When I run the ROMS model, I got the following informaton:
NETCDF_PUT_FVAR_1D - error while writing variable: ocean_time
in input file: ./Lee.nc
call from: wrt_his.F
ROMS/TOMS - Output error ............ exit_flag: 3
ERROR: Abnormal termination: NetCDF OUTPUT.
REASON: NetCDF: Not a valid ID
Part information in my '.in'file is:
! Time-Stepping parameters.
NTIMES == 2449920 ! 1276 days(2009-1-1 to 2012-06-30) x 1920 x 1 baroclinic steps/day
DT == 45.0d0
NDTFAST == 30
! Model iteration loops parameters.
ERstr = 1
ERend = 1
Nouter = 1
Ninner = 1
Nintervals = 1
! Number of eigenvalues (NEV) and eigenvectors (NCV) to compute for the
! Lanczos/Arnoldi problem in the Generalized Stability Theory (GST)
! analysis. NCV must be greater than NEV (see documentation below).
NEV = 2 ! Number of eigenvalues
NCV = 10 ! Number of eigenvectors
! Input/Output parameters.
NRREC == 0 ! no Restart
LcycleRST == T ! restart saved every NRST times
NRST == 19200 ! 10 day x 1920 steps/day rst
NSTA == 1
NFLT == 1
NINFO == 40 ! display on the screen
! Output history, average, diagnostic files parameters.
LDEFOUT == T
NHIS == 320 ! 4 hours
NDEFHIS == 57600 ! 30 days
NTSAVG == 1
NAVG == 1920 ! 24 hours
NDEFAVG == 57600 ! 30 days
NTSDIA == 1
NDIA == 1920 ! 24 hours
NDEFDIA == 57600 ! 30 days
! Output tangent linear and adjoint models parameters.
LcycleTLM == F
NTLM == 72
NDEFTLM == 0
LcycleADJ == F
NADJ == 72
NDEFADJ == 0
NSFF == 72 ! new variables from ROMS 333
NOBC == 72 ! new variables from ROMS 333
Please help me. Any help from you will be highly appreciated!
ERROR: Abnormal termination: NetCDF OUTPUT.
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
Help! Help! I am waiting for you online. 
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
Sorry, I don't know what's wrong. Have you successfully run ROMS in a simpler domain? Have you tested your NetCDF library in any way? I would investigate this in a debugger, poking to find out what ID is in error - the file ID or the variable ID? You might get the same answer from print statements (only the Master should print).
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
Hi, Kate, Thanks for your kind reply.kate wrote:Sorry, I don't know what's wrong. Have you successfully run ROMS in a simpler domain? Have you tested your NetCDF library in any way? I would investigate this in a debugger, poking to find out what ID is in error - the file ID or the variable ID? You might get the same answer from print statements (only the Master should print).
I have run the Upwelling case successfully, Does it mean the NetCDF library is ok?
I looked up on the internet, somenone suggested I should change the NDEFHIS's value to 0, When I tried that, it was killed when wrote history fields:
Code: Select all
NLM: GET_STATE - Read state initial conditions, t = 972 00:00:00
(File: cpb_ini_160x240_Lee.nc, Rec=0001, Index=1)
- free-surface
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- vertically integrated u-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- vertically integrated v-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- u-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- v-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- potential temperature
(Min = 1.62402554E+01 Max = 2.77315388E+01)
- salinity
(Min = -1.28079161E-01 Max = 3.36495667E+01)
GET_NGFLD - river runoff XI-positions at RHO-points
(Min = 3.00000000E+00 Max = 1.58000000E+02)
GET_NGFLD - river runoff ETA-positions at RHO-points
(Min = 1.20000000E+01 Max = 2.37000000E+02)
GET_NGFLD - river runoff direction
(Min = 0.00000000E+00 Max = 1.00000000E+00)
GET_NGFLD - river runoff mass transport vertical profile
(Min = 5.00000007E-02 Max = 5.00000007E-02)
GET_NGFLD - river runoff mass transport, t = 972 00:00:00
(Rec=0097, Index=2, File: cpb_frc_160x240_Lee_river.nc)
(Tmin= 971.0000 Tmax= 1276.9896)
(Min = -7.92876511E+01 Max = 2.34748071E+03)
GET_2DFLD - surface u-wind component, t = 972 00:00:00
(Rec=0025, Index=1, File: cpb_frc_160x240_Lee_bulk_Uwind.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = -3.95848322E+00 Max = 4.64155614E-01)
GET_2DFLD - surface v-wind component, t = 972 00:00:00
(Rec=0025, Index=1, File: cpb_frc_160x240_Lee_bulk_Vwind.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = -6.86217356E+00 Max = 2.74473858E+00)
GET_2DFLD - surface air pressure, t = 972 00:00:00
(Rec=0025, Index=1, File: cpb_frc_160x240_Lee_bulk_Pair.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 9.97142212E+02 Max = 1.01894214E+03)
GET_2DFLD - solar shortwave radiation flux, t = 972 00:00:00
