model blow up

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slvester
Posts: 32
Joined: Mon Jun 01, 2009 12:59 pm
Location: second institution of oceanography,state oceanic administration China

model blow up

#1 Post by slvester » Mon Dec 14, 2009 2:50 am

hello everyone,I just want to set up my own application ,my domin is northwest pacific(9.08°N-46.80°N,105.39°E-179°E),but the model blowing up just 1 step.
----------------------------------------------------------
NORTHWEST PACIFIC OCEAN

Operating system : Linux
CPU/hardware : x86_64
Compiler system : pgi
Compiler command : /opt/mpi/mvapich/1.1/gcc.pgf90/bin/mpif90
Compiler flags : -O3 -tp k8-64 -Mfree

Input Script : /dcfs2/users/slvester/roms/example/nwpacific/input/ocean_nwpacific.in

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 416M

Local Root : /dcfs2/users/slvester/roms
Header Dir : /dcfs2/users/slvester/roms/ROMS/Include
Header file : nwpacific.h
Analytical Dir: /dcfs2/users/slvester/roms/ROMS/Functionals

Resolution, Grid 01: 0134x0082x035, Parallel Nodes: 16, Tiling: 002x008


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

8640 ntimes Number of timesteps for 3-D equations.
3600.000 dt Timestep size (s) for 3-D equations.
50 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).
360 nHIS Number of timesteps between the writing fields
into history file.
8640 ndefHIS Number of timesteps between creation of new
history files.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
720 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
8640 ndefAVG Number of timesteps between creation of new
time-averaged file.
2.0000E+01 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
2.0000E+01 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
4.0000E+01 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/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.
4.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
1 lmd_Jwt Jerlov water type.
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
5.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E-01 theta_b S-coordinate bottom control parameter.
20.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
15.000 dstart Time-stamp assigned to model initialization (days).
-1.00 time_ref Reference time for units attribute (yyyymmdd.dd)
1.5000E+01 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
1.5000E+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.
14.000 T0 Background potential temperature (C) constant.
35.000 S0 Background salinity (PSU) constant.
1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
T 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

Output/Input Files:

Output Restart File: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-rst.nc
Prefix for History Files: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-his
Prefix for Averages Files: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-avg
Input Grid File: /dcfs2/users/slvester/roms/example/nwpacific/input/nwpacific-grid.nc
Input Nonlinear Initial File: /dcfs2/users/slvester/roms/example/nwpacific/input/nwpacific-init.nc
Input Forcing File 01: /dcfs2/users/slvester/roms/example/nwpacific/input/nwpacific-forc.nc
Input Boundary File: /dcfs2/users/slvester/roms/example/nwpacific/input/nwpacific-bry.nc

Tile partition information for Grid 01: 0134x0082x0035 tiling: 002x008

tile Istr Iend Jstr Jend Npts

0 1 67 1 8 18760
1 68 134 1 8 18760
2 1 67 9 19 25795
3 68 134 9 19 25795
4 1 67 20 30 25795
5 68 134 20 30 25795
6 1 67 31 41 25795
7 68 134 31 41 25795
8 1 67 42 52 25795
10 1 67 53 63 25795
11 68 134 53 63 25795
12 1 67 64 74 25795
13 68 134 64 74 25795
14 1 67 75 82 18760
15 68 134 75 82 18760

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 67.50 0.50 8.50 RHO-points
1 67.50 134.50 0.50 8.50 RHO-points
2 0.50 67.50 8.50 19.50 RHO-points
3 67.50 134.50 8.50 19.50 RHO-points
4 0.50 67.50 19.50 30.50 RHO-points
5 67.50 134.50 19.50 30.50 RHO-points
6 0.50 67.50 30.50 41.50 RHO-points
7 67.50 134.50 30.50 41.50 RHO-points
8 0.50 67.50 41.50 52.50 RHO-points
9 67.50 134.50 41.50 52.50 RHO-points
10 0.50 67.50 52.50 63.50 RHO-points
11 67.50 134.50 52.50 63.50 RHO-points
12 0.50 67.50 63.50 74.50 RHO-points
13 67.50 134.50 63.50 74.50 RHO-points
14 0.50 67.50 74.50 82.50 RHO-points
15 67.50 134.50 74.50 82.50 RHO-points

0 1.00 67.50 0.50 8.50 U-points
1 67.50 134.00 0.50 8.50 U-points
2 1.00 67.50 8.50 19.50 U-points
3 67.50 134.00 8.50 19.50 U-points
4 1.00 67.50 19.50 30.50 U-points
5 67.50 134.00 19.50 30.50 U-points
6 1.00 67.50 30.50 41.50 U-points
7 67.50 134.00 30.50 41.50 U-points
8 1.00 67.50 41.50 52.50 U-points
9 67.50 134.00 41.50 52.50 U-points
10 1.00 67.50 52.50 63.50 U-points
11 67.50 134.00 52.50 63.50 U-points
12 1.00 67.50 63.50 74.50 U-points
13 67.50 134.00 63.50 74.50 U-points
14 1.00 67.50 74.50 82.50 U-points
15 67.50 134.00 74.50 82.50 U-points

0 0.50 67.50 1.00 8.50 V-points
1 67.50 134.50 1.00 8.50 V-points
2 0.50 67.50 8.50 19.50 V-points
3 67.50 134.50 8.50 19.50 V-points
4 0.50 67.50 19.50 30.50 V-points
5 67.50 134.50 19.50 30.50 V-points
6 0.50 67.50 30.50 41.50 V-points
7 67.50 134.50 30.50 41.50 V-points
8 0.50 67.50 41.50 52.50 V-points
9 67.50 134.50 41.50 52.50 V-points
10 0.50 67.50 52.50 63.50 V-points
11 67.50 134.50 52.50 63.50 V-points
12 0.50 67.50 63.50 74.50 V-points
13 67.50 134.50 63.50 74.50 V-points
14 0.50 67.50 74.50 82.00 V-points
15 67.50 134.50 74.50 82.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 158
HaloSizeJ(1) = 46
TileSide(1) = 73
TileSize(1) = 1241


Activated C-preprocessing Options:

NWPACIFIC NORTHWEST PACIFIC OCEAN
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged fields.
AVERAGES_FLUXES Writing out time-averaged surface fluxes.
CURVGRID Orthogonal curvilinear grid.
DIURNAL_SRFLUX Modulate shortwave radiation by the local diurnal cycle.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EAST_FSGRADIENT Eastern edge, free-surface, gradient condition.
EAST_M2RADIATION Eastern edge, 2D momentum, radiation condition.
EAST_M3CLAMPED Eastern edge, 3D momentum, Clamped condition.
EAST_TRADIATION Eastern edge, tracers, radiation condition.
EAST_VOLCONS Eastern edge, enforce mass conservation.
LMD_CONVEC LMD convective mixing due to shear instability.
LMD_MIXING Large/McWilliams/Doney interior mixing.
LMD_NONLOCAL LMD convective nonlocal transport.
LMD_RIMIX LMD diffusivity due to shear instability.
LMD_SKPP KPP surface boundary layer mixing.
MASKING Land/Sea masking.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NORTH_VOLCONS Northern edge, enforce mass conservation.
NORTH_FSGRADIENT Northern edge, free-surface, gradient condition.
NORTH_M2NUDGING Northern edge, 2D momentum, passive/active outflow/inflow.
NORTH_M2RADIATION Northern edge, 2D momentum, radiation condition.
NORTH_M3CLAMPED Northern edge, 3D momentum, Clamped condition.
NORTH_TRADIATION Northern edge, tracers, radiation condition.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
QCORRECTION Surface net heat flux correction.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SCORRECTION Surface salinity flux correction.
SOLAR_SOURCE Solar Radiation Source Term.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSGRADIENT Southern edge, free-surface, gradient condition.
SOUTH_M2NUDGING Southern edge, 2D momentum, passive/active outflow/inflow.
SOUTH_M2RADIATION Southern edge, 2D momentum, radiation condition.
SOUTH_M3CLAMPED Southern edge, 3D momentum, Clamped condition.
SOUTH_TRADIATION Southern edge, tracers, radiation condition.
SOUTH_VOLCONS Southern edge, enforce mass conservation.
SPONGE Enhanced horizontal mixing in the sponge areas.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_SVADVECTION Parabolic splines 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.
WESTERN_WALL Wall boundary at Western edge.

INITIAL: Configuring and initializing forward nonlinear model ...
Node # 11 (pid= 5026) is active.
Node # 10 (pid= 5025) is active.
Node # 8 (pid= 5023) is active.
Node # 13 (pid= 5028) is active. Node # 12 (pid= 5027) is active. Node # 14 (pid= 5029) is active. Node # 15 (pid= 5030) is active.




Vertical S-coordinate System:

level S-coord Cs-curve at_hmin over_slope at_hmax

35 0.0000000 0.0000000 0.000 0.000 0.000
34 -0.0285714 -0.0020485 -0.571 -7.524 -14.477
33 -0.0571429 -0.0044087 -1.143 -16.106 -31.070
32 -0.0857143 -0.0071955 -1.714 -26.137 -50.559
31 -0.1142857 -0.0105514 -2.286 -38.098 -73.910
30 -0.1428571 -0.0146531 -2.857 -52.591 -102.325
29 -0.1714286 -0.0197192 -3.429 -70.357 -137.286
28 -0.2000000 -0.0260168 -4.000 -92.303 -180.607
27 -0.2285714 -0.0338662 -4.571 -119.516 -234.461
26 -0.2571429 -0.0436408 -5.143 -153.264 -301.385
25 -0.2857143 -0.0557579 -5.714 -194.962 -384.209
24 -0.3142857 -0.0706549 -6.286 -246.095 -485.904
23 -0.3428571 -0.0887464 -6.857 -308.070 -609.284
22 -0.3714286 -0.1103591 -7.429 -381.997 -756.566
21 -0.4000000 -0.1356491 -8.000 -468.405 -928.811
20 -0.4285714 -0.1645179 -8.571 -566.960 -1125.349
19 -0.4571429 -0.1965563 -9.143 -676.273 -1343.403
18 -0.4857143 -0.2310465 -9.714 -793.907 -1578.100
17 -0.5142857 -0.2670460 -10.286 -916.664 -1823.042
16 -0.5428571 -0.3035415 -10.857 -1041.104 -2071.352
15 -0.5714286 -0.3396314 -11.429 -1164.168 -2316.908
14 -0.6000000 -0.3746809 -12.000 -1283.701 -2555.402
13 -0.6285714 -0.4084071 -12.571 -1398.742 -2784.913
12 -0.6571429 -0.4408839 -13.143 -1509.543 -3005.943
11 -0.6857143 -0.4724895 -13.714 -1617.387 -3221.059
10 -0.7142857 -0.5038269 -14.286 -1724.320 -3434.354
9 -0.7428571 -0.5356467 -14.857 -1832.891 -3650.924
8 -0.7714286 -0.5687892 -15.429 -1945.951 -3876.473
7 -0.8000000 -0.6041494 -16.000 -2066.538 -4117.076
6 -0.8285714 -0.6426630 -16.571 -2197.828 -4379.085
5 -0.8571429 -0.6853090 -17.143 -2343.144 -4669.145
4 -0.8857143 -0.7331227 -17.714 -2505.999 -4994.285
3 -0.9142857 -0.7872163 -18.286 -2690.169 -5362.053
2 -0.9428571 -0.8488037 -18.857 -2899.774 -5780.691
1 -0.9714286 -0.9192295 -19.429 -3139.377 -6259.326
0 -1.0000000 -1.0000000 -20.000 -3414.091 -6808.182

