My seashore test

[fancer]

Hi all ROMS users!))))
Please, help me with my application for compute sediment transport in seashore with input real grid and forcing from SWAN.
I have installed MCT and have run his examples. All works well. When I start ROMS with mpif90, assign next error:

[xxx@host] roms3 # mpirun -np 2 ./oceanG ROMS/External/ocean_seashore.in
Coupled Input File name = ROMS/External/ocean_seashore.in
rank 0 in job 47 host_51380 caused collective abort of all ranks
exit status of rank 0: return code 0

When I run without SWAN and MCT with gfortran ROMS stop after first line of calculations:

Process Information:

Thread # 0 (pid= 3237) is active.

Model Input Parameters: ROMS/TOMS version 3.2
Tuesday - June 16, 2009 - 7:39:22 PM
-----------------------------------------------------------------------------

Seashore sediment transport

Operating system : Linux
CPU/hardware : i686
Compiler system : gfortran
Compiler command : /usr/bin/gfortran
Compiler flags : -frepack-arrays -g -fbounds-check -ffree-form -ffree-line-length-none

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 353M

Local Root : /root/program_files/ROMS/roms3
Header Dir : /root/program_files/ROMS/roms3/ROMS/Include
Header file : seashore.h
Analytical Dir: /root/program_files/ROMS/roms3/ROMS/Functionals

Resolution, Grid 01: 0040x0164x020, Parallel Threads: 1, Tiling: 001x001


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

34546 ntimes Number of timesteps for 3-D equations.
10.000 dt Timestep size (s) for 3-D equations.
20 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.
720 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).
720 nHIS Number of timesteps between the writing fields
into history file.
1.0000E-03 visc2 Horizontal, harmonic mixing coefficient (m2/s)
for momentum.
5.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
5.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
5.0000E-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).
2.5000E-02 rdrg2 Quadratic bottom drag coefficient.
1.5000E-02 Zob Bottom roughness (m).
5.0000E-01 Zos Surface roughness (m).
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
1.0000E+00 theta_s S-coordinate surface control parameter.
1.0000E+00 theta_b S-coordinate bottom control parameter.
0.000 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.
15.000 T0 Background potential temperature (C) constant.
30.000 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).
7.6000E-04 Scoef Saline contraction coefficient (1/PSU).
1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
T Hout(idBath) Write out time-dependent bathymetry.
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
T Hout(idUsms) Write out surface U-momentum stress.
T Hout(idVsms) Write out surface V-momentum stress.
T Hout(idUbms) Write out bottom U-momentum stress.
T Hout(idVbms) Write out bottom V-momentum stress.
T Hout(idUbrs) Write out bottom U-current stress.
T Hout(idVbrs) Write out bottom V-current stress.
T Hout(idUbws) Write out wind-induced, bottom U-wave stress.
T Hout(idVbws) Write out wind-induced, bottom V-wave stress.
T Hout(idUbcs) Write out max wind + current, bottom U-wave stress.
T Hout(idVbcs) Write out max wind + current, bottom V-wave stress.
T Hout(idW2xx) Write out 2D radiation stress, Sxx.
T Hout(idW2xy) Write out 2D radiation stress, Sxy.
T Hout(idW2yy) Write out 2D radiation stress, Syy.
T Hout(idWamp) Write out wave height.
T Hout(idWlen) Write out wave length.
T Hout(idWdir) Write out wave direction.
T Hout(idBott) Write out bottom property 01: grain_diameter
T Hout(idBott) Write out bottom property 02: grain_density
T Hout(idBott) Write out bottom property 03: settling_vel
T Hout(idBott) Write out bottom property 04: erosion_stress
T Hout(idBott) Write out bottom property 05: ripple_length
T Hout(idBott) Write out bottom property 06: ripple_height
T Hout(idBott) Write out bottom property 07: bed_wave_amp
T Hout(idBott) Write out bottom property 08: Zo_def
T Hout(idBott) Write out bottom property 09: Zo_app

Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Input Grid File: Data/ROMS/Grid/seashore_grid.nc

Tile partition information for Grid 01: 0040x0164x0020 tiling: 001x001

tile Istr Iend Jstr Jend Npts

0 1 40 1 164 131200

Tile minimum and maximum fractional grid coordinates:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 -0.50 42.50 -0.50 166.50 RHO-points