(Rec=0025, Index=1, File: cpb_frc_160x240_Lee_bulk_swrad.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - downwelling longwave radiation flux, t = 972 00:00:00
(Rec=0025, Index=1, File: cpb_frc_160x240_Lee_bulk_lwrad_down.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 7.64621511E-05 Max = 9.41647260E-05)
GET_2DFLD - surface air temperature, t = 972 00:00:00
(Rec=0025, Index=1, File: cpb_frc_160x240_Lee_bulk_Tair.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 1.48792343E+01 Max = 2.67672482E+01)
GET_2DFLD - surface air relative humidity, t = 972 00:00:00
(Rec=0025, Index=1, File: cpb_frc_160x240_Lee_bulk_Qair.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 5.50962982E-01 Max = 9.31274948E-01)
GET_NGFLD - free-surface eastern boundary condition, t = 972 00:00:00
(Rec=0025, Index=2, File: cpb_bry_160x240_Lee.nc)
(Tmin= 971.0000 Tmax= 1276.9584)
(Min = -5.35676098E+00 Max = 8.69854867E-01)
GET_NGFLD - 2D u-momentum eastern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: cpb_bry_160x240_Lee.nc)
(Tmin= 0.0000 Tmax= 0.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_NGFLD - 2D v-momentum eastern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: cpb_bry_160x240_Lee.nc)
(Tmin= 0.0000 Tmax= 0.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_NGFLD - temperature eastern boundary condition, t = 956 00:00:00
(Rec=0020, Index=2, File: cpb_bry_160x240_Lee.nc)
(Tmin= 379.0000 Tmax= 1809.0000)
(Min = 1.92486763E+01 Max = 2.60051193E+01)
GET_NGFLD - salinity eastern boundary condition, t = 956 00:00:00
(Rec=0020, Index=2, File: cpb_bry_160x240_Lee.nc)
(Tmin= 379.0000 Tmax= 1809.0000)
(Min = 3.16055031E+01 Max = 3.38161812E+01)
Maximum grid stiffness ratios: rx0 = 7.842086E-01 (Beckmann and Haidvogel)
rx1 = 3.429667E+01 (Haney)
Initial basin volumes: TotVolume = 2.7576155885E+11 m3
MinVolume = 2.5670776751E+04 m3
MaxVolume = 4.4602063582E+07 m3
Max/Min = 1.7374645113E+03
NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 01866241 - 02449920)
GET_NGFLD - river runoff mass transport, t = 972 00:15:01
(Rec=0098, Index=1, File: cpb_frc_160x240_Lee_river.nc)
(Tmin= 971.0000 Tmax= 1276.9896)
(Min = -7.78717957E+01 Max = 2.34181738E+03)
GET_2DFLD - surface u-wind component, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_Uwind.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = -3.60082650E+00 Max = 5.00677049E-01)
GET_2DFLD - surface v-wind component, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_Vwind.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = -6.79969215E+00 Max = 2.13858318E+00)
GET_2DFLD - surface air pressure, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_Pair.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 9.97390686E+02 Max = 1.01985712E+03)
GET_2DFLD - solar shortwave radiation flux, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_swrad.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - downwelling longwave radiation flux, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_lwrad_down.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 7.59754687E-05 Max = 9.35231107E-05)
GET_2DFLD - surface air temperature, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_Tair.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 1.39307537E+01 Max = 2.66532497E+01)
GET_2DFLD - surface air relative humidity, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_Qair.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 5.54842453E-01 Max = 9.33233109E-01)
GET_NGFLD - free-surface eastern boundary condition, t = 972 01:00:01
(Rec=0026, Index=1, File: cpb_bry_160x240_Lee.nc)
(Tmin= 971.0000 Tmax= 1276.9584)
(Min = -4.71466017E+00 Max = 9.39512134E-01)
GET_NGFLD - temperature eastern boundary condition, t = 987 00:00:00
(Rec=0021, Index=1, File: cpb_bry_160x240_Lee.nc)
(Tmin= 379.0000 Tmax= 1809.0000)
(Min = 2.05826626E+01 Max = 2.47020512E+01)
GET_NGFLD - salinity eastern boundary condition, t = 987 00:00:00
(Rec=0021, Index=1, File: cpb_bry_160x240_Lee.nc)
(Tmin= 379.0000 Tmax= 1809.0000)
(Min = 3.23332100E+01 Max = 3.39163857E+01)
STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
1866240 972 00:00:00 0.000000E+00 7.957775E+01 7.957775E+01 3.542731E+11
DEF_HIS - creating history file: ./Lee.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
Killed
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
Processes usually get killed for running beyond some limit - time limit, open files limit, memory limit. I can't tell which you ran into. How big is your grid? Did it hang there trying to write for a very long time? Did you get any output file at all?
