model terminates if 'DIAGNOSTICS_UV' is activated

[xwu]

Hi,all!

I run across this errors with a ROMS+SWAN coupled case. The case runs well if 'DIAGNOSTICS_UV' is unactivated. But once this cpp gets activated, the running terminates at the very beginning with the details shown as the following:

Coupled Input File name = Projects/Stormsrun/TS/Nest_TS/Factor7/bcf_coupling.in

Model Coupling:


Ocean Model MPI nodes: 000 - 001

Waves Model MPI nodes: 002 - 005

Model Input Parameters: ROMS/TOMS version 3.7
Friday - April 24, 2015 - 5:42:06 PM
-----------------------------------------------------------------------------

SWAN grid 1 is preparing computation


BCF TEST

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

Input Script :

SVN Root URL : https:://myroms.org/svn/src
SVN Revision : 889:931M

Local Root : /home/wxd/COAWST
Header Dir : /home/wxd/COAWST/Projects/Stormsrun/TS/Nest_TS/Factor7
Header file : bcf_test.h
Analytical Dir: /home/wxd/COAWST/Projects/Stormsrun/TS/Nest_TS/Factor7

Resolution, Grid 01: 0945x0210x004, Parallel Nodes: 2, Tiling: 002x001


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

33480 ntimes Number of timesteps for 3-D equations.
10.000 dt Timestep size (s) for 3-D equations.
10 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.
3480 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).
180 nHIS Number of timesteps between the writing fields
into history file.
31 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
180 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
1.0000E-01 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
F LuvSponge Turning OFF sponge on horizontal momentum.
F LtracerSponge(01) Turning OFF sponge on tracer 01: temp
F LtracerSponge(02) Turning OFF sponge on tracer 02: salt
1.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-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.
0.000 wec_alpha WEC factor for roller/breaking energy distribution.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
2.5000E-02 rdrg2 Quadratic bottom drag coefficient.
1.0000E-04 Zob Bottom roughness (m).
5.0000E-02 Zos Surface roughness (m).
1.0000E+00 Dcrit Minimum depth for wetting and drying (m).
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
3.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E-01 theta_b S-coordinate bottom control parameter.
50.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
53046.125 dstart Time-stamp assigned to model initialization (days).
18581124.00 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.
1.0000E+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).
F LuvSrc Turning OFF momentum point Sources/Sinks.
F LwSrc Turning OFF volume influx point Sources/Sinks.
F LtracerSrc(01) Turning OFF point Sources/Sinks on tracer 01: temp
F LtracerSrc(02) Turning OFF point Sources/Sinks on tracer 02: salt
F LsshCLM Turning OFF processing of SSH climatology.
F Lm2CLM Turning OFF processing of 2D momentum climatology.
F Lm3CLM Turning OFF processing of 3D momentum climatology.
F LtracerCLM(01) Turning OFF processing of climatology tracer 01: temp
F LtracerCLM(02) Turning OFF processing of climatology tracer 02: salt
F LnudgeM2CLM Turning OFF nudging of 2D momentum climatology.
F LnudgeM3CLM Turning OFF nudging of 3D momentum climatology.
F LnudgeTCLM(01) Turning OFF nudging of climatology tracer 01: temp
F LnudgeTCLM(02) Turning OFF nudging of climatology tracer 02: salt
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(idUbms) Write out bottom U-momentum stress.
T Hout(idVbms) Write out bottom V-momentum stress.
T Hout(idU2rs) Write out total 2D u-radiation stress.
T Hout(idV2rs) Write out total 2D v-radiation stress.
T Hout(idU2Sd) Write out 2D u-momentum stokes velocity.
T Hout(idV2Sd) Write out 2D v-momentum stokes velocity.
T Hout(idU3Sd) Write out 3D u-momentum stokes velocity.
T Hout(idV3Sd) Write out 3D v-momentum stokes velocity.
T Hout(idWztw) Write out WEC quasi-static sea level adjustment.
T Hout(idWqsp) Write out WEC quasi-static pressure.
T Hout(idWbeh) Write out WEC Bernoulli head.
T Hout(idWamp) Write out wave height.
T Hout(idWlen) Write out wavelength.
T Hout(idWdir) Write out wave direction.
T Hout(idWptp) Write out wave surface period.
T Hout(idWpbt) Write out wave bottom period.
T Hout(idWorb) Write out wave bottom orbital velocity.
T Hout(idVvis) Write out vertical viscosity: AKv.



