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PostPosted: Mon Nov 26, 2018 10:41 am 
Offline

Joined: Thu Jan 25, 2018 3:23 pm
Posts: 11
Location: South China Sea institude of Oceanology
Hello,
I have a problem need to solve. The log file is:

--------------------------------------------------------------------------------
Model Input Parameters: ROMS/TOMS version 3.7
Monday - November 26, 2018 - 10:15:09 AM
--------------------------------------------------------------------------------

South China Sea Test

Operating system : Linux
CPU/hardware : x86_64
Compiler system : ifort
Compiler command : /opt/software/mpich2/bin/mpif90
Compiler flags : -fp-model precise -ip -O3 -free -free -free

Input Script : ocean_eddy.in

SVN Root URL : https:://myroms.org/svn/src
SVN Revision : 911M

Local Root : /home/customer/roms
Header Dir : /home/customer/roms/Projects/test/eddy_dipole
Header file : eddy.h
Analytical Dir: /home/customer/roms/Projects/test/eddy_dipole

Resolution, Grid 01: 0269x0241x030, Parallel Nodes: 2, Tiling: 001x002


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

175200 ntimes Number of timesteps for 3-D equations.
360.000 dt Timestep size (s) for 3-D equations.
45 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.
F LcycleRST Switch to recycle time-records in restart file.
240 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).
240 nHIS Number of timesteps between the writing fields
into history file.
0 nQCK Number of timesteps between the writing fields
into quicksave file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
240 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
240 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
4.0000E+01 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
4.0000E+01 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
2.0000E+02 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-05 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-05 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.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
2.0000E+00 blk_ZQ Height (m) of surface air humidity measurement.
2.0000E+00 blk_ZT Height (m) of surface air temperature measurement.
1.0000E+01 blk_ZW Height (m) of surface winds measurement.
1 lmd_Jwt Jerlov water type.
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
7.0000E+00 theta_s S-coordinate surface control parameter.
1.0000E+00 theta_b S-coordinate bottom control parameter.
10.000 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)
1.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
1.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
1.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
1.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
1.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
1.0000E+01 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.
35.000 S0 Background salinity (PSU) constant.
-1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
T LuvSrc Turning ON 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
T LtracerSrc(02) Turning ON 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.
T LtracerCLM(01) Turning ON processing of climatology tracer 01: temp
T LtracerCLM(02) Turning ON 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(idOvel) Write out omega vertical velocity.
T Hout(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt
T Hout(idpthR) Write out time-varying dephts of RHO-points.
T Hout(idTsur) Write out surface net heat flux.
T Hout(idSrad) Write out shortwave radiation flux.
T Hout(idLrad) Write out longwave radiation flux.
T Hout(idLhea) Write out latent heat flux.
T Hout(idShea) Write out sensible heat flux.
T Hout(idDano) Write out density anomaly.
T Hout(idVvis) Write out vertical viscosity: AKv.
T Hout(idTdif) Write out vertical diffusion: AKt(itemp).
T Hout(idSdif) Write out vertical diffusion: AKt(isalt).
T Hout(idHsbl) Write out depth of surface boundary layer.

T Aout(idFsur) Write out averaged free-surface.
T Aout(idUbar) Write out averaged 2D U-momentum component.
T Aout(idVbar) Write out averaged 2D V-momentum component.
T Aout(idUvel) Write out averaged 3D U-momentum component.
T Aout(idVvel) Write out averaged 3D V-momentum component.
T Aout(idWvel) Write out averaged W-momentum component.
T Aout(idOvel) Write out averaged omega vertical velocity.
T Aout(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt


Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc
Output Diagnostics File: ocean_dia.nc
Input Grid File: Data/croco_grd.nc
Input Nonlinear Initial File: Data/croco_ini.nc
Input Sources/Sinks File: Data/myrivers.nc
Input Forcing File 01: Data/croco_frc_6h.nc
Input Forcing File 02: Data/croco_blk_6h.nc
Input Climatology File: Data/croco_clm.nc
Input Boundary File: Data/croco_bry_SODA.nc
Biology Parameters File: npzd_Powell.in

