swan+roms test

[fereshteh]

Dear
For inlet test I have updates its files as suggested in forum. I could compile it but for running, some errors appear. forum has been checked for solving them but its suggestions (for example set 1 cpu for swan) cannot help me therefore I send .log file contains created after run command:

Code: Select all

$ Mpirun –np 8 ./oceanG coupling_inlet_test.in>run.log

(for Ntilei=2 Ntilej=2 Nthreads(oceans0=4) and Nthreads (waves)=4)


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 12, 2013 - 5:00:00 PM
-----------------------------------------------------------------------------

Inlet Test Case
Operating system : Linux
CPU/hardware : i686
Compiler system : gfortran
Compiler command : /home/fkomijani/mpich2/bin/mpif90
Compiler flags : -frepack-arrays -g -fbounds-check -I/home/fkomijani/MCT/include -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none
Input Script : /home/fkomijani/projects/INLET_test/inlet_test/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/INLET_test/inlet_test
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/INLET_test/inlet_test/ocean_inlet_test.in
Input Grid File: /home/fkomijani/projects//INLET_test/inlet_test/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_MELLOR05 Nearshore Radiation Stress Terms (Mellor 2005).
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.

CHECKDEFS - only one radiation stress formulation is allowed.
Elapsed CPU time (seconds):
ROMS/TOMS - Output NetCDF summary for Grid 01:

ROMS/TOMS - Configuration error ..... exit_flag: 5
ERROR: Illegal model configuration.

as you can see there is not any thing that shows swan model is computing.
And also in linux shell this error appears:
MCT::m_MCTWorld::clean_: deallocate(MCTW,...) error, stat =2
That MCT_world.mod located in mct/include directory.
And I get Terminating error: Inputfile missing Message in PRINT and Errfile files.
i need your experience to sort out what cause these problems.
thanks in advance for your attention and guidance
cheers
fereshte

[redhat007]

dear
i can solve above problem ( ) by
#define nearshore_mellor08
inlet test is running from 2 days ago .
would you please tell me estimated time for this test when use 8 processors.
Is there any way that while it is running, i find that every thing is OK.
thank you
fereshte

[fereshteh]

dear all
in inlet test, after solving some errors which appear in Print_xx files and Errofile_xx files, now mentioned test is running but again some empty Print_xx files and Errofile_xx files created in project directory while linux shell shows model is still running.
i check created .log file. End of it shows nodes for ocean model are active but there is not any thing about swan nodes. i set 4 cpu for swan test
Process Information
node # 0 (pid= 2055) is active
node # 2 (pid= 2075) is active
node # 1 (pid= 2055) is active
node # 3 (pid= 2055) is active
but after 2 weeks running does not finished also no thing change.
it seems that model running has problem. would you please help me find what is the problem?
also is there any command which shows processes when model is running?
all the best
fereshte

[jcwarner]

how about trying it with just one proc for roms, and one for swan.
that job should only take about 20 minutes to run, or something like that. the ocean_his.nc should be written to, and you would see output immediately. IF you are getting Err* files, then there is something wrong with SWAN. most likely it can not find the bathy.bot or grd file.

[fereshteh]

dear Warner
At first thanks for your suggestion . i use it and set
Ntilei=1, Ntilej=1 ,Nthreads (ocean)=1 and Nthreads (waves)=1
but in every run which 1 cpu set for swan model (in this example:also 1 procc for ocean model) it reply

Code: Select all

mpirun -np 2 ./oceanG coupling_inlet-test.in>mpi.log 
application called MPI_Abort(comm=0x84000002, 4) - process 0

and in Errorfile and print files, input file missing error appears.
those problems happen when ever 1 cpu set for swan while different number set for ocean model ( 1 to 4)
it is necessary to say that i bring out _coor.grd and _bathy.bot files from Data folder and put them beside swan_inlet_test.in, then in READGRID and READINP portions, just call those file's names, respectively.
i don't have idea how can solve this error therefore i request you guide me.
all the best
fereshte

[jafar1979]

dear Warner
i am sure that MPICH2 (release 1.4.1p1 )installation was correct

Code: Select all

/configure FC=gfortran CC=gcc  --prefix=/home/<user>/mpich2_install_new 2>&1 |tee c.txt
make 2>&1 |tee m.txt
make install  2>&1 |tee mi.txt

because i was able to run upwelling test in parallel mode successfully.
and about MCT i do
export USE_MPI=on # distributed-memory parallelism
export USE_MPIF90=on # compile with mpif90 script
#export which_MPI=mpich # compile with MPICH library
export which_MPI=mpich2 # compile with MPICH2 library
#export which_MPI=openmpi
.
.
.
if [ -n "${USE_MPI:+1}" ]; then
if [ "${which_MPI}" = "mpich2" ]; then
export ESMF_DIR=/opt/gfortransoft/mpich2/esmf
##export MCT_INCDIR=/opt/gfortransoft/mpich2/mct/include
##export MCT_LIBDIR=/opt/gfortransoft/mpich2/mct/lib
export MCT_INCDIR=/home/fkomijani/MCT_install/include
export MCT_LIBDIR=/home/fkomijani/MCT_install/lib
in build.bash file and
ifdef USE_MCT
MCT_INCDIR ?= /home/fkomijani/MCT_install/include
MCT_LIBDIR ?= /home/fkomijani/MCT_install/lib
FFLAGS += -I$(MCT_INCDIR)
LIBS += -L$(MCT_LIBDIR) -lmct -lmpeu
in linux_gfortran.mk file.
also read all posts about inlet test. but i dont know what is the problem.
would you please help me to sort out it.
thanks in advance
all the best
fereshte