0 -0.50 42.50 -0.50 166.50 U-points

0 -0.50 42.50 -0.50 166.50 V-points


Sediment Parameters, Grid: 01
=============================


Size Sd50 Csed Srho Wsed Erate poros
Class (mm) (kg/m3) (kg/m3) (mm/s) (kg/m2/s) (nondim)

1 1.0000E+00 0.0000E+00 2.6500E+03 1.0000E+00 1.0000E-05 5.0000E-01

tau_ce tau_cd tnu2 tnu4 Akt_bak Tnudg
(N/m2) (N/m2) (m2/s) (m4/s) (m2/s) (day)

1 7.0000E-02 2.0000E-02 0.0000E+00 0.0000E+00 5.0000E-06 0.0000E+00

morph_fac
(nondim)

1 1.0000E+00

New bed layer formed when deposition exceeds 0.10000E-01 (m).
Two first layers are combined when 2nd layer smaller than 0.00000E+00 (m).
Rate coefficient for bed load transport = 0.15000E+00

T Hout(idTvar) Write out sediment01: sand_01
T Hout(idfrac) Write out bed fraction, sediment 01: sandfrac_01
T Hout(idfrac) Write out mass, sediment 01: sandmass_01
T Hout(idSbed) Write out BED property 01: bed_thickness
T Hout(idSbed) Write out BED property 02: bed_age
T Hout(idSbed) Write out BED property 03: bed_porosity

Activated C-preprocessing Options:

SEASHORE Seashore sediment transport
ANA_BPFLUX Analytical bottom passive tracers fluxes.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_FSOBC Analytical free-surface boundary conditions.
ANA_INITIAL Analytical initial conditions.
ANA_M2OBC Analytical 2D momentum boundary conditions.
ANA_SEDIMENT Analytical sediment initial conditions.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_SPFLUX Analytical surface passive tracer fluxes.
ANA_SSFLUX Analytical kinematic surface salinity flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ANA_WWAVE Analytical wind induced waves.
ASSUMED_SHAPE Using assumed-shape arrays.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EAST_FSGRADIENT Eastern edge, free-surface, gradient condition.
EAST_M2GRADIENT Eastern edge, 2D momentum, gradient condition.
EAST_M3GRADIENT Eastern edge, 3D momentum, gradient condition.
FSOBC_REDUCED Using free-surface data in reduced physics condtions
GLS_MIXING Generic Length-Scale turbulence closure.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
MIX_S_UV Mixing of momentum along constant S-surfaces.
NEARSHORE_MELLOR Nearshore RAdiation Stress Terms.
NONLINEAR Nonlinear Model.
!NONLIN_EOS Linear 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.
SEDIMENT Cohesive and noncohesive sediments.
SED_MORPH Allow bottom model elevation to evolve.
SUSPLOAD Activate suspended sediment transport.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSGRADIENT Southern edge, free-surface, gradient condition.
SOUTH_M2REDUCED Southern edge, 2D momentum, reduced-physics condition.
SOUTH_M3GRADIENT Southern edge, 3D momentum, gradient condition.
SPLINES Conservative parabolic spline reconstruction.
SSW_BBL Styles and Glenn Bottom Boundary Layer - modified.
SSW_CALC_ZNOT Internal computation of bottom roughness.
TS_MPDATA Recursive flux corrected MPDATA 3D advection of tracers.
UV_ADV Advection of momentum.
UV_U3HADVECTION Third-order upstream horizontal advection of 3D momentum.
UV_C4VADVECTION Fourth-order centered vertical advection of momentum.
UV_VIS2 Harmonic mixing of momentum.
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