Output/Input Files:

Output Restart File: land_ocean_rst.nc
Output History File: TSnest_ocean_his_Max2wMdLtd_f7.nc
Output Diagnostics File: TSnest_ocean_dia_Max2wMdLtd_f7.nc
Physical parameters File:
Input Grid File: Projects/Stormsrun/TS/Nest_TS/Factor7/zland_gridfine7.nc
Input Nonlinear Initial File: Projects/Stormsrun/TS/Nest_TS/Factor7/TSnest_Max2wMdLtd_inic7.nc
Input Forcing File 01: Projects/Stormsrun/TS/Nest_TS/Factor7/TSnest_wind_Max2wMdLtd.nc
Input Boundary File 01: Projects/Stormsrun/TS/Nest_TS/Factor7/TSnest_Max2wMdLtd_bdyc7.nc

Tile partition information for Grid 01: 0945x0210x0004 tiling: 002x001

tile Istr Iend Jstr Jend Npts

Number of tracers: 2
0 1 473 1 210 397320
1 474 945 1 210 396480

Tile minimum and maximum fractional coordinates for Grid 01:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 0.50 473.50 0.50 210.50 RHO-points
1 473.50 945.50 0.50 210.50 RHO-points

0 1.00 473.50 0.50 210.50 U-points
1 473.50 945.00 0.50 210.50 U-points

0 0.50 473.50 1.00 210.00 V-points
1 473.50 945.50 1.00 210.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 968
HaloSizeJ(1) = 442
TileSide(1) = 478
TileSize(1) = 102770


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

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

zeta 1 Clamped Clamped Clamped Closed

ubar 1 Clamped Clamped Clamped Closed

vbar 1 Clamped Clamped Clamped Closed

u 1 Rad + Nud Rad + Nud Rad + Nud Closed

v 1 Rad + Nud Rad + Nud Rad + Nud Closed

temp 1 Gradient Gradient Gradient Closed

salt 1 Gradient Gradient Gradient Closed

tke 1 Gradient Gradient Gradient Closed

ubar_stokes 1 Gradient Gradient Gradient Closed

vbar_stokes 1 Gradient Gradient Gradient Closed

u_stokes 1 Gradient Gradient Gradient Closed

v_stokes 1 Gradient Gradient Gradient Closed

Activated C-preprocessing Options:

BCF_TEST BCF TEST
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SSFLUX Analytical kinematic surface salinity flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
CURVGRID Orthogonal curvilinear grid.
DIAGNOSTICS_UV Computing and writing momen Node # 1 (pid= 31238) is active.
tum diagnostic terms.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
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.
WEC_VF Vortex Force wave current interaction- UNDER DEVELOPMENT!!!!.
WDISS_WAVEMOD Wave energy dissipation acquired from coupled wave model.
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.
SOLVE3D Solving 3D Primitive Equations.
SPLINES Conservative parabolic spline reconstruction.
SWAN_COUPLING SWAN model coupling.
TS_C2HADVECTION Second-order centered horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection of tracers.
UV_ADV Advection of momentum.
UV_COR Coriolis term.
UV_C2ADVECTION Second-order centered differences advection of momentum.
UV_KIRBY Compute uwave and vwave Kirby avg velocities.
UV_LOGDRAG Logarithmic bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
WAVES_OCEAN Two-way wave-ocean models coupling.
WET_DRY Wetting and drying activated.

Process Information:

Node # 0 (pid= 31237) is active.
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 31237 on node usc exited on signal 9 (Killed)
--------------------------------------------------------------------------


I donot know how to fix this problem. If anyone could help me out of this?

Thanks!

Xiaodong

[jcwarner]

i just a test with Inlet_test and added output for the diagnostics. It ran fine for me.
please do an update and try again.
thanks,
john

[xwu]

Thanks, John!

I got the reason for my problem. The high resolution grid plus 'diagnostics' overburden the the desktop, thus it terminates in the very beginning. It runs well on cluster now.

Xiaodong