Tile partition information for Grid 01: 0269x0241x0030 tiling: 001x002

tile Istr Iend Jstr Jend Npts

0 1 269 1 121 976470
1 1 269 122 241 968400

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 269.50 0.50 121.50 RHO-points
1 0.50 269.50 121.50 241.50 RHO-points

0 1.00 269.00 0.50 121.50 U-points
1 1.00 269.00 121.50 241.50 U-points

0 0.50 269.50 1.00 121.50 V-points
1 0.50 269.50 121.50 241.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 837
HaloSizeJ(1) = 399
TileSide(1) = 273
TileSize(1) = 34671



NPZD Model Parameters, Grid: 01
===============================

1 BioIter Number of iterations for nonlinear convergence.
4.3000E-01 PARfrac Fraction of shortwave radiation that is
photosynthetically active (nondimensional).
6.7000E-02 AttSW Light attenuation of seawater (m-1).
9.5000E-03 AttPhy Light attenuation by phytoplankton (m2/mmole_N).
2.5000E-02 PhyIS Phytoplankton growth, initial slope of P-I curve
(m2/W).
1.5000E+00 Vm_NO3 Nitrate upatake rate (day-1).
1.0000E-01 PhyMRD Phytoplankton mortality rate to Detritus (day-1)
0.0000E+00 PhyMRN Phytoplankton mortality rate to Nitrogen (day-1)
1.0000E+00 K_NO3 Inverse half-saturation for phytoplankton NO3
uptake (1/(mmol m-3)).
8.4000E-01 Ivlev Ivlev constant for zooplankton grazing
(nondimensional).
5.2000E-01 ZooGR Zooplankton maximum growth rate (day-1).
0.0000E+00 ZooEED Zooplankton excretion efficiency to Detritus
pool (nondimensional).
3.0000E-01 ZooEEN Zooplankton excretion efficiency to Nitrogen
pool (nondimensional).
1.4500E-01 ZooMRD Zooplankton mortality rate to Detritus (day-1).
0.0000E+00 ZooMRN Zooplankton mortality rate to Nitrogen (day-1).
1.0300E+00 DetRR Detritus remineralization rate (day-1).
0.0000E+00 wPhy Phytoplankton sinking rate (m/day).
8.0000E+00 wDet Detrital sinking rate (m/day).
4.0000E+01 nl_tnu2(03) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 03: NO3
4.0000E+01 nl_tnu2(04) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 04: phytoplankton
4.0000E+01 nl_tnu2(05) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 05: zooplankton
4.0000E+01 nl_tnu2(06) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 06: detritus
F LtracerSponge(03) Turning OFF sponge on tracer 03: NO3
F LtracerSponge(04) Turning OFF sponge on tracer 04: phytoplankton
F LtracerSponge(05) Turning OFF sponge on tracer 05: zooplankton
F LtracerSponge(06) Turning OFF sponge on tracer 06: detritus
5.0000E-06 Akt_bak(03) Background vertical mixing coefficient (m2/s)
for tracer 03: NO3
5.0000E-06 Akt_bak(04) Background vertical mixing coefficient (m2/s)
for tracer 04: phytoplankton
5.0000E-06 Akt_bak(05) Background vertical mixing coefficient (m2/s)
for tracer 05: zooplankton
5.0000E-06 Akt_bak(06) Background vertical mixing coefficient (m2/s)
for tracer 06: detritus
0.0000E+00 Tnudg(03) Nudging/relaxation time scale (days)
for tracer 03: NO3
0.0000E+00 Tnudg(04) Nudging/relaxation time scale (days)
for tracer 04: phytoplankton
0.0000E+00 Tnudg(05) Nudging/relaxation time scale (days)
for tracer 05: zooplankton
0.0000E+00 Tnudg(06) Nudging/relaxation time scale (days)
for tracer 06: detritus
F LtracerSrc(03) Turning OFF point sources/Sink on tracer 03: NO3
F LtracerSrc(04) Turning OFF point sources/Sink on tracer 04: phytoplankton
F LtracerSrc(05) Turning OFF point sources/Sink on tracer 05: zooplankton
F LtracerSrc(06) Turning OFF point sources/Sink on tracer 06: detritus
F LtracerCLM(03) Turning OFF processing of climatology tracer 03: NO3
F LtracerCLM(04) Turning OFF processing of climatology tracer 04: phytoplankton
F LtracerCLM(05) Turning OFF processing of climatology tracer 05: zooplankton
F LtracerCLM(06) Turning OFF processing of climatology tracer 06: detritus
F LnudgeTCLM(03) Turning OFF nudging of climatology tracer 03: NO3
F LnudgeTCLM(04) Turning OFF nudging of climatology tracer 04: phytoplankton
F LnudgeTCLM(05) Turning OFF nudging of climatology tracer 05: zooplankton
F LnudgeTCLM(06) Turning OFF nudging of climatology tracer 06: detritus

