Help My first application

[bibi951]

Hello,everyone.I am new to Roms.
I just have build up my first application program.As I ween,there is something wrong. It is just an imatation of windbasin.I use my grid-The area range is 3-41N,100-137E.I didn't do much preprocess on bathymethy.And I use four wall boundry conditions,surface and bottom both with momentum and heat flux.It just blowup in the first step. Would somebody help me find what's the problem?
As follows:
NANHAI SHUZHISHIYAN

Operating system : CYGWIN
CPU/hardware : i686
Compiler system : g95
Compiler command : /usr/local/bin/g95
Compiler flags : -fno-second-underscore -O3 -ffast-math -ffree-form -ffree-line-length-huge

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 333M

Local Root : /home/Sun/roms/trunk
Header Dir : /home/Sun/roms/Projects/nanhai
Header file : nanhai.h
Analytical Dir: /home/Sun/roms/Projects/nanhai/Functionals

Resolution, Grid 01: 0521x0440x020, Parallel Threads: 1, Tiling: 001x001


Activated C-preprocessing Options:

NANHAI NANHAI SHUZHISHIYAN
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_INITIAL Analytical initial conditions.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
CURVGRID Orthogonal curvilinear grid.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EASTERN_WALL Wall boundary at Eastern edge.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
MY25_MIXING Mellor/Yamada Level-2.5 mixing closure.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NORTHERN_WALL Wall boundary at Northern edge.
N2S2_HORAVG Horizontal smoothing of buoyancy and shear.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
K_GSCHEME Third-order upstream advection of TKE fields.
!RST_SINGLE Double precision fields in restart NetCDF file.
SOLVE3D Solving 3D Primitive Equations.
SOUTHERN_WALL Wall boundary at Southern edge.
SPLINES Conservative parabolic spline reconstruction.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_SVADVECTION Parabolic splines vertical advection of tracers.
UV_ADV Advection of momentum.
UV_COR Coriolis term.
UV_U3HADVECTION Third-order upstream horizontal advection of 3D momentum.
UV_C4VADVECTION Fourth-order centered vertical advection of momentum.
UV_QDRAG Quadratic bottom stress.
VAR_RHO_2D Variable density barotropic mode.
WESTERN_WALL Wall boundary at Western edge.

INITIAL: Configuring and initializing forward nonlinear model ...


Vertical S-coordinate System:

level S-coord Cs-curve at_hmin over_slope at_hmax


Minimum X-grid spacing, DXmin = 6.58820368E+00 km
Maximum X-grid spacing, DXmax = 8.58514811E+00 km
Minimum Y-grid spacing, DYmin = 6.80046120E+00 km
Maximum Y-grid spacing, DYmax = 8.86173180E+00 km
Minimum Z-grid spacing, DZmin = NaN m
Maximum Z-grid spacing, DZmax = NaN m

Minimum barotropic Courant Number = 0.00000000E+00
Maximum barotropic Courant Number = 3.06178799E-01
Maximum Coriolis Courant Number = 1.12416582E-02


Maximum grid stiffness ratios: rx0 = 1.000000E+00 (Beckmann and Haidvogel)
rx1 = 2.141787E+01 (Haney)


Initial basin volumes: TotVolume = NaN m3
MinVolume = NaN m3
MaxVolume = 6.62990960088657E+10 m3
Max/Min = 0.00000000000000E+00

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00068400)

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 515 24:00:00 NaN NaN NaN NaN

Elapsed CPU time (seconds):

Thread # 0 CPU: 128.453
Total: 128.453

Nonlinear model elapsed time profile:

Initialization ................................... 70.406 (54.8109 %)
Computation of global information integrals ...... 7.047 ( 5.4860 %)
2D/3D coupling, vertical metrics ................. 11.359 ( 8.8432 %)
Omega vertical velocity .......................... 5.156 ( 4.0141 %)
Equation of state for seawater ................... 52.422 (40.8101 %)
Total: 146.391 113.9642

All percentages are with respect to total time = 128.453

ROMS/TOMS - Output NetCDF summary for Grid 01:

Analytical header files used:

/home/Sun/roms/Projects/nanhai/Functionals/ana_btflux.h
/home/Sun/roms/Projects/nanhai/Functionals/ana_initial.h
/home/Sun/roms/Projects/nanhai/Functionals/ana_smflux.h
/home/Sun/roms/Projects/nanhai/Functionals/ana_stflux.h

ROMS/TOMS - Blows up ................ exit_flag: 1

[gouillon]

I never tried that test case but if there is no land in your basin, try to undefine the MASKING option.
It seems that you have a NAN value for your min basin volume and a 0 value for your barotropic courant number. Start from there to debug.