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
Thank you.kate wrote:Processes usually get killed for running beyond some limit - time limit, open files limit, memory limit. I can't tell which you ran into. How big is your grid? Did it hang there trying to write for a very long time? Did you get any output file at all?
It took about several minutes(not very long) to get killed. Actually, I have got two output files: Lee.nc and Lee_rst.nc. The code of the Lee.nc is as follows:
Code: Select all
dimensions:
xi_rho = 162 ;
xi_u = 161 ;
xi_v = 162 ;
xi_psi = 161 ;
eta_rho = 242 ;
eta_u = 242 ;
eta_v = 241 ;
eta_psi = 241 ;
N = 20 ;
s_rho = 20 ;
s_w = 21 ;
tracer = 2 ;
boundary = 4 ;
ocean_time = UNLIMITED ; // (1 currently)
variables:
int ntimes ;
ntimes:long_name = "number of long time-steps" ;
int ndtfast ;
ndtfast:long_name = "number of short time-steps" ;
double dt ;
dt:long_name = "size of long time-steps" ;
dt:units = "second" ;
double dtfast ;
dtfast:long_name = "size of short time-steps" ;
dtfast:units = "second" ;
double dstart ;
dstart:long_name = "time stamp assigned to model initilization" ;
dstart:units = "days since 0001-01-01 00:00:00" ;
dstart:calendar = "julian" ;
int nHIS ;
nHIS:long_name = "number of time-steps between history records" ;
int ndefHIS ;
ndefHIS:long_name = "number of time-steps between the creation of history files" ;
int nRST ;
nRST:long_name = "number of time-steps between restart records" ;
nRST:cycle = "only latest two records are maintained" ;
int ntsAVG ;
ntsAVG:long_name = "starting time-step for accumulation of time-averaged fields" ;
int nAVG ;
nAVG:long_name = "number of time-steps between time-averaged records" ;
int ndefAVG ;
ndefAVG:long_name = "number of time-steps between the creation of average files" ;
double Falpha ;
Falpha:long_name = "Power-law shape barotropic filter parameter" ;
double Fbeta ;
Fbeta:long_name = "Power-law shape barotropic filter parameter" ;
double Fgamma ;
Fgamma:long_name = "Power-law shape barotropic filter parameter" ;
double nl_tnu2(tracer) ;
nl_tnu2:long_name = "nonlinear model Laplacian mixing coefficient for tracers" ;
nl_tnu2:units = "meter2 second-1" ;
double nl_visc2 ;
nl_visc2:long_name = "nonlinear model Laplacian mixing coefficient for momentum" ;
nl_visc2:units = "meter2 second-1" ;
double Akt_bak(tracer) ;
Akt_bak:long_name = "background vertical mixing coefficient for tracers" ;
Akt_bak:units = "meter2 second-1" ;
double Akv_bak ;
Akv_bak:long_name = "background vertical mixing coefficient for momentum" ;
Akv_bak:units = "meter2 second-1" ;
double Akk_bak ;
Akk_bak:long_name = "background vertical mixing coefficient for turbulent energy" ;
Akk_bak:units = "meter2 second-1" ;
double Akp_bak ;
Akp_bak:long_name = "background vertical mixing coefficient for length scale" ;
Akp_bak:units = "meter2 second-1" ;
double rdrg ;
rdrg:long_name = "linear drag coefficient" ;
rdrg:units = "meter second-1" ;
double rdrg2 ;
rdrg2:long_name = "quadratic drag coefficient" ;
double Zob ;
Zob:long_name = "bottom roughness" ;
Zob:units = "meter" ;
double Zos ;
Zos:long_name = "surface roughness" ;
Zos:units = "meter" ;
double gls_p ;
gls_p:long_name = "stability exponent" ;
double gls_m ;
gls_m:long_name = "turbulent kinetic energy exponent" ;
double gls_n ;
gls_n:long_name = "turbulent length scale exponent" ;
double gls_cmu0 ;
gls_cmu0:long_name = "stability coefficient" ;
double gls_c1 ;
gls_c1:long_name = "shear production coefficient" ;
double gls_c2 ;
gls_c2:long_name = "dissipation coefficient" ;
double gls_c3m ;
gls_c3m:long_name = "buoyancy production coefficient (minus)" ;
double gls_c3p ;
gls_c3p:long_name = "buoyancy production coefficient (plus)" ;
double gls_sigk ;