[jcwarner]

i think you mean:
mpirun -np 2 ./oceanG coupling_inlet_test.in>mpi.log
( undescores in the input file name, not dash -)

If you move the files, then you need to tell it the new paths. I have not run the test case as distributed by Rutgers lately. But you should just follow the input files.
It first points to the coupling_inlet_test.in
In that file, it should list the paths to the ocn and wav input files. in those files they list the paths to the grids etc. the way i had it set up, you would not have needed to move any files.

check the paths to the files and see if they are correct. is there anything in the PRINT or ERR* files?

[jafar1979]

hi
i guess that bug in mpich2 release 1.4.1p1 cause above problem, therefore i installed release 3.0.4 but it can not help me. as i told before when more that 1 cpu used for swan, PRINT or ERR* files are empty but when 1 cpu used for it, there is input file missing error in those files and in terminal page

Code: Select all

application called MPI_Abort(comm=0x84000002, 4) - process 0

arise.
about input files change:
swan_inlet_test.in keeps with out any changes.
in couplig_inlet_test changes are as: 1-INPname(ocean)=/home/..../test/ocean_inlet_test.in 2- INPname(waves)=/home/..../test/swan-inlet-test.in 3-CLPname=/home/.../test/coupling.dat
in ocean_inlet_test.in changes are as: 1- VARNAME=/home/.../test/varinfo.dat 2- GRDNAME=/home/.../test/inlet_test_grid.nc
as well as some changes in build.bash file for MCT requested path, USE_MPI,USE_MPIF90,mpich2 and so on.
with regard this post what you think about reason of this problem?
thanks

[jcwarner]

if the Err and Print files have errors, then the errors are with swan, not roms.
did you relly have the swan input file listed as
2- INPname(waves)=/home/..../test/swan-inlet-test.in
or
2- INPname(waves)=/home/..../test/swan_inlet_test.in

is that the real path, all those dots?
sometimes swan does not like the path name to be more than 72 characters.
-j

[jafar1979]

Dear Warner
many many thanks
i can not believe that my fault is long path name. now Swan is preparing computation. but recent error is:
at line 420 of file ocpids.f90
Fortran runtime error:actual string length is shorter than the declared one for dummy argument 'timstr' (15/24)
base on NTIMES=34560, DT=5 s ocean model run time is 2 days. and base on swan model' s input, this model run for 25 days. 20000101 25 DAY 20000126
does following error appear for this different run times? but why after modifing swan run time for 2 days, this error arise again
thanks again for your attention

[jafar1979]

dear Warner
about my last post:

At line 420 of file ocpids.f90
Fortran runtime error: Actual string length is shorter than the declared one for dummy argument 'timstr' (15/24)

swan model break when it what to give current from ROMS model.
i check ocpids.f90 file (and ocpids.F) it includes :

Code: Select all

  --------Fortran 90 date-time routines --------

  CHARACTER TIMSTR *24, CDUMMY *5                                     30.82
      INTEGER   IDUMMY(8)                                                 30.82
      CALL DATE_AND_TIME (TIMSTR(1:8), TIMSTR(10:20), CDUMMY, IDUMMY)     30.70
:     CALL DTSTTI (1, TIMSTR, PRCTIM)                                     30.70
      RETURN
      END SUBROUTINE OCDTIM
!*****************************************************************                                                               
 line420:     SUBROUTINE DTSTTI (IOPT, TIMSTR, DTTIME)
!                                             

which this information taken from ocpids.F that located in Trunk/Waves/SWAN/Src .it seem that timstr length in SWAN and ROMS model are not equal. as you can see its length in SWAN model is 24 and in ROMS model is 15 (base on above error message). at first i tried to set timstr to 15 length but with regard that it called in different function it can help me.
Now would you pleas give me an idea to fix this error
thanks in advance

[jcwarner]

i remember this error, and it has been corrected in future versions of swan. If you really want to do roms+swan coupling, perhaps you could use our coawst system which has an updated version of swan, and vortex force instead of mellor method, grid refinement in swan, etc. send me an email at
jcwarner@usgs.gov
and i can set you up.
-john

[m567tej]

dear fereshteh
Do you have any change into roms grid file and make swan files again or no? I ran all four INLET_Test cases without any error. As Warner said, try to run them by 1 processor for ROMS and 1 processor for SWAN. In general, the coupled model can be run only when your number of processor are equal to number of grids*sub_models. Although you can use an unlimited number of processors when you run only ROMS. If you want to run a coupled model with more processors, make mosaic sub-grids and then make swan files for each sub_grid again.

[jafar1979]

dear m567tej
thanks for your kindly reply.
actually i used 1 processor for ROMS and 1 processor for SWAN but that error appear. also i did not make change into ROMS grid file.
i think you use COAWST which has SWAN40.91. is not it? because as Warner said in Rutgers version (SWAN40.51) there is such error

it has been corrected in future versions of swan

thanks