blowing up with ubar and vbar with min and max as NaNs

[fagundesmo]

Dear all,

my model is blowing up and, therefore, I was wondering if it has anything to do with ubar and vbar having min and max as NAN values. If so, how could I fix this problem since I've checked my ubar e vbar and both have values except in the borders which are masked with NAN values.


Model Input Parameters: ROMS/TOMS version 3.7
Monday - May 30, 2016 - 3:10:23 PM
-----------------------------------------------------------------------------

Atlantic Equatorial

Operating system : Linux
CPU/hardware : x86_64
Compiler system : ifort
Compiler command : /usr/local/bin/mpif90
Compiler flags : -heap-arrays -fp-model precise -ip -O3 -free -free -free

Input Script :

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

Local Root : /models/roms
Header Dir : /home/roms/projects_roms/matheus/atleq/benchmark/proc2
Header file : atleq.h
Analytical Dir: /home/roms/projects_roms/matheus/atleq/benchmark/proc2/ROMS/Functionals

Resolution, Grid 01: 0903x0321x050, Parallel Nodes: 2, Tiling: 002x001


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

10800 ntimes Number of timesteps for 3-D equations.
1800.000 dt Timestep size (s) for 3-D equations.
30 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.
360 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).
5400 nHIS Number of timesteps between the writing fields
into history file.
360 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
360 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
5400 ndefAVG Number of timesteps between creation of new
time-averaged file.
0.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
0.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
1.0500E-06 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.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
4.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E+00 theta_b S-coordinate bottom control parameter.
300.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
29222.500 dstart Time-stamp assigned to model initialization (days).
19000101.00 time_ref Reference time for units attribute (yyyymmdd.dd)
6.0000E+01 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
6.0000E+01 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
3.0000E+01 Znudg Nudging/relaxation time scale (days)
for free-surface.
3.0000E+01 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
3.0000E+01 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.
5.000 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).
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(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(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt

T Aout(idFsur) Write out averaged free-surface.
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(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt

Output/Input Files:

Output Restart File: river_rst.nc
Output History File: atleq_his.nc
Prefix for Averages Files: atleq_avg
Input Grid File: /home/roms/DATA/grade/Atleq112.nc
Input Nonlinear Initial File: /home/roms/DATA/oceano/roms_ini_SODA_Y1980M1D3.nc
Input Forcing File 01: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-prate.nc
Input Forcing File 02: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-pressfc.nc
Input Forcing File 03: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-q2m.nc
Input Forcing File 04: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-tmp2m.nc
Input Forcing File 05: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-uwnd10m.nc
Input Forcing File 06: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-vwnd10m.nc
Input Boundary File: /home/roms/DATA/oceano/Atleq_bry.nc

Tile partition information for Grid 01: 0903x0321x0050 tiling: 002x001

tile Istr Iend Jstr Jend Npts

0 1 452 1 321 7254600
1 453 903 1 321 7238550

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 452.50 0.50 321.50 RHO-points
1 452.50 903.50 0.50 321.50 RHO-points

0 1.00 452.50 0.50 321.50 U-points
1 452.50 903.00 0.50 321.50 U-points

0 0.50 452.50 1.00 321.00 V-points
1 452.50 903.50 1.00 321.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 926
HaloSizeJ(1) = 662
TileSide(1) = 457
TileSize(1) = 148525


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

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

zeta 1 Chapman Imp Chapman Imp Closed Chapman Imp

ubar 1 Flather Flather Closed Flather

vbar 1 Flather Flather Closed Flather

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

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

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

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

tke 1 Radiation Radiation Closed Radiation

Activated C-preprocessing Options:

ATLEQ Atlantic Equatorial
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
CURVGRID Orthogonal curvilinear grid.
DIFF_GRID Horizontal diffusion coefficient scaled by grid size.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
MIX_GEO_TS Mixing of tracers along geopotential surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
MY25_MIXING Mellor/Yamada Level-2.5 mixing closure.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NO_LBC_ATT Not checking NetCDF global attribute NLM_LBC during restart.
NO_WRITE_GRID Not Writing grid arrays into NetCDF ouput files.
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 Single precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SPLINES Conservative parabolic spline reconstruction.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical 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.
VISC_3DCOEF Horizontal, time-dependent 3D viscosity coefficient.

