ROMS blows up

[chaos4u2]

Hello, I have a problem with ROMS, when I execute my case it blows up at the 2nd iteration. Here I show you the log, if you see something wrong because I've tried many things but it keeps on blowing. Thanks in advanced.

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

17280 ntimes Number of timesteps for 3-D equations.
15.000 dt Timestep size (s) for 3-D equations.
100 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.
288 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).
1 nHIS Number of timesteps between the writing fields
into history file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
1 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
1 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
5.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
5.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
2.0000E+00 nl_tnu4(01) NLM Horizontal, biharmonic mixing coefficient
(m4/s) for tracer 01: temp
2.0000E+00 nl_tnu4(02) NLM Horizontal, biharmonic mixing coefficient
(m4/s) for tracer 02: salt
5.0000E+00 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
5.0000E+00 nl_visc4 NLM Horizontal, biharmonic mixing coefficient
(m4/s) for momentum.
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.
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.
2 Vstretching S-coordinate stretching function.
3.0000E+00 theta_s S-coordinate surface control parameter.
1.0000E+00 theta_b S-coordinate bottom control parameter.
1.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
3.000 dstart Time-stamp assigned to model initialization (days).
20121011.00 time_ref Reference time for units attribute (yyyymmdd.dd)
5.0000E+01 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
5.0000E+01 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
0.0000E+00 Znudg Nudging/relaxation time scale (days)
for free-surface.
0.0000E+00 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
0.0000E+00 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
0.0000E+00 obcfac Factor between passive and active
open boundary conditions.
F VolCons(1) NLM western edge boundary volume conservation.
F VolCons(2) NLM southern edge boundary volume conservation.
F VolCons(3) NLM eastern edge boundary volume conservation.
F VolCons(4) NLM northern edge boundary volume conservation.
17.500 T0 Background potential temperature (C) constant.
37.400 S0 Background salinity (PSU) constant.
1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
T Hout(idFsur) Write out free-surface.
T Hout(idUbar) Write out 2D U-momentum component.
T Hout(idVbar) Write out 2D V-momentum component.
T Hout(idUvel) Write out 3D U-momentum component.
T Hout(idVvel) Write out 3D V-momentum component.
T Hout(idWvel) Write out W-momentum component.
T Hout(idOvel) Write out omega vertical velocity.
T Hout(idTvar) Write out tracer 01: temp
T Hout(idTvar) Write out tracer 02: salt
T Hout(idVvis) Write out vertical viscosity: AKv.
T Hout(idTdif) Write out vertical diffusion: AKt(itemp).
T Hout(idSdif) Write out vertical diffusion: AKt(isalt).

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

T Dout(M2rate) Write out 2D momentun acceleration.
T Dout(M2pgrd) Write out 2D momentum pressure gradient.
T Dout(M2fcor) Write out 2D momentum Coriolis force.
T Dout(M2hadv) Write out 2D momentum horizontal advection.
T Dout(M2xadv) Write out 2D momentum horizontal X-advection.
T Dout(M2yadv) Write out 2D momentum horizontal Y-advection.
T Dout(M2hvis) Write out 2D momentum horizontal viscosity.
T Dout(M2xvis) Write out 2D momentum horizontal X-viscosity.
T Dout(M2yvis) Write out 2D momentum horizontal Y-viscosity.
T Dout(M2sstr) Write out 2D momentum surface stress.
T Dout(M2bstr) Write out 2D momentum bottom stress.

T Dout(M3rate) Write out 3D momentun acceleration.
T Dout(M3pgrd) Write out 3D momentum pressure gradient.
T Dout(M3fcor) Write out 3D momentum Coriolis force.
T Dout(M3hadv) Write out 3D momentum horizontal advection.
T Dout(M3xadv) Write out 3D momentum horizontal X-advection.
T Dout(M3yadv) Write out 3D momentum horizontal Y-advection.
T Dout(M3vadv) Write out 3D momentum vertical advection.
T Dout(M3hvis) Write out 3D momentum horizontal viscosity.
T Dout(M3xvis) Write out 3D momentum horizontal X-viscosity.
T Dout(M3yvis) Write out 3D momentum horizontal Y-viscosity.
T Dout(M3vvis) Write out 3D momentum vertical viscosity.