Flav

[jcwarner]

"Minimum Z-grid spacing, DZmin = NaN m
Maximum Z-grid spacing, DZmax = NaN m

Minimum barotropic Courant Number = 0.00000000E+00"

do you have any 'zeros' in your bathymetry?

[kate]

Note that you can't have zero depth, even if it is inside the land mask.

[bibi951]

Hi.Thanks for your replies.
I have modified the bathymetre,and it works.
Very nice.
Thank you all

[bibi951]

Hello,everyone.
Back again.
I now use OTPS to make tide forcing.I use Cygwin for windows,and G95,Gfortran are my fortran compiler.Now it seem that G95 don't recognize this.Any advice?
$ make extract_HC
g95 -o extract_HC extract_HC.f subs.f -L/usr/local/lib -lnetcdf -I/usr/local/include
In file extract_HC.f:227
write(11,fmt)lat(k),lon0(k),((abs(z1(ic)),atan2(-imag(z1(ic)),real(z1(ic)))*180/3.141593),ic=1,ncon)
....................................................(1)

Error: Expected a right parenthesis in expression at (1)

[kate]

Hello,everyone.
Back again.
I now use OTPS to make tide forcing.I use Cygwin for windows,and G95,Gfortran are my fortran compiler.Now it seem that G95 don't recognize this.Any advice?
$ make extract_HC
g95 -o extract_HC extract_HC.f subs.f -L/usr/local/lib -lnetcdf -I/usr/local/include
In file extract_HC.f:227
write(11,fmt)lat(k),lon0(k),((abs(z1(ic)),atan2(-imag(z1(ic)),real(z1(ic)))*180/3.141593),ic=1,ncon)
....................................................(1)

Error: Expected a right parenthesis in expression at (1)

Have you tried gfortran? If that doesn't work, I would rewrite that implied do loop on ic into an explicit do loop. I have a vague memory of the above style not being accepted by some gnu compiler even though it may be valid Fortran.

[bibi951]

Hi,Kate.
I tried Gfortran,it also failed to do it.
I have rewrite this section to a explicit do loop.
As follows:
line 25 : character*2000 fmt1,fmt2,ftmp
aroud 176: c output format
fmt1='(f9.3,f9.3)'
if(APRI)then
fmt2='(f8.3,f8.1)'
else
fmt2='(f8.3,f8.3)'
endif
aroud 227: if(APRI)then
write(11,trim(fmt1),advance='no') lat(k),lon0(k)
do ic=1,ncon
write(11,trim(fmt2),advance='no') abs(z1(ic)),
* atan2(-imag(z1(ic)),real(z1(ic)))*180/3.141593
enddo
write(11,*)
else
write(11,trim(fmt1),advance='no') lat(k),lon0(k)
do ic=1,ncon
write(11,trim(fmt2),advance='no') real(z1(ic)),imag(z1(ic))
enddo
write(11,*)
endif

[bibi951]

Hi,everyone
I created my domain grid with seagrid.The first corner(*) is southwest(in real world),so the first edge is south(in real world).But what is the west boundary in Roms Model? Is it the first edge(south in real world)? Or ...?
If one boundary is half open,(there is a gap ),I should use OBC without further consideration, right?
Thanks in advance.

[kate]

I believe the answers are yes and yes.

[mathieu]

Inside of roms the attributes south, east, north, west refer to the Grid.
More precisely if the grid has size (eta_rho,xi_rho),
then:

• The points of the southern boundaries are all the points (1,iXi) for iXi between 1 and xi_rho.
  The points of the eastern boundary are all the points (iEta,xi_rho) for iEta between 1 and eta_rho.
  The points of the western boundary are all the points (iEta,1) for iEta between 1 and eta_rho.
  The points of the northern boundaries are all the points (eta_rho,iXi) for iXi between 1 and xi_rho.

All the options SOUTH_* and others refer to those points. The grid thus has its own notions of south, north, west, east. They coincide with the the corresponding geographical south, north, west and east only if the angle of the grid (variable angle in the netcdf grid file) is zero.
So, I would advise you to plot the grid and see if it matches with the above description.