T Hout(idTvar) Write out tracer 03: NO3
T Hout(idTvar) Write out tracer 04: phytoplankton
T Hout(idTvar) Write out tracer 05: zooplankton
T Hout(idTvar) Write out tracer 06: detritus

T Aout(idTvar) Write out averaged tracer 03: NO3
T Aout(idTvar) Write out averaged tracer 04: phytoplankton
T Aout(idTvar) Write out averaged tracer 05: zooplankton
T Aout(idTvar) Write out averaged tracer 06: detritus

T Dout(iTrate) Write out rate of change of tracer 03: NO3
T Dout(iTrate) Write out rate of change of tracer 04: phytoplankton
T Dout(iTrate) Write out rate of change of tracer 05: zooplankton
T Dout(iTrate) Write out rate of change of tracer 06: detritus
T Dout(iThadv) Write out horizontal advection, tracer 03: NO3
T Dout(iThadv) Write out horizontal advection, tracer 04: phytoplankton
T Dout(iThadv) Write out horizontal advection, tracer 05: zooplankton
T Dout(iThadv) Write out horizontal advection, tracer 06: detritus
T Dout(iTxadv) Write out horizontal X-advection, tracer 03: NO3
T Dout(iTxadv) Write out horizontal X-advection, tracer 04: phytoplankton
T Dout(iTxadv) Write out horizontal X-advection, tracer 05: zooplankton
T Dout(iTxadv) Write out horizontal X-advection, tracer 06: detritus
T Dout(iTyadv) Write out horizontal Y-advection, tracer 03: NO3
T Dout(iTyadv) Write out horizontal Y-advection, tracer 04: phytoplankton
T Dout(iTyadv) Write out horizontal Y-advection, tracer 05: zooplankton
T Dout(iTyadv) Write out horizontal Y-advection, tracer 06: detritus
T Dout(iTvadv) Write out vertical advection, tracer 03: NO3
T Dout(iTvadv) Write out vertical advection, tracer 04: phytoplankton
T Dout(iTvadv) Write out vertical advection, tracer 05: zooplankton
T Dout(iTvadv) Write out vertical advection, tracer 06: detritus
T Dout(iThdif) Write out horizontal diffusion, tracer 03: NO3
T Dout(iThdif) Write out horizontal diffusion, tracer 04: phytoplankton
T Dout(iThdif) Write out horizontal diffusion, tracer 05: zooplankton
T Dout(iThdif) Write out horizontal diffusion, tracer 06: detritus
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 05: zooplankton
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 06: detritus
T Dout(iTydif) Write out horizontal Y-diffusion, tracer 03: NO3
T Dout(iTydif) Write out horizontal Y-diffusion, tracer 04: phytoplankton
T Dout(iTydif) Write out horizontal Y-diffusion, tracer 05: zooplankton
T Dout(iTydif) Write out horizontal Y-diffusion, tracer 06: detritus
T Dout(iTsdif) Write out horizontal S-diffusion, tracer 03: NO3
T Dout(iTsdif) Write out horizontal S-diffusion, tracer 04: phytoplankton
T Dout(iTsdif) Write out horizontal S-diffusion, tracer 05: zooplankton
T Dout(iTsdif) Write out horizontal S-diffusion, tracer 06: detritus
T Dout(iTvdif) Write out vertical diffusion, tracer 03: NO3
T Dout(iTvdif) Write out vertical diffusion, tracer 04: phytoplankton
T Dout(iTvdif) Write out vertical diffusion, tracer 05: zooplankton
T Dout(iTvdif) Write out vertical diffusion, tracer 06: detritus