gls_sigk:long_name = "constant Schmidt number for TKE" ;
double gls_sigp ;
gls_sigp:long_name = "constant Schmidt number for PSI" ;
double gls_Kmin ;
gls_Kmin:long_name = "minimum value of specific turbulent kinetic energy" ;
double gls_Pmin ;
gls_Pmin:long_name = "minimum Value of dissipation" ;
double Charnok_alpha ;
Charnok_alpha:long_name = "Charnok factor for surface roughness" ;
double Zos_hsig_alpha ;
Zos_hsig_alpha:long_name = "wave amplitude factor for surface roughness" ;
double sz_alpha ;
sz_alpha:long_name = "surface flux from wave dissipation" ;
double CrgBan_cw ;
CrgBan_cw:long_name = "surface flux due to Craig and Banner wave breaking" ;
double Znudg ;
Znudg:long_name = "free-surface nudging/relaxation inverse time scale" ;
Znudg:units = "day-1" ;
double M2nudg ;
M2nudg:long_name = "2D momentum nudging/relaxation inverse time scale" ;
M2nudg:units = "day-1" ;
double M3nudg ;
M3nudg:long_name = "3D momentum nudging/relaxation inverse time scale" ;
M3nudg:units = "day-1" ;
double Tnudg(tracer) ;
Tnudg:long_name = "Tracers nudging/relaxation inverse time scale" ;
Tnudg:units = "day-1" ;
double FSobc_in(boundary) ;
FSobc_in:long_name = "free-surface inflow, nudging inverse time scale" ;
FSobc_in:units = "second-1" ;
double FSobc_out(boundary) ;
FSobc_out:long_name = "free-surface outflow, nudging inverse time scale" ;
FSobc_out:units = "second-1" ;
double M2obc_in(boundary) ;
M2obc_in:long_name = "2D momentum inflow, nudging inverse time scale" ;
M2obc_in:units = "second-1" ;
double M2obc_out(boundary) ;
M2obc_out:long_name = "2D momentum outflow, nudging inverse time scale" ;
M2obc_out:units = "second-1" ;
double Tobc_in(boundary, tracer) ;
Tobc_in:long_name = "tracers inflow, nudging inverse time scale" ;
Tobc_in:units = "second-1" ;
double Tobc_out(boundary, tracer) ;
Tobc_out:long_name = "tracers outflow, nudging inverse time scale" ;
Tobc_out:units = "second-1" ;
double M3obc_in(boundary) ;
M3obc_in:long_name = "3D momentum inflow, nudging inverse time scale" ;
M3obc_in:units = "second-1" ;
double M3obc_out(boundary) ;
M3obc_out:long_name = "3D momentum outflow, nudging inverse time scale" ;
M3obc_out:units = "second-1" ;
double rho0 ;
rho0:long_name = "mean density used in Boussinesq approximation" ;
rho0:units = "kilogram meter-3" ;
double gamma2 ;
gamma2:long_name = "slipperiness parameter" ;
int LtracerSrc(tracer) ;
LtracerSrc:long_name = "tracer point sources and sink activation switch" ;
LtracerSrc:flag_values = 0, 1 ;
LtracerSrc:flag_meanings = ".FALSE. .TRUE." ;
int spherical ;
spherical:long_name = "grid type logical switch" ;
spherical:flag_values = 0, 1 ;
spherical:flag_meanings = "Cartesian spherical" ;
double xl ;
xl:long_name = "domain length in the XI-direction" ;
xl:units = "meter" ;
double el ;
el:long_name = "domain length in the ETA-direction" ;
el:units = "meter" ;
int Vtransform ;
Vtransform:long_name = "vertical terrain-following transformation equation" ;
int Vstretching ;
Vstretching:long_name = "vertical terrain-following stretching function" ;
double theta_s ;
theta_s:long_name = "S-coordinate surface control parameter" ;
double theta_b ;
theta_b:long_name = "S-coordinate bottom control parameter" ;
double Tcline ;
Tcline:long_name = "S-coordinate surface/bottom layer width" ;
Tcline:units = "meter" ;
double hc ;
hc:long_name = "S-coordinate parameter, critical depth" ;
hc:units = "meter" ;
double s_rho(s_rho) ;
s_rho:long_name = "S-coordinate at RHO-points" ;
s_rho:valid_min = -1. ;
s_rho:valid_max = 0. ;
s_rho:positive = "up" ;
s_rho:standard_name = "ocean_s_coordinate_g1" ;
s_rho:formula_terms = "s: s_rho C: Cs_r eta: zeta depth: h depth_c: hc" ;
s_rho:field = "s_rho, scalar" ;
double s_w(s_w) ;
s_w:long_name = "S-coordinate at W-points" ;