[hugobastos]

Inside of roms the attributes south, east, north, west refer to the Grid.
More precisely if the grid has size (eta_rho,xi_rho),
then:

• The points of the southern boundaries are all the points (1,iXi) for iXi between 1 and xi_rho.
  The points of the eastern boundary are all the points (iEta,xi_rho) for iEta between 1 and eta_rho.
  The points of the western boundary are all the points (iEta,1) for iEta between 1 and eta_rho.
  The points of the northern boundaries are all the points (eta_rho,iXi) for iXi between 1 and xi_rho.

All the options SOUTH_* and others refer to those points. The grid thus has its own notions of south, north, west, east. They coincide with the the corresponding geographical south, north, west and east only if the angle of the grid (variable angle in the netcdf grid file) is zero.
So, I would advise you to plot the grid and see if it matches with the above description.

Hello community,


A nice way to verify this in with ncview, and check the mask_rho or others mask's variables and see if they match with your geographic location (coastline position).

Because ncview read like mathieu says, and if the mask's (rho,psi) r not likely your real coast on the ncview display, your put some point on the wrong sequence!

Yhis happen to me on the GUIFG tool, when u forgot the order of Roll points hehe, my ocean boundary became clamped and the point's next to the land masks stay with nudging to NaN values hehe .

Another issue is to check de U,V masks, since when i use some routines from the collection of .m scripts, one or two routine messed up the masks on U and V!

So, to avoid this type of errors( and others stuff), ncview is very nice!


Thnkz
hugo

[bibi951]

Thanks for the above replies,they are very clear.

I get this error message:
Minimum barotropic Courant Number = 9.63854617E-03
Maximum barotropic Courant Number = 2.99427149E-01
Maximum Coriolis Courant Number = 1.12416582E-02

GET_NGFLD - tidal period
(Min = 4.32000000E+04 Max = 9.29494800E+04)
GET_2DFLD - tidal elevation amplitude
(Min = 0.00000000E+00 Max = 3.23688018E+00)
GET_2DFLD - tidal elevation phase angle
(Min = 1.25512765E-04 Max = 6.28311161E+00)
GET_2DFLD - tidal current inclination angle
(Min = 0.00000000E+00 Max = 6.28318531E+00)
GET_2DFLD - tidal current phase angle
(Min = 0.00000000E+00 Max = 6.28318217E+00)
GET_2DFLD - maximum tidal current, ellipse major axis
(Min = 0.00000000E+00 Max = 5.91933030E+00)
GET_2DFLD - minimum tidal current, ellipse minor axis
(Min = -1.30634990E+00 Max = 1.62644441E+00)
assertion "extent != 0" failed: file "posixio.c", line 412
Aborted (core dumped)
And I find a oceanS.exe.stackdump file which says:
Stack trace:
Frame Function Args
0022BBC8 7C802532 (00000678, 0000EA60, 000000A4, 0022BC10)
0022BCE8 61097F54 (00000000, 7C8025F0, 7C802532, 000000A4)
0022BDD8 61095AEB (00000000, 003B0023, 00230000, 0022CE68)
0022BE38 61095FCB (0022BE50, 00000000, 00000094, 61020C1B)
0022BEF8 61096182 (00000E34, 00000006, 0022BF28, 61096383)
0022BF08 610961AC (00000006, 0022CE88, 0000D44C, 6109A7DF)
0022BF28 61096383 (6110D008, 005405ED, 005404D4, 0000019C)
0022BF58 61001087 (005404D4, 0000019C, 005405ED, 00000000)
0022BFC8 610935A8 (00000000, 00000000, 00000000, 00000000)
0022BFF8 0052C66B (00ACFF30, 0022C058, FFFFFFFF, 00000000)
0022C0A8 0052D450 (00ACFEC8, 00000000, 00000000, 00000000)
0022C0E8 005145A8 (0096A270, 00000000, 00000000, 00000000)
0022C108 0051466C (0096A270, 00000000, 00000000, 0022C148)
0022C128 00514695 (0096A270, 00000000, 0022C148, 698043F1)
0022C158 0050E6A1 (0096A260, 0053CE70, 0022C434, 00000009)
0022C2B8 004C573D (0022CC84, 00532280, 00962310, 0053CE70)
End of stack trace (more stack frames may be present)
Is it because of my PC memory isn't enough?
Besides,I have run the example cases such as cblast,it's OK.And they run fast.My case runs very slowly. I always find it's almost the maximum memory.
I attach my .h file. Somewhere improper?
/*
** svn $Id: .h 169 2007-04-09 21:01:01Z $
*******************************************************************************
** Copyright (c) 2002-2007 The ROMS/TOMS Group **
** Licensed under a MIT/X style license **
** See License_ROMS.txt **
*******************************************************************************
**
** Options for Coupled Boundary Layers and Air-Sea Transfer Application.
**
** Application flag: ** Input script: .in
*/
/* Basic physics options */
#define UV_ADV
#define UV_COR
#define UV_VIS2
#define UV_QDRAG
#define MIX_S_UV
#define SOLVE3D
#define NONLIN_EOS
#undef SALINITY

