About the TEST_HEAD case

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

About the TEST_HEAD case

#1 Post by liangliang » Fri Jan 01, 2010 2:07 pm

Dear everyone:
Happy new year!
Now i try to run the TEST_HEAD case,i know that it is a case of coupling between roms and swan.I have installed the MCT and MPI,and then i want to install the ARPACK lib,but i have a trouble in compling it.I want to ask whether the version of MPI is specified,or the MPICH2 is better? And for the TEST_HEAD,is the ARPACK essential? under what condition is the ARPACK is essential ?
Thank you !

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

Re: About the TEST_HEAD case

#2 Post by liangliang » Mon Jan 04, 2010 3:51 am

Everyone:
Hello!
I have succeeded in compiling the case of TEST_HEAD without ARPACK and created the "oceanM".
And then ,when I ran the model,i writed the command line "mpirun -np 2 oceanM coupling_test_head.in",
but the result is only one line "coupled input file = coupling_test_head.in",then it's over,without any other error information.
whether is my command line wrong? It's my first to run the coupling model,please help me!
Thank you !

jcwarner
Posts: 869
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: About the TEST_HEAD case

#3 Post by jcwarner » Mon Jan 04, 2010 3:54 am

did you give the full location of the coupling file?
did swan create any files?
were there any error or output files created?

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

Re: About the TEST_HEAD case

#4 Post by liangliang » Mon Jan 04, 2010 1:34 pm

jcwarner:
Thank you very much! You are right,my input file's location is wrong.
but after i corrected the location,the model still didn't run.The difference is that it created some files
Now ,my computer is a two-kernel PC,and i have installed MCT and MPI,which have been tested.


next is the information on the screen:
root@c12:/home/roms/projects/TEST_HEAD# mpirun -np 2 oceanM coupling_test_head.in
root@localhost's password:
Coupled Input File name = coupling_test_head.in

Model Coupling Parallel Threads:

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


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


Process Information:

Node # 0 (pid= 3127) is active.

Model Input Parameters: ROMS/TOMS version 3.2
Monday - January 4, 2010 - 7:03:30 PM
-----------------------------------------------------------------------------
p1_3133: p4_error: : 4
rm_l_1_3136: (0.030020) net_send: could not write to fd=5, errno = 32
[1] MPI Abort by user Aborting program !
[1] Aborting program!
p1_3133: (0.030660) net_send: could not write to fd=5, errno = 32



next is the information in the "log" file:
bm_list_25268: p4_error: interrupt SIGx: 1
p0_25267: p4_error: Timeout in making connection to remote process on localhost: 0
p0_25267: (151314.414767) net_send: could not write to fd=4, errno = 32



next is the information in the "PI1585" file:
c12 0 /home/roms/projects/TEST_HEAD/oceanM
localhost 1 /home/roms/projects/TEST_HEAD/oceanM



Besides there are 3 files created by SWAN: "PRINT"、"Errfile"、"swanint"

the "Errfile" say 'Terminating error: Input file missing'.
I think that swan is no problem .The "Input file missing" should result from the abnormal end of roms.

jcwarner
Posts: 869
Joined: Wed Dec 31, 2003 6:16 pm
Location: USGS, USA

Re: About the TEST_HEAD case

#5 Post by jcwarner » Mon Jan 04, 2010 2:56 pm

you need to be careful about the paths. When you go to run the program, you need to point to the coupling input file. That file has paths to the input files for roms and swan. Those paths need to be relative to the location of oceanM. Within the roms and swan input files, there are paths to their forcing files and output files. So check that all the paths are correct.

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

Re: About the TEST_HEAD case

#6 Post by liangliang » Tue Jan 05, 2010 6:45 am

jcwarner:
Thank you for your suggestion!
Before,i use the absolute path,which is wrong.now,i have changed the path relative to the oceanM.It is available.
But there are some other problems.
I think the program have read the input files,but i don't know what lead the program aborted.