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

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

zeta 1 Chapman Imp Chapman Imp Chapman Imp Chapman Imp

ubar 1 Flather Flather Flather Flather

vbar 1 Flather Flather Flather Flather

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

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

temp 1 Rad + Nud Rad + Nud Rad + Nud Rad + Nud

salt 1 Rad + Nud Rad + Nud Rad + Nud Rad + Nud

NO3 1 Clamped Clamped Clamped Clamped

phytoplankton 1 Clamped Clamped Clamped Clamped

zooplankton 1 Clamped Clamped Clamped Clamped

detritus 1 Clamped Clamped Clamped Clamped

Activated C-preprocessing Options:

SCS_BIOARGO South China Sea Test
ANA_BPFLUX Analytical bottom passive tracers fluxes.
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SPFLUX Analytical surface passive tracer fluxes.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
!BOUNDARY_ALLGATHER Using mpi_allreduce in mp_boundary routine.
BULK_FLUXES Surface bulk fluxes parameterization.
!COLLECT_ALL... Using mpi_isend/mpi_recv in mp_collect routine.
CURVGRID Orthogonal curvilinear grid.
DIAGNOSTICS_TS Computing and writing tracer diagnostic terms.
DIAGNOSTICS_UV Computing and writing momentum diagnostic terms.
DIFF_GRID Horizontal diffusion coefficient scaled by grid size.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
LMD_CONVEC LMD convective mixing due to shear instability.
LMD_MIXING Large/McWilliams/Doney interior mixing.
LMD_NONLOCAL LMD convective nonlocal transport.
LMD_RIMIX LMD diffusivity due to shear instability.
LMD_SKPP KPP surface boundary layer mixing.
MASKING Land/Sea masking.
MIX_GEO_TS Mixing of tracers along geopotential surfaces.
MIX_GEO_UV Mixing of momentum along geopotential surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NPZD_POWELL NPZD Biological Model, Powell et al. fomulation.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
QCORRECTION Surface net heat flux correction.
REDUCE_ALLGATHER Using mpi_allgather in mp_reduce routine.
RI_SPLINES Parabolic Spline Reconstruction for Richardson Number.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SRELAXATION Surface salinity relaxation as surface flux.
SOLAR_SOURCE Solar Radiation Source Term.
SOLVE3D Solving 3D Primitive Equations.
SPLINES_VDIFF Parabolic Spline Reconstruction for Vertical Diffusion.
SPLINES_VVISC Parabolic Spline Reconstruction for Vertical Viscosity.
SPHERICAL Spherical grid configuration.
TS_MPDATA Recursive flux corrected MPDATA 3D advection of tracers.
TS_DIF2 Harmonic mixing of tracers.
UV_ADV Advection of momentum.
UV_COR Coriolis term.
UV_U3HADVECTION Third-order upstream horizontal advection of 3D momentum.
UV_C4VADVECTION Fourth-order centered vertical advection of momentum.
UV_QDRAG Quadratic bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
VISC_GRID Horizontal viscosity coefficient scaled by grid size.

Process Information:

Node # 0 (pid= 481) is active.
Node # 1 (pid= 482) is active.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
oceanM 00000000009C9481 Unknown Unknown Unknown
oceanM 00000000009C7BD7 Unknown Unknown Unknown
oceanM 0000000000976CB4 Unknown Unknown Unknown
oceanM 0000000000976AC6 Unknown Unknown Unknown
oceanM 000000000092F26F Unknown Unknown Unknown
oceanM 000000000093324D Unknown Unknown Unknown
libpthread.so.0 000000396DA0F500 Unknown Unknown Unknown
oceanM 00000000009231B5 Unknown Unknown Unknown
oceanM 0000000000877110 Unknown Unknown Unknown
oceanM 0000000000841C33 Unknown Unknown Unknown
oceanM 0000000000875624 Unknown Unknown Unknown
oceanM 00000000007E8D47 Unknown Unknown Unknown
oceanM 0000000000405A72 Unknown Unknown Unknown
oceanM 000000000040504C Unknown Unknown Unknown
oceanM 0000000000404F0E Unknown Unknown Unknown
libc.so.6 000000396D61ECDD Unknown Unknown Unknown
oceanM 0000000000404E19 Unknown Unknown Unknown