/* Basic numerics options */
/*#define UV_SADVECTION*/
#define TS_U3HADVECTION
#define TS_SVADVECTION
#define DJ_GRADPS
#define SPLINES
#define CURVGRID
#define MASKING

/* Outputs */
/*#define AVERAGES
/*#define AVERAGES_QUADRATIC /* for full diagnostics of mean and eddy heat fluxes */
/*#define AVERAGES_FLUXES /* for full diagnostics of mean and eddy heat fluxes */
/*#define DIAGNOSTICS_UV
/*#define DIAGNOSTICS_TS /* for full diagnostics of mean and eddy heat fluxes */
/*#define STATIONS*/
#undef OUT_DOUBLE

/* Surface and bottom boundary conditions */
/*#define SOLAR_SOURCE /* solar radiation penetrates through water column */
#define ANA_SMFLUX
#define ANA_STFLUX
#define ANA_BTFLUX
#define ANA_BMFLUX

#define ANA_INITIAL

/* Vertical subgridscale turbulence closure */
#undef LMD_MIXING
#define MY25_MIXING
#ifdef MY25_MIXING
# define N2S2_HORAVG
# define KANTHA_CLAYSON
#endif
#ifdef LMD_MIXING
# define LMD_RIMIX
# define LMD_CONVEC
# define LMD_SKPP
# define LMD_BKPP
# define ANA_CLOUD
#endif


#define EASTERN_WALL
#define NORTHERN_WALL
/* Open boundary conditions */
#define ANA_FSOBC
#define ANA_M2OBC
#define RADIATION_2D
#define RAMP_TIDES
#define SSH_TIDES
#define ADD_FSOBC
#define WEST_FSCHAPMAN
#define SOUTH_FSCHAPMAN
#define UV_TIDES
#define ADD_M2OBC
#define WEST_M2FLATHER
#define WEST_M3RADIATION
#define WEST_M3NUDGING
#define WEST_TRADIATION
#define WEST_TNUDGING
#define SOUTH_M2FLATHER
#define SOUTH_M3RADIATION
#define SOUTH_M3NUDGING
#define SOUTH_TRADIATION
#define SOUTH_TNUDGING

[kate]

Have you tried compiling with USE_DEBUG? You might get a more useful stack trace then. What is your grid size? You can get a feel for how big is too big by running the BENCHMARK case with the three different input files.

[bibi951]

Hi,everyone.
I want to use only real tides on the open boundry.So I write this in my .h file
/* Basic physics options */
#define UV_ADV
#define UV_COR
#define UV_VIS2
#define UV_QDRAG
#define MIX_S_UV
#define SOLVE3D
#define NONLIN_EOS
#undef SALINITY

/* Basic numerics options */
/*#define UV_SADVECTION*/
#define TS_U3HADVECTION
#define TS_SVADVECTION
#define DJ_GRADPS
#define SPLINES
#define CURVGRID
#define MASKING

/#undef OUT_DOUBLE

/* Surface and bottom boundary conditions */
/*#define SOLAR_SOURCE /* solar radiation penetrates through water column */
#define ANA_SMFLUX
#define ANA_STFLUX
#define ANA_BTFLUX
#define ANA_BMFLUX

#define ANA_INITIAL

/* Vertical subgridscale turbulence closure */
#undef LMD_MIXING
#define MY25_MIXING
#ifdef MY25_MIXING
# define N2S2_HORAVG
# define KANTHA_CLAYSON
#endif
#ifdef LMD_MIXING
# define LMD_RIMIX
# define LMD_CONVEC
# define LMD_SKPP
# define LMD_BKPP
# define ANA_CLOUD
#endif