s_w:valid_min = -1. ;
s_w:valid_max = 0. ;
s_w:positive = "up" ;
s_w:standard_name = "ocean_s_coordinate_g1" ;
s_w:formula_terms = "s: s_w C: Cs_w eta: zeta depth: h depth_c: hc" ;
s_w:field = "s_w, scalar" ;
double Cs_r(s_rho) ;
Cs_r:long_name = "S-coordinate stretching curves at RHO-points" ;
Cs_r:valid_min = -1. ;
Cs_r:valid_max = 0. ;
Cs_r:field = "Cs_r, scalar" ;
double Cs_w(s_w) ;
Cs_w:long_name = "S-coordinate stretching curves at W-points" ;
Cs_w:valid_min = -1. ;
Cs_w:valid_max = 0. ;
Cs_w:field = "Cs_w, scalar" ;
double ocean_time(ocean_time) ;
ocean_time:long_name = "time since initialization" ;
ocean_time:units = "seconds since 0001-01-01 00:00:00" ;
ocean_time:calendar = "julian" ;
ocean_time:field = "time, scalar, series" ;
float zeta(ocean_time, eta_rho, xi_rho) ;
zeta:long_name = "free-surface" ;
zeta:units = "meter" ;
zeta:time = "ocean_time" ;
zeta:coordinates = "lon_rho lat_rho ocean_time" ;
zeta:field = "free-surface, scalar, series" ;
zeta:_FillValue = 1.e+37f ;
float ubar(ocean_time, eta_u, xi_u) ;
ubar:long_name = "vertically integrated u-momentum component" ;
ubar:units = "meter second-1" ;
ubar:time = "ocean_time" ;
ubar:coordinates = "lon_u lat_u ocean_time" ;
ubar:field = "ubar-velocity, scalar, series" ;
ubar:_FillValue = 1.e+37f ;
float vbar(ocean_time, eta_v, xi_v) ;
vbar:long_name = "vertically integrated v-momentum component" ;
vbar:units = "meter second-1" ;
vbar:time = "ocean_time" ;
vbar:coordinates = "lon_v lat_v ocean_time" ;
vbar:field = "vbar-velocity, scalar, series" ;
vbar:_FillValue = 1.e+37f ;
float u(ocean_time, s_rho, eta_u, xi_u) ;
u:long_name = "u-momentum component" ;
u:units = "meter second-1" ;
u:time = "ocean_time" ;
u:coordinates = "lon_u lat_u s_rho ocean_time" ;
u:field = "u-velocity, scalar, series" ;
u:_FillValue = 1.e+37f ;
float v(ocean_time, s_rho, eta_v, xi_v) ;
v:long_name = "v-momentum component" ;
v:units = "meter second-1" ;
v:time = "ocean_time" ;
v:coordinates = "lon_v lat_v s_rho ocean_time" ;
v:field = "v-velocity, scalar, series" ;
v:_FillValue = 1.e+37f ;
float w(ocean_time, s_w, eta_rho, xi_rho) ;
w:long_name = "vertical momentum component" ;
w:units = "meter second-1" ;
w:time = "ocean_time" ;
w:coordinates = "lon_rho lat_rho s_w ocean_time" ;
w:field = "w-velocity, scalar, series" ;
w:_FillValue = 1.e+37f ;
float temp(ocean_time, s_rho, eta_rho, xi_rho) ;
temp:long_name = "potential temperature" ;
temp:units = "Celsius" ;
temp:time = "ocean_time" ;
temp:coordinates = "lon_rho lat_rho s_rho ocean_time" ;
temp:field = "temperature, scalar, series" ;
temp:_FillValue = 1.e+37f ;
float salt(ocean_time, s_rho, eta_rho, xi_rho) ;
salt:long_name = "salinity" ;
salt:time = "ocean_time" ;
salt:coordinates = "lon_rho lat_rho s_rho ocean_time" ;
salt:field = "salinity, scalar, series" ;
salt:_FillValue = 1.e+37f ;
float rho(ocean_time, s_rho, eta_rho, xi_rho) ;
rho:long_name = "density anomaly" ;
rho:units = "kilogram meter-3" ;
rho:time = "ocean_time" ;
rho:coordinates = "lon_rho lat_rho s_rho ocean_time" ;
rho:field = "density, scalar, series" ;
rho:_FillValue = 1.e+37f ;
float AKv(ocean_time, s_w, eta_rho, xi_rho) ;
AKv:long_name = "vertical viscosity coefficient" ;
AKv:units = "meter2 second-1" ;
AKv:time = "ocean_time" ;
AKv:coordinates = "lon_rho lat_rho s_w ocean_time" ;
AKv:field = "AKv, scalar, series" ;
float AKs(ocean_time, s_w, eta_rho, xi_rho) ;
AKs:long_name = "salinity vertical diffusion coefficient" ;
AKs:units = "meter2 second-1" ;
AKs:time = "ocean_time" ;
AKs:coordinates = "lon_rho lat_rho s_w ocean_time" ;
AKs:field = "AKs, scalar, series" ;
float tke(ocean_time, s_w, eta_rho, xi_rho) ;
tke:long_name = "turbulent kinetic energy" ;
tke:units = "meter2 second-2" ;
tke:time = "ocean_time" ;
