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ROMS/TOMS

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PostPosted: Wed Jun 22, 2016 1:40 pm 
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Joined: Fri Jun 17, 2016 1:55 pm
Posts: 4
Location: INDIA
Hi,
I am quite new to ROMS and from computer science domain.
I want to do some bench marking on our server (Linux OS,256Gb Memory,40 cores) for that I am trying to run it .

but while running I am getting Error like

ROMS/TOMS - Blows up ................ exit_flag: 1


MAIN: Abnormal termination: BLOWUP.



the input .in file configuration is like
Lm == 599 ! Number of I-direction INTERIOR RHO-points
Mm == 881 ! Number of J-direction INTERIOR RHO-points
N == 40 ! Number of vertical levels
and
NtileI == 4 ! I-direction partition
NtileJ == 10 ! J-direction partition

the .nc file grid dimension is
xi_rho = 601 ;
xi_u = 600 ;
xi_v = 601 ;
eta_rho = 883 ;
eta_u = 883 ;
eta_v = 882 ;
s_rho = 40 ;
s_w = 41 ;

The OutPut/Error I am getting is (mpiexec.hydra -np 40 ./oceanM ocean_india.in )



INITIAL: Configuring and initializing forward nonlinear model ...
*******

Vertical S-coordinate System, Grid 01:

level S-coord Cs-curve Z at hmin at hc half way at hmax

40 0.0000000 0.0000000 0.000 0.000 0.000 0.000
39 -0.0250000 -0.0000309 0.000 0.000 0.000 0.000
38 -0.0500000 -0.0001247 0.000 0.000 0.000 0.000
37 -0.0750000 -0.0002842 0.000 0.000 0.000 0.000
36 -0.1000000 -0.0005144 0.000 0.000 0.000 0.000
35 -0.1250000 -0.0008222 0.000 0.000 0.000 0.000
34 -0.1500000 -0.0012170 0.000 0.000 0.000 0.000
33 -0.1750000 -0.0017111 0.000 0.000 0.000 0.000
32 -0.2000000 -0.0023196 0.000 0.000 0.000 0.000
31 -0.2250000 -0.0030610 0.000 0.000 0.000 0.000
30 -0.2500000 -0.0039582 0.000 0.000 0.000 0.000
29 -0.2750000 -0.0050385 0.000 0.000 0.000 0.000
28 -0.3000000 -0.0063350 0.000 0.000 0.000 0.000
27 -0.3250000 -0.0078873 0.000 0.000 0.000 0.000
26 -0.3500000 -0.0097429 0.000 0.000 0.000 0.000
25 -0.3750000 -0.0119584 0.000 0.000 0.000 0.000
24 -0.4000000 -0.0146013 0.000 0.000 0.000 0.000
23 -0.4250000 -0.0177522 0.000 0.000 0.000 0.000
22 -0.4500000 -0.0215067 0.000 0.000 0.000 0.000
21 -0.4750000 -0.0259789 0.000 0.000 0.000 0.000
20 -0.5000000 -0.0313040 0.000 0.000 0.000 0.000
19 -0.5250000 -0.0376427 0.000 0.000 0.000 0.000
18 -0.5500000 -0.0451859 0.000 0.000 0.000 0.000
17 -0.5750000 -0.0541596 0.000 0.000 0.000 0.000
16 -0.6000000 -0.0648314 0.000 0.000 0.000 0.000
15 -0.6250000 -0.0775180 0.000 0.000 0.000 0.000
14 -0.6500000 -0.0925932 0.000 0.000 0.000 0.000
13 -0.6750000 -0.1104976 0.000 0.000 0.000 0.000
12 -0.7000000 -0.1317496 0.000 0.000 0.000 0.000
11 -0.7250000 -0.1569575 0.000 0.000 0.000 0.000
10 -0.7500000 -0.1868327 0.000 0.000 0.000 0.000
9 -0.7750000 -0.2222045 0.000 0.000 0.000 0.000
8 -0.8000000 -0.2640351 0.000 0.000 0.000 0.000
7 -0.8250000 -0.3134348 0.000 0.000 0.000 0.000
6 -0.8500000 -0.3716761 0.000 0.000 0.000 0.000
5 -0.8750000 -0.4402058 0.000 0.000 0.000 0.000
4 -0.9000000 -0.5206513 0.000 0.000 0.000 0.000
3 -0.9250000 -0.6148197 0.000 0.000 0.000 0.000
2 -0.9500000 -0.7246838 0.000 0.000 0.000 0.000
1 -0.9750000 -0.8523498 0.000 0.000 0.000 0.000
0 -1.0000000 -1.0000000 0.000 0.000 0.000 0.000

Time Splitting Weights for Grid 01: ndtfast = 5 nfast = 7
==================================