#define EASTERN_WALL
#define NORTHERN_WALL
/* Open boundary conditions */
#define ANA_FSOBC
#define ANA_M2OBC
#define RADIATION_2D
#define RAMP_TIDES
#define SSH_TIDES
#define ADD_FSOBC
#define WEST_FSCHAPMAN
#define SOUTH_FSCHAPMAN
#define UV_TIDES
#define ADD_M2OBC
#define WEST_M2FLATHER
#define WEST_M3RADIATION
#define WEST_M3NUDGING
#define WEST_TRADIATION
#define WEST_TNUDGING
#define SOUTH_M2FLATHER
#define SOUTH_M3RADIATION
#define SOUTH_M3NUDGING
#define SOUTH_TRADIATION
#define SOUTH_TNUDGING

on the open boundry,I use ana_fsobc.h and ana_m2obc.h to give zero for all the vars. And I modified the parts of ana_initial.h ana_bmflux.h ana_btflux.h ana_smflux.h ana_stflux.h for my application.
It is a very simple case, but I encounted this error,and spent days in finding what's wrong.
It seems that a boundry file is requested.But I think I use ana_*.h to assign them zeros.I just want an analytic boundry values and the tide.Besides I have give a tidal forcing file but seems model didn't need it.
NFFILES == 1 ! number of forcing files
FRCNAME == test_HC.nc
This is the error message:
Output/Input Files:

Output Restart File: ./rst_nanhai_ex.nc
Prefix for History Files: ./his_nanhai_ex
Input Grid File: zhongguon.nc
Input Boundary File: /dev/null
This is Activated C-preprocessing Options:

NANHAI NANHAI SHUZHISHIYAN
ADD_FSOBC Adding tidal elevation to proccesed OBC data.

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 0 00:00:00 0.000000E+00 3.233154E+05 3.233154E+05 2.468722E+16

Would some one help me ?

[hugobastos]

You cant use this together:

#define ANA_FSOBC
#define ANA_M2OBC
with
#define SSH_TIDES
#define ADD_FSOBC
#define ADD_M2OBC


U probably are overwriting the values in the boundary, using this 2 options !

The first's options set the elevation on the boundary to the values in ana_fsobc.F & ana_m2obc.F , call by analytical.F!

The last options r for realistic cases! u need to provide the tidal parameters on a netcdf file, and add this values in the model boundary.

Usually, we make a file from TPXO tide model, set this file to forcing file, add the options of SSH_TIDES,ADD_FSOBC,ADD_M2OBC and the respectivly boundary conditions .

See https://www.myroms.org/wiki/index.php/Tidal_Forcing For realistic tide forcing

and this https://www.myroms.org/wiki/index.php/FJORD_TIDAL_CASE , for a simple test on your grid!

Search in the wiki & forum about the CPP FLAGS and cases u want to use/test!

Clearly u will skip some of these types of problems.

[bibi951]

Hello,I have a simple question to ask.
I don't quite understand this :
In set_tides.F line 434 and below,
! To avoid having two boundary
! points for these arrays, the values of "zeta_west" and "zeta_east"
! are averaged at u-points.
# ifdef ADD_FSOBC
zeta_west(j)=zeta_west(j)+ &
& 0.5_r8*(Etide(Istr-1,j)+Etide(Istr,j))
It seems that the programer want " zeta averaged at u-points",to be consistant with Ubar,maybe? zeta should be associated with divergence through continuity equation,So zeta should be on Rho grid point and u v on u,v grid point,isn't it? But then, Add tidal currents (m/s) to 2D momentum climatologies.
Uwrk(i,j)=UV_Tmajor(i,j,itide)*Cangle*Cphase- &
& UV_Tminor(i,j,itide)*Sangle*Sphase
Vwrk(i,j)=UV_Tmajor(i,j,itide)*Sangle*Cphase+ &
& UV_Tminor(i,j,itide)*Cangle*Sphase
And Utide(i,j)=Utide(i,j)+ &
& ramp*0.5_r8*(Uwrk(i-1,j)+Uwrk(i,j))
It seems back to zeta.I am confused about this.
What is that indeed? And what boundry condition (variables on which grid point?) do I need to provide for climatory?
I am a beginer to ROMS? Please give me some guide.
Thanks in advance.