tke:coordinates = "lon_rho lat_rho s_w ocean_time" ;
tke:field = "tke, scalar, series" ;
float gls(ocean_time, s_w, eta_rho, xi_rho) ;
gls:long_name = "turbulent generic length scale" ;
gls:units = "meter3 second-2" ;
gls:time = "ocean_time" ;
gls:coordinates = "lon_rho lat_rho s_w ocean_time" ;
gls:field = "gls, scalar, series" ;
float bustr(ocean_time, eta_u, xi_u) ;
bustr:long_name = "bottom u-momentum stress" ;
bustr:units = "newton meter-2" ;
bustr:time = "ocean_time" ;
bustr:coordinates = "lon_u lat_u ocean_time" ;
bustr:field = "bottom u-momentum stress, scalar, series" ;
bustr:_FillValue = 1.e+37f ;
float bvstr(ocean_time, eta_v, xi_v) ;
bvstr:long_name = "bottom v-momentum stress" ;
bvstr:units = "newton meter-2" ;
bvstr:time = "ocean_time" ;
bvstr:coordinates = "lon_v lat_v ocean_time" ;
bvstr:field = "bottom v-momentum stress, scalar, series" ;
bvstr:_FillValue = 1.e+37f ;
// global attributes:
:file = "./Lee.nc" ;
:format = "netCDF-3 classic file" ;
:Conventions = "CF-1.4" ;
:type = "ROMS/TOMS history file" ;
:title = "ROMS3.0 - Chesapeake Bay Application" ;
:rst_file = "./Lee_rst.nc" ;
:his_file = "./Lee.nc" ;
:avg_base = "./Lee_avg" ;
:grd_file = "/home/wzhu/chesapeake_sed/input/cpb_grd_160x240.nc" ;
:ini_file = "/home/wzhu/chesapeake_sed/input/cpb_ini_160x240_Lee.nc" ;
:frc_file_01 = "/home/wzhu/chesapeake_sed/input/cpb_frc_160x240_Lee_bulk_lwrad_down.nc" ;
:frc_file_02 = "/home/wzhu/chesapeake_sed/input/cpb_frc_160x240_Lee_bulk_Pair.nc" ;
:frc_file_03 = "/home/wzhu/chesapeake_sed/input/cpb_frc_160x240_Lee_bulk_Qair.nc" ;
:frc_file_04 = "/home/wzhu/chesapeake_sed/input/cpb_frc_160x240_Lee_bulk_swrad.nc" ;
:frc_file_05 = "/home/wzhu/chesapeake_sed/input/cpb_frc_160x240_Lee_bulk_Tair.nc" ;
:frc_file_06 = "/home/wzhu/chesapeake_sed/input/cpb_frc_160x240_Lee_bulk_Uwind.nc" ;
:frc_file_07 = "/home/wzhu/chesapeake_sed/input/cpb_frc_160x240_Lee_bulk_Vwind.nc" ;
:frc_file_08 = "/home/wzhu/chesapeake_sed/input/cpb_frc_160x240_Lee_river.nc" ;
:bry_file = "/home/wzhu/chesapeake_sed/input/cpb_bry_160x240_Lee.nc" ;
:svn_url = "https://www.myroms.org/svn/src/trunk" ;
:svn_rev = "exported" ;
:code_dir = "/home/wzhu/chesapeake_sed/roms34_revised" ;
:header_dir = "/home/wzhu/chesapeake_sed" ;
:header_file = "chesapeake.h" ;
:os = "Linux" ;
:cpu = "x86_64" ;
:compiler_system = "ifort" ;
:compiler_command = "/usr/bin/ifort" ;
:compiler_flags = "-heap-arrays -fp-model precise -ip -O3 -xW -free" ;
:tiling = "004x004" ;
:history = "ROMS/TOMS, Version 3.4, Tuesday - November 6, 2012 - 3:43:37 PM" ;
:ana_file = "ROMS/Functionals/ana_btflux.h, ROMS/Functionals/ana_nudgcoef.h, ROMS/Functionals/ana_rain.h, ROMS/Functionals/ana_stflux.h" ;
:CPP_options = "chesapeake, ATM_PRESS, ANA_BSFLUX, ANA_BTFLUX, ANA_RAIN, ANA_SSFLUX, ASSUMED_SHAPE, AVERAGES, BULK_FLUXES, CURVGRID, DOUBLE_PRECISION, EAST_FSCHAPMAN, EAST_M2FLATHER, EAST_M3RADIATION, EAST_TNUDGING, EAST_TRADIATION, EMINUSP, GLS_MIXING, KANTHA_CLAYSON, LONGWAVE_OUT, MASKING, MIX_GEO_TS, MIX_GEO_UV, NONLINEAR, NONLIN_EOS, NORTHERN_WALL, NO_WRITE_GRID, POWER_LAW, PRSGRD31, PROFILE, *PSOURCE_FSCHAPMAN, K_GSCHEME, RHO_SURF, !RST_SINGLE, SALINITY, SOLVE3D, SOUTHERN_WALL, SPLINES, TS_MPDATA, TS_DIF2, TS_PSOURCE, UV_ADV, UV_COR, UV_U3HADVECTION, UV_SADVECTION, UV_LOGDRAG, UV_PSOURCE, UV_VIS2, VAR_RHO_2D, WESTERN_WALL" ;
}
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
I think the grid is 160x240. The contents in my last reply are the header information of the Lee.nc.kate wrote:Processes usually get killed for running beyond some limit - time limit, open files limit, memory limit. I can't tell which you ran into. How big is your grid? Did it hang there trying to write for a very long time? Did you get any output file at all?