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
When I Turn off point Source/Sinks switches:

LuvSrc == F ! horizontal momentum transport
LwSrc == F ! volume vertical influx
LtracerSrc == F F ! temperature, salinity, inert
The model can run properyly.

When I turn on any one of them,I will get a result of above with segmentation error.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I checked my river file, and there seems no wrong.
Here is the head file of my river:
netcdf myrivers {
dimensions:
xi_rho = 271 ;
xi_u = 270 ;
xi_v = 271 ;
eta_rho = 243 ;
eta_u = 243 ;
eta_v = 242 ;
s_rho = 30 ;
river = 3 ;
river_time = 365 ;
time = UNLIMITED ; // (365 currently)
variables:
double time(time) ;
time:long_name = "river time" ;
time:units = "days since 2014-01-01 00:00:00 GMT" ;
time:field = "river_time, scalar, series" ;
double river(river) ;
river:long_name = "river runoff identification number" ;
river:units = "nondimensional" ;
river:field = "river, scalar" ;
double river_Xposition(river) ;
river_Xposition:long_name = "river XI-position at RHO-points" ;
river_Xposition:units = "nondimensional" ;
river_Xposition:valid_min = 1. ;
river_Xposition:valid_max = 270. ;
river_Xposition:field = "river_Xposition, scalar" ;
double river_Eposition(river) ;
river_Eposition:long_name = "river ETA-position at RHO-points" ;
river_Eposition:units = "nondimensional" ;
river_Eposition:valid_min = 1. ;
river_Eposition:valid_max = 242. ;
river_Eposition:field = "river_Eposition, scalar" ;
double river_direction(river) ;
river_direction:long_name = "river runoff direction" ;
river_direction:units = "nondimensional" ;
river_direction:field = "river_direction, scalar" ;
double river_flag(river) ;
river_flag:long_name = "river runoff tracer flag" ;
river_flag:option_0 = "all tracers are off" ;
river_flag:option_1 = "only temperature is on" ;
river_flag:option_2 = "only salinity is on" ;
river_flag:option_3 = "both temperature and salinity are on" ;
river_flag:units = "nondimensional" ;
river_flag:field = "river_flag, scalar" ;
double river_Vshape(s_rho, river) ;
river_Vshape:long_name = "river runoff mass transport vertical profile" ;
river_Vshape:units = "nondimensional" ;
river_Vshape:field = "river_Vshape, scalar" ;
double river_time(river_time) ;
river_time:long_name = "river runoff time" ;
river_time:units = "days since 2014-01-01 00:00:00" ;
river_time:calendar = "365.25 days in every year" ;
river_time:cycle_length = 365.25 ;
river_time:field = "river_time, scalar, series" ;
double river_transport(river_time, river) ;
river_transport:long_name = "river runoff vertically integrated mass transport" ;
river_transport:units = "meter3 second-1" ;
river_transport:field = "river_transport, scalar, series" ;
river_transport:time = "river_time" ;
double river_temp(river_time, s_rho, river) ;
river_temp:long_name = "river runoff potential temperature" ;
river_temp:units = "Celsius" ;
river_temp:time = "river_time" ;
river_temp:field = "river_temp, scalar, series" ;
double river_salt(river_time, s_rho, river) ;
river_salt:long_name = "river runoff salinity" ;
river_salt:units = "PSU" ;
river_salt:time = "river_time" ;
river_salt:field = "river_salt, scalar, series" ;
double river_NO3(river_time, s_rho, river) ;
river_NO3:long_name = "river runoff NO3" ;
river_NO3:units = "mMol N m-3" ;
river_NO3:time = "river_time" ;
river_NO3:field = "river_NO3, scalar, series" ;
double river_phyt(river_time, s_rho, river) ;
river_phyt:long_name = "river runoff phytoplankton" ;
river_phyt:units = "mMol N m-3" ;
river_phyt:time = "river_time" ;
river_phyt:field = "river_phyt, scalar, series" ;
double river_zoop(river_time, s_rho, river) ;
river_zoop:long_name = "river runoff zooplankton" ;
river_zoop:units = "mMol N m-3" ;
river_zoop:time = "river_time" ;
river_zoop:field = "river_zoop, scalar, series" ;
double river_detritus(river_time, s_rho, river) ;
river_detritus:long_name = "river runoff detritus" ;
river_detritus:units = "mMol N m-3" ;
river_detritus:time = "river_time" ;
river_detritus:field = "river_detritus, scalar, series" ;