The information on the screen is such as:
root@c12:/home/roms/trunk# mpirun -np 2 ./oceanM coupling_test_head.in
root@localhost's password:
Coupled Input File name = coupling_test_head.in

Model Coupling Parallel Threads:

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


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


Process Information:

Node # 0 (pid= 8611) is active.

Model Input Parameters: ROMS/TOMS version 3.2
Tuesday - January 5, 2010 - 11:09:42 AM
-----------------------------------------------------------------------------

Sediment Test Headland Case

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

Input Script : ocean_test_head.in

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

Local Root : /home/roms/trunk
Header Dir : /home/roms/projects/TEST_HEAD
Header file : test_head.h
Analytical Dir: /home/roms/trunk/ROMS/Functionals

Resolution, Grid 01: 0056x0026x010, Parallel Nodes: 1, Tiling: 001x001


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

1440 ntimes Number of timesteps for 3-D equations.
30.000 dt Timestep size (s) for 3-D equations.
20 ndtfast Number of timesteps for 2-D equations between
each 3D timestep.

(……………………elide)

Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Physical parameters File: ocean_test_head.in
Input Grid File: test_head_curv_grd.nc
Input Nonlinear Initial File: test_head_ini.nc

Tile partition information for Grid 01: 0056x0026x0010 tiling: 001x001

tile Istr Iend Jstr Jend Npts

0 1 56 1 26 14560

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 56.50 0.50 26.50 RHO-points

0 1.00 56.00 0.50 26.50 U-points

0 0.50 56.50 1.00 26.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = HaloSizeI(1) = 201p1_8619: p4_error: : 172879
rm_l_1_8622: (0.081741) net_send: could not write to fd=5, errno = 32
p1_8619: (0.082079) net_send: could not write to fd=5, errno = 32



SWAN is preparing computation ...

1 - <NO ERROR MESSAGE> : Could not convert index -1082024444 into a pointer
The index may be an incorrect argument.
Possible sources of this problem are a missing "include 'mpif.h'",
a misspelled MPI object (e.g., MPI_COM_WORLD instead of MPI_COMM_WORLD)
or a misspelled user variable for an MPI object (e.g.,
com instead of comm).
[1] Aborting program !
[1] Aborting program!
MCT::m_MCTWorld::initm_: MP_comm_size() error, "Communicator argument is not a valid communicator
Special bit pattern 6 in communicator is incorrect. May indicate an
out-of-o"
001.MCT(MPEU)::die.: from MCT::m_MCTWorld::initm_()
MCT::m_MCTWorld::initm_: MP_comm_rank() error, "Communicator argument is not a valid communicator
Special bit pattern 6 in communicator is incorrect. May indicate an
out-of-o"
001.MCT(MPEU)::die.: from MCT::m_MCTWorld::initm_()
MCT::m_MCTWorld::initm_: MPI_SEND(mysize) error, "Communicator argument is not a valid communicator
Special bit pattern 6 in communicator is incorrect. May indicate an
out-of-o"
001.MCT(MPEU)::die.: from MCT::m_MCTWorld::initm_()
MCT::m_MCTWorld::initm_: MPI_SEND(Gprocids) error, "Communicator argument is not a valid communicator
Special bit pattern 6 in communicator is incorrect. May indicate an
out-of-o"
001.MCT(MPEU)::die.: from MCT::m_MCTWorld::initm_()
MCT::m_MCTWorld::initr_: MP_comm_size() error, "Communicator argument is not a valid communicator
Special bit pattern 6 in communicator is incorrect. May indicate an
out-of-o"
001.MCT(MPEU)::die.: from MCT::m_MCTWorld::initr_()
MCT::m_MCTWorld::initr_: MP_comm_rank() error, "Communicator argument is not a valid communicator
Special bit pattern 6 in communicator is incorrect. May indicate an
out-of-o"
001.MCT(MPEU)::die.: from MCT::m_MCTWorld::initr_()
MCT::m_MCTWorld::initr_: MP_comm_dup() error, "Invalid communicator"
001.MCT(MPEU)::die.: from MCT::m_MCTWorld::initr_()



Sometimes,the information on the screen is also like this:

root@c12:/home/roms/trunk# mpirun -np 2 ./oceanM coupling_test_head.in
root@localhost's password:
Coupled Input File name = coupling_test_head.in

Model Coupling Parallel Threads:

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


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


Process Information:

Node # 0 (pid= 8700) is active.