Primary Secondary Accumulated to Current Step

1 0.0119306869089341 0.2000000000000000 0.0119306869089341 0.2000000000000000
2 0.0475049776008205 0.1976138626182131 0.0594356645097546 0.3976138626182131
3 0.1047629417620785 0.1881128670980491 0.1641986062718331 0.5857267297162622
4 0.1760826281731955 0.1671602787456334 0.3402812344450286 0.7528870084618955
5 0.2416469636634478 0.1319437531109943 0.5819281981084765 0.8848307615728898
6 0.2602974116474964 0.0836143603783047 0.8422256097559729 0.9684451219511945
7 0.1577743902440273 0.0315548780488055 1.0000000000000002 0.9999999999999999

ndtfast, nfast = 5 7 nfast/ndtfast = 1.40000

Centers of gravity and integrals (values must be 1, 1, approx 1/2, 1, 1):

1.000000000000 1.084198606272 0.542099303136 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.00000

Metrics information for Grid 01:
===============================

Minimum X-grid spacing, DXmin = 1.00000000E+00 km
Maximum X-grid spacing, DXmax = 1.00000000E+00 km
Minimum Y-grid spacing, DYmin = 1.00000000E+00 km
Maximum Y-grid spacing, DYmax = 1.00000000E+00 km
Minimum Z-grid spacing, DZmin = 0.00000000E+00 m
Maximum Z-grid spacing, DZmax = 0.00000000E+00 m

Minimum barotropic Courant Number = 0.00000000E+00
Maximum barotropic Courant Number = 0.00000000E+00
Maximum Coriolis Courant Number = 2.47800000E-03

GET_NGFLD - free-surface western boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -4.61830586E-01 Max = 0.00000000E+00)
GET_NGFLD - free-surface southern boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -2.39182904E-01 Max = 0.00000000E+00)
GET_NGFLD - 2D u-momentum western boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -1.99090600E-01 Max = 6.18652590E-02)
GET_NGFLD - 2D v-momentum western boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -4.85758297E-02 Max = 3.84716615E-02)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -1.44191995E-01 Max = 3.66550982E-02)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -4.45211306E-02 Max = 3.96983512E-02)
GET_NGFLD - 3D u-momentum western boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -2.52713412E-01 Max = 2.72067100E-01)
GET_NGFLD - 3D v-momentum western boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -1.51217207E-01 Max = 1.91503897E-01)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -2.91490614E-01 Max = 5.03728628E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -9.51866090E-01 Max = 4.69759792E-01)
GET_NGFLD - temperature western boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = 0.00000000E+00 Max = 3.02323895E+01)
GET_NGFLD - salinity western boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = 0.00000000E+00 Max = 3.65302200E+01)
GET_NGFLD - temperature southern boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = 0.00000000E+00 Max = 3.17947292E+01)
GET_NGFLD - salinity southern boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = 0.00000000E+00 Max = 3.63209915E+01)

Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = NaN (Beckmann and Haidvogel)
rx1 = NaN (Haney)

Initial basin volumes: TotVolume = 0.0000000000E+00 m3
MinVolume = 0.0000000000E+00 m3
MaxVolume = 0.0000000000E+00 m3
Max/Min = 0.0000000000E+00

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00028800)

GET_NGFLD - free-surface western boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -4.62206513E-01 Max = 0.00000000E+00)
GET_NGFLD - free-surface southern boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -2.40414307E-01 Max = 0.00000000E+00)
GET_NGFLD - 2D u-momentum western boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -1.70969397E-01 Max = 6.63159266E-02)
GET_NGFLD - 2D v-momentum western boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -4.88123894E-02 Max = 3.76734100E-02)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -2.32917905E-01 Max = 3.50951888E-02)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -4.49662507E-02 Max = 1.17154799E-01)
GET_NGFLD - 3D u-momentum western boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -2.05577299E-01 Max = 2.85452396E-01)
GET_NGFLD - 3D v-momentum western boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -1.71727493E-01 Max = 2.02047005E-01)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -4.01514113E-01 Max = 5.12598574E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = -7.88119018E-01 Max = 4.51970607E-01)
GET_NGFLD - temperature western boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = 0.00000000E+00 Max = 3.02420902E+01)
GET_NGFLD - salinity western boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = 0.00000000E+00 Max = 3.65283089E+01)
GET_NGFLD - temperature southern boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = 0.00000000E+00 Max = 3.18051491E+01)
GET_NGFLD - salinity southern boundary condition, t = 9136 12:00:00
(Rec=0000371, Index=1, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = 0.00000000E+00 Max = 3.63229103E+01)

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed

0 9135 12:00:00 NaN NaN NaN 0.000000E+00
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 2.337052E-04

Elapsed CPU time (seconds):