20 0.0000000 0.0000000 0.000 0.000 0.000
19 -0.0500000 -0.0435151 0.293 -0.064 -0.420
18 -0.1000000 -0.0889041 0.586 -0.143 -0.871
17 -0.1500000 -0.1360495 0.878 -0.236 -1.350
16 -0.2000000 -0.1848065 1.171 -0.343 -1.856
15 -0.2500000 -0.2350037 1.464 -0.461 -2.386
14 -0.3000000 -0.2864445 1.757 -0.590 -2.936
13 -0.3500000 -0.3389099 2.049 -0.727 -3.503
12 -0.4000000 -0.3921616 2.342 -0.870 -4.082
11 -0.4500000 -0.4459462 2.635 -1.018 -4.670
10 -0.5000000 -0.5000000 2.928 -1.168 -5.263
9 -0.5500000 -0.5540538 3.220 -1.318 -5.856
8 -0.6000000 -0.6078384 3.513 -1.465 -6.444
7 -0.6500000 -0.6610901 3.806 -1.609 -7.024
6 -0.7000000 -0.7135555 4.099 -1.746 -7.590
5 -0.7500000 -0.7649963 4.392 -1.874 -8.140
4 -0.8000000 -0.8151935 4.684 -1.993 -8.670
3 -0.8500000 -0.8639505 4.977 -2.099 -9.176
2 -0.9000000 -0.9110959 5.270 -2.193 -9.655
1 -0.9500000 -0.9564849 5.563 -2.272 -10.106
0 -1.0000000 -1.0000000 5.855 -2.335 -10.526

Time Splitting Weights: ndtfast = 20 nfast = 29

Primary Secondary Accumulated to Current Step

1-0.0009651193358779 0.0500000000000000-0.0009651193358779 0.0500000000000000
2-0.0013488780126037 0.0500482559667939-0.0023139973484816 0.1000482559667939
3-0.0011514592651645 0.0501156998674241-0.0034654566136461 0.1501639558342180
4-0.0003735756740661 0.0501732728306823-0.0038390322877122 0.2003372286649003
5 0.0009829200513762 0.0501919516143856-0.0028561122363360 0.2505291802792859
6 0.0029141799764308 0.0501428056118168 0.0000580677400948 0.3006719858911028
7 0.0054132615310267 0.0499970966129953 0.0054713292711215 0.3506690825040981
8 0.0084687837865133 0.0497264335364439 0.0139401130576348 0.4003955160405420
9 0.0120633394191050 0.0493029943471183 0.0260034524767397 0.4496985103876603
10 0.0161716623600090 0.0486998273761630 0.0421751148367487 0.4983983377638233
11 0.0207585511322367 0.0478912442581626 0.0629336659689855 0.5462895820219859
12 0.0257765478740990 0.0468533167015507 0.0887102138430845 0.5931428987235365
13 0.0311633730493854 0.0455644893078458 0.1198735868924699 0.6387073880313823
14 0.0368391158442262 0.0440063206553765 0.1567127027366961 0.6827137086867587
15 0.0427031802506397 0.0421643648631652 0.1994158829873358 0.7248780735499240
16 0.0486309868367617 0.0400292058506332 0.2480468698240975 0.7649072794005571
17 0.0544704302037592 0.0375976565087951 0.3025173000278567 0.8025049359093522
18 0.0600380921294286 0.0348741349986072 0.3625553921572853 0.8373790709079594
19 0.0651152103984763 0.0318722303921357 0.4276706025557617 0.8692513013000951
20 0.0694434033194840 0.0286164698722119 0.4971140058752457 0.8978677711723070
21 0.0727201499285570 0.0251442997062377 0.5698341558038027 0.9230120708785448
22 0.0745940258796570 0.0215082922098099 0.6444281816834597 0.9445203630883546
23 0.0746596950216180 0.0177785909158270 0.7190878767050777 0.9622989540041816
24 0.0724526566618460 0.0140456061647461 0.7915405333669236 0.9763445601689278
25 0.0674437485167025 0.0104229733316538 0.8589842818836262 0.9867675335005817
26 0.0590334053485719 0.0070507859058187 0.9180176872321981 0.9938183194064003
27 0.0465456732896125 0.0040991156383901 0.9645633605218106 0.9979174350447904
28 0.0292219798521904 0.0017718319739095 0.9937853403740009 0.9996892670186999
29 0.0062146596259991 0.0003107329813000 1.0000000000000000 0.9999999999999998

ndtfast, nfast = 20 29 nfast/ndtfast = 1.45000

Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):

1.000000000000 1.060707743385 0.530353871693 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.14200