Process Information:

Node # 0 (pid= 45510) is active.
Node # 1 (pid= 45511) is active.

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

50 0.0000000 0.0000000 0.000 0.000 0.000 0.000
49 -0.0200000 -0.0004958 -0.098 -3.074 -6.466 -7.999
48 -0.0400000 -0.0019848 -0.197 -6.298 -15.151 -20.683
47 -0.0600000 -0.0044722 -0.295 -9.671 -26.067 -38.076
46 -0.0800000 -0.0079665 -0.394 -13.195 -39.233 -60.219
45 -0.1000000 -0.0124794 -0.493 -16.872 -54.675 -87.167
44 -0.1200000 -0.0180260 -0.592 -20.704 -72.428 -118.991
43 -0.1400000 -0.0246241 -0.691 -24.694 -92.529 -155.774
42 -0.1600000 -0.0322941 -0.790 -28.844 -115.027 -197.614
41 -0.1800000 -0.0410591 -0.889 -33.159 -139.971 -244.618
40 -0.2000000 -0.0509440 -0.988 -37.642 -167.417 -296.906
39 -0.2200000 -0.0619756 -1.087 -42.296 -197.426 -354.602
38 -0.2400000 -0.0741814 -1.186 -47.127 -230.059 -417.837
37 -0.2600000 -0.0875898 -1.286 -52.138 -265.380 -486.744
36 -0.2800000 -0.1022287 -1.385 -57.334 -303.450 -561.456
35 -0.3000000 -0.1181254 -1.485 -62.719 -344.330 -642.101
34 -0.3200000 -0.1353048 -1.585 -68.296 -388.078 -728.796
33 -0.3400000 -0.1537894 -1.685 -74.068 -434.741 -821.648
32 -0.3600000 -0.1735973 -1.785 -80.040 -484.362 -920.742
31 -0.3800000 -0.1947414 -1.885 -86.211 -536.968 -1026.138
30 -0.4000000 -0.2172277 -1.985 -92.584 -592.574 -1137.866
29 -0.4200000 -0.2410540 -2.085 -99.158 -651.175 -1255.915
28 -0.4400000 -0.2662085 -2.186 -105.931 -712.743 -1380.229
27 -0.4600000 -0.2926672 -2.286 -112.900 -777.226 -1510.694
26 -0.4800000 -0.3203933 -2.387 -120.059 -844.541 -1647.138
25 -0.5000000 -0.3493346 -2.488 -127.400 -914.571 -1789.314
24 -0.5200000 -0.3794221 -2.588 -134.913 -987.163 -1936.897
23 -0.5400000 -0.4105683 -2.689 -142.585 -1062.120 -2089.473
22 -0.5600000 -0.4426658 -2.790 -150.400 -1139.203 -2246.537
21 -0.5800000 -0.4755864 -2.891 -158.338 -1218.126 -2407.483
20 -0.6000000 -0.5091798 -2.993 -166.377 -1298.552 -2571.603
19 -0.6200000 -0.5432741 -3.094 -174.491 -1380.097 -2738.085
18 -0.6400000 -0.5776758 -3.195 -182.651 -1462.329 -2906.018
17 -0.6600000 -0.6121712 -3.296 -190.826 -1544.771 -3074.392
16 -0.6800000 -0.6465284 -3.397 -198.979 -1626.904 -3242.115
15 -0.7000000 -0.6805007 -3.498 -207.075 -1708.177 -3408.022
14 -0.7200000 -0.7138307 -3.599 -215.075 -1788.014 -3570.900
13 -0.7400000 -0.7462556 -3.701 -222.938 -1865.829 -3729.508
12 -0.7600000 -0.7775137 -3.801 -230.627 -1941.036 -3882.612
11 -0.7800000 -0.8073512 -3.902 -238.103 -2013.069 -4029.015
10 -0.8000000 -0.8355308 -4.003 -245.330 -2081.398 -4167.598
9 -0.8200000 -0.8618395 -4.103 -252.276 -2145.545 -4297.356
8 -0.8400000 -0.8860972 -4.204 -258.915 -2205.109 -4417.440
7 -0.8600000 -0.9081638 -4.304 -265.225 -2259.778 -4527.188
6 -0.8800000 -0.9279462 -4.404 -271.192 -2309.341 -4626.161
5 -0.9000000 -0.9454027 -4.504 -276.810 -2353.707 -4714.163
4 -0.9200000 -0.9605452 -4.603 -282.082 -2392.903 -4791.251
3 -0.9400000 -0.9734393 -4.703 -287.016 -2427.074 -4857.733
2 -0.9600000 -0.9842008 -4.802 -291.630 -2456.480 -4914.155
1 -0.9800000 -0.9929894 -4.901 -295.948 -2481.476 -4961.271
0 -1.0000000 -1.0000000 -5.000 -300.000 -2502.500 -5000.000

