Error about inlet test cae

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liangliang
Posts: 61
Joined: Mon Jul 20, 2009 2:41 pm
Location: Port And Costal Engineering Laboratory

Error about inlet test cae

#1 Post by liangliang » Sun Jan 13, 2013 1:50 am

Dear everyone:
I try to run the inlet test case ,I know that it is a case of coupling between roms and swan.
I have succeed compiling it . My platform is unbuntu 12.10 ,mpif90 gfortran mpich2 mct
When I want to run it ,I get an error ! Please help me ! Thank you !
next is the information on the screen


chenzhen@chenzhen-ThinkPad-T410:~/Projects/inlet_test$ mpiexec -np 4 ./oceanM coupling_inlet_test.in
Coupled Input File name = coupling_inlet_test.in



Model Coupling Parallel Threads:



Ocean Model MPI nodes: 000 - 001
Waves Model MPI nodes: 002 - 003


Ocean Export: bath:SSH:Ubar:Vbar:ZO
Waves Export: Wdir:Wamp:Wlen:Wptop:Wpbot:Wubot





Model Input Parameters: ROMS/TOMS version 3.6
Sunday - January 13, 2013 - 9:36:39 AM
-----------------------------------------------------------------------------

SWAN is preparing computation ...


Inlet Test Case

Operating system : Linux
CPU/hardware : i686
Compiler system : gfortran
Compiler command : /usr/bin/mpif90
Compiler flags : -frepack-arrays -O3 -ffast-math -I/home/chenzhen/ROMS/MCT/mct -I/home/chenzhen/ROMS/MCT/mpeu -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-

Input Script : ocean_inlet_test.in

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 643M

Local Root : /home/chenzhen/roms
Header Dir : /home/chenzhen/Projects/inlet_test
Header file : inlet_test.h
Analytical Dir: /home/chenzhen/Projects/inlet_test

Resolution, Grid 01: 0075x0070x008, Parallel Nodes: 2, Tiling: 002x001


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

34560 ntimes Number of timesteps for 3-D equations.
5.000 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 nl_visc2 NLM 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.
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.
10.000 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(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 wavelength.
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
Physical parameters File: ocean_inlet_test.in
Input Grid File: Data/inlet_test_grid.nc

Tile partition information for Grid 01: 0075x0070x0008 tiling: 002x001

tile Istr Iend Jstr Jend Npts

0 1 38 1 70 21280
1 39 75 1 70 20720

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 38.50 0.50 70.50 RHO-points
1 38.50 75.50 0.50 70.50 RHO-points

0 1.00 38.50 0.50 70.50 U-points
1 38.50 75.00 0.50 70.50 U-points

0 0.50 38.50 1.00 70.00 V-points
1 38.50 75.50 1.00 70.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 150
HaloSizeJ(1) = 243
TileSide(1) = 75
TileSize(1) = 3300



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

tau_ce tau_cd nl_tnu2 nl_tnu4 Akt_bak Tnudg
(N/m2) (N/m2) (m2/s) (m4/s) (m2/s) (day)

1 1.0000E-01 1.0000E-02 0.0000E+00 0.0000E+00 5.0000E-06 0.0000E+00

morph_fac
(nondim)

1 1.0000E+01

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: mud_01
T Hout(idfrac) Write out bed fraction, sediment 01: mudfrac_01
T Hout(idfrac) Write out mass, sediment 01: mudmass_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

Lateral Boundary Conditions: NLM
============================

Variable Grid West Edge South Edge East Edge North Edge
--------- ---- ---------- ---------- ---------- ----------

zeta 1 Gradient Closed Gradient Gradient

ubar 1 Gradient Closed Gradient Reduced

vbar 1 Gradient Closed Gradient Reduced

u 1 Gradient Closed Gradient Gradient

v 1 Gradient Closed Gradient Gradient

temp 1 Gradient Closed Gradient Gradient

salt 1 Gradient Closed Gradient Gradient

mud_01 1 Gradient Closed Gradient Gradient

tke 1 Gradient Closed Gradient Gradient

Activated C-preprocessing Options:

INLET_TEST Inlet Test Case
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.
ASSUMED_SHAPE Using assumed-shape arrays.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
FSOBC_REDUCED Using free-surface data in reduced physics conditions
GLS_MIXING Generic Length-Scale turbulence closure.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
MCT_LIB Using Model Coupling Toolkit library.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NEARSHORE_MELLOR05 Nearshore Radiation Stress Terms (Mellor 2005).
NONLINEAR Nonlinear Model.
!NONLIN_EOS Linear Equation of State for seawater.
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.
SPLINES Conservative parabolic spline reconstruction.
SSW_BBL Styles and Glenn Bottom Boundary Layer - modified.
SSW_CALC_ZNOT Internal computation of bottom roughness.
SWAN_COUPLING Two-way SWAN/ROMS coupling.
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.
WAVES_OCEAN Two-way wave-ocean models coupling.