Minimum X-grid spacing, DXmin = 3.00002090E-02 km
Maximum X-grid spacing, DXmax = 3.00002093E-02 km
Minimum Y-grid spacing, DYmin = 3.00000000E-02 km
Maximum Y-grid spacing, DYmax = 3.00000007E-02 km
Minimum Z-grid spacing, DZmin = -2.92767293E-01 m
Maximum Z-grid spacing, DZmax = 5.92723058E-01 m

Minimum barotropic Courant Number = 2.82583748E-03
Maximum barotropic Courant Number = 2.39516077E-01
Maximum Coriolis Courant Number = 1.08104461E-03


Maximum grid stiffness ratios: rx0 = 9.926508E-01 (Beckmann and Haidvogel)
rx1 = 2.196218E+04 (Haney)


Initial basin volumes: TotVolume = 3.01841820631482E+07 m3
MinVolume = -3.41170348265188E+01 m3
MaxVolume = 5.27200400404144E+02 m3
Max/Min = -1.54527028238209E+01

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00034546)

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 0 00:00:00 0.000000E+00 3.841801E+01 3.841801E+01 2.838443E+07
DEF_HIS - creating history file: ocean_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
---------------------------------------------------------------

A week I solve this problem... Please help!
I attach the necessary files...

[fancer]

If longer to wait:

1 0 00:00:10 NaN NaN NaN NaN

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=2,2) into time record = 0000001

Elapsed CPU time (seconds):

Thread # 0 CPU: 150.749
Total: 150.749

Nonlinear model elapsed time profile:

Initialization ................................... 0.040 ( 0.0265 %)
Processing of input data ......................... 0.008 ( 0.0053 %)
Computation of global information integrals ...... 0.988 ( 0.6554 %)
Writing of output data ........................... 0.152 ( 0.1008 %)
Model 2D kernel .................................. 26.730 (17.7312 %)
2D/3D coupling, vertical metrics ................. 0.912 ( 0.6050 %)
Omega vertical velocity .......................... 0.352 ( 0.2335 %)
Equation of state for seawater ................... 0.724 ( 0.4803 %)
Sediment tranport module, source/sink terms ...... 2.884 ( 1.9132 %)
GLS vertical mixing parameterization ............. 5.432 ( 3.6036 %)
3D equations right-side terms .................... 1.248 ( 0.8279 %)
3D equations predictor step ...................... 0.028 ( 0.0186 %)
Pressure gradient ................................ 0.028 ( 0.0186 %)
Harmonic stress tensor, S-surfaces ............... 0.032 ( 0.0212 %)
Corrector time-step for 3D momentum .............. 5.744 ( 3.8105 %)
Corrector time-step for tracers .................. 104.423 (69.2689 %)
Bottom boundary layer module ..................... 0.008 ( 0.0053 %)
Total: 149.733 99.3260

All percentages are with respect to total time = 150.749

ROMS/TOMS - Output NetCDF summary for Grid 01:
number of time records written in HISTORY file = 00000001
number of time records written in RESTART file = 00000001

Analytical header files used:

ROMS/Functionals/ana_btflux.h
ROMS/Functionals/ana_fsobc.h
ROMS/Functionals/ana_initial.h
ROMS/Functionals/ana_m2obc.h
ROMS/Functionals/ana_sediment.h
ROMS/Functionals/ana_smflux.h
ROMS/Functionals/ana_stflux.h
ROMS/Functionals/ana_wwave.h

ROMS/TOMS: DONE... Wednesday - June 17, 2009 - 10:20:17 AM

[fancer]

When I run with ana_wwave and const Dwave Hwave and Lwave:
Hwave(i,j)=2.0_r8
Dwave(i,j)=90.0_r8*deg2rad
Lwave(i,j)=20.0_r8

ROMS blowing up after 4 step:
NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00034546)

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 0 00:00:00 0.000000E+00 3.610191E+01 3.610191E+01 3.027612E+07
DEF_HIS - creating history file: ocean_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
1 0 00:00:02 4.502087E-06 3.610212E+01 3.610213E+01 3.027613E+07
2 0 00:00:04 1.656315E-02 3.609990E+01 3.611646E+01 3.027768E+07
3 0 00:00:06 1.905550E-02 3.610085E+01 3.611990E+01 3.027745E+07
4 0 00:00:08 NaN NaN NaN NaN

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=1,1) into time record = 0000001

[jcwarner]

ok. So if you look in the restart file, does that provide any information?? Is the blow up (nan creation) at the boundary, coastline,
maybe you need to
#define WET_DRY
??