Time Splitting Weights: ndtfast = 50 nfast = 69

Primary Secondary Accumulated to Current Step

1-0.0004563262418391 0.0200000000000000-0.0004563262418391 0.0200000000000000
2-0.0008555246732536 0.0200091265248368-0.0013118509150927 0.0400091265248368
3-0.0011975957891734 0.0200262370183019-0.0025094467042661 0.0600353635431387
4-0.0014825415143255 0.0200501889340853-0.0039919882185915 0.0800855524772240
5-0.0017103668530001 0.0200798397643718-0.0057023550715916 0.1001653922415958
6-0.0018810821987231 0.0201140471014318-0.0075834372703147 0.1202794393430276
7-0.0019947063038349 0.0201516687454063-0.0095781435741496 0.1404311080884340
8-0.0020512699089757 0.0201915628714830-0.0116294134831253 0.1606226709599169
9-0.0020508200324769 0.0202325882696625-0.0136802335156022 0.1808552592295795
10-0.0019934249196594 0.0202736046703121-0.0156736584352616 0.2011288638998915
11-0.0018791796520380 0.0203134731687052-0.0175528380872996 0.2214423370685968
12-0.0017082124164322 0.0203510567617460-0.0192610505037318 0.2417933938303428
13-0.0014806914339834 0.0203852210100746-0.0207417419377152 0.2621786148404174
14-0.0011968325490789 0.0204148348387543-0.0219385744867941 0.2825934496791717
15-0.0008569074781817 0.0204387714897359-0.0227954819649758 0.3030322211689075
16-0.0004612527185669 0.0204559096392995-0.0232567346835427 0.3234881308082070
17-0.0000102791169649 0.0204651346936709-0.0232670138005077 0.3439532655018779
18 0.0004955179018893 0.0204653402760102-0.0227714958986183 0.3644186057778880
19 0.0010555474468010 0.0204554299179724-0.0217159484518173 0.3848740356958604
20 0.0016691116117526 0.0204343189690364-0.0200468368400647 0.4053083546648968
21 0.0023353932676362 0.0204009367368013-0.0177114435724285 0.4257092914016981
22 0.0030534431940779 0.0203542288714486-0.0146580003783505 0.4460635202731467
23 0.0038221665513568 0.0202931600075670-0.0108358338269937 0.4663566802807137
24 0.0046403086924171 0.0202167166765399-0.0061955251345765 0.4865733969572536
25 0.0055064403149742 0.0201239105026915-0.0006890848196024 0.5066973074599451
26 0.0064189419537136 0.0200137816963921 0.0057298571341112 0.5267110891563371
27 0.0073759878125848 0.0198854028573178 0.0131058449466960 0.5465964920136549
28 0.0083755289371871 0.0197378831010661 0.0214813738838831 0.5663343751147210
29 0.0094152757272501 0.0195703725223223 0.0308966496111332 0.5859047476370433
30 0.0104926797892080 0.0193820670077773 0.0413893294003412 0.6052868146448206
31 0.0116049151288660 0.0191722134119932 0.0529942445292072 0.6244590280568137
32 0.0127488586841624 0.0189401151094159 0.0657431032133696 0.6433991431662296
33 0.0139210701980223 0.0186851379357326 0.0796641734113919 0.6620842811019622
34 0.0151177714313064 0.0184067165317722 0.0947819448426983 0.6804909976337343
35 0.0163348247158524 0.0181043611031460 0.1111167695585507 0.6985953587368804
36 0.0175677108476106 0.0177776646088290 0.1286844804061612 0.7163730233457094
37 0.0188115063198728 0.0174263103918768 0.1474959867260340 0.7337993337375862
38 0.0200608598965948 0.0170500802654793 0.1675568466226288 0.7508494140030655
39 0.0213099685258127 0.0166488630675474 0.1888668151484416 0.7674982770706129
40 0.0225525525931525 0.0162226636970312 0.2114193677415941 0.7837209407676441
41 0.0237818305154335 0.0157716126451681 0.2352011982570276 0.7994925534128122
42 0.0249904926743652 0.0152959760348595 0.2601916909313928 0.8147885294476717
43 0.0261706746903379 0.0147961661813722 0.2863623656217307 0.8295846956290438
44 0.0273139300363068 0.0142727526875654 0.3136762956580375 0.8438574483166091
45 0.0284112019917697 0.0137264740868393 0.3420874976498072 0.8575839224034484
46 0.0294527949368383 0.0131582500470039 0.3715402925866456 0.8707421724504523
47 0.0304283449864031 0.0125691941482671 0.4019686375730487 0.8833113665987193
48 0.0313267899643920 0.0119606272485390 0.4332954275374407 0.8952719938472583
49 0.0321363387181221 0.0113340914492512 0.4654317662555627 0.9066060852965095
50 0.0328444397727456 0.0106913646748887 0.4982762060283084 0.9172974499713983
51 0.0334377493257894 0.0100344758794338 0.5317139553540977 0.9273319258508321
52 0.0339020985817871 0.0093657208929180 0.5656160539358848 0.9366976467437502
53 0.0342224604270064 0.0086876789212823 0.5998385143628912 0.9453853256650325
54 0.0343829154442684 0.0080032297127422 0.6342214298071596 0.9533885553777747
55 0.0343666172678620 0.0073155714038568 0.6685880470750215 0.9607041267816315
56 0.0341557572785502 0.0066282390584996 0.7027438043535718 0.9673323658401310
57 0.0337315286386720 0.0059451239129286 0.7364753329922438 0.9732774897530596
58 0.0330740896673358 0.0052704933401551 0.7695494226595796 0.9785479830932148
59 0.0321625265557082 0.0046090115468084 0.8017119492152878 0.9831569946400232
60 0.0309748154223953 0.0039657610156942 0.8326867646376830 0.9871227556557174
61 0.0294877837089178 0.0033462647072463 0.8621745483466008 0.9904690203629637
62 0.0276770709152801 0.0027565090330680 0.8898516192618808 0.9932255293960317
63 0.0255170886756324 0.0022029676147624 0.9153687079375131 0.9954284970107941
64 0.0229809801740268 0.0016926258412497 0.9383496881115398 0.9971211228520438
65 0.0200405789002670 0.0012330062377692 0.9583902670118067 0.9983541290898130
66 0.0166663667458513 0.0008321946597639 0.9750566337576579 0.9991863237495768
67 0.0128274314400094 0.0004988673248468 0.9878840651976674 0.9996851910744237
68 0.0084914233258330 0.0002423186960466 0.9963754885235003 0.9999275097704703
69 0.0036245114764992 0.0000724902295300 0.9999999999999996 1.0000000000000000

ndtfast, nfast = 50 69 nfast/ndtfast = 1.38000

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

1.000000000000 1.033396903681 0.516698451840 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.22720

Minimum X-grid spacing, DXmin = 4.15066970E+01 km
Maximum X-grid spacing, DXmax = 5.98704509E+01 km
Minimum Y-grid spacing, DYmin = 4.03208592E+01 km
Maximum Y-grid spacing, DYmax = 5.81602728E+01 km
Minimum Z-grid spacing, DZmin = 5.71428571E-01 m
Maximum Z-grid spacing, DZmax = 5.48856052E+02 m

Minimum barotropic Courant Number = 2.42400022E-02
Maximum barotropic Courant Number = 6.22377843E-01
Maximum Coriolis Courant Number = 3.82603640E-01


NLM: GET_STATE - Read state initial conditions, t = 15 00:00:00
(File: nwpacific-init.nc, Rec=0001, Index=1)
- free-surface
(Min = -8.99822056E-01 Max = 4.12949800E-01)
- vertically integrated u-momentum component
(Min = -1.05592263E+00 Max = 2.47805142E+00)
- vertically integrated v-momentum component
(Min = -3.63884521E+00 Max = 8.69620323E-01)
- u-momentum component
(Min = -1.48831594E+00 Max = 3.85862422E+00)
- v-momentum component
(Min = -6.83433580E+00 Max = 1.57864392E+00)
- potential temperature
(Min = -6.43691063E+00 Max = 2.83319798E+01)
- salinity
(Min = 2.30707073E+01 Max = 3.54776268E+01)
GET_2DFLD - surface u-momentum stress, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.19034103E-04 Max = 1.79930181E-04)
GET_2DFLD - surface v-momentum stress, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.16289256E-04 Max = 3.27086142E-05)
GET_2DFLD - solar shortwave radiation flux, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 1.61595730E-05 Max = 6.07030323E-05)
GET_2DFLD - surface net heat flux, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.20427728E-04 Max = 9.40330967E-06)
GET_2DFLD - sea surface temperature climatology, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -6.43691039E+00 Max = 2.83319797E+01)
GET_2DFLD - surface net heat flux sensitivity to SST, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -7.73167560E-08 Max = 1.03143543E-07)
GET_2DFLD - sea surface salinity climatology, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 2.30707066E+01 Max = 3.54776267E+01)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -3.70964128E-01 Max = 6.65950744E-01)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.25458286E+00 Max = 2.99424436E-01)
GET_NGFLD - 2D u-momentum northern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.20164766E-01 Max = 1.34822336E-01)
GET_NGFLD - 2D v-momentum northern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -7.09751111E-02 Max = 1.30982775E-01)
GET_NGFLD - 3D u-momentum eastern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.71648280E-01 Max = 1.37739662E-01)
GET_NGFLD - 3D v-momentum eastern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -7.61510512E-02 Max = 1.94683157E-02)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -9.71257878E-01 Max = 1.11143594E+00)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -4.42478684E+00 Max = 4.82727350E-01)
GET_NGFLD - 3D u-momentum northern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -3.08496689E-01 Max = 1.95377816E-01)
GET_NGFLD - 3D v-momentum northern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.24919656E-01 Max = 2.38742540E-01)
Maximum grid stiffness ratios: rx0 = 9.286866E-01 (Beckmann and Haidvogel)
rx1 = 3.120519E+01 (Haney)