// global attributes:
:type = "ROMS FORCING file" ;
:title = "NENA River Forcing" ;
:grd_file = "/home/customer/roms/Projects/test/eddy_dipole/Data/croco_grd.nc" ;
:rivers = "1" ;
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%
I hope someone can share your experience and help me solve the problem.I'd aprreciate it very much.


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PostPosted: Tue Nov 27, 2018 12:43 am 
Offline

Joined: Thu Jan 25, 2018 3:23 pm
Posts: 11
Location: South China Sea institude of Oceanology
I recompiled my model. And this is the debugged result:


forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
oceanG 00000000026A0AF1 Unknown Unknown Unknown
oceanG 000000000269F247 Unknown Unknown Unknown
oceanG 000000000264E954 Unknown Unknown Unknown
oceanG 000000000264E766 Unknown Unknown Unknown
oceanG 0000000002606F0F Unknown Unknown Unknown
oceanG 000000000260AEED Unknown Unknown Unknown
libpthread.so.0 000000396DA0F500 Unknown Unknown Unknown
oceanG 00000000025FAE55 Unknown Unknown Unknown
oceanG 000000000254EDB8 Unknown Unknown Unknown
oceanG 0000000002469367 mod_netcdf_mp_net 852 mod_netcdf.f90
oceanG 000000000253DC6C mod_sources_mp_al 109 mod_sources.f90
oceanG 00000000021E99A3 mod_arrays_ 81 mod_arrays.f90
oceanG 0000000000406462 ocean_control_mod 123 ocean_control.f90
oceanG 000000000040509A MAIN__ 95 master.f90

oceanG 0000000000404EBE Unknown Unknown Unknown
libc.so.6 000000396D61ECDD Unknown Unknown Unknown
oceanG 0000000000404DC9 Unknown Unknown Unknown


Last edited by Shuaiyiping on Tue Nov 27, 2018 12:56 am, edited 2 times in total.

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PostPosted: Tue Nov 27, 2018 12:54 am 
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Posts: 741
Location: USGS, USA
so this is telling you something:

oceanG 0000000002469367 mod_netcdf_mp_net 852 mod_netcdf.f90
oceanG 000000000253DC6C mod_sources_mp_al 109 mod_sources.f90

look in Build/mod_sources.f90 line 109 and it is probably calling mod_netcdf with some information.
Look in Build/mod_netcdf.f90 line 852 and see what it is try to read or write. that might be the variable that is causing trouble.

-john


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PostPosted: Tue Nov 27, 2018 12:58 am 
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Location: South China Sea institude of Oceanology
Thank you very much ,John :)


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PostPosted: Tue Nov 27, 2018 6:46 am 
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Joined: Thu Jan 25, 2018 3:23 pm
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Location: South China Sea institude of Oceanology
I checked the mod_netcdf.f90.It seems that the ncread problem. I checked my input river file and I don't know where is it wrong. I attached my ncfile. Hope you can point out my problem. Thanks very much.

mod_source.f90:

! Inquire about the number of point sources.
!