[fancer]

Without wet and dry ROMS blowing up on second time-step.
With wet and dry ROMS blowing up on fourth time-step.
I many times started the program with different parametres and have noticed that most part of time is spent on Corrector time-step for tracers. And blowing up when kinetic energy becomes more than certain value(~2.0E-2).
No zero in bath, but NaN in vbar and ubar, u and v(((( - Border where is NaN and where is not NaN present for ubar and vbar very strange (look at the picture). NaN in the ubar and vbar where white color.
I attach two restart files with wet and dry and without it.

My bathymetry

mybath.png (16.61 KiB) Viewed 41076 times

vbar

vbar.png (4.44 KiB) Viewed 41073 times

ubar

ubar.png (4.05 KiB) Viewed 41072 times

PS my second post without wet and dry;
my third post with wet and dry.
And that can be with SWAN???

[jcwarner]

run it w/ wet_dry on, save every time step and see what the history files tell you.

[fancer]

If I do Hwave less when 2.0 when kinetic energy becomes less and ROMS work more long.

[jcwarner]

i am looking at the ocean_his.nc file.
There are no values for the x,y, lon, or lat, so I con only pcolor the values of the arrays, not in any spatial sense.
One of the problems is that the wave heigths are rather large, especially in the shallow areas. Typically the ration of Hwave/depth ~ 0.8 maximum (or so). Since you specificy a const Hwave of 2 m, that value is rather large in the shallow regions. So you say that it runs longer when Hwave is reduced. Try Hwave = 0.2 m to start, just to see if it runs.
then we can step to the next problem.

[fancer]

Ok, I run app with Hwave 0.2 and he work fine with small kinetic energy. Kinetic energy fluctuates, but the tendency growing.
What can I do with SWAN, because const wave is bad way for research my region?
ps I had suspicions towards height of a wave about coast))

[fancer]

my app blowing up after 5 records in history file after every 360 steps((((

[jcwarner]

getting there.
try running it with
#undef SED_MORPH

[fancer]

Again blowing up((((

I have noticed the tendency:
At first kinetic energy fluctuates, is then levelled and starts to grow, but then again starts to fluctuate (((

[fancer]

easygrid displayed:
COPY-PASTE the following parameters into your ocean.in file
----------------------------------------------------------------------------------------------


Lm == 40 ! Number of I-direction INTERIOR RHO-points
Mm == 164 ! Number of J-direction INTERIOR RHO-points
N == 20 ! Number of vertical levels


Make sure the Baroclinic time-step (DT) in your ocean.in file is less than: 2.3146 seconds

Can ROMS fall because a time step more than the specified? My dt=20.

[fancer]

At dt=2.3 ROMS falls in 2.5 hours of real time((((

[jcwarner]

well, here is when you need to take the reigns of the horse and start to go down the trail. I am trying to show you some guidance of how to do these things. So if it now runs for 3 hours , then start to save the his file every 10 minutes and that will give you 18 steps to look at and start to get a feel for what is happening in the sytsem. When it blows up, look at that loast itme step in the restart file. What is happening. You need to dig in here.

[fancer]

But what can I do with SWAN and did You see my swan_seashore.in file?

ps and ncview can't open restart file((((

[jcwarner]

i am not sure why ncview can not open restart file.
Do you use matlab?

For SWAN - do you know how to develop a coupled roms-swan application?
It would be best to look at the INLET_TEST as an example.

