Illegal model configuration

[shiyf]

Hello everyone, I have got an error as follow: ( I don't know the reason, I am confused. Anyone can tell me how to fix it?)


Model Input Parameters: ROMS/TOMS version 3.6
Friday - November 15, 2013 - 3:50:05 PM
-----------------------------------------------------------------------------

SHIYF

Operating system : Linux
CPU/hardware : x86_64
Compiler system : ifort
Compiler command : /lustre/inspur/mpi/openmpi-intel/bin/mpif90
Compiler flags : -heap-arrays -fp-model precise -ip -O3 -free -free -free

Input Script : ocean_shiyf.in

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

Local Root : /lustre/home/shiyongfangWKJ/roms/trunk
Header Dir : /lustre/home/shiyongfangWKJ/roms/projects/roms_test
Header file : shiyf.h
Analytical Dir: /lustre/home/shiyongfangWKJ/roms/projects/roms_test

Resolution, Grid 01: 0449x0160x016, Parallel Nodes: 9, Tiling: 003x003


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

1440 ntimes Number of timesteps for 3-D equations.
300.000 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.
1 nSTA Number of timesteps between the writing of data
the stations file.
1 nFLT Number of timesteps between the writing of data
into floats file.
T ldefout Switch to create a new output NetCDF file(s).
72 nHIS Number of timesteps between the writing fields
into history 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.
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.
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.
5.0000E-06 Akk_bak Background vertical mixing coefficient (m2/s)
for turbulent energy.
5.0000E-06 Akp_bak Background vertical mixing coefficient (m2/s)
for turbulent generic statistical field.
3.000 gls_p GLS stability exponent.
1.500 gls_m GLS turbulent kinetic energy exponent.
-1.000 gls_n GLS turbulent length scale exponent.
7.6000E-06 gls_Kmin GLS minimum value of turbulent kinetic energy.
1.0000E-12 gls_Pmin GLS minimum value of dissipation.
5.4770E-01 gls_cmu0 GLS stability coefficient.
1.4400E+00 gls_c1 GLS shear production coefficient.
1.9200E+00 gls_c2 GLS dissipation coefficient.
-4.0000E-01 gls_c3m GLS stable buoyancy production coefficient.
1.0000E+00 gls_c3p GLS unstable buoyancy production coefficient.
1.0000E+00 gls_sigk GLS constant Schmidt number for TKE.
1.3000E+00 gls_sigp GLS constant Schmidt number for PSI.
1400.000 charnok_alpha Charnok factor for Zos calculation.
0.500 zos_hsig_alpha Factor for Zos calculation using Hsig(Awave).
0.250 sz_alpha Factor for Wave dissipation surface tke flux .
100.000 crgban_cw Factor for Craig/Banner surface tke flux.
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).
2.0000E-02 Zos Surface roughness (m).
1 lmd_Jwt Jerlov water type.
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

READ_PHYPAR - Invalid input parameter, Tnudg(isalt) = 0.0000E+00
Must be greater than zero for salt flux correction.

Elapsed CPU time (seconds):


ROMS/TOMS - Output NetCDF summary for Grid 01:

ROMS/TOMS - Configuration error ..... exit_flag: 5


ERROR: Illegal model configuration.

[kate]

It says you can't have Tnudg(2) set to zero, yet you have it set to zero. Have you tried changing it in your ocean.in file?

[shiyf]

It says you can't have Tnudg(2) set to zero, yet you have it set to zero. Have you tried changing it in your ocean.in file?