Initial basin volumes: TotVolume = 1.0195732167E+17 m3
MinVolume = 1.0437166820E+09 m3
MaxVolume = 1.7929222638E+12 m3
Max/Min = 1.7178246690E+03

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00008640)
GET_2DFLD - surface u-momentum stress, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.14788056E-04 Max = 1.76329951E-04)
GET_2DFLD - surface v-momentum stress, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.61363824E-04 Max = 5.47849092E-05)
GET_2DFLD - solar shortwave radiation flux, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 2.57406058E-05 Max = 6.66155416E-05)
GET_2DFLD - surface net heat flux, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -9.55788731E-05 Max = 1.79752348E-05)
GET_2DFLD - sea surface temperature climatology, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -6.71732477E+00 Max = 2.81421771E+01)
GET_2DFLD - surface net heat flux sensitivity to SST, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 1.00000000E+37 Max = -1.00000000E+37)
GET_2DFLD - surface net freswater flux, (E-P), t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -6.58397719E-08 Max = 9.03918527E-08)
GET_2DFLD - sea surface salinity climatology, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 2.13265627E+01 Max = 3.56467295E+01)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 45 00:00:00
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.96658265E-01 Max = 6.56010728E-01)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.26393990E+00 Max = 3.14500955E-01)
GET_NGFLD - 2D u-momentum northern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.44200644E-01 Max = 7.42109354E-02)
GET_NGFLD - 2D v-momentum northern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -7.11725877E-02 Max = 5.97144657E-02)
GET_NGFLD - 3D u-momentum eastern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.47918548E-01 Max = 1.33245331E-01)
GET_NGFLD - 3D v-momentum eastern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -6.11355318E-02 Max = 2.50364556E-02)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -8.31879226E-01 Max = 1.09808463E+00)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -4.46979576E+00 Max = 4.85713673E-01)
GET_NGFLD - 3D u-momentum northern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -3.17924362E-01 Max = 1.19590537E-01)
GET_NGFLD - 3D v-momentum northern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.12817657E-01 Max = 1.03162162E-01)

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 15 00:00:00 1.168903E-02 2.509908E+04 2.509909E+04 1.021807E+17
DEF_HIS - creating history file: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-his_0001.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-avg_0001.nc
1 15 01:00:00 NaN NaN NaN NaN

Blowing-up: Saving latest model state into RESTART file

WRT_RST - wrote re-start fields (Index=2,2) into time record = 0000001
Elapsed CPU time (seconds):

Node # 0 CPU: 1.729
Node # 1 CPU: 1.729 Node # 2 CPU: 1.729 Node # 7 CPU: 1.730 Node # 6 CPU: 1.730 Node # 5 CPU: 1.730 Node # 4 CPU: 1.730





Node # 3 CPU: 1.729
Node # 8 CPU: 1.729 Node # 9 CPU: 1.730 Node # 10 CPU: 1.730 Node # 11 CPU: 1.730
Node # 15 CPU: 1.729 Node # 12 CPU: 1.729 Node # 13 CPU: 1.729 Node # 14 CPU: 1.729

Total: 27.670

Nonlinear model elapsed time profile:

Initialization ................................... 9.415 (34.0252 %)
Reading of input data ............................ 5.588 (20.1965 %)
Processing of input data ......................... 0.040 ( 0.1430 %)
Processing of output time averaged data .......... 0.001 ( 0.0035 %)
Computation of vertical boundary conditions ...... 0.004 ( 0.0144 %)
Computation of global information integrals ...... 0.045 ( 0.1610 %)
Writing of output data ........................... 6.530 (23.6006 %)
Model 2D kernel .................................. 1.083 ( 3.9138 %)
2D/3D coupling, vertical metrics ................. 0.083 ( 0.3014 %)
Omega vertical velocity .......................... 0.068 ( 0.2442 %)
Equation of state for seawater ................... 0.342 ( 1.2365 %)
KPP vertical mixing parameterization ............. 0.232 ( 0.8389 %)
3D equations right-side terms .................... 0.082 ( 0.2957 %)
3D equations predictor step ...................... 0.225 ( 0.8135 %)
Pressure gradient ................................ 0.080 ( 0.2887 %)
Harmonic mixing of tracers, S-surfaces ........... 0.030 ( 0.1095 %)
Harmonic stress tensor, S-surfaces ............... 0.055 ( 0.1982 %)
Corrector time-step for 3D momentum .............. 0.140 ( 0.5072 %)
Corrector time-step for tracers .................. 0.151 ( 0.5465 %)
Total: 24.194 87.4384

Nonlinear model message Passage profile:

Message Passage: 2D halo exchanges ............... 0.397 ( 1.4343 %)
Message Passage: 3D halo exchanges ............... 0.341 ( 1.2311 %)
Message Passage: 4D halo exchanges ............... 0.094 ( 0.3413 %)
Message Passage: data broadcast .................. 15.369 (55.5455 %)
Message Passage: data reduction .................. 0.129 ( 0.4675 %)
Message Passage: data gathering .................. 2.710 ( 9.7941 %)
Message Passage: data scattering.................. 1.685 ( 6.0884 %)
Total: 20.725 74.9022

All percentages are with respect to total time = 27.670

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_srflux.h

ROMS/TOMS: DONE... Monday - December 14, 2009 - 10:14:32 AM
------------------------------------------------------------------
and I check the nwpacific-rst.nc file ,the variable temp,salt,zeta,u,v et al are NAN or empty values.That is not right,but I don't konw why?may be the initial file is not ok,and all the nc file I just use the RNT to generate(MAIN_ncfiles.m).
and cpp?I really don't konw the open boundary condition ,and there are so much diffrent choice
Any advice?
Thank you

User avatar
kate
Posts: 3780
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: model blow up

#2 Post by kate » Mon Dec 14, 2009 4:58 pm

The first thing to try is a shorter timestep. Try something half as long and see what happens.

slvester
Posts: 32
Joined: Mon Jun 01, 2009 12:59 pm
Location: second institution of oceanography,state oceanic administration China

Re: model blow up

#3 Post by slvester » Tue Dec 15, 2009 1:31 am

Hi kate,thanks for your reply,you are so kind.
I just try more shorter timestp,and I set dt=1800;900;100;20;4;0.5 ,but unfortunately,all the result is the same:
--------------------------------------------------------
dt=20
half a year

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 15 00:00:00 1.168903E-02 2.509908E+04 2.509909E+04 1.021807E+17
DEF_HIS - creating history file: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-his_0001.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-avg_0001.nc
1 15 00:00:20 NaN NaN NaN NaN