[fancer]

I have made all as in Inlet_test, could You check up in first my post?

ps Inlet test exit with error too(((( :
Coupled Input File name = ./ROMS/External/ocean_inlet_test.in
rank 0 in job 4 host_53124 caused collective abort of all ranks
exit status of rank 0: return code 0

[mathieu]

The thing that is wrong with the application is the smoothing of the very high roughness. You had

Maximum grid stiffness ratios: rx0 = 9.926508E-01 (Beckmann and Haidvogel)
rx1 = 2.196218E+04 (Haney)

Those are incredibly large value. Maximum rx0 should be 0.2 and maximum rx1 should be 6. Above those values the situation is unstable and here it is the cause of the problem.
I would also advise you to check the masks: I recently had a similar problem caused by incoherent mask_u, mask_v mask_rho when using editmask.
If the issue is really bathymetry smoothing I have programs to do this, which is now much faster and available from my web site.

[fancer]

Hi, mathieu))
Thank You for your participation))
http://www.liga.ens.fr/~dutour/Bathymetry/index.html - is this Your web site with Your program?
ps I'm sorry, my english is bad)))
pss In GRID_SmoothPositive_ROMS_rx1.m :
If Vstretching == 1 need rewrite hc on ARVD.hc)))

[jacopo]

Hi all ROMS users!))))
Please, help me with my application for compute sediment transport in seashore with input real grid and forcing from SWAN.
I have installed MCT and have run his examples. All works well. When I start ROMS with mpif90, assign next error:

[xxx@host] roms3 # mpirun -np 2 ./oceanG ROMS/External/ocean_seashore.in
Coupled Input File name = ROMS/External/ocean_seashore.in
rank 0 in job 47 host_51380 caused collective abort of all ranks
exit status of rank 0: return code 0

in coupled applications you have to use coupling_ocean.in, not the ocean.in.
That's why you are not able to run the INLET test too.
These informations are available in ROMS website (somewhere)

[fancer]

Thanks very much to All: jacopo mathieu jcwarner for Your help)))
Two hours of estimated time ROMS works normally. Then the scheme begin to be shaken. It is visible from kinetic energy, then the scheme falls (((
But with smooth of grid ROMS work longer)))
rx0=1.2E-01
rx1=5.6E+00
I don't know what to do. Can somebody suggest?
What settings should I change?
With SWAN scheme blow up too((((

[fancer]

Blowing up with less time step(((
dt=4.
Before falling unreal parametres are observed, for example 148.879 kg/m3 suspended cohesive sediment(((
ps Oscillations begin around mid-calculated time(((

In ubar next :

[fancer]

What can be it??? (With dt=40)

60 0 00:40:00 4.231106E-03 3.573977E+01 3.574400E+01 3.072280E+07
61 0 00:40:40 1.664284+150 NaN NaN -6.095703E+51

Blowing-up: Saving latest model state into RESTART file

[fancer]

In ubar inf (with dt=40):
1.0e+66 *
...
NaN NaN NaN NaN NaN 0.0000 0.0000 0.0000
NaN NaN NaN NaN 0.0000 0.0000 0.0000 -0.0000
NaN NaN NaN NaN 0.0000 -0.0000 -0.0000 -0.0000
NaN NaN NaN NaN 0.0000 0.0000 -0.0000 -0.0000
NaN NaN NaN NaN -0.0000 -0.0000 -0.0000 -0.0000
NaN NaN NaN NaN 0.0000 0.0000 -0.0000 -0.0000
NaN NaN NaN NaN 0.0000 0.0000 0.0000 0.0000
NaN NaN NaN NaN -0.0000 0.0000 -0.0000 0.0000
NaN NaN NaN NaN 0.0000 -0.0000 0.0000 0.0000
NaN NaN NaN NaN -0.0000 -0.0000 -0.0000 0.0000
NaN NaN NaN NaN 0 -0.0000 0.0000 0.0000
NaN NaN NaN NaN 0 0 -0.0000 -0.0000
NaN NaN NaN -0.0000 0.0000 0.0000 0 -0.0000
NaN NaN NaN -0.0000 0.0000 0.0000 0.0000 0
NaN NaN NaN 0.0974 0.0001 0.0000 0 0
NaN NaN NaN 0.9606 0.1708 0.0001 -0.0000 0
NaN NaN 6.6829 -6.5159 1.0553 0.0735 0.0001 0.0000
NaN NaN -1.0045 0.9921 0.1450 0.0002 -0.0287 -0.0000
NaN NaN -0.0706 0.0718 0.0001 0 0.0000 0
NaN NaN NaN -0.0000 0.0000 0.0000 0 0
NaN NaN NaN -0.0000 0.0000 -0.0000 0.0000 -0.0000
NaN NaN NaN 0.0000 0.0000 0.0000 0 0.0000
NaN NaN NaN -0.0000 0.0000 0 0.0000 -0.0000
NaN NaN NaN 0.0000 0 0.0000 -0.0000 0.0000
NaN NaN NaN -0.0000 0.0000 -0.0000 -0.0000 0.0000
NaN NaN NaN NaN -0.0000 -0.0000 0.0000 0.0000
NaN NaN NaN NaN 0.0000 -0.0000 -0.0000 0.0000
NaN NaN NaN NaN 0.0000 -0.0000 0.0000 0.0000
NaN NaN NaN NaN 0.0000 -0.0000 0.0000 0.0000
NaN NaN NaN NaN -0.0000 -0.0000 -0.0000 0.0000
NaN NaN NaN NaN -0.0000 -0.0000 -0.0000 -0.0000
NaN NaN NaN NaN -0.0000 -0.0000 -0.0000 -0.0000
NaN NaN NaN NaN -0.0000 -0.0000 -0.0000 -0.0000
NaN NaN NaN NaN -0.0000 -0.0000 -0.0000 -0.0000
NaN NaN NaN NaN -0.0000 -0.0000 -0.0000 -0.0000
...
With vbar, zeta this too))) Zeta should be zero ashore?