T Dout(iTrate) Write out rate of change of tracer 01: temp
T Dout(iTrate) Write out rate of change of tracer 02: salt
T Dout(iThadv) Write out horizontal advection, tracer 01: temp
T Dout(iThadv) Write out horizontal advection, tracer 02: salt
T Dout(iTxadv) Write out horizontal X-advection, tracer 01: temp
T Dout(iTxadv) Write out horizontal X-advection, tracer 02: salt
T Dout(iTyadv) Write out horizontal Y-advection, tracer 01: temp
T Dout(iTyadv) Write out horizontal Y-advection, tracer 02: salt
T Dout(iTvadv) Write out vertical advection, tracer 01: temp
T Dout(iTvadv) Write out vertical advection, tracer 02: salt
T Dout(iThdif) Write out horizontal diffusion, tracer 01: temp
T Dout(iThdif) Write out horizontal diffusion, tracer 02: salt
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 01: temp
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 02: salt
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 01: temp
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 02: salt
T Dout(iTvdif) Write out vertical diffusion, tracer 01: temp
T Dout(iTvdif) Write out vertical diffusion, tracer 02: salt

Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc
Output Diagnostics File: ocean_dia.nc
Input Grid File: /home/sergi/Projects/BOCANA/bocananou_grid.nc
Input Nonlinear Initial File: /home/sergi/Projects/BOCANA/bocananou_initial.nc
Input Boundary File: /home/sergi/Projects/BOCANA/bocana_bry.nc

Tile partition information for Grid 01: 0040x0191x0005 tiling: 001x001

tile Istr Iend Jstr Jend Npts

0 1 40 1 191 38200

Tile minimum and maximum fractional grid coordinates:
(interior points only)

tile Xmin Xmax Ymin Ymax grid

0 0.50 41.50 0.50 191.50 RHO-points

0 0.00 41.00 0.50 191.50 U-points

0 0.50 41.50 0.00 191.00 V-points

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

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

zeta 1 Closed Closed Clamped Clamped

ubar 1 Closed Closed Clamped Clamped

vbar 1 Closed Closed Clamped Clamped

u 1 Closed Closed Clamped Clamped

v 1 Closed Closed Clamped Clamped

temp 1 Closed Closed Clamped Clamped

salt 1 Closed Closed Clamped Clamped

Activated C-preprocessing Options:

BOCANA Bocana Sud al Port de Barcelona
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_SSFLUX Analytical kinematic surface salinity 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.
DIAGNOSTICS_TS Computing and writing tracer diagnostic terms.
DIAGNOSTICS_UV Computing and writing momentum diagnostic terms.
DIFF_GRID Horizontal diffusion coefficient scaled by grid size.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
LMD_MIXING Large/McWilliams/Doney interior mixing.
MASKING Land/Sea masking.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
!RST_SINGLE Double 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_SVADVECTION Parabolic splines vertical advection of tracers.
TS_DIF2 Harmonic mixing of tracers.
TS_DIF4 Biharmonic 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.
UV_VIS4 Biharmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
VISC_GRID Horizontal viscosity coefficient scaled by grid size.

Process Information:

Thread # 0 (pid= 4822) is active.

INITIAL: Configuring and initializing forward nonlinear model ...


Vertical S-coordinate System:

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

5 0.0000000 0.0000000 0.000 0.000 0.000 0.000
4 -0.2000000 -0.0294071 -0.000 -0.115 -0.454 -0.760
3 -0.4000000 -0.1484182 -0.000 -0.274 -1.736 -3.253
2 -0.6000000 -0.3829205 -0.000 -0.491 -4.085 -7.982
1 -0.8000000 -0.7112727 -0.000 -0.756 -7.302 -14.526
0 -1.0000000 -1.0000000 -0.000 -1.000 -10.152 -20.304