Thank you very much！the error has been solved,But when I run again,it is shown that
Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc
Output Stations File: ocean_sta.nc
Output Floats File: ocean_flt.nc
Input Grid File: /lustre/home/shiyongfangWKJ/roms/projects/roms_test/shiyf_grd.nc
Input Nonlinear Initial File: /lustre/home/shiyongfangWKJ/roms/projects/roms_test/shiyf_ini.nc
Input Forcing File 01: /lustre/home/shiyongfangWKJ/roms/projects/roms_test/shiyf_frc.nc
Input Boundary File: /lustre/home/shiyongfangWKJ/roms/projects/roms_test/shiyf_bry.nc

READ_PHYPAR - could not find input file:
do you encounter such a problem,could you help me?
my *.h file is :
/*
**
** Options for SHIYF.
**
** Application flag: SHIYF
** Input script: ocean_shiyf.in
*/

#define NO_HIS
#undef NETCDF4
#undef PARALLEL_IO
#undef OFFLINE_FLOATS



#define CURVGRID
#define MASKING
#define NONLIN_EOS
#define SOLVE3D
#define SALINITY
#ifdef SOLVE3D
#define SPLINES
#endif
#define FLOATS
#define STATIONS
#undef WET_DRY

#undef T_PASSIVE
#ifdef T_PASSIVE
#define ANA_PASSIVE
#define TRC_PSOURCE
#define ANA_TRC_PSOURCE
#define AGE_PASSIVE
#endif


#define NO_WRITE_GRID
#undef OUT_DOUBLE
#define RST_SINGLE
#define AVERAGES
#define AVERAGES2
#ifdef SOLVE3D
#undef AVERAGES_DETIDE
#undef DIAGNOSTICS_TS
#endif
#undef DIAGNOSTICS_UV


#ifdef SOLVE3D
#define DJ_GRADPS
#endif

#define UV_ADV
#define UV_COR
#undef UV_SADVECTION

#ifdef SOLVE3D
#define TS_U3HADVECTION
#define TS_C4VADVECTION
#undef TS_MPDATA
#endif

#define UV_VIS2
#undef UV_SMAGORINSKY
#undef VISC_3DCOEF
#define MIX_S_UV
#define VISC_GRID
#undef SPONGE

#ifdef SOLVE3D
#define TS_DIF2
#define MIX_GEO_TS
#define DIFF_GRID
#endif


#ifdef SOLVE3D
#define SOLAR_SOURCE
#define WTYPE_GRID
#undef LMD_MIXING
#ifdef LMD_MIXING
#define LMD_RIMIX
#define LMD_CONVEC
#define LMD_SKPP
#undef LMD_BKPP
#define LMD_NONLOCAL
#define LMD_SHAPIRO
#undef LMD_DDMIX
#endif

#define GLS_MIXING
#undef MY25_MIXING

#if defined GLS_MIXING || defined MY25_MIXING
#define KANTHA_CLAYSON
#define N2S2_HORAVG
#endif
#endif

#ifdef SOLVE3D
#define NCEP_FLUXES
#endif


#ifdef SOLVE3D
#define SCORRECTION
#undef QCORRECTION
#undef TCLIMATOLOGY
#undef TCLM_NUDGING
#endif



#define RADIATION_2D

#ifdef SOLVE3D
#define ANA_BSFLUX
#define ANA_BTFLUX
#else
#define ANA_SMFLUX
#endif

[kate]

That looks scarily like one of my cppdefs.h files. I see you have both floats and stations on. Do you have the floats and stations input files for it to read? I would debug this in a debugger to see where it's failing because it's not all that obvious from what you sent.

[shiyf]

That looks scarily like one of my cppdefs.h files. I see you have both floats and stations on. Do you have the floats and stations input files for it to read? I would debug this in a debugger to see where it's failing because it's not all that obvious from what you sent.

In fact,I only want to simulate the ocean temperature and salinity, Because i am a new user,I want to first be familiar with the process of the roms.As you suggest,I try to modify my shiyf.h file,Thank you very much !
could you help me have a look Whether the input files are correctly?