Time Splitting Weights for Grid 01: ndtfast = 30 nfast = 42
==================================

Primary Secondary Accumulated to Current Step

1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
12 0.0043042707117221 0.0335513677379153-0.0022367614257356 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864348 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708920 0.0329439123123590 0.0216737068001213 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565097 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906204 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716643 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402368 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399432 0.6603333185976138
21 0.0256737146312911 0.0297153720153352 0.1342125541712342 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524359 0.7189082721405746
23 0.0316613792205220 0.0279045862015855 0.1945237931729578 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236653 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893981 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886213 0.8237939964192927
27 0.0432936737565710 0.0230872677537126 0.3506756411451924 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772280 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880565 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442384 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256415 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325521 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348098 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479478 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213239 0.9738247715198165
36 0.0503158038019030 0.0080591141492892 0.8085423793232269 0.9818838856691057
37 0.0473537721847153 0.0063819206892258 0.8558961515079423 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497611 0.9930692679747334
39 0.0376397765791564 0.0033640675316746 0.9367177506289175 0.9964333355064080
40 0.0305543017255206 0.0021094083123694 0.9672720523544381 0.9985427438187774
41 0.0217382098544504 0.0010909315881854 0.9890102622088885 0.9996336754069628
42 0.0109897377911118 0.0003663245930371 1.0000000000000004 0.9999999999999999

ndtfast, nfast = 30 42 nfast/ndtfast = 1.40000

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

1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.18933

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

Minimum X-grid spacing, DXmin = 8.96492125E+00 km
Maximum X-grid spacing, DXmax = 9.27662045E+00 km
Minimum Y-grid spacing, DYmin = 8.99525215E+00 km
Maximum Y-grid spacing, DYmax = 9.30386323E+00 km
Minimum Z-grid spacing, DZmin = 9.84012919E-02 m
Maximum Z-grid spacing, DZmax = 1.68374265E+02 m

Minimum barotropic Courant Number = 6.39676115E-02
Maximum barotropic Courant Number = 2.09270051E+00
Maximum Coriolis Courant Number = 6.76708721E-02

Horizontal mixing scaled by grid size, GRDMAX = 9.29023185E+00 km

Minimum horizontal viscosity coefficient = 7.48339491E+01 m2/s
Maximum horizontal viscosity coefficient = 7.74185988E+01 m2/s

NLM: GET_STATE - Read state initial conditions, t = 29222 12:00:00
(Grid 01, File: roms_ini_SODA_Y1980M1D3.nc, Rec=0001, Index=1)
- free-surface
(Min = -3.70100817E-01 Max = 2.66125192E-01)
- vertically integrated u-momentum component
(Min = NaN Max = NaN)
- vertically integrated v-momentum component
(Min = NaN Max = NaN)
- u-momentum component
(Min = -1.19349110E+00 Max = 1.48280624E+00)
- v-momentum component
(Min = -9.64514274E-01 Max = 1.18053425E+00)
- potential temperature
(Min = 4.36085150E-01 Max = 2.88065167E+01)
- salinity
(Min = 3.01144427E+01 Max = 3.71944949E+01)
GET_NGFLD - free-surface western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -7.63329480E-02 Max = 0.00000000E+00)
GET_NGFLD - free-surface southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.06996103E-01 Max = 2.28605348E-01)
GET_NGFLD - free-surface northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -1.79728888E-01 Max = 5.65656418E-03)
GET_NGFLD - 2D u-momentum western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -1.24101975E-01 Max = -5.94207262E-03)
GET_NGFLD - 2D v-momentum western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 2.49592586E-04 Max = 6.28793664E-02)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = NaN Max = NaN)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = NaN Max = NaN)
GET_NGFLD - 2D u-momentum northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = NaN Max = NaN)
GET_NGFLD - 2D v-momentum northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = NaN Max = NaN)
GET_NGFLD - 3D u-momentum western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.99767774E-01 Max = 6.75020457E-02)
GET_NGFLD - 3D v-momentum western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.89718544E-02 Max = 2.41981859E-01)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.42197277E-01 Max = 1.57265507E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.45226682E-01 Max = 2.45044268E-01)
GET_NGFLD - 3D u-momentum northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.69608758E-01 Max = 2.43040919E-01)
GET_NGFLD - 3D v-momentum northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.41488585E-01 Max = 2.80939748E-01)
GET_NGFLD - temperature western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 2.72299778E+01)
GET_NGFLD - salinity western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 3.67487356E+01)
GET_NGFLD - temperature southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 2.75865267E+01)
GET_NGFLD - salinity southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 3.70214136E+01)
GET_NGFLD - temperature northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 2.79680253E+01)
GET_NGFLD - salinity northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 3.69891889E+01)

Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 2.100000E-01 (Beckmann and Haidvogel)
rx1 = 5.306240E+01 (Haney)

Initial basin volumes: TotVolume = 6.6573679764E+16 m3
MinVolume = 8.1416838766E+06 m3
MaxVolume = 1.4532114761E+10 m3
Max/Min = 1.7849028507E+03

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00010800)

GET_NGFLD - free-surface western boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -1.15312136E-01 Max = 0.00000000E+00)
GET_NGFLD - free-surface southern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.03842956E-01 Max = 2.32551762E-01)
GET_NGFLD - free-surface northern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -1.87306332E-01 Max = 1.55312279E-02)
GET_NGFLD - 2D u-momentum western boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -1.95107994E-01 Max = -1.06365148E-02)
GET_NGFLD - 2D v-momentum western boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 3.16437822E-04 Max = 1.10563738E-01)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = NaN Max = NaN)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = NaN Max = NaN)
GET_NGFLD - 2D u-momentum northern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = NaN Max = NaN)
GET_NGFLD - 2D v-momentum northern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = NaN Max = NaN)
GET_NGFLD - 3D u-momentum western boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -4.21467055E-01 Max = 1.67933650E-02)
GET_NGFLD - 3D v-momentum western boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -1.64072255E-02 Max = 2.86393429E-01)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.25998970E-01 Max = 1.48051707E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.29652536E-01 Max = 2.65987746E-01)
GET_NGFLD - 3D u-momentum northern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -2.85973209E-01 Max = 3.60502392E-01)
GET_NGFLD - 3D v-momentum northern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = -1.88582333E-01 Max = 2.68122847E-01)
GET_NGFLD - temperature western boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 2.72902457E+01)
GET_NGFLD - salinity western boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 3.67482209E+01)
GET_NGFLD - temperature southern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 2.77164009E+01)
GET_NGFLD - salinity southern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 3.70264769E+01)
GET_NGFLD - temperature northern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 2.79277273E+01)
GET_NGFLD - salinity northern boundary condition, t = 29227 12:00:00
(Rec=0000003, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 30212.5000)
(Min = 0.00000000E+00 Max = 3.69862032E+01)

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

0 29222 12:00:00 2.718432E-03 2.158603E+04 2.158604E+04 6.661190E+16
(171,260,46) 2.679433E-01 1.431780E-01 0.000000E+00 1.571628E+00
DEF_HIS - creating history file, Grid 01: atleq_his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file, Grid 01: atleq_avg_0001.nc
1 29222 12:30:00 NaN NaN NaN NaN
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 NaN

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=1,2) into time record = 0000001

Elapsed CPU time (seconds):

Node # 0 CPU: 16.849
Node # 1 CPU: 16.857
Total: 33.706

Nonlinear model elapsed time profile:

Allocation and array initialization .............. 2.436 ( 7.2276 %)
Ocean state initialization ....................... 0.512 ( 1.5191 %)
Reading of input data ............................ 0.052 ( 0.1543 %)
Processing of input data ......................... 0.008 ( 0.0237 %)
Computation of vertical boundary conditions ...... 0.008 ( 0.0237 %)
Computation of global information integrals ...... 0.548 ( 1.6259 %)
Writing of output data ........................... 2.920 ( 8.6637 %)
Model 2D kernel .................................. 4.920 (14.5977 %)
2D/3D coupling, vertical metrics ................. 0.636 ( 1.8870 %)
Omega vertical velocity .......................... 0.396 ( 1.1749 %)
Equation of state for seawater ................... 2.512 ( 7.4531 %)
My2.5 vertical mixing parameterization ........... 3.184 ( 9.4470 %)
3D equations right-side terms .................... 1.176 ( 3.4892 %)
3D equations predictor step ...................... 1.120 ( 3.3230 %)
Pressure gradient ................................ 0.924 ( 2.7415 %)
Harmonic mixing of tracers, geopotentials ........ 1.708 ( 5.0676 %)
Harmonic stress tensor, S-surfaces ............... 0.852 ( 2.5279 %)
Corrector time-step for 3D momentum .............. 1.224 ( 3.6316 %)
Corrector time-step for tracers .................. 0.952 ( 2.8246 %)
Total: 26.090 77.4033

Nonlinear model message Passage profile:

Message Passage: 2D halo exchanges ............... 0.376 ( 1.1156 %)
Message Passage: 3D halo exchanges ............... 0.092 ( 0.2730 %)
Message Passage: 4D halo exchanges ............... 0.040 ( 0.1187 %)
Message Passage: data broadcast .................. 2.516 ( 7.4650 %)
Message Passage: data reduction .................. 0.052 ( 0.1543 %)
Message Passage: data gathering .................. 2.548 ( 7.5599 %)
Message Passage: data scattering.................. 1.072 ( 3.1806 %)
Total: 6.696 19.8671

All percentages are with respect to total time = 33.706

ROMS/TOMS - Output NetCDF summary for Grid 01:
number of time records written in HISTORY file = 00000001
number of time records written in RESTART file = 00000001

Analytical header files used:

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

ROMS/TOMS: DONE... Monday - May 30, 2016 - 3:10:40 PM

[kate]

If all the NaNs are in the land mask, you shouldn't see it in the GET_XXX reports like that. You need to clean the Nans out of your input files.

[fagundesmo]

Hi Kate,

ok, I'll try it here. Thank you.

[wilkin]

You say:

I've checked my ubar e vbar and both have values except in the borders which are masked with NAN values.

You can't have NaNs anywhere, not even on the perimeter, because ROMS computes with all values then applies land mask and boundary conditions. So NaNs anywhere propagate to NaNs everywhere.

Even with the Flather open boundary condition for ubar/vbar, you need initial values on the perimeter because these enter into the calculation for the next time step. Flather does not fix the perimeter as the boundary condition file, but merges this in with the gravity wave calculation.

Since you have valid u,v everywhere, including on the boundary (or so it seems from the standard output), just compute corresponding ubar/vbar as you have elsewhere.

[Helios]

After fixing the NaN issue, I think you should change your time step, in order to reduce your Maximum barotropic Courant Number.

[fagundesmo]

Hi wilkin and Helios,

I have fixed the NAN problem and now I'm playing with the courant number. Although, I have a max courant number 0.83 it keeps blowing up, I am trying to play with my DT in order to keep my courant number equals to 0.83 and my barotropic time step equals 24 sec. Since, it keeps blowing up I wonder what the problem is now. The following is my output:

Resolution, Grid 01: 0903x0321x050, Parallel Nodes: 6, Tiling: 003x002


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

360 ntimes Number of timesteps for 3-D equations.
360.000 dt Timestep size (s) for 3-D equations.
15 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.
360 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).
5400 nHIS Number of timesteps between the writing fields
into history file.
360 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
360 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
360 ndefAVG Number of timesteps between creation of new
time-averaged file.
0.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
0.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
5.0000E-06 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.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
4.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E+00 theta_b S-coordinate bottom control parameter.
300.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
29217.500 dstart Time-stamp assigned to model initialization (days).
19000101.00 time_ref Reference time for units attribute (yyyymmdd.dd)
6.0000E+01 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
6.0000E+01 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
3.0000E+01 Znudg Nudging/relaxation time scale (days)
for free-surface.
3.0000E+01 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
3.0000E+01 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.
5.000 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).
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(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(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt

T Aout(idFsur) Write out averaged free-surface.
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(idTvar) Write out averaged tracer 01: temp
T Aout(idTvar) Write out averaged tracer 02: salt

Output/Input Files:

Output Restart File: river_rst.nc
Prefix for Averages Files: atleq_avg
Input Grid File: /home/roms/DATA/grade/Atleq112.nc
Input Nonlinear Initial File: /home/roms/DATA/oceano/roms_ini_SODA_Y1979M12D29.nc
Input Forcing File 01: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-prate.nc
Input Forcing File 02: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-pressfc.nc
Input Forcing File 03: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-q2m.nc
Input Forcing File 04: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-tmp2m.nc
Input Forcing File 05: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-uwnd10m.nc
Input Forcing File 06: /home/roms/DATA/atmosfera/CFSR-blk-TSA-roms-vwnd10m.nc
Input Boundary File: /home/roms/DATA/oceano/Atleq_bry.nc

Tile partition information for Grid 01: 0903x0321x0050 tiling: 003x002

tile Istr Iend Jstr Jend Npts

0 1 301 1 161 2423050
1 302 602 1 161 2423050
2 603 903 1 161 2423050
3 1 301 162 321 2408000
4 302 602 162 321 2408000
5 603 903 162 321 2408000

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 301.50 0.50 161.50 RHO-points
1 301.50 602.50 0.50 161.50 RHO-points
2 602.50 903.50 0.50 161.50 RHO-points
3 0.50 301.50 161.50 321.50 RHO-points
4 301.50 602.50 161.50 321.50 RHO-points
5 602.50 903.50 161.50 321.50 RHO-points

0 1.00 301.50 0.50 161.50 U-points
1 301.50 602.50 0.50 161.50 U-points
2 602.50 903.00 0.50 161.50 U-points
3 1.00 301.50 161.50 321.50 U-points
4 301.50 602.50 161.50 321.50 U-points
5 602.50 903.00 161.50 321.50 U-points

0 0.50 301.50 1.00 161.50 V-points
1 301.50 602.50 1.00 161.50 V-points
2 602.50 903.50 1.00 161.50 V-points
3 0.50 301.50 161.50 321.00 V-points
4 301.50 602.50 161.50 321.00 V-points
5 602.50 903.50 161.50 321.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 626
HaloSizeJ(1) = 344
TileSide(1) = 307
TileSize(1) = 50962


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

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

zeta 1 Chapman Imp Chapman Imp Closed Chapman Imp

ubar 1 Flather Flather Closed Flather

vbar 1 Flather Flather Closed Flather

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

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

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

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

tke 1 Rad + Nud Rad + Nud Closed Rad + Nud

Activated C-preprocessing Options:

ATLEQ Atlantic Equatorial
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_STFLUX Analytical kinematic surface temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
CURVGRID Orthogonal curvilinear grid.
DIFF_GRID Horizontal diffusion coefficient scaled by grid size.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
MIX_GEO_TS Mixing of tracers along geopotential surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
MY25_MIXING Mellor/Yamada Level-2.5 mixing closure.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NO_LBC_ATT Not checking NetCDF global attribute NLM_LBC during restart.
NO_WRITE_GRID Not Writing grid arrays into NetCDF ouput files.
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 Single precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SPLINES Conservative parabolic spline reconstruction.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical 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.
VISC_3DCOEF Horizontal, time-dependent 3D viscosity coefficient.

......

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

Minimum X-grid spacing, DXmin = 8.96492125E+00 km
Maximum X-grid spacing, DXmax = 9.27662045E+00 km
Minimum Y-grid spacing, DYmin = 8.99525215E+00 km
Maximum Y-grid spacing, DYmax = 9.30386323E+00 km
Minimum Z-grid spacing, DZmin = 9.84012919E-02 m
Maximum Z-grid spacing, DZmax = 1.68374265E+02 m

Minimum barotropic Courant Number = 2.55870446E-02
Maximum barotropic Courant Number = 8.37080204E-01
Maximum Coriolis Courant Number = 1.35341744E-02

Horizontal mixing scaled by grid size, GRDMAX = 9.29023185E+00 km

Minimum horizontal viscosity coefficient = 7.48339491E+01 m2/s
Maximum horizontal viscosity coefficient = 7.74185988E+01 m2/s