Time Splitting Weights: ndtfast = 100 nfast = 136

Primary Secondary Accumulated to Current Step

1-0.0001594457047349 0.0100000000000000-0.0001594457047349 0.0100000000000000
2-0.0003102043539849 0.0100015944570474-0.0004696500587199 0.0200015944570474
3-0.0004522759527012 0.0100046965005872-0.0009219260114211 0.0300062909576346
4-0.0005856605201383 0.0100092192601142-0.0015075865315593 0.0400155102177488
5-0.0007103581063581 0.0100150758653156-0.0022179446379175 0.0500305860830644
6-0.0008263688153356 0.0100221794463792-0.0030443134532531 0.0600527655294436
7-0.0009336928346655 0.0100304431345325-0.0039780062879186 0.0700832086639761
8-0.0010323304718712 0.0100397800628792-0.0050103367597898 0.0801229887268553
9-0.0011222821973150 0.0100501033675979-0.0061326189571048 0.0901730920944532
10-0.0012035486937100 0.0100613261895711-0.0073361676508148 0.1002344182840242
11-0.0012761309122332 0.0100733616765082-0.0086122985630481 0.1103077799605324
12-0.0013400301352409 0.0100861229856305-0.0099523286982889 0.1203939029461629
13-0.0013952480455848 0.0100995232869829-0.0113475767438737 0.1304934262331457
14-0.0014417868025304 0.0101134757674387-0.0127893635464041 0.1406069020005845
15-0.0014796491242768 0.0101278936354640-0.0142690126706810 0.1507347956360485
16-0.0015088383770778 0.0101426901267068-0.0157778510477588 0.1608774857627553
17-0.0015293586709646 0.0101577785104776-0.0173072097187233 0.1710352642732329
18-0.0015412149620705 0.0101730720971872-0.0188484246807938 0.1812083363704202
19-0.0015444131615570 0.0101884842468079-0.0203928378423508 0.1913968206172281
20-0.0015389602511410 0.0102039283784235-0.0219317980934918 0.2016007489956516
21-0.0015248644052242 0.0102193179809349-0.0234566624987159 0.2118200669765865
22-0.0015021351196239 0.0102345666249872-0.0249587976183398 0.2220546336015737
23-0.0014707833469051 0.0102495879761834-0.0264295809652450 0.2323042215777571
24-0.0014308216383147 0.0102642958096525-0.0278604026035597 0.2425685173874096
25-0.0013822642923165 0.0102786040260356-0.0292426668958762 0.2528471214134452
26-0.0013251275097287 0.0102924266689588-0.0305677944056048 0.2631395480824039
27-0.0012594295554622 0.0103056779440561-0.0318272239610670 0.2734452260264600
28-0.0011851909268611 0.0103182722396107-0.0330124148879281 0.2837634982660707
29-0.0011024345286441 0.0103301241488793-0.0341148494165722 0.2940936224149500
30-0.0010111858544481 0.0103411484941657-0.0351260352710203 0.3044347709091157
31-0.0009114731749732 0.0103512603527102-0.0360375084459935 0.3147860312618259
32-0.0008033277327288 0.0103603750844599-0.0368408361787223 0.3251464063462858
33-0.0006867839433822 0.0103684083617872-0.0375276201221045 0.3355148147080730
34-0.0005618796037077 0.0103752762012210-0.0380894997258122 0.3458900909092941
35-0.0004286561061383 0.0103808949972581-0.0385181558319504 0.3562709859065522
36-0.0002871586599182 0.0103851815583195-0.0388053144918686 0.3666561674648717
37-0.0001374365188575 0.0103880531449187-0.0389427510107261 0.3770442206097904
38 0.0000204567843123 0.0103894275101073-0.0389222942264138 0.3874336481198977
39 0.0001864631969805 0.0103892229422641-0.0387358310294333 0.3978228710621618
40 0.0003605198990979 0.0103873583102943-0.0383753111303355 0.4082102293724562
41 0.0005425590490165 0.0103837531113034-0.0378327520813190 0.4185939824837595
42 0.0007325075227271 0.0103783275208132-0.0371002445585919 0.4289723100045727
43 0.0009302866464954 0.0103710024455859-0.0361699579120965 0.4393433124501586
44 0.0011358119228966 0.0103616995791210-0.0350341459891999 0.4497050120292796
45 0.0013489927502484 0.0103503414598920-0.0336851532389515 0.4600553534891716