Model Input Parameters: ROMS/TOMS version 3.2
Tuesday - January 5, 2010 - 11:10:17 AM
-----------------------------------------------------------------------------

Sediment Test Headland Case

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

Input Script : ocean_test_head.in

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

Local Root : /home/roms/trunk
Header Dir : /home/roms/projects/TEST_HEAD
Header file : test_head.h
Analytical Dir: /home/roms/trunk/ROMS/Functionals

Resolution, Grid 01: 0056x0026x010, Parallel Nodes: 1, Tiling: 001x001


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

1440 ntimes Number of timesteps for 3-D equations.
30.000 dt Timestep size (s) for 3-D equations.
20 ndtfast Number of timesteps for 2-D equations between
each 3D timestep.

(…………………………………………elide)

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


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

1 2.5000E-01 0.0000E+00 2.6500E+03 3.0000E+01 5.0000E-04 9.0000E-01

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

1 1.9000E-01 6.0000E-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 = 0.50000E-01

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(idUbld) Write out bed load at U-points, sediment 01: bedload_Usand_01
T Hout(idVbld) Write out bed load at V-points, sediment 01: bedload_Vsand_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
T Hout(idSbed) Write out BED property 04: bed_biodiff

Activated C-preprocessing Options:

TEST_HEAD Sediment Test Headland 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_M2OBC Analytical 2D momentum boundary 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.
BEDLOAD_MPM Activate bed load sediment transport Meyer-Peter-Mueller.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EAST_FSCLAMPED Eastern edge, free-surface, Clamped condition.
EAST_M2REDUCED Eastern edge, 2D momentum, reduced-physics condition.
EAST_M3RADIATION Eastern edge, 3D momentum, radiation condition.
EAST_TGRADIENT Eastern edge, tracers, gradient condition.
FSOBC_REDUCED Using free-surface data in reduced physics condtions
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
MCT_LIB Using Model Coupling Toolkit library.
MPI MPI distributed-memory configuration.
MY25_MIXING Mellor/Yamada Level-2.5 mixing closure.
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.
OUT_DOUBLE Double precision output fields in NetCDF files.
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.
SOUTHERN_WALL Wall boundary at Southern edge.
SPLINES Conservative parabolic spline reconstruction.
SSH_TIDES Add tidal elevation to SSH climatology.
SWAN_COUPLING Two-way SWAN/ROMS coupling.
THREE_GHOST Using three Ghost Points in halo regions.
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_LOGDRAG Logarithmic bottom stress.
UV_TIDES Add tidal currents to 2D momentum climatologies.
VAR_RHO_2D Variable density barotropic mode.
WAVES_OCEAN Two-way wave-ocean models coupling.
WEST_FSCLAMPED Western edge, free-surface, Clamped condition.
WEST_M2REDUCED Western edge, 2D momentum, reduced-physics condition.
WEST_M3RADIATION Western edge, 3D momentum, radiation condition.
WEST_TGRADIENT Western edge, tracers, gradient condition.
WET_DRY Wetting and drying activated.
0 - MPI_IRECV : Invalid count argument is -1209793328
[0] Aborting program !
[0] Aborting program!
p0_8700: p4_error: : 8258
p0_8700: (1.866909) net_send: could not write to fd=4, errno = 32
root@c12:/home/roms/trunk#


Besides,the swan created 'PRINT' and 'swanint' file,no Errfile.
the PRINT file is such as:
1

Execution started at 20100105.111017



---------------------------------------
SWAN
SIMULATION OF WAVES IN NEAR SHORE AREAS
VERSION NUMBER 40.51AB
---------------------------------------



PROJECT 'TEST HEAD' ''

'ocean_test_head test case to drive ROMS'

''

''