Blowing-up: Saving latest model state into RESTART file

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

dt=4
half a year

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 15 00:00:00 1.168903E-02 2.509908E+04 2.509909E+04 1.021807E+17
DEF_HIS - creating history file: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-avg.nc
1 15 00:00:04 NaN NaN NaN NaN

Blowing-up: Saving latest model state into RESTART file

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

dt=0.5
half a year

STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 15 00:00:00 1.168903E-02 2.509908E+04 2.509909E+04 1.021807E+17
DEF_HIS - creating history file: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-his.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-avg.nc
1 15 00:00:00 NaN NaN NaN NaN

Blowing-up: Saving latest model state into RESTART file

----------------------------------------------------------------------------
for dt=0.4,the result is the same ,so the model is blow up at once,maybe I need to check the cpp,initial condition,obc,et al?So what can I do?
Thank you!

lfowler
Posts: 2
Joined: Thu Oct 08, 2009 6:53 pm
Location: Imperial College London

Re: model blow up

#4 Post by lfowler » Tue Dec 15, 2009 12:21 pm

-
Last edited by lfowler on Fri Sep 10, 2010 2:05 pm, edited 1 time in total.

slvester
Posts: 32
Joined: Mon Jun 01, 2009 12:59 pm
Location: second institution of oceanography,state oceanic administration China

Re: model blow up

#5 Post by slvester » Tue Dec 15, 2009 1:43 pm

Thank you lfowler.
I just check my initial nc files ,the temp,salt value are all normal,the same with zeta,u,v,ubar,vbar,and some u,v are 0,but others are not 0.
Is it dt<sqrt(((dx^2+dy^2)/(9.8*h))?If it is,then dt<4132?
Minimum X-grid spacing, DXmin = 4.15066970E+01 km
Maximum X-grid spacing, DXmax = 5.98704509E+01 km
Minimum Y-grid spacing, DYmin = 4.03208592E+01 km
Maximum Y-grid spacing, DYmax = 5.81602728E+01 km
and my minimum depth of water is 20m
But I still set the dt=20,and the model blow up at 1st,the same with dt=1800,3600.
Then I set the u=0,v=0,ubar=0.vbar=0.zeta=0,just don't change the temp and salt,but the model blow up all the same.I don't know why?Maybe cpp?My cpp is:
--------------------------------
NWPACIFIC NORTHWEST PACIFIC OCEAN
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged fields.
AVERAGES_FLUXES Writing out time-averaged surface fluxes.
CURVGRID Orthogonal curvilinear grid.
DIURNAL_SRFLUX Modulate shortwave radiation by the local diurnal cycle.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EAST_FSGRADIENT Eastern edge, free-surface, gradient condition.
EAST_M2RADIATION Eastern edge, 2D momentum, radiation condition.
EAST_M3CLAMPED Eastern edge, 3D momentum, Clamped condition.
EAST_TRADIATION Eastern edge, tracers, radiation condition.
EAST_VOLCONS Eastern edge, enforce mass conservation.
LMD_CONVEC LMD convective mixing due to shear instability.
LMD_MIXING Large/McWilliams/Doney interior mixing.
LMD_NONLOCAL LMD convective nonlocal transport.
LMD_RIMIX LMD diffusivity due to shear instability.
LMD_SKPP KPP surface boundary layer mixing.
MASKING Land/Sea masking.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NORTH_VOLCONS Northern edge, enforce mass conservation.
NORTH_FSGRADIENT Northern edge, free-surface, gradient condition.
NORTH_M2NUDGING Northern edge, 2D momentum, passive/active outflow/inflow.
NORTH_M2RADIATION Northern edge, 2D momentum, radiation condition.
NORTH_M3CLAMPED Northern edge, 3D momentum, Clamped condition.
NORTH_TRADIATION Northern edge, tracers, radiation condition.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
QCORRECTION Surface net heat flux correction.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SCORRECTION Surface salinity flux correction.
SOLAR_SOURCE Solar Radiation Source Term.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSGRADIENT Southern edge, free-surface, gradient condition.
SOUTH_M2NUDGING Southern edge, 2D momentum, passive/active outflow/inflow.
SOUTH_M2RADIATION Southern edge, 2D momentum, radiation condition.
SOUTH_M3CLAMPED Southern edge, 3D momentum, Clamped condition.
SOUTH_TRADIATION Southern edge, tracers, radiation condition.
SOUTH_VOLCONS Southern edge, enforce mass conservation.
SPONGE Enhanced horizontal mixing in the sponge areas.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_SVADVECTION Parabolic splines 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.
WESTERN_WALL Wall boundary at Western edge.
--------------------
I really don't understand how to choose the diffrent conditions in the cpp?
Thanks!

User avatar
kate
Posts: 3780
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: model blow up

#6 Post by kate » Tue Dec 15, 2009 8:54 pm

OK, you've ruled out the timestep as the culprit. Now I would turn to a debugger to figure out where things go bad. I didn't notice anything odd in the min/max values for the read in values - no NaN there. Zero is a valid temperature, so it's not that. Alternately, you could try cutting back on model processes, say try a 2-D run or a run with TS_FIXED.

slvester
Posts: 32
Joined: Mon Jun 01, 2009 12:59 pm
Location: second institution of oceanography,state oceanic administration China

Re: model blow up

#7 Post by slvester » Wed Dec 16, 2009 5:22 am

Thanks kate.I redefine TS_FIXED,and test again,but unfortunatly it blow up again
and I close all 3-D and traces(alos test include open that),just run the 2-D(I don't know whether it is right?)
Also,test with different dt,dt=2,1800,...
I really have no ideal for that.
What's the matter?
Thanks
Physical Parameters, Grid: 01
=============================

7776000 ntimes Number of timesteps for 3-D equations.
2.000 dt Timestep size (s) for 3-D equations.
50 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.
600 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).
648000 nHIS Number of timesteps between the writing fields
into history file.
7776000 ndefHIS Number of timesteps between creation of new
history files.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.