46 0.0015697321354425 0.0103368515323895-0.0321154211035089 0.4703922050215611
47 0.0017979264001745 0.0103211542110351-0.0303174947033344 0.4807133592325962
48 0.0020334648805720 0.0103031749470333-0.0282840298227624 0.4910165341796295
49 0.0022762296202215 0.0102828402982276-0.0260078002025408 0.5012993744778572
50 0.0025260950565934 0.0102600780020254-0.0234817051459475 0.5115594524798827
51 0.0027829277008656 0.0102348170514595-0.0206987774450819 0.5217942695313421
52 0.0030465858111454 0.0102069877744508-0.0176521916339365 0.5320012573057930
53 0.0033169190590902 0.0101765219163394-0.0143352725748463 0.5421777792221323
54 0.0035937681899260 0.0101433527257485-0.0107415043849203 0.5523211319478808
55 0.0038769646758645 0.0101074150438492-0.0068645397090558 0.5624285469917299
56 0.0041663303629196 0.0100686453970906-0.0026982093461362 0.5724971923888205
57 0.0044616771111203 0.0100269820934614 0.0017634677649840 0.5825241744822819
58 0.0047628064281242 0.0099823653223502 0.0065262741931083 0.5925065398046321
59 0.0050695090962281 0.0099347372580689 0.0115957832893363 0.6024412770627010
60 0.0053815647927771 0.0098840421671066 0.0169773480821135 0.6123253192298076
61 0.0056987417039731 0.0098302265191789 0.0226760897860865 0.6221555457489865
62 0.0060207961320800 0.0097732391021391 0.0286968859181665 0.6319287848511256
63 0.0063474720960293 0.0097130311408183 0.0350443580141958 0.6416418159919439
64 0.0066785009254227 0.0096495564198580 0.0417228589396184 0.6512913724118020
65 0.0070136008479335 0.0095827714106038 0.0487364597875519 0.6608741438224058
66 0.0073524765701069 0.0095126354021245 0.0560889363576588 0.6703867792245303
67 0.0076948188515579 0.0094391106364234 0.0637837552092167 0.6798258898609537
68 0.0080403040725683 0.0093621624479078 0.0718240592817851 0.6891880523088616
69 0.0083885937950820 0.0092817594071822 0.0802126530768671 0.6984698117160437
70 0.0087393343170983 0.0091978734692313 0.0889519873939654 0.7076676851852750
71 0.0090921562204639 0.0091104801260603 0.0980441436144293 0.7167781653113353
72 0.0094466739120640 0.0090195585638557 0.1074908175264933 0.7257977238751910
73 0.0098024851584103 0.0089250918247351 0.1172933026849036 0.7347228156999261
74 0.0101591706136288 0.0088270669731510 0.1274524732985323 0.7435498826730771
75 0.0105162933408455 0.0087254752670147 0.1379687666393778 0.7522753579400918
76 0.0108733983269705 0.0086203123336062 0.1488421649663484 0.7608956702736981
77 0.0112300119908805 0.0085115783503365 0.1600721769572289 0.7694072486240346
78 0.0115856416849999 0.0083992782304277 0.1716578186422288 0.7778065268544624
79 0.0119397751902801 0.0082834218135777 0.1835975938325090 0.7860899486680401
80 0.0122918802045775 0.0081640240616749 0.1958894740370864 0.7942539727297150
81 0.0126414038244295 0.0080411052596291 0.2085308778615159 0.8022950779893441
82 0.0129877720202296 0.0079146912213848 0.2215186498817456 0.8102097692107290
83 0.0133303891048003 0.0077848135011825 0.2348490389865459 0.8179945827119115
84 0.0136686371953643 0.0076515096101345 0.2485176761819102 0.8256460923220460
85 0.0140018756689153 0.0075148232381809 0.2625195518508255 0.8331609155602269
86 0.0143294406109853 0.0073748044814917 0.2768489924618108 0.8405357200417186
87 0.0146506442578125 0.0072315100753819 0.2914996367196234 0.8477672301171005
88 0.0149647744319058 0.0070850036328038 0.3064644111515292 0.8548522337499043
89 0.0152710939710086 0.0069353558884847 0.3217355051225378 0.8617875896383890
90 0.0155688401504611 0.0067826449487746 0.3373043452729989 0.8685702345871636
91 0.0158572240989607 0.0066269565472700 0.3531615693719596 0.8751971911344336
