blowing up: Diag Speed Trouble

Bug reports, work arounds and fixes

Moderators: arango, robertson

Post Reply
Message
Author
jitraporn13
Posts: 12
Joined: Mon May 02, 2016 12:54 pm
Location: Kasetsart University

blowing up: Diag Speed Trouble

#1 Unread post by jitraporn13 »

Dear All,

I'm trying to run ROMs by forcing with u,v,p components
It was blowing up since the beginning.
The error:

Diag Speed Trouble
Diag speed ijk

I don't know why the max speed is so big

Please help me to figure out the problem.

Thank you so much

Here is part of my log file
____________________________________________

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

3600 ntimes Number of timesteps for 3-D equations.
150.000 dt Timestep size (s) for 