IF (ng.eq.1) THEN
DO mg=1,Ngrids
foundit=.FALSE.
IF (LuvSrc(mg).or.LwSrc(mg).or.ANY(LtracerSrc(:,mg))) THEN
CALL netcdf_inq_var (ng, iNLM, SSF(mg)%name, &
& MyVarName = TRIM(Vname(1,idRxpo)), &
& SearchVar = foundit, &
& VarID = Vid, &
& nVardim = nvdim, &
& nVarAtt = nvatt)
IF (FoundError(exit_flag, NoError, 136, &
& "ROMS/Modules/mod_sources.F"//", allocate_sources")) RETURN
IF (foundit) THEN
Nsrc(mg)=var_Dsize(1) ! first dimension
Msrc(mg)=Nsrc(mg)
END IF
END IF
END DO
END IF









mod_netcdf.f90:

!
! Inquire global attribute names and their external data type.
!
DO i=1,MIN(Matts,n_gatt)
att_id=i
status=nf90_inq_attname(ncid, nf90_global, att_id, &
& att_name(i))
IF (status.eq.nf90_noerr) THEN
status=nf90_inquire_attribute(ncid, nf90_global, &
& TRIM(att_name(i)), &
& xtype = att_kind(i), &
& attnum = att_id)
IF (status.ne.nf90_noerr) THEN
WRITE (stdout,5) i, TRIM(ncname), TRIM(SourceFile)
exit_flag=2
ioerror=status
EXIT
END IF
ELSE
WRITE (stdout,5) i, TRIM(ncname), TRIM(SourceFile)
exit_flag=2
ioerror=status
EXIT
END IF
END DO


Last edited by Shuaiyiping on Thu Nov 29, 2018 9:33 am, edited 1 time in total.

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PostPosted: Tue Nov 27, 2018 1:10 pm 
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Posts: 741
Location: USGS, USA
a few things:
- does it work with just
LuvSrc == T ! horizontal momentum transport
and the rest == F ? that way we know it is just for river info, and not the tracers.

- the mod sources has
MyVarName = TRIM(Vname(1,idRxpo)), &
so it is trying to read idRxpo,
and trying to read attributes of that var.

look in varinfo.dat and see

'river_Xposition' ! Input
'river runoff XI-positions at RHO-points'
'nondimensional' ! [nondimensional]
'river_Xposition, scalar'
'river'
'idRxpo'
'nulvar'
1.0d0

so it is reading river_Xposition,

ncdisp of your nc file has (in part)

river_Xposition
Size: 3x1
Dimensions: river
Datatype: double
Attributes:
long_name = 'river XI-position at RHO-points'
units = 'nondimensional'
valid_min = 1
valid_max = 270
field = 'river_Xposition, scalar'



I now ask: Is this Rutgers roms or croco?


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PostPosted: Wed Nov 28, 2018 3:37 am 
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I turned off all the swiches except LuvSrc. There result is also like before with segmentation fault.
My roms is Rutgers roms,but I used Roms_tools with revised to create the input files.


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PostPosted: Wed Nov 28, 2018 3:40 am 
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I turned off all the swiches except LuvSrc. There result is also like before with segmentation fault.
My roms is Rutgers roms,but I used Roms_tools with revised to create the input files.
The header file of river is from roms_cdl.


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PostPosted: Wed Nov 28, 2018 1:42 pm 
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this section of mod_netcdf is newly modified.
which one of these is line 852:

DO i=1,MIN(Matts,n_gatt)
att_id=i
status=nf90_inq_attname(ncid, nf90_global, att_id, &
& att_name(i))
IF (status.eq.nf90_noerr) THEN
status=nf90_inquire_attribute(ncid, nf90_global, &
& TRIM(att_name(i)), &
& xtype = att_kind(i), &
& attnum = att_id)
IF (status.ne.nf90_noerr) THEN
WRITE (stdout,5) i, TRIM(ncname), TRIM(SourceFile)
exit_flag=2
ioerror=status
EXIT
END IF
ELSE
WRITE (stdout,5) i, TRIM(ncname), TRIM(SourceFile)
exit_flag=2
ioerror=status
EXIT
END IF
END DO


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PostPosted: Thu Nov 29, 2018 9:33 am 
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Posts: 11
Location: South China Sea institude of Oceanology
Thkan you very much. Today I updated my roms. And replaced the older package ROMS with the latest and it worked. Thanks again for helping me :D


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