My memory information is as follows:
Code: Select all
total used free shared buffers cached
Mem: 7117260 156812 6960448 0 2936 22316
-/+ buffers/cache: 131560 6985700
Swap: 7335932 24032 7311900
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
The memory seems big enough - that is a smallish grid. What are your personal limits? In csh/tcsh, try:
In bash, try:
Code: Select all
delta.arsc.edu 216% limit
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 10240 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 41984
Code: Select all
bash-3.2$ ulimit -a
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 41984
max locked memory (kbytes, -l) 32
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 10240
cpu time (seconds, -t) unlimited
max user processes (-u) 41984
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
Thank you for reply.
When I typed 'ulimit -a', it displayed:
When I typed 'ulimit -a', it displayed:
Code: Select all
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 55260
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 55260
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
The only thing I see there is the stack size limit, though my experience has been a seg fault, rather than "killed" as the message.
One thing you can try with the upwelling problem is simply increasing the values of Lm, Mm, N to see if larger values fail as your domain did.
One thing you can try with the upwelling problem is simply increasing the values of Lm, Mm, N to see if larger values fail as your domain did.
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
Thank you.kate wrote:The only thing I see there is the stack size limit, though my experience has been a seg fault, rather than "killed" as the message.
One thing you can try with the upwelling problem is simply increasing the values of Lm, Mm, N to see if larger values fail as your domain did.
But what and where are the Lm, Mm, and N? Are they in the 'build.bash' file?
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
No, they're in the ocean_upwelling.in.
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
I have done that, when I double increase the values, it is OK; when I thrice increase the values or more, it says 'Segmentation fault (core dumped)', but does not dispaly 'killed'.kate wrote:No, they're in the ocean_upwelling.in.
Then I compared the 'ocean_upwelling.in' file with my domain 'Lee.in' file, I found that the most different segment was the 'Time-Stepping parameters'.
In the ocean_upwelling.in, it is:
Code: Select all
NTIMES == 1440
DT == 300.0d0
NDTFAST == 30
Code: Select all
NTIMES == 2449920 ! 1276 days(2009-1-1 to 2012-06-30) x 1920 x 1 baroclinic steps/day
DT == 45.0d0
NDTFAST == 30
In the upwelling.log file:
Code: Select all
NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00001440)
STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
0 0 00:00:00 0.000000E+00 6.579497E+02 6.579497E+02 3.884376E+11
DEF_HIS - creating history file: ocean_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file: ocean_avg.nc
DEF_DIAGS - creating diagnostics file: ocean_dia.nc
1 0 00:05:00 3.268255E-13 6.579497E+02 6.579497E+02 3.884376E+11
2 0 00:10:00 6.503587E-12 6.579497E+02 6.579497E+02 3.884376E+11
Code: Select all
NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 01866241 - 02449920)
GET_NGFLD - river runoff mass transport, t = 972 00:15:01
(Rec=0098, Index=1, File: cpb_frc_160x240_Lee_river.nc)
(Tmin= 971.0000 Tmax= 1276.9896)
(Min = -7.78717957E+01 Max = 2.34181738E+03)
GET_2DFLD - surface u-wind component, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_Uwind.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = -3.60082650E+00 Max = 5.00677049E-01)
GET_2DFLD - surface v-wind component, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_Vwind.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = -6.79969215E+00 Max = 2.13858318E+00)
GET_2DFLD - surface air pressure, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_Pair.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 9.97390686E+02 Max = 1.01985712E+03)
GET_2DFLD - solar shortwave radiation flux, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_swrad.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - downwelling longwave radiation flux, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_lwrad_down.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 7.59754687E-05 Max = 9.35231107E-05)
GET_2DFLD - surface air temperature, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_Tair.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 1.39307537E+01 Max = 2.66532497E+01)
GET_2DFLD - surface air relative humidity, t = 972 01:00:01
(Rec=0026, Index=2, File: cpb_frc_160x240_Lee_bulk_Qair.nc)
(Tmin= 971.0000 Tmax= 1276.0000)
(Min = 5.54842453E-01 Max = 9.33233109E-01)
GET_NGFLD - free-surface eastern boundary condition, t = 972 01:00:01
(Rec=0026, Index=1, File: cpb_bry_160x240_Lee.nc)
(Tmin= 971.0000 Tmax= 1276.9584)
(Min = -4.71466017E+00 Max = 9.39512134E-01)
GET_NGFLD - temperature eastern boundary condition, t = 987 00:00:00
(Rec=0021, Index=1, File: cpb_bry_160x240_Lee.nc)
(Tmin= 379.0000 Tmax= 1809.0000)
(Min = 2.05826626E+01 Max = 2.47020512E+01)
GET_NGFLD - salinity eastern boundary condition, t = 987 00:00:00
(Rec=0021, Index=1, File: cpb_bry_160x240_Lee.nc)
(Tmin= 379.0000 Tmax= 1809.0000)
(Min = 3.23332100E+01 Max = 3.39163857E+01)
STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
1866240 972 00:00:00 0.000000E+00 7.957775E+01 7.957775E+01 3.542731E+11
DEF_HIS - creating history file: Lee_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file: Lee_avg.nc
Killed
Code: Select all
! Output history, average, diagnostic files parameters.