[shiyf]

That looks scarily like one of my cppdefs.h files. I see you have both floats and stations on. Do you have the floats and stations input files for it to read? I would debug this in a debugger to see where it's failing because it's not all that obvious from what you sent.

hi, I delete the cpp options-' FLOATS and STATIONS'in my cppdefs file, and compile build.bash again,but i get anther error:
Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc
Output Stations File: ocean_sta.nc
Output Floats File: ocean_flt.nc
Input Grid File: /lustre/home/shiyongfangWKJ/roms/projects/roms_test/shiyf_grd.nc
Input Nonlinear Initial File: /lustre/home/shiyongfangWKJ/roms/projects/roms_test/shiyf_ini.nc
Input Forcing File 01: /lustre/home/shiyongfangWKJ/roms/projects/roms_test/shiyf_frc.nc
Input Boundary File: /lustre/home/shiyongfangWKJ/roms/projects/roms_test/shiyf_bry.nc

READ_PHYPAR - could not find input file: ROMS/External/stations.in

Elapsed CPU time (seconds):


ROMS/TOMS - Output NetCDF summary for Grid 01:

ROMS/TOMS - I/O error ............... exit_flag: 4

I am very confused,How to locate the source of the error?
I am greatly appreciated for your help!

[kate]

Checking the read_phypar.F code shows that it will only try to read the stations file if STATIONS is defined. You can check the read_phypar.f90 intermediate file to check for the lines inside the #ifdef:

Code: Select all

#ifdef STATIONS
          fname=sposnam
          IF (.not.find_file(ng, fname, 'SPOSNAM')) GO TO 30
          WRITE (out,230) '        Station positions File:  ',          &    
     &                    TRIM(fname)
#endif

If it is still there, you haven't fully recompiled after changing your cppdefs.h file. Try "make clean" and a fresh build.

[shiyf]

Checking the read_phypar.F code shows that it will only try to read the stations file if STATIONS is defined. You can check the read_phypar.f90 intermediate file to check for the lines inside the #ifdef:

Code: Select all

#ifdef STATIONS
          fname=sposnam
          IF (.not.find_file(ng, fname, 'SPOSNAM')) GO TO 30
          WRITE (out,230) '        Station positions File:  ',          &    
     &                    TRIM(fname)
#endif

If it is still there, you haven't fully recompiled after changing your cppdefs.h file. Try "make clean" and a fresh build.

thank you very much! the problem have solved,but there is anther error:CHECKDEFS - no bottom stress formulation is selected.
i am very confused,because i have defined UV_LDRAG,it is same as the above problem, when i delete the station options in cpp.h as you suggest,then compile build.bash again, the error is still,Until I delete all files, including roms code,and upload all files,compile build.bash again,Problem can be solved. I do not know why it is? Can you give me some advice?

[kate]

You should not need to download ROMS all over again. When you build ROMS, it creates intermediate files in some $SCRATCH_DIR location. Do you know where that is? You want to find that location and investigate what those files look like when there are problems like your bottom drag problem.

Then when you modify your shiyf.h file, you want to restart the build. One way to do that is to delete the whole $SCRATCH_DIR directory and let build.bash recreate it. Also, the clean=1 in build.bash should be doing that for you automatically. Thirdly, if all the MakeDepend things are working, it should know to recompile almost everything when shiyf.h is modified.

As for the bottom drag, I don't know, but the place to investigate is in $SCRATCH_DIR/checkdefs.f90. Search it for "ibbl". Compare that to what's in checkdefs.F. Did it pick up any of your cpp options? If not, perhaps it's because your shiyf.h file is in dos format, I don't know.

[shiyf]

You should not need to download ROMS all over again. When you build ROMS, it creates intermediate files in some $SCRATCH_DIR location. Do you know where that is? You want to find that location and investigate what those files look like when there are problems like your bottom drag problem.

Then when you modify your shiyf.h file, you want to restart the build. One way to do that is to delete the whole $SCRATCH_DIR directory and let build.bash recreate it. Also, the clean=1 in build.bash should be doing that for you automatically. Thirdly, if all the MakeDepend things are working, it should know to recompile almost everything when shiyf.h is modified.

As for the bottom drag, I don't know, but the place to investigate is in $SCRATCH_DIR/checkdefs.f90. Search it for "ibbl". Compare that to what's in checkdefs.F. Did it pick up any of your cpp options? If not, perhaps it's because your shiyf.h file is in dos format, I don't know.

Thank you very much for your answer patiently,I found the cause of the error, it is because that i only modify my shiyf.h file under the projects file,but not modify the shiyf.h in trunk/ROMS/include path, I'm sorry to delay your time,but your advise is very useful for me!