1296000 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
7776000 ndefAVG Number of timesteps between creation of new
time-averaged file.
2.0000E+01 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
2.0000E+01 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
3.0000E+01 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/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).
1 lmd_Jwt Jerlov water type.
15 levsfrc Deepest level to apply surface stress as a
bodyforce.
1 levbfrc Shallowest level to apply bottom stress as a
bodyforce.
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
5.0000E+00 theta_s S-coordinate surface control parameter.
4.0000E-01 theta_b S-coordinate bottom control parameter.
20.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
15.000 dstart Time-stamp assigned to model initialization (days).
-1.00 time_ref Reference time for units attribute (yyyymmdd.dd)
1.5000E+01 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
1.5000E+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.
14.000 T0 Background potential temperature (C) constant.
35.000 S0 Background salinity (PSU) constant.
1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
T 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(idOvel) Write out omega vertical velocity.
----------------------------------------------------------------------------
Activated C-preprocessing Options:

NWPACIFIC NORTHWEST PACIFIC OCEAN
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SMFLUX Analytical kinematic surface momentum flux.
ANA_SRFLUX Analytical kinematic shortwave radiation flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged fields.
AVERAGES_FLUXES Writing out time-averaged surface fluxes.
BODYFORCE Momentum stresses as body-forces.
CURVGRID Orthogonal curvilinear grid.
DIURNAL_SRFLUX Modulate shortwave radiation by the local diurnal cycle.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EAST_FSRADIATION Eastern edge, free-surface, radiation condition.
EAST_M2RADIATION Eastern edge, 2D momentum, radiation condition.
EAST_VOLCONS Eastern edge, enforce mass conservation.
LMD_CONVEC LMD convective mixing due to shear instability.
LMD_MIXING Large/McWilliams/Doney interior mixing.
LMD_NONLOCAL LMD convective nonlocal transport.
LMD_RIMIX LMD diffusivity due to shear instability.
LMD_SKPP KPP surface boundary layer mixing.
MASKING Land/Sea masking.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NORTH_VOLCONS Northern edge, enforce mass conservation.
NORTH_FSGRADIENT Northern edge, free-surface, gradient condition.
NORTH_M2NUDGING Northern edge, 2D momentum, passive/active outflow/inflow.
NORTH_M2RADIATION Northern edge, 2D momentum, radiation condition.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
QCORRECTION Surface net heat flux correction.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SCORRECTION Surface salinity flux correction.
SOLAR_SOURCE Solar Radiation Source Term.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSGRADIENT Southern edge, free-surface, gradient condition.
SOUTH_M2NUDGING Southern edge, 2D momentum, passive/active outflow/inflow.
SOUTH_M2RADIATION Southern edge, 2D momentum, radiation condition.
SOUTH_VOLCONS Southern edge, enforce mass conservation.
SPONGE Enhanced horizontal mixing in the sponge areas.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_SVADVECTION Parabolic splines vertical advection of tracers.
TS_DIF2 Harmonic mixing of tracers.
TS_FIXED Diagnostic configuration, no evolution of tracer.
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_LDRAG Linear bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
WESTERN_WALL Wall boundary at Western edge.
--------------------------------------------------------------------------------
STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 15 00:00:00 0.000000E+00 2.509864E+04 2.509864E+04 1.021797E+17
DEF_HIS - creating history file: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-his_0001.nc
WRT_HIS - wrote history fields (Index=1,1) into time record = 0000001
DEF_AVG - creating average file: /dcfs2/users/slvester/roms/example/nwpacific/out/nwpacific-avg_0001.nc
1 15 00:00:02 NaN NaN NaN NaN

christianmohn
Posts: 1
Joined: Mon Nov 02, 2009 4:41 pm
Location: NERI, Aarhus University

Re: model blow up

#8 Post by christianmohn » Wed Dec 16, 2009 8:13 am

Hi, in addition to Kate's recommendations I would try to run the model on 1 CPU as a quick check to make sure that there is no issue with MPI parallelization. If memory is a constraint, you could do this test with a coarser horizontal grid. Good luck, Christian

User avatar
susonic
Posts: 160
Joined: Tue Aug 21, 2007 5:44 pm
Location: Jeju National University
Contact:

Re: model blow up

#9 Post by susonic » Thu Dec 17, 2009 4:21 am

First of all, I doubt the cpp option. In cpp they are warning try not to use 'TS_SADVECTION' unless it's a shallow and high vertical resolution application. If it's not a solution, then what about changing the ROMS version? Say, go back to svn 390.

slvester
Posts: 32
Joined: Mon Jun 01, 2009 12:59 pm
Location: second institution of oceanography,state oceanic administration China

Re: model blow up

#10 Post by slvester » Thu Dec 17, 2009 9:08 am

Thanks kate,christianmohn and susonic,you are all so kind.
slvester wrote:I would try to run the model on 1 CPU as a quick check to make sure that there is no issue with MPI parallelization. If memory is a constraint, you could do this test with a coarser horizontal grid.
Yes,I just test it with 1 CPU,but it blow up again. The memeory is not a problem :P
susonic wrote:First of all, I doubt the cpp option. In cpp they are warning try not to use 'TS_SADVECTION' unless it's a shallow and high vertical resolution application. If it's not a solution, then what about changing the ROMS version? Say, go back to svn 390.
Yes,I closed the TS_SADVECTION and opne the TS_C4ADVECTION in cpp.but it blow up again.
My ROMS version is 424.
And I try to set the new nwpacific-grid.nc again ,then all the nc files(clima.oby.init ,forc),run the model ,it blow up ,but something is diffrent :
--------------------------------------
STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 15 00:00:00 NaN NaN NaN NaN

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


MAIN: Abnormal termination: BLOWUP.

------------------------
So first I should try to go back to svn 390 and then run the model,if it blow up,I should set the gridfile (then all the input nc files)once again.
Thanks!

klyons

Re: model blow up

#11 Post by klyons » Thu Dec 17, 2009 9:26 am

From the model output you posted, there appears to be a problem with one of your forcing values:

GET_2DFLD - surface net heat flux sensitivity to SST, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 1.00000000E+37 Max = -1.00000000E+37)

This might be your problem.

Kieran

slvester
Posts: 32
Joined: Mon Jun 01, 2009 12:59 pm
Location: second institution of oceanography,state oceanic administration China

Re: model blow up

#12 Post by slvester » Fri Dec 18, 2009 8:39 am

Thanks klyons.
klyons wrote:GET_2DFLD - surface net heat flux sensitivity to SST, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 1.00000000E+37 Max = -1.00000000E+37)
This is really a question.I set up the ncfiles(MAIN_ncfiles.m)once again and get the dQdSST.
I find a strange question,In the program rnt_2s.m line 63:
in=find(isnan(Tn) == 1); Tn(in)=-9999999.0 ;
If use this order the temp and salt value in the clima.nc et al include -9999999.0(It is just take place of the NaN value),But when I run the model,in the log file ,there are something like this
GET_2DFLD - sea surface temperature climatology, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -9.999999E+07 Max = 3.20000000E+01)
It is mean that the model take the -9999999.0 as the min value of temp and salt
When I set:
%in=find(isnan(Tn) == 1); Tn(in)=-9999999.0 ;
so the clim.nc et al file have NaN value,and I run the model,in the log file ,there are something like this:
GET_2DFLD - sea surface temperature climatology, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = NaN Max = NaN)
so how can I resolve this NaN value?
Another question,I get the dQdSST value in the forc.nc file and use the rnc_PlotNCfiles.m to figure the clim.nc,forc.nc,init.nc files ,It is just ok,and I can't see somthing is abnormal,and in the figure.the dQdSST value in the forc.nc file is
-87~3.04,but when I run the model,in the log file,
there are somthing like this:
GET_2DFLD - surface net heat flux sensitivity to SST, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.05970393E-05 Max = -4.33922053E-06)
Dose This mean the model variable value not consistant with the input nc files?I am confused.
Unfortunately,The model blows up again
I have struggled this question for some days

klyons

Re: model blow up

#13 Post by klyons » Mon Dec 21, 2009 10:57 am

Do you have any land in your model domain? Do the NaNs exist on land or sea grid points (or both)? If the NaNs exist at sea points then you need to use a realistic local value for those points not a value like -9999999.0.

slvester
Posts: 32
Joined: Mon Jun 01, 2009 12:59 pm
Location: second institution of oceanography,state oceanic administration China

Re: model blow up

#14 Post by slvester » Mon Dec 21, 2009 3:25 pm

Thanks klyons.
klyons wrote:Do you have any land in your model domain?
yes,I have land in my model domain,sometimes,I set up the grid.nc file once again,this question is not exit,but sometimes it still exit.In the programe rnt_2s.m ,I think the
-9999999.0 just take place of the deficit value of the variable.
one tiem,two times ,three times .....I redifine my cpp and set up the ncfiles again and again.but the model still blow up.I really don't know why
cna you help me?
thanks !
wishes!