92 0.0161354302077207 0.0064683843062804 0.3692969995796802 0.8816655754407140
93 0.0164026155330280 0.0063070300042032 0.3856996151127082 0.8879726054449172
94 0.0166579091921988 0.0061430038488729 0.4023575243049070 0.8941156092937901
95 0.0169004117529326 0.0059764247569509 0.4192579360578396 0.9000920340507410
96 0.0171291946160649 0.0058074206394216 0.4363871306739044 0.9058994546901626
97 0.0173432993917185 0.0056361286932610 0.4537304300656229 0.9115355833834236
98 0.0175417372688526 0.0054626956993438 0.4712721673344755 0.9169982790827673
99 0.0177234883782110 0.0052872783266552 0.4889956557126865 0.9222855574094225
100 0.0178875011486682 0.0051100434428731 0.5068831568613548 0.9273956008522957
101 0.0180326916569743 0.0049311684313865 0.5249158485183291 0.9323267692836821
102 0.0181579429708980 0.0047508415148167 0.5430737914892271 0.9370776107984988
103 0.0182621044857684 0.0045692620851077 0.5613358959749954 0.9416468728836066
104 0.0183439912544149 0.0043866410402500 0.5796798872294103 0.9460335139238566
105 0.0184023833105056 0.0042032011277059 0.5980822705399159 0.9502367150515625
106 0.0184360249852842 0.0040191772946008 0.6165182955252001 0.9542558923461634
107 0.0184436242177053 0.0038348170447480 0.6349619197429054 0.9580907093909113
108 0.0184238518579681 0.0036503808025709 0.6533857716008735 0.9617410901934823
109 0.0183753409644487 0.0034661422839913 0.6717611125653222 0.9652072324774735
110 0.0182966860940303 0.0032823888743468 0.6900577986593526 0.9684896213518203
111 0.0181864425858324 0.0030994220134065 0.7082442412451850 0.9715890433652268
112 0.0180431258383383 0.0029175575875482 0.7262873670835234 0.9745066009527750
113 0.0178652105799207 0.0027371263291648 0.7441525776634440 0.9772437272819398
114 0.0176511301327661 0.0025584742233656 0.7618037077962101 0.9798022015053053
115 0.0173992756701974 0.0023819629220379 0.7792029834664075 0.9821841644273431
116 0.0171079954673953 0.0022079701653359 0.7963109789338028 0.9843921345926790
117 0.0167755941455171 0.0020368902106620 0.8130865730793199 0.9864290248033410
118 0.0164003319092156 0.0018691342692068 0.8294869049885354 0.9882981590725478
119 0.0159804237775546 0.0017051309501146 0.8454673287660900 0.9900032900226624
120 0.0155140388083243 0.0015453267123391 0.8609813675744143 0.9915486167350015
121 0.0149992993157544 0.0013901863242559 0.8759806668901687 0.9929388030592573
122 0.0144342800816253 0.0012401933310983 0.8904149469717940 0.9941789963903556
123 0.0138170075597787 0.0010958505302821 0.9042319545315728 0.9952748469206376
124 0.0131454590740262 0.0009576804546843 0.9173774136055990 0.9962325273753219
125 0.0124175620094553 0.0008262258639440 0.9297949756150543 0.9970587532392658
126 0.0116311929971360 0.0007020502438495 0.9414261686121903 0.9977608034831154
127 0.0107841770922233 0.0005857383138781 0.9522103457044137 0.9983465417969934
128 0.0098742869454606 0.0004778965429559 0.9620846326498743 0.9988244383399493
129 0.0088992419680793 0.0003791536735013 0.9709838746179537 0.9992035920134505
130 0.0078567074900984 0.0002901612538205 0.9788405821080520 0.9994937532672710
131 0.0067442939120218 0.0002115941789195 0.9855848760200738 0.9997053474461904
132 0.0055595558499341 0.0001441512397993 0.9911444318700079 0.9998494986859897
133 0.0042999912739952 0.0000885556812999 0.9954444231440031 0.9999380543672897
134 0.0029630406403326 0.0000455557685600 0.9984074637843356 0.9999836101358497
135 0.0015460860163330 0.0000159253621566 0.9999535498006686 0.9999995354980064
136 0.0000464501993315 0.0000004645019933 1.0000000000000002 0.9999999999999997