LDEFOUT == T
NHIS == 1920 ! 4 hours
NDEFHIS == 0!57600 ! 30 days
NTSAVG == 1
NAVG == 1920 ! 24 hours
NDEFAVG == 0!57600 ! 30 days
NTSDIA == 1
NDIA == 1920 ! 24 hours
NDEFDIA == 0!57600 ! 30 days
Code: Select all
! Output NetCDF file names, [1:Ngrids].
GSTNAME == /dev/null !./test_gst.nc
RSTNAME == Lee_rst.nc
HISNAME == Lee_his.nc
TLMNAME == /dev/null !/home/jiapeng/yunli/case_1996_amp_wind/test_tlm.nc
TLFNAME == /dev/null !/home/jiapeng/yunli/case_1996_amp_wind/test_tlf.nc
ADJNAME == /dev/null !/home/jiapeng/yunli/case_1996_amp_wind/test_adj.nc
AVGNAME == Lee_avg.nc
DIANAME == Lee_dia.nc
STANAME == /dev/null !/home/jiapeng/yunli/case_1996_amp_wind/test_sta.nc
FLTNAME == /dev/null !/home/jiapeng/yunli/case_1996_amp_wind/test_flt.nc
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
I have had this error message before when my set-up files are in a directory which is several sub-directories away from my home directory eg. /home/subdir1/subdir2/subdir3/subdir4/run
By copying the exact same set-up files to a folder /home/run for example I no longer got the error.
I don't understand why but thought I'd mention it in case it solves your problem.
By copying the exact same set-up files to a folder /home/run for example I no longer got the error.
I don't understand why but thought I'd mention it in case it solves your problem.
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
Hi ckerry, thanks for your help.ckerry wrote:I have had this error message before when my set-up files are in a directory which is several sub-directories away from my home directory eg. /home/subdir1/subdir2/subdir3/subdir4/run
By copying the exact same set-up files to a folder /home/run for example I no longer got the error.
I don't understand why but thought I'd mention it in case it solves your problem.
I have done that as you suggested, but I got the same result. Did you see the whole conversations between Kate and I? and do you have any other suggestions?
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
Hi Friends， How are you doing these days?kate wrote:No, they're in the ocean_upwelling.in.
I have not got the problem silved yet, but when I type:sudo tail -f /var/log/syslog to see the syslog:
Code: Select all
Nov 14 18:33:18 lsvm kernel: [1244276.692068] [22113] 1003 22113 5902 1 0 0 0 bash
Nov 14 18:33:18 lsvm kernel: [1244276.692072] [ 1927] 1003 1927 13527 0 3 0 0 vi
Nov 14 18:33:18 lsvm kernel: [1244276.692075] [21270] 0 21270 19951 1 0 0 0 sshd
Nov 14 18:33:18 lsvm kernel: [1244276.692078] [21448] 1003 21448 20131 19 2 0 0 sshd
Nov 14 18:33:18 lsvm kernel: [1244276.692081] [21449] 1003 21449 3288 1 0 0 0 sftp-server
Nov 14 18:33:18 lsvm kernel: [1244276.692091] [23332] 1003 23332 6818 27 0 0 0 bash
Nov 14 18:33:18 lsvm kernel: [1244276.692094] [23466] 1003 23466 4901315 1731830 0 0 0 oceanS
Nov 14 18:33:18 lsvm kernel: [1244276.692098] [23582] 0 23582 1077 20 0 0 0 sleep
Nov 14 18:33:18 lsvm kernel: [1244276.692100] Out of memory: Kill process 23466 (oceanS) score 986 or sacrifice child
Nov 14 18:33:18 lsvm kernel: [1244276.692124] Killed process 23466 (oceanS) total-vm:19605260kB, anon-rss:6927320kB, file-rss:0kB
Any help will be highly appreciated!
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
If you are running on Linux, a friend here suggests using valgrind to find memory leaks:
1) compile with -g
then run program with:
2a) valgrind --leak-check=summary --track-origins=yes ./a.out
or
2b) valgrind --leak-check=full --track-origins=yes ./a.out
Re: ERROR: Abnormal termination: NetCDF OUTPUT.
The problem was ultimately solved. The server is a single-processor machine, it is not so powerful to run this model. when I changed to a more powerful server, it worked.
Thanks to all the kind people: kate and ckerry.
Best.
Thanks to all the kind people: kate and ckerry.
Best.