[mpich-discuss] coupling
fereshteh komijani
fereshtehkomijani at gmail.com
Sun Oct 27 05:33:54 CDT 2013
Sure.
ROMS and SWAN models are models for ocean and wave models, respectively.
Coupling of them require 3 input files: coupling_test.in, swan_test.in and
roms_test.in which first one is coupled input file and also one build.bash
file which in it user called requested libraries, cpp optins, header file,
compilers (for me gcc and gfortran). For example in build.bash file I set
USE_MPI=on = on
USE_MPIF90 =on
WHICH_MPI=mpich2
FORT = gfortran
also with regard that for coupling model, MCT (model coupling toolkit)
is necessary I have installed it and set its include and lib directories
in build.bash file.
In coupling_test.in user call swan_test.in and roms_test.in as wave and
ocean model's inputs.
In roms_test.in some coefficients, solving technique and some input forcing
file determined.
for choosing number of nodes for each model there are NtileI and Ntilej in
roms_test.in and Nthreads (ocean) and Nthreads (wave) in
coupling_test.infile ( Nthreads (ocean)=NtileI *Ntilej )
and total nodes are equal to Nthreads (ocean)+Nthreads (wave).
whenever i set one node for wave model (SWAN) (Nthreads (wave)=1) after
running by
mpirun -np 2 ./oceanG coupling_inlet-test.in>mpi.log
it replies:
application called MPI_Abort(comm=0x84000002, 4) - process 0
But when set Nthreads (wave)>1 (and everything for Nthreads (ocean)) for
example
mpirun -np 8 ./oceanG coupling_inlet-test.in>mpi.log
mpi.log file (attaché file) shows that roms model does not have problems
and its nodes are active but nothing happen for swan model after 2 weeks
than running.
I hope that this information be sufficient.
All the best
fereshte
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? Coupled Input File name = coupling_inlet_test.in
Model Coupling Parallel Threads:
Ocean Model MPI nodes: 000 - 003
Waves Model MPI nodes: 004 - 007
Ocean Export: bath:SSH:Ubar:Vbar:ZO
Waves Export: Wdir:Wamp:Wlen:Wptop:Wpbot:Wubot
Model Input Parameters: ROMS/TOMS version 3.6
Sunday - October 13, 2013 - 1:02:55 PM
-----------------------------------------------------------------------------
Inlet Test Case
Operating system : Linux
CPU/hardware : i686
Compiler system : gfortran
Compiler command : /home/fkomijani/mpich2_install_new/bin/mpif90
Compiler flags : -frepack-arrays -g -fbounds-check -I/home/fkomijani/MCT_install/include -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none
Input Script : /home/fkomijani/projects/my_test/INLET_test/inlet_test_4/ocean_inlet_test.in
SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : exported
Local Root : /home/fkomijani/ROMS/TRUNK
Header Dir : /home/fkomijani/projects/my_test/INLET_test/inlet_test_4
Header file : inlet_test.h
Analytical Dir: /home/fkomijani/ROMS/TRUNK/ROMS/Functionals
Resolution, Grid 01: 0075x0070x008, Parallel Nodes: 4, Tiling: 002x002
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: /home/fkomijani/projects/my_test/INLET_test/inlet_test_4/ocean_inlet_test.in
Input Grid File: /home/fkomijani/projects/my_test/INLET_test/inlet_test_4/inlet_test_grid.nc
Tile partition information for Grid 01: 0075x0070x0008 tiling: 002x002
tile Istr Iend Jstr Jend Npts
0 1 38 1 35 10640
1 39 75 1 35 10360
2 1 38 36 70 10640
3 39 75 36 70 10360
Tile minimum and maximum fractional grid coordinates:
(interior points only)
tile Xmin Xmax Ymin Ymax grid
0 0.50 38.50 0.50 35.50 RHO-points
1 38.50 75.50 0.50 35.50 RHO-points
2 0.50 38.50 35.50 70.50 RHO-points
3 38.50 75.50 35.50 70.50 RHO-points
0 1.00 38.50 0.50 35.50 U-points
1 38.50 75.00 0.50 35.50 U-points
2 1.00 38.50 35.50 70.50 U-points
3 38.50 75.00 35.50 70.50 U-points
0 0.50 38.50 1.00 35.50 V-points
1 38.50 75.50 1.00 35.50 V-points
2 0.50 38.50 35.50 70.00 V-points
3 38.50 75.50 35.50 70.00 V-points
Maximum halo size in XI and ETA directions:
HaloSizeI(1) = 150
HaloSizeJ(1) = 144
TileSide(1) = 44
TileSize(1) = 1848
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_MELLOR08 Nearshore Radiation Stress Terms (Mellor 2008).
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= 11842) is active.
Node # 3 (pid= 11845) is active.
Node # 1 (pid= 11843) is active.
Node # 2 (pid= 11844) is active.
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