ndtfast, nfast = 100 136 nfast/ndtfast = 1.36000

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

1.000000000000 1.019196655660 0.509598327830 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.25560

Minimum X-grid spacing, DXmin = 7.04111612E-03 km
Maximum X-grid spacing, DXmax = 1.41390377E-01 km
Minimum Y-grid spacing, DYmin = 2.84936236E-03 km
Maximum Y-grid spacing, DYmax = 7.57004872E-02 km
Minimum Z-grid spacing, DZmin = 0.00000000E+00 m
Maximum Z-grid spacing, DZmax = 6.54458965E+00 m

Minimum barotropic Courant Number = 3.40823462E-02
Maximum barotropic Courant Number = 3.88832768E-01
Maximum Coriolis Courant Number = 1.44504081E-03

Horizontal mixing scaled by grid size, GRDMAX = 1.01077164E-01 km

NLM: GET_STATE - Read state initial conditions, t = 0 00:00:00
(File: bocananou_initial.nc, Rec=0001, Index=1)
- free-surface
(Min = 3.90000000E-01 Max = 3.90000000E-01)
- vertically integrated u-momentum component
(Min = -1.14800000E-01 Max = -1.14800000E-01)
- vertically integrated v-momentum component
(Min = -2.77200000E-01 Max = -2.77200000E-01)
- u-momentum component
(Min = -1.14800000E-01 Max = -1.14800000E-01)
- v-momentum component
(Min = -2.77200000E-01 Max = -2.77200000E-01)
- potential temperature
(Min = 1.75000000E+01 Max = 1.75000000E+01)
- salinity
(Min = 3.74000000E+01 Max = 3.74000000E+01)
GET_NGFLD - free-surface eastern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 3.89999986E-01 Max = 3.89999986E-01)
GET_NGFLD - free-surface northern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 3.89999986E-01 Max = 3.89999986E-01)
GET_NGFLD - 2D u-momentum eastern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -1.14799999E-01 Max = -1.14799999E-01)
GET_NGFLD - 2D v-momentum eastern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -2.77200013E-01 Max = -2.77200013E-01)
GET_NGFLD - 2D u-momentum northern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -1.14799999E-01 Max = -1.14799999E-01)
GET_NGFLD - 2D v-momentum northern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -2.77200013E-01 Max = -2.77200013E-01)
GET_NGFLD - 3D u-momentum eastern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -1.14799999E-01 Max = -1.14799999E-01)
GET_NGFLD - 3D v-momentum eastern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -2.77200013E-01 Max = -2.77200013E-01)
GET_NGFLD - 3D u-momentum northern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -1.14799999E-01 Max = -1.14799999E-01)
GET_NGFLD - 3D v-momentum northern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -2.77200013E-01 Max = -2.77200013E-01)
GET_NGFLD - temperature eastern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 1.75000000E+01 Max = 1.75000000E+01)
GET_NGFLD - salinity eastern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 3.74000015E+01 Max = 3.74000015E+01)
GET_NGFLD - temperature northern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 1.75000000E+01 Max = 1.75000000E+01)
GET_NGFLD - salinity northern boundary condition, t = 0 00:00:00
(Rec=0001, Index=2, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 3.74000015E+01 Max = 3.74000015E+01)

Maximum grid stiffness ratios: rx0 = 1.000000E+00 (Beckmann and Haidvogel)
rx1 = 6.171319E+00 (Haney)


Initial basin volumes: TotVolume = 7.8565623992E+07 m3
MinVolume = 1.2594844108E+02 m3
MaxVolume = 1.9061957055E+04 m3
Max/Min = 1.5134730443E+02


NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00017280)

