in 2021!