MODE NONSTATIONARY TWODIMENSIONAL

SET INRHOG 1 NAUTICAL

COORDINATES CARTESIAN



&& KEYWORDS TO CREATE AND READ COMPUTATIONAL GRID &&
CGRID CURVILINEAR 57 27 EXC 9.999000e+003 9.999000e+003 &
CIRCLE 36 0.04 1.0 30
Resolution in sigma-space: df/f = 0.1133

READGRID COORDINATES 1 'Waves/SWAN/External/test_head_curv_grid_coord.grd' 4 0 0 FREE



&& KEYWORDS TO CREATE AND READ BATHYMETRY GRID &&
INPGRID BOTTOM CURVILINEAR 0 0 57 27 EXC 9.999000e+003

READINP BOTTOM 1 'Waves/SWAN/External/test_head_curv_bathy.bot' 4 0 FREE



&& KEYWORD TO CREATE CURRENT GRID &&
INPGRID CURRENT CURVILINEAR 0 0 57 27 EXC 9.999000e+003 &
NONSTATIONARY 20030101.0000 30 DAY 20030131.0000



&& KEYWORD TO CREATE WATER LEVEL GRID &&
INPGRID WLEV CURVILINEAR 0 0 57 27 EXC 9.999000e+003 &
NONSTATIONARY 20030101.0000 30 DAY 20030131.0000



&& KEYWORD TO CREATE FRICTION LEVEL GRID &&
INPGRID FRIC CURVILINEAR 0 0 57 27 EXC 9.999000e+003 &
NONSTATIONARY 20030101.0000 30 DAY 20030131.0000



BOUNDPAR1 SHAPESPEC JONSWAP 3.3 PEAK DSPR DEGREES

BOUNDPAR2 SEGMENT IJ 0 27 57 27 CONSTANT PAR 2.0 10.0 0. 20.



& Restart name **********************************
&INIT HOTSTART 'swan_restart.dat'


& PHYSICS ****************************************
&BREAKING CONSTANT 1.0 0.73
FRICTION MADSEN 0.05

OFF QUAD

GEN3



PROP BSBT



BLOCK 'COMPGRID' NOHEADER 'depth.mat' LAY 4 DEPTH 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'dissip.mat' LAY 4 DISSIP 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'force.mat' LAY 4 FORCE 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'fric.mat' LAY 4 FRCOEEF 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'hsig.mat' LAY 4 HSIGN 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'rtp.mat' LAY 4 RTP 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'tm01.mat' LAY 4 TM01 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'setup.mat' LAY 4 SETUP 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'tmbot.mat' LAY 4 TMBOT 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'ubot.mat' LAY 4 UBOT 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'vel.mat' LAY 4 VEL 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'wdir.mat' LAY 4 DIR 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'wlen.mat' LAY 4 WLEN 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'xp.mat' LAY 4 XP 1. OUTPUT 20030101.000000 2 HR

BLOCK 'COMPGRID' NOHEADER 'yp.mat' LAY 4 YP 1. OUTPUT 20030101.000000 2 HR



COMPUTE NONSTAT 20030101.000000 120 SEC 20030101.120000
** Warning : Limiter is de-activated in case of no quadruplets

what dose the "Warning" mean?
And dose my MPI have problem ? why is the program aborted?

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

Re: About the TEST_HEAD case

#7 Post by liangliang » Wed Jan 06, 2010 4:44 pm

jcwarner:
I have succeeded in running the case of TEST_HEAD.
the problem is from MCT.When i install mct ,i use the mpi-serial and the real4double8.that is wrong.
Thanks for your help! Best wish to you!
besides,some variables in the "test_head_ini.nc" are wrong.

zhaoqian
Posts: 45
Joined: Tue Nov 11, 2008 5:45 pm
Location: National Marine Environmental Mornitoring Center

Re: About the TEST_HEAD case

#8 Post by zhaoqian » Thu Mar 11, 2010 7:56 am

Hi liangliang:
Is the variable Tcline? In ocean_test_head.in, it is 0.1 while in *.nc file it is very large.

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