Activated C-preprocessing Options:

NWPACIFIC NORTHWEST PACIFIC OCEAN
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged fields.
AVERAGES_FLUXES Writing out time-averaged surface fluxes.
BODYFORCE Momentum stresses as body-forces.
CURVGRID Orthogonal curvilinear grid.
DIURNAL_SRFLUX Modulate shortwave radiation by the local diurnal cycle.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EAST_FSRADIATION Eastern edge, free-surface, radiation condition.
EAST_M2RADIATION Eastern edge, 2D momentum, radiation condition.
EAST_M3NUDGING Eastern edge, 3D momentum, passive/active outflow/inflow.
EAST_M3RADIATION Eastern edge, 3D momentum, radiation condition.
EAST_TNUDGING Eastern edge, tracers, passive/active outflow/inflow.
EAST_TRADIATION Eastern edge, tracers, radiation condition.
EAST_VOLCONS Eastern edge, enforce mass conservation.
LMD_CONVEC LMD convective mixing due to shear instability.
LMD_MIXING Large/McWilliams/Doney interior mixing.
LMD_NONLOCAL LMD convective nonlocal transport.
LMD_RIMIX LMD diffusivity due to shear instability.
LMD_SKPP KPP surface boundary layer mixing.
MASKING Land/Sea masking.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NORTH_VOLCONS Northern edge, enforce mass conservation.
NORTH_FSGRADIENT Northern edge, free-surface, gradient condition.
NORTH_M2NUDGING Northern edge, 2D momentum, passive/active outflow/inflow.
NORTH_M2RADIATION Northern edge, 2D momentum, radiation condition.
NORTH_M3NUDGING Northern edge, 3D momentum, passive/active outflow/inflow.
NORTH_M3RADIATION Northern edge, 3D momentum, radiation condition.
NORTH_TNUDGING Northern edge, tracers, passive/active outflow/inflow.
NORTH_TRADIATION Northern edge, tracers, radiation condition.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
QCORRECTION Surface net heat flux correction.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SCORRECTION Surface salinity flux correction.
SOLAR_SOURCE Solar Radiation Source Term.
SOLVE3D Solving 3D Primitive Equations.
SOUTH_FSGRADIENT Southern edge, free-surface, gradient condition.
SOUTH_M2NUDGING Southern edge, 2D momentum, passive/active outflow/inflow.
SOUTH_M2RADIATION Southern edge, 2D momentum, radiation condition.
SOUTH_M3NUDGING Southern edge, 3D momentum, passive/active outflow/inflow.
SOUTH_M3RADIATION Southern edge, 3D momentum, radiation condition.
SOUTH_TNUDGING Southern edge, tracers, passive/active outflow/inflow.
SOUTH_TRADIATION Southern edge, tracers, radiation condition.
SOUTH_VOLCONS Southern edge, enforce mass conservation.
SPONGE Enhanced horizontal mixing in the sponge areas.
TS_C4HADVECTION Fourth-order centered 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.
WESTERN_WALL Wall boundary at Western edge.

INITIAL: Configuring and initializing forward nonlinear model ...
Power filter parameters, Fgamma, gamma = 0.28400 0.22720

Minimum X-grid spacing, DXmin = 4.23136053E+01 km
Maximum X-grid spacing, DXmax = 6.02183574E+01 km
Minimum Y-grid spacing, DYmin = 4.04665581E+01 km
Maximum Y-grid spacing, DYmax = 5.75900316E+01 km
Minimum Z-grid spacing, DZmin = 5.71428285E-01 m
Maximum Z-grid spacing, DZmax = 4.99190573E+02 m

Minimum barotropic Courant Number = 6.88497524E-04
Maximum barotropic Courant Number = 1.67364700E-02
Maximum Coriolis Courant Number = 1.05119596E-02
------------------------------------------------------------------

NLM: GET_STATE - Read state initial conditions, t = 15 00:00:00
(File: nwpacific-init.nc, Rec=0001, Index=1)
- free-surface
(Min = -9.30930793E-01 Max = 4.33212429E-01)
- vertically integrated u-momentum component
(Min = -1.54409245E-01 Max = 2.28290752E-01)
- vertically integrated v-momentum component
(Min = -5.71699917E-01 Max = 1.54866859E-01)
- u-momentum component
(Min = -5.31272352E-01 Max = 4.15556252E-01)
- v-momentum component
(Min = -1.14637828E+00 Max = 3.80686015E-01)
- potential temperature
(Min = -6.33812141E+00 Max = 2.82483559E+01)
- salinity
(Min = 2.32816772E+01 Max = 3.54774704E+01)
GET_2DFLD - surface u-momentum stress, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.18950366E-04 Max = 1.79853842E-04)
GET_2DFLD - surface v-momentum stress, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.15845773E-04 Max = 3.20990087E-05)
GET_2DFLD - solar shortwave radiation flux, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 1.68663096E-05 Max = 6.04279528E-05)
GET_2DFLD - surface net heat flux, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.20201810E-04 Max = 9.09955497E-06)
GET_2DFLD - sea surface temperature climatology, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -6.33812163E+00 Max = 2.82483550E+01)
GET_2DFLD - surface net heat flux sensitivity to SST, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.02486617E-05 Max = 2.68244872E-06)
GET_2DFLD - surface net freswater flux, (E-P), t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -7.12789420E-08 Max = 1.03241965E-07)
GET_2DFLD - sea surface salinity climatology, t = 15 00:00:00
(Rec=0001, Index=1, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 2.32816772E+01 Max = 3.54774693E+01)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -7.92952144E-02 Max = 1.31777762E-01)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -5.71699943E-01 Max = 1.54866852E-01)
GET_NGFLD - 2D u-momentum northern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -6.51845436E-02 Max = 9.12738077E-02)
GET_NGFLD - 2D v-momentum northern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.45121726E-02 Max = 4.03309134E-02)
GET_NGFLD - 3D u-momentum eastern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.85900558E-01 Max = 9.91482220E-02)
GET_NGFLD - 3D v-momentum eastern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -5.22824901E-02 Max = 2.28374821E-02)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.18395698E-01 Max = 2.19592159E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.14637830E+00 Max = 2.49603807E-01)
GET_NGFLD - 3D u-momentum northern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.29776488E-01 Max = 1.37148187E-01)
GET_NGFLD - 3D v-momentum northern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -3.59251858E-02 Max = 6.43606695E-02)
GET_NGFLD - temperature eastern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 1.24072863E+00 Max = 2.76062501E+01)
GET_NGFLD - salinity eastern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 3.31574597E+01 Max = 3.54221402E+01)
GET_NGFLD - temperature southern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 1.24072863E+00 Max = 2.82483550E+01)
GET_NGFLD - salinity southern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 3.32591299E+01 Max = 3.50171344E+01)
GET_NGFLD - temperature northern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -6.33812163E+00 Max = 5.37533818E+00)
GET_NGFLD - salinity northern boundary condition, t = 15 00:00:00
(Rec=0001, Index=2, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 2.32816772E+01 Max = 3.46979379E+01)