[jcwarner]

i am trying to help but you are going to have to do some things here.
The last restart file was for dt=10, and the figures you posted are for dt =40. Looks like you are trying different things. With a dt of 40, the Courant number is real close to 1. Lets lower that a little to make sure we stay away from problems.
Try this:
dt = 30
ndtfast =30
Run it.
Set the history file so that when it blows up, there is at least 10 steps in the history file.
So if it blows at 60 steps, then set nhis = 10.
Set the nrst to be the same as nhis.
post those files when it dies.

[mathieu]

Dear fancer, thank you for bug report. I corrected my program.
Otherwise, for your problem, look at the following:

• --Your maximum barotropic number is about 0.958 which is almost at the limit of 1. Try running with a reduced dt and a value of 0.2 for maximum barotropic.
  --Try to get a running system with as few fancy option as possible: disable waves and sediment and see if it works now.
  --Some time ago, I experienced problem with ifort compiler which was introducing some numerical error. Try with a different compiler and see if problems occur.
  --Your initial state has maybe too strong variability of temperature and salinity, which cause some initial large currents for correction. One solution to this problem is to run your application with no forcing in order to smooth things out.

[fancer]

Hi, sorry for the delay)))
Now dt=20 dtfast=50 and max Courant number is 1.91612862E-01. But scheme still blowing up(((
I can not upload the history file because it is too large (106 MB), but I can upload picture with necessary data.
For example:
Ubar (from history) 8 step:

ubar history 8

ubar_nhis_8.png (13.99 KiB) Viewed 40707 times

Ubar (from history) 9 step:

ubar history 9

ubar_nhis_9.png (14.32 KiB) Viewed 40708 times

Ubar (from restart) 10 step:

ubar restart 1

ubar_1.png (14.34 KiB) Viewed 40707 times

Ubar (from restart) 11 step:

ubar restart 2

ubar_2.png (14.78 KiB) Viewed 40704 times

Ubar (from restart) last step:

ubar restart 3

ubar_3.png (14.26 KiB) Viewed 40705 times

And Sxx(Sxy, Syy) starts fluctuate:
Sxx (from history) 9 step:

Sxx history 9

Sxx_9.png (21.44 KiB) Viewed 40705 times

Sxx (from history) 10 step:

Sxx history 10

Sxx_10.png (21.07 KiB) Viewed 40704 times

Sxx (from history) 11 step:

Sxx history 11

Sxx_11.png (21.57 KiB) Viewed 40705 times

My restart and log file attached next.

seashore_ocean_rst.nc

Restart file

(35.95 MiB) Downloaded 701 times

seashore.log

Log file

(71.08 KiB) Downloaded 511 times

[fancer]

and sand_01:
Near the bottom (from restart):