GET_NGFLD - free-surface eastern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 4.00000006E-01 Max = 4.00000006E-01)
GET_NGFLD - free-surface northern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 4.00000006E-01 Max = 4.00000006E-01)
GET_NGFLD - 2D u-momentum eastern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -1.14799999E-01 Max = -1.14799999E-01)
GET_NGFLD - 2D v-momentum eastern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -2.77200013E-01 Max = -2.77200013E-01)
GET_NGFLD - 2D u-momentum northern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -1.14799999E-01 Max = -1.14799999E-01)
GET_NGFLD - 2D v-momentum northern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -2.77200013E-01 Max = -2.77200013E-01)
GET_NGFLD - 3D u-momentum eastern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -1.14799999E-01 Max = -1.14799999E-01)
GET_NGFLD - 3D v-momentum eastern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -2.77200013E-01 Max = -2.77200013E-01)
GET_NGFLD - 3D u-momentum northern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -1.14799999E-01 Max = -1.14799999E-01)
GET_NGFLD - 3D v-momentum northern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = -2.77200013E-01 Max = -2.77200013E-01)
GET_NGFLD - temperature eastern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 1.75000000E+01 Max = 1.75000000E+01)
GET_NGFLD - salinity eastern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 3.74000015E+01 Max = 3.74000015E+01)
GET_NGFLD - temperature northern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 1.75000000E+01 Max = 1.75000000E+01)
GET_NGFLD - salinity northern boundary condition, t = 1 12:00:00
(Rec=0002, Index=1, File: bocana_bry.nc)
(Tmin= 0.0000 Tmax= 3.0000)
(Min = 3.74000015E+01 Max = 3.74000015E+01)

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

0 0 00:00:00 4.405872E-02 6.817282E+01 6.821688E+01 8.099713E+07
(40,089,5) 4.587076E-02 4.426591E-01 0.000000E+00 3.000315E-01
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 00:00:15 NaN NaN NaN NaN
(00,000,0) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00

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):

Thread # 0 CPU: 118.803
Total: 118.803

Nonlinear model elapsed time profile:

Allocation and array initialization .............. 0.408 ( 0.3434 %)
Ocean state initialization ....................... 0.024 ( 0.0202 %)
Reading of input data ............................ 0.032 ( 0.0269 %)
Computation of global information integrals ...... 0.188 ( 0.1583 %)
Writing of output data ........................... 0.100 ( 0.0842 %)
Model 2D kernel .................................. 115.231 (96.9932 %)
2D/3D coupling, vertical metrics ................. 0.096 ( 0.0808 %)
Omega vertical velocity .......................... 0.044 ( 0.0370 %)
Equation of state for seawater ................... 0.244 ( 0.2054 %)
KPP vertical mixing parameterization ............. 0.008 ( 0.0067 %)
3D equations right-side terms .................... 0.104 ( 0.0875 %)
3D equations predictor step ...................... 0.124 ( 0.1044 %)
Pressure gradient ................................ 0.060 ( 0.0505 %)
Harmonic mixing of tracers, S-surfaces ........... 0.032 ( 0.0269 %)
Biharmonic mixing of tracers, S-surfaces ......... 0.068 ( 0.0572 %)
Harmonic stress tensor, S-surfaces ............... 0.048 ( 0.0404 %)
Biharmonic stress tensor, S-surfaces ............. 0.068 ( 0.0572 %)
Corrector time-step for 3D momentum .............. 1.032 ( 0.8687 %)
Corrector time-step for tracers .................. 0.780 ( 0.6566 %)
Total: 118.691 99.9057

All percentages are with respect to total time = 118.803

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_hmixcoef.h
ROMS/Functionals/ana_nudgcoef.h
ROMS/Functionals/ana_smflux.h
ROMS/Functionals/ana_stflux.h

ROMS/TOMS: DONE... Monday - April 22, 2013 - 6:30:39 PM


Also here is the header file:

/* Model Physics */
#define SOLVE3D
#define CURVGRID
#define UV_COR
#define UV_ADV
#define UV_VIS2
#define UV_VIS4
#define TS_DIF2
#define TS_DIF4
#define SALINITY
#define NONLIN_EOS /*Activate if Tº or Salt is activated*/
#define LMD_MIXING /*MY25_MIXING or GLS_MIXING*/


/* Numerical Schemes Options */
#define TS_U3HADVECTION /*Horizontal advection*/
#define TS_SVADVECTION /*Use if splines vertical advection*/
#define DJ_GRADPS /*Use if splines density jacobian*/
#define VISC_GRID /*Scale viscosity coeff by grid size*/
#define MIX_S_UV /*Mixing along constant S-surfaces*/
#define DIFF_GRID /*Scale diffusion coeff by grid size*/
#define MIX_S_TS /*Mixing along constant S-surfaces*/
#define SPLINES
#define MASKING