Node # 0 CPU: 3.243
Node # 2 CPU: 3.103
Node # 4 CPU: 3.095
Node # 8 CPU: 3.111
Node # 10 CPU: 3.103
Node # 13 CPU: 3.087
Node # 14 CPU: 3.087
Node # 15 CPU: 3.087
Node # 17 CPU: 3.095
Node # 18 CPU: 3.088
Node # 23 CPU: 3.086
Node # 33 CPU: 3.098
Node # 36 CPU: 3.098
Node # 21 CPU: 3.087
Node # 25 CPU: 3.086
Node # 30 CPU: 3.086
Node # 35 CPU: 3.086
Node # 37 CPU: 3.087
Node # 19 CPU: 3.087
Node # 26 CPU: 3.085
Node # 28 CPU: 3.087
Node # 29 CPU: 3.086
Node # 32 CPU: 3.099
Node # 34 CPU: 3.099
Node # 38 CPU: 3.086
Node # 39 CPU: 3.083
Node # 27 CPU: 3.086
Node # 31 CPU: 3.087
Node # 1 CPU: 3.089
Node # 3 CPU: 3.088
Node # 9 CPU: 3.086
Node # 12 CPU: 3.087
Node # 16 CPU: 3.109
Node # 20 CPU: 3.087
Node # 24 CPU: 3.087
Node # 5 CPU: 3.088
Node # 7 CPU: 3.088
Node # 6 CPU: 3.088
Node # 11 CPU: 3.088
Node # 22 CPU: 3.086
Total: 123.768

Nonlinear model elapsed time profile, Grid: 01

Allocation and array initialization .............. 30.878 (24.9481 %)
Ocean state initialization ....................... 90.291 (72.9520 %)
Reading of input data ............................ 82.147 (66.3716 %)
Processing of input data ......................... 0.132 ( 0.1064 %)
Computation of global information integrals ...... 0.412 ( 0.3331 %)
2D/3D coupling, vertical metrics ................. 2.718 ( 2.1963 %)
Omega vertical velocity .......................... 0.313 ( 0.2526 %)
Equation of state for seawater ................... 0.946 ( 0.7647 %)
Total: 207.837 167.9249

Nonlinear model message Passage profile, Grid: 01

Message Passage: 2D halo exchanges ............... 2.960 ( 2.3917 %)
Message Passage: 3D halo exchanges ............... 0.918 ( 0.7416 %)
Message Passage: 4D halo exchanges ............... 0.124 ( 0.1000 %)
Message Passage: data broadcast .................. 79.873 (64.5346 %)
Message Passage: data reduction .................. 0.182 ( 0.1473 %)
Total: 84.057 67.9153

All percentages are with respect to total time = 123.768


ROMS/TOMS - Output NetCDF summary for Grid 01:

Analytical header files used:

ROMS/Functionals/ana_btflux.h
ROMS/Functionals/ana_grid.h
ROMS/Functionals/ana_initial.h
ROMS/Functionals/ana_smflux.h
ROMS/Functionals/ana_stflux.h

ROMS/TOMS - Blows up ................ exit_flag: 1


MAIN: Abnormal termination: BLOWUP.


Please help me to solve this issue,
thanks in advance


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PostPosted: Thu Jun 23, 2016 1:11 am 
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Posts: 3487
Location: IMS/UAF, USA
You have:

Code:
level S-coord Cs-curve Z at hmin at hc half way at hmax

40 0.0000000 0.0000000 0.000 0.000 0.000 0.000
39 -0.0250000 -0.0000309 0.000 0.000 0.000 0.000
38 -0.0500000 -0.0001247 0.000 0.000 0.000 0.000
37 -0.0750000 -0.0002842 0.000 0.000 0.000 0.000
36 -0.1000000 -0.0005144 0.000 0.000 0.000 0.000
35 -0.1250000 -0.0008222 0.000 0.000 0.000 0.000
34 -0.1500000 -0.0012170 0.000 0.000 0.000 0.000
You cannot have zero depth. How are you providing the depth?


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PostPosted: Thu Jun 23, 2016 9:42 am 
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Joined: Fri Jun 17, 2016 1:55 pm
Posts: 4
Location: INDIA
Hi Kate,
Thanks for you quick reply...

I tried to figure out the issue but couldn't ,So I compiled a different version(3.7) but I was stuck with some other error like
GET_VARCOORDS - Cannot find "coordinates" attribute for variable: U10
in file: /home/somanath/INCUSE/input_files/U10.nc

This attribute is needed to interpolate input data
to model grid. Following CF compliance, we need:

float my_var(time, lat, lon) ;
my_var:long_name = "my variable long name" ;
my_var:units = "my variable units" ;
my_var:coordinates = "lon lat" ;
my_var:time = "my_var_time" ;


GET_2DFLD - error while reading variable: U10 at TIME index = 19

Elapsed CPU time (seconds):

Node # 0 CPU: 12.928

ROMS/TOMS - Output NetCDF summary for Grid 01:

ROMS/TOMS - Input error ............. exit_flag: 2



The U10.nc file is something like
netcdf U10 {
dimensions:
lon = 401 ;
lat = 281 ;
T_00Z = UNLIMITED ; // (121 currently)
variables:
double lon(lon) ;


The value of U10 in varinfo.dat

'U10' ! Input
'surface u-wind component'
'meter second-1' ! [m/s]
'u-wind, scalar, series'
'T_00Z'
'idUair'
'r2dvar'
1.0d0


The Dimension in cean_avg_9136.nc is

netcdf ocean_avg_9136 {
dimensions:
xi_rho = 601 ;
xi_u = 600 ;
xi_v = 601 ;
xi_psi = 600 ;
eta_rho = 883 ;
eta_u = 883 ;
eta_v = 882 ;
eta_psi = 882 ;
s_rho = 40 ;
s_w = 41 ;
tracer = 14 ;
boundary = 4 ;
ocean_time = UNLIMITED ; // (1 currently)


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PostPosted: Fri Jun 24, 2016 5:01 am 
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I can't get to my winds files at the moment, but the ncdump of the U10 variable should look like:
Code:
float U10(time, lat, lon) ;
U10:long_name = "my variable long name" ;
U10:units = "my variable units" ;
U10:coordinates = "lon lat" ;
U10:time = "my_var_time" ;
Can you show us the full "ncdump -h" of that file? I assume U10 is on some regular lat,lon grid and you want ROMS to interpolate it to your grid?


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PostPosted: Fri Jun 24, 2016 10:22 am 
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Posts: 4
Location: INDIA
Hi kate,
Thanks a lot, It worked what I did I just added the value in variables part of U10.nc file as you mentioned.
But Now I am stuck with another error
INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.


GET_NGFLD - O2 western boundary condition, t = 9135 12:00:00
(Rec=0000370, Index=2, File: roms_bry_1x48_2014_2015.nc)
(Tmin= 8766.5000 Tmax= 9495.5000)
(Min = 0.00000000E+00 Max = 2.08586807E+02)

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

Elapsed CPU time (seconds):


INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.
Node # 0 CPU: 15.129

ROMS/TOMS - Output NetCDF summary for Grid 01:

ROMS/TOMS - Input error ............. exit_flag: 2

Node # 3 CPU: 15.118
Node # 4 CPU: 15.118
Node # 5 CPU: 15.118
Node # 6 CPU: 15.117
Node # 8 CPU: 15.117
Node # 9 CPU: 15.117
Node # 10 CPU: 15.117
Node # 11 CPU: 15.117

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.
Node # 12 CPU: 15.117

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.
Node # 13 CPU: 15.117

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.
Node # 14 CPU: 15.117

INQUIRE - unable to find requested variable: NO3_east
in file:
file name is blank, cannot be determined.
Node # 15 CPU: 15.117

ERROR: Abnormal termination: NetCDF INPUT.
REASON: No error
Node # 1 CPU: 15.118
Node # 2 CPU: 15.118
Node # 7 CPU: 15.118


Please check this out


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PostPosted: Fri Jun 24, 2016 2:16 pm 
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The only thing that needs nitrate boundary conditions is one of the biology submodules. Did you turn one of them on?


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PostPosted: Mon Jun 27, 2016 6:57 am 
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yes, I am using the biology module bio_Fennel.in.


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PostPosted: Tue Jun 28, 2016 5:11 am 
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Posts: 449
Location: Rutgers University
Quote:
Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = NaN (Beckmann and Haidvogel)
rx1 = NaN (Haney)

Initial basin volumes: TotVolume = 0.0000000000E+00 m3
MinVolume = 0.0000000000E+00 m3
MaxVolume = 0.0000000000E+00 m3
Max/Min = 0.0000000000E+00


Your ocean depth is zero everywhere.

ROMS reports that you are using an analytical grid from the ana_grid.h functional in your main source trunk:

Quote:
Analytical header files used:

ROMS/Functionals/ana_btflux.h
ROMS/Functionals/ana_grid.h
ROMS/Functionals/ana_initial.h
ROMS/Functionals/ana_smflux.h
ROMS/Functionals/ana_stflux.h


So the modifications you made to ana_grid.h have not set a finite positive bottom depth. You won't get far until you fix that.

_________________
John Wilkin: IMCS Rutgers University
71 Dudley Rd, New Brunswick, NJ 08901-8521, USA. ph: 609-630-0559 jwilkin@rutgers.edu


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PostPosted: Tue Jun 28, 2016 5:38 am 
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Joined: Wed Jul 02, 2003 5:29 pm
Posts: 3487
Location: IMS/UAF, USA
What boundary conditions are you providing for the ecosystem components? How are its LBC options set? Some values require external boundary fields. Do you have some you think it should be reading or do you not have them?


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