Sand_01 restart 11 (bottom)

sand_01_1.png (8.25 KiB) Viewed 40748 times

On a surface (from restart):

Sand_01 restart 11 (surface)

sand_01_20.png (11.61 KiB) Viewed 40744 times

[jacopo]

in addition to Mathieu's list, using k-epsilon can cause instabilities. try out something else (MY2.5, k-w) or use half the timestep

[fancer]

1) I'm run the application without forcing app work for 12 hours of estimated time: Lwave=0.0_r8 Hwave=0.0_r8. but scheme blowing up((
2) I'm run the application without sediment: undef sediment, undef ana_sediment, define UV_QDRAG, undef SSW_BBL.
3) I'm run the application without sediment and forcing: for this case kinetic energy begin fluctuate too, then blow up(((

seashore.log

Wihout wwave and sediment

(203.66 KiB) Downloaded 476 times

4) I'm compile the program with gfortran and mpif90, but application blowing up in both cases(((
5) temp=10, and salt=0 - Is this contrary?

For my application almost all parameters such us in INLET_TEST. Except dt, dtfast, Hwave=0.2 m, Lwave=2 m, Dwave=135 degrees, my grid file.
A don't understand why kinetic energy begin fluctuate? Do I have anything to correct in the ocean_seashore.in file?

[fancer]

Whether it is necessary to declare NORTHERN_WALL if a land along northern border?

With options for the Mellor/Yamada level 2.5 closure app blow up too(((

With options for K-profile vertical mixing parameterization app blow up too(((

[fancer]

In my application fsobc was setup how in INLET_TEST:
# ifdef EAST_FSOBC
IF (EASTERN_EDGE) THEN
cff=-1.0_r8*sin(2.0_r8*pi*time(ng)/(12.0_r8*3600.0_r8))
DO j=JstrR,JendR
BOUNDARY(ng)%zeta_east(j)=cff
END DO
END IF
# endif
Now I'm change this on:
# ifdef EAST_FSOBC
IF (EASTERN_EDGE) THEN
cff=tan(1.0_r8/(time(ng)+3600))
DO j=JstrR,JendR
BOUNDARY(ng)%zeta_east(j)=cff
END DO
END IF
# endif
And now ROMS work 4 hours estimated time and continues to work)) I don't know why ROMS blew up with previous boundary conditions)))

[mathieu]

Ok, so it is not compiler.
What I would do in your place is:

• --Disable NEARSHORE_MELLOR, this radiation stress can be large and has some problems.
  --Do not use waves. I am not sure what you mean with Lwave=0.0 but if it means constant values of Lwave and Hwave in your ocean_frc.nc file then it is maybe not a good idea. The philosopphy should be to start with a simple setting and then complexify it.
  --Use UV_LOGDRAG instead of UV_QDRAG, the form of the stress is still quadratic but the value of the coefficient is then based on the physical basis of similarity theory.
  --Change the boundary parameterization: The boundary condition can create problems, even in region far from the boundary. A better combination is FSCHAPMAN and M2FLATHER, see elsewhere in the forum.

[fancer]

--I already run ROMS with FSCHAPMAN and M2FLATHER boundary conditions and app blew up on 3th hours of estimated time.
--About Lwave... Yes, I have written nonsense)))) I do not have ocean_frc.nc file, therefore I use analytical values or SWAN. I'm define ana_wwave and set this values in ana_wwave.h. If I set undef ANA_WWAVE then compiler give me error: "I can't find ocean_frc.nc." If undef NEARSHORE_MELLOR then compiler write: "I don't know Hwave and Lwave"))) Should I undef that and another?
--I think (look at my prev post) what problem with stability was from EAST fsobc))

About other points I will write a bit later, then ROMS end to work.

[fancer]

Thanks to All: mr. jcwarner, mr. jacopo especially mr. mathieu!)))
Now I set 0.0 on fsobc and define FSCHAPMAN and M2FLATHER for boundary and ROMS work very long)))
Once again many thanks to all for the help))) and many thanks for the ROMS!!!))))
A question about SWAN:
I maked all how in INLET_TEST. But my coupling app blowing up. Here my swan_seashore.in, seashore_ocean_his.nc.

[feroda]

You may want to pay special attention to your water/land mask.