/* Surface Boundary Conditions */
#define ANA_SMFLUX /*Surface momentum stress*/
#define ANA_STFLUX /*Surface temperature flux*/
#define ANA_SSFLUX /*Surface salinity flux*/


/* Bottom Boundary Conditions */
#define UV_QDRAG /* Turn on quadratic bottom friction */
#define ANA_BTFLUX
#define ANA_BSFLUX


/* Other Options */
#define AVERAGES
#define AVERAGES_FLUXES
#define AVERAGES_AKV
#define AVERAGES_AKT
#define AVERAGES_AKS
#define DIAGNOSTICS_TS
#define DIAGNOSTICS_UV

[kate]

I believe this is your problem:

Vertical S-coordinate System:

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

5 0.0000000 0.0000000 0.000 0.000 0.000 0.000
4 -0.2000000 -0.0294071 -0.000 -0.115 -0.454 -0.760
3 -0.4000000 -0.1484182 -0.000 -0.274 -1.736 -3.253
2 -0.6000000 -0.3829205 -0.000 -0.491 -4.085 -7.982
1 -0.8000000 -0.7112727 -0.000 -0.756 -7.302 -14.526
0 -1.0000000 -1.0000000 -0.000 -1.000 -10.152 -20.304

This says that your minimum depth is 0. You must have some non-zero depth even inside the land mask because there are places where terms are divided by the depth.

This is also worrisome:

Maximum grid stiffness ratios: rx0 = 1.000000E+00 (Beckmann and Haidvogel

but may be related.

[chaos4u2]

Thank you Kate for your fast answer.

I've changed manually the h and mask_rho matrix to make all 0 at the same positions in both matrix.

It keeps blowing up.

My teacher told me to change too the mask_psi, mask_u and mask_v.

But my question is that these matrix have different dimensions:

mask_rho (42x193)
mask_psi (41x192)
mask_u (41x193)
mask_v (42x193).

He told me that mask_u and mask_v are 1 if the number in mask_rho in both sides is also 1. But I've checked my original matrix, and there are many numbers that don't follow this law. Also, mask_psi is different.

How can I change mask_psi, u and v according to mask_rho?

Thanks in advanced!

[kate]

You never want to have any of your h values be zero. Period.

Don't worry about mask_psi - ROMS recomputes it anyways. It should probably recompute the u,v masks too, but they are simple. Here is the python code for computing them from the rho mask:

Code: Select all

def uvp_masks(rmask):
    '''
    return u-, v-, and psi-masks based on input rho-mask
    
    Parameters
    ----------
    
    rmask : ndarray
        mask at CGrid rho-points
    
    Returns
    -------
    (umask, vmask, pmask) : ndarrays
        masks at u-, v-, and psi-points
    '''
    rmask = np.asarray(rmask)
    assert rmask.ndim == 2, 'rmask must be a 2D array'
    assert np.all((rmask==0)|(rmask==1)), 'rmask array must contain only ones and zeros.'

    umask = rmask[:, :-1] * rmask[:, 1:]
    vmask = rmask[:-1, :] * rmask[1:, :]
    pmask = rmask[:-1, :-1] * rmask[:-1, 1:] * rmask[1:, :-1] * rmask[1:, 1:]

    return umask, vmask, pmask

[drews]

You never want to have any of your h values be zero. Period.

h is the bathymetry at rho-points (positive downward). For my model domain the Shuttle Radar Topography Mission at 3 arc-seconds reports an elevation of 0 meters at several portions of the shoreline. Am I supposed to increase those values? Or decrease them to some alternate value?

[kate]

Your situation is different in that you are using WET_DRY while the OP (original poster) was not. The WET_DRY code adds some small water depth so that (h+zeta) is never zero -> in those parts not covered by the fixed land mask. You cannot have zero depths inside the fixed land mask where zeta is always zero. If your domain is running, don't worry about it.

[fdaryabor]

Dear Chaos4u2,

What kate suggest you is the one way to resolving problem. I recomend you, please try to avoiding option "Output Diagnostics File: ocean_dia.nc" for Output/Input Files in your simulation, and see how. Few reason can be for "BLOWS UP".

1- Input data, such as forcings and boundary data are too low resolution in comparing with model resolution, even though after interpolation on the model grid points.
2- time step for 2d and 3d in comparing with your resolution.

Good Luck