Maximum grid stiffness ratios: rx0 = 3.794281E-01 (Beckmann and Haidvogel)
rx1 = 1.276845E+01 (Haney)
Initial basin volumes: TotVolume = 9.4937769891E+16 m3
MinVolume = 1.1675001395E+09 m3
MaxVolume = 1.6606996579E+12 m3
Max/Min = 1.4224406505E+03

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00017280)
GET_2DFLD - surface u-momentum stress, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.14796599E-04 Max = 1.76354535E-04)
GET_2DFLD - surface v-momentum stress, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.61328160E-04 Max = 5.37323299E-05)
GET_2DFLD - solar shortwave radiation flux, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 2.64384669E-05 Max = 6.62480614E-05)
GET_2DFLD - surface net heat flux, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -9.55642005E-05 Max = 1.79407637E-05)
GET_2DFLD - sea surface temperature climatology, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -6.66470056E+00 Max = 2.80981529E+01)
GET_2DFLD - surface net heat flux sensitivity to SST, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.96546601E-05 Max = 3.15062258E-06)
GET_2DFLD - surface net freswater flux, (E-P), t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -5.83796569E-08 Max = 9.08026485E-08)
GET_2DFLD - sea surface salinity climatology, t = 45 00:00:00
(Rec=0002, Index=2, File: nwpacific-forc.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 2.15810763E+01 Max = 3.56455211E+01)
GET_NGFLD - 2D u-momentum southern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -5.60895822E-02 Max = 1.27304133E-01)
GET_NGFLD - 2D v-momentum southern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -5.69311173E-01 Max = 7.98094603E-02)
GET_NGFLD - 2D u-momentum northern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -6.42640638E-02 Max = 5.87949578E-02)
GET_NGFLD - 2D v-momentum northern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.70152575E-02 Max = 2.74919483E-02)
GET_NGFLD - 3D u-momentum eastern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -1.61698103E-01 Max = 8.86258898E-02)
GET_NGFLD - 3D v-momentum eastern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -5.27395814E-02 Max = 2.75172195E-02)
GET_NGFLD - 3D u-momentum southern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -2.96090991E-01 Max = 2.28041112E-01)
GET_NGFLD - 3D v-momentum southern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
GET_NGFLD - temperature eastern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 1.23730097E+00 Max = 2.75135253E+01)
GET_NGFLD - salinity eastern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 3.32835609E+01 Max = 3.53265716E+01)
GET_NGFLD - temperature southern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 1.23730097E+00 Max = 2.80992727E+01)
GET_NGFLD - salinity southern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = 3.31870841E+01 Max = 3.49282135E+01)
GET_NGFLD - temperature northern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
(Min = -6.66470056E+00 Max = 4.76900141E+00)
GET_NGFLD - salinity northern boundary condition, t = 45 00:00:00
(Rec=0002, Index=1, File: nwpacific-bry.nc)
(Tmin= 15.0000 Tmax= 345.0000)
STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME

0 15 00:00:00 NaN NaN NaN NaN

Elapsed CPU time (seconds):

Node # 0 CPU: 1.158 Node # 1 CPU: 1.185 Node # 2 CPU: 1.185 Node # 3 CPU: 1.185


Node # 6 CPU: 1.189 Node # 4 CPU: 1.189 Node # 5 CPU: 1.189 Node # 7 CPU: 1.189



Total: 9.472

Nonlinear model elapsed time profile:

Initialization ................................... 6.299 (66.5030 %)
Reading of input data ............................ 4.184 (44.1770 %)
Processing of input data ......................... 0.018 ( 0.1946 %)
Computation of global information integrals ...... 0.019 ( 0.1989 %)
2D/3D coupling, vertical metrics ................. 0.035 ( 0.3713 %)
Omega vertical velocity .......................... 0.015 ( 0.1576 %)
Equation of state for seawater ................... 0.188 ( 1.9820 %)
Total: 10.759 113.5844

Nonlinear model message Passage profile:

Message Passage: 2D halo exchanges ............... 0.153 ( 1.6130 %)
Message Passage: 3D halo exchanges ............... 0.101 ( 1.0629 %)
Message Passage: 4D halo exchanges ............... 0.013 ( 0.1396 %)
Message Passage: data broadcast .................. 5.042 (53.2295 %)
Message Passage: data reduction .................. 0.008 ( 0.0859 %)
Message Passage: data scattering.................. 0.794 ( 8.3774 %)
Total: 6.110 64.5085

All percentages are with respect to total time = 9.472

ROMS/TOMS - Output NetCDF summary for Grid 01:

Analytical header files used:

ROMS/Functionals/ana_btflux.h
ROMS/Functionals/ana_hmixcoef.h
ROMS/Functionals/ana_nudgcoef.h
ROMS/Functionals/ana_srflux.h

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


MAIN: Abnormal termination: BLOWUP.
--------------------------------------------------------------------

klyons

Re: model blow up

#15 Post by klyons » Mon Dec 21, 2009 4:11 pm

My suspicion is that the input data remains the source of your problem but I can't see anything obviously wrong in the latest output you posted. I think that you should take Kate's earlier advice and use debugging to step through the code and find where the NaNs are being created.

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arango
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Re: model blow up

#16 Post by arango » Mon Dec 21, 2009 5:28 pm

If you have an NaN in the first time step is either a CFL time-step violation or a configuration problem in your input initial conditions or forcing files. If you have NetCDF files, you need to check that the data is correct and the input NetCDF variable have the correct attributes and the variables are CF compliant. Check distributed directory Data/ROMS/CDL for the official NetCDF metadata for ROMS.

There are a lot of matlab scripts out there. The ones that are officially tested are distributed in the matlab repository with the following svn URL:

https://www.myroms.org/svn/src/matlab

Other scripts are not supported. You need to used them at your own risk. Many users write scripts and ignore ROMS metadata design and CF compliance.

slvester
Posts: 32
Joined: Mon Jun 01, 2009 12:59 pm
Location: second institution of oceanography,state oceanic administration China

Re: model blow up

#17 Post by slvester » Tue Dec 22, 2009 12:14 am

Thanks arango and klyons.I just use the RNT to set up my ncfiles.
Thanks for your suggestion,I will try
Thanks!

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