Process Information:

Node # 0 (pid= 6492) is active.
Node # 1 (pid= 6493) is active.
Fatal error in MPI_Send: Invalid datatype, error stack:
MPI_Send(173): MPI_Send(buf=0xbfe64e78, count=1, INVALID DATATYPE, dest=0, tag=2, MPI_COMM_WORLD) failed
MPI_Send(111): Null Datatype pointer

liangliang
Posts: 61
Joined: Mon Jul 20, 2009 2:41 pm
Location: Port And Costal Engineering Laboratory

Re: Error about inlet test cae

#2 Post by liangliang » Tue Jan 15, 2013 1:23 am

I have succeed compiling it . My machine had mpich2 and openmpi before . And I uninstalled openmpi .
Then I compiled it again . Then I typed mpirun -np 4 ./oceanM coupling_inlet_test.in
It works well . It seems there is a conflict between mpich2 and openmpi .
But I still have a question about it .
If i type mpirun -np 4 ./oceanM coupling_inlet_test.in > & log &
The screen show -bash: syntax error near unexpected token `&'
But if I type mpirun -np 4 ./oceanM coupling_inlet_test.in ,it woks well .
Could you tell you why ?

User avatar
kate
Posts: 3798
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: Error about inlet test cae

#3 Post by kate » Tue Jan 15, 2013 7:17 pm

It is because some of us are so stuck in our ways as to be using a Unix shell in the csh family. Job redirection is different between the sh family (including bash) and the other family. In this statement:

Code: Select all

oceanM coupling_inlet_test.in > & log &
the first "&" sends the error output to the file log along with the standard output, while the second "&" puts the whole job into the background. The bash redirection is described here (search on "bash redirect stderr").

liangliang
Posts: 61
Joined: Mon Jul 20, 2009 2:41 pm
Location: Port And Costal Engineering Laboratory

Re: Error about inlet test cae

#4 Post by liangliang » Thu Jan 17, 2013 8:52 am

kate wrote:It is because some of us are so stuck in our ways as to be using a Unix shell in the csh family. Job redirection is different between the sh family (including bash) and the other family. In this statement:

Code: Select all

oceanM coupling_inlet_test.in > & log &
the first "&" sends the error output to the file log along with the standard output, while the second "&" puts the whole job into the background. The bash redirection is described here (search on "bash redirect stderr").
Thank you ! I have another question . i didn't succeed installing hdf5-1.8.6. So I installed netcdf4 without hdf5. And I didn't set NETCDF4 in build.bash(#export USE_NETCDF4=on).It seems works well in inlet test case. Then I want to couple roms with swan.Does it affect the result ?

User avatar
kate
Posts: 3798
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: Error about inlet test cae

#5 Post by kate » Thu Jan 17, 2013 5:26 pm

I can't say for SWAN, but the ROMS story is a little confusing. As it is now, USE_NETCDF4 means that the build system can count on the existence of nc-config (or perhaps it is sometimes nf-config). It can ask nc-config how to link things together, whether hdf is needed or not, whether -lnetcdff is needed or not, and so on. Therefore, you can USE_NETCDF4 even if your build didn't include HDF5.

Inside ROMS, there's a cppdefs of NETCDF4 - that one does need HDF5. It means to create NETCDF output in the new HDF5 format.

liangliang
Posts: 61
Joined: Mon Jul 20, 2009 2:41 pm
Location: Port And Costal Engineering Laboratory

Re: Error about inlet test cae

#6 Post by liangliang » Sun Jan 20, 2013 11:47 am

kate wrote:I can't say for SWAN, but the ROMS story is a little confusing. As it is now, USE_NETCDF4 means that the build system can count on the existence of nc-config (or perhaps it is sometimes nf-config). It can ask nc-config how to link things together, whether hdf is needed or not, whether -lnetcdff is needed or not, and so on. Therefore, you can USE_NETCDF4 even if your build didn't include HDF5.

Inside ROMS, there's a cppdefs of NETCDF4 - that one does need HDF5. It means to create NETCDF output in the new HDF5 format.
Thank you for your reply !

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