NLM: GET_STATE - Read state initial conditions, t = 29217 12:00:00
(Grid 01, File: roms_ini_SODA_Y1979M12D29.nc, Rec=0001, Index=1)
- free-surface
(Min = -3.56767006E-01 Max = 2.55167816E-01)
- vertically integrated u-momentum component
(Min = -5.00194538E-01 Max = 1.08272027E-01)
- vertically integrated v-momentum component
(Min = -9.59396706E-02 Max = 3.79799400E-01)
- u-momentum component
(Min = -1.28447083E+00 Max = 1.53294544E+00)
- v-momentum component
(Min = -9.05112139E-01 Max = 1.27386835E+00)
- potential temperature
(Min = 4.37372040E-01 Max = 2.89420652E+01)
- salinity
(Min = 3.03602513E+01 Max = 3.72483137E+01)
GET_NGFLD - free-surface western boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -4.18840224E-02 Max = 0.00000000E+00)
GET_NGFLD - free-surface southern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.11230831E-01 Max = 2.36514993E-01)
GET_NGFLD - free-surface northern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -1.80912646E-01 Max = 2.36783240E-02)
GET_NGFLD - 2D u-momentum western boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -5.03907755E-02 Max = 7.54603368E-03)
GET_NGFLD - 2D v-momentum western boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 1.87037196E-02)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.75992599E-02 Max = 1.11919609E-02)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -3.44734838E-02 Max = 3.66260725E-02)
GET_NGFLD - 2D u-momentum northern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -4.10003673E-02 Max = 1.49573967E-02)
GET_NGFLD - 2D v-momentum northern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -5.03430284E-02 Max = 3.63252747E-02)
GET_NGFLD - 3D u-momentum western boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -1.62394764E-01 Max = 8.25405164E-02)
GET_NGFLD - 3D v-momentum western boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -3.42322665E-02 Max = 1.34523490E-01)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.10556234E-01 Max = 1.66392674E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.27173665E-01 Max = 2.50497737E-01)
GET_NGFLD - 3D u-momentum northern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -3.02971686E-01 Max = 2.89232909E-01)
GET_NGFLD - 3D v-momentum northern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.86692981E-01 Max = 3.27474357E-01)
GET_NGFLD - temperature western boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 2.72470425E+01)
GET_NGFLD - salinity western boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 3.67573813E+01)
GET_NGFLD - temperature southern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 2.75734003E+01)
GET_NGFLD - salinity southern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 3.70147834E+01)
GET_NGFLD - temperature northern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 2.79495202E+01)
GET_NGFLD - salinity northern boundary condition, t = 29217 12:00:00
(Rec=0000001, Index=2, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 3.69997306E+01)

Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 2.100000E-01 (Beckmann and Haidvogel)
rx1 = 5.306240E+01 (Haney)

Initial basin volumes: TotVolume = 6.6573679764E+16 m3
MinVolume = 8.1416838766E+06 m3
MaxVolume = 1.4532114761E+10 m3
Max/Min = 1.7849028507E+03

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00000360)

GET_NGFLD - free-surface western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -7.63329480E-02 Max = 0.00000000E+00)
GET_NGFLD - free-surface southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.06996103E-01 Max = 2.28605348E-01)
GET_NGFLD - free-surface northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -1.79728888E-01 Max = 5.65656418E-03)
GET_NGFLD - 2D u-momentum western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -1.24302509E-01 Max = 0.00000000E+00)
GET_NGFLD - 2D v-momentum western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 6.68999065E-02)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.29775982E-02 Max = 1.39900757E-02)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -3.55426819E-02 Max = 3.15084993E-02)
GET_NGFLD - 2D u-momentum northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -3.94047850E-02 Max = 2.82735992E-02)
GET_NGFLD - 2D v-momentum northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -3.81182828E-02 Max = 2.30277945E-02)
GET_NGFLD - 3D u-momentum western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.99767774E-01 Max = 6.74589893E-02)
GET_NGFLD - 3D v-momentum western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -1.84976252E-02 Max = 2.39752689E-01)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.42197277E-01 Max = 1.55991417E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.45226543E-01 Max = 2.45045739E-01)
GET_NGFLD - 3D u-momentum northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.69608758E-01 Max = 2.40859870E-01)
GET_NGFLD - 3D v-momentum northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = -2.41489694E-01 Max = 2.80939464E-01)
GET_NGFLD - temperature western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 2.72299778E+01)
GET_NGFLD - salinity western boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 3.67487356E+01)
GET_NGFLD - temperature southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 2.75865267E+01)
GET_NGFLD - salinity southern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 3.70214136E+01)
GET_NGFLD - temperature northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 2.79680253E+01)
GET_NGFLD - salinity northern boundary condition, t = 29222 12:00:00
(Rec=0000002, Index=1, File: Atleq_bry.nc)
(Tmin= 29217.5000 Tmax= 29627.5000)
(Min = 0.00000000E+00 Max = 3.69891889E+01)

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

0 29217 12:00:00 2.705264E-03 2.158604E+04 2.158604E+04 6.661195E+16
(159,218,50) 3.274578E-02 4.877767E-02 0.000000E+00 1.616027E+00
1 29217 12:06:00 2.705822E-03 2.158605E+04 2.158605E+04 6.661195E+16
(262,141,01) 5.879897E-03 2.746851E-05 1.978124E-01 1.615546E+00
2 29217 12:12:00 2.709873E-03 2.158606E+04 2.158607E+04 6.661195E+16
(197,308,01) 8.911839E-04 1.942702E-02 6.250043E-01 1.615115E+00
3 29217 12:18:00 2.715865E-03 2.158608E+04 2.158609E+04 6.661195E+16
(197,308,01) 1.063690E-03 2.947815E-02 1.248464E+00 1.614952E+00
4 29217 12:24:00 2.723602E-03 2.158610E+04 2.158610E+04 6.661195E+16
(197,308,01) 1.333597E-03 3.953959E-02 1.858658E+00 1.614558E+00
5 29217 12:30:00 2.732771E-03 2.158611E+04 2.158612E+04 6.661194E+16
(197,308,01) 1.711901E-03 4.935311E-02 2.439046E+00 1.672696E+00
6 29217 12:36:00 2.742932E-03 2.158612E+04 2.158613E+04 6.661194E+16
(197,308,01) 2.165261E-03 5.868695E-02 2.969803E+00 1.944916E+00
7 29217 12:42:00 2.753643E-03 2.158613E+04 2.158613E+04 6.661193E+16
(198,308,01) 2.516981E-03 6.848169E-02 3.430140E+00 2.168316E+00
8 29217 12:48:00 2.764259E-03 2.158614E+04 2.158614E+04 6.661193E+16
(200,308,01) 7.072145E-03 7.507266E-02 3.912601E+00 2.320211E+00
9 29217 12:54:00 2.774303E-03 2.158614E+04 2.158614E+04 6.661193E+16
(200,308,01) 9.035620E-03 8.074783E-02 4.301604E+00 8.676547E+00
10 29217 13:00:00 2.790531E-03 2.158615E+04 2.158615E+04 6.661192E+16
(195,162,27) 2.035074E-01 3.795590E-03 7.230745E+00 9.995135E+01

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=1,1) into time record =

I am doing a benchmark with DT=240 and NDFAST=40 and it gives me a barotropic time step of 6sec which I think it's too much, but when I try to increase it and also my baroclinic value it blows up even with courant number less than 1. Is there anything else I could do to fix it?

Thank you,

[fagundesmo]

If all the NaNs are in the land mask, you shouldn't see it in the GET_XXX reports like that. You need to clean the Nans out of your input files.

Hi Kate,

I have fixed that in python since I'm still doing the benchmark I'm still waiting for the output.

Thank you,

[kate]

I would still play with the timestep. Just because your Courant number based on the initial conditions is less than one, you're not out of the woods. In fact, I don't think 0.83 is out of the woods. Plus, as soon as things start evolving, your forcing, etc. could lead to larger currents than are in your initial conditions.

[fagundesmo]

I would still play with the timestep. Just because your Courant number based on the initial conditions is less than one, you're not out of the woods. In fact, I don't think 0.83 is out of the woods. Plus, as soon as things start evolving, your forcing, etc. could lead to larger currents than are in your initial conditions.

Hi Kate,

I'll certify about that. Thank you again.

Regards

[mathieu]

If you compile with ifort, you can detect the precise line where the NaN first occur with the compile option -fpe0. With gfortran the option is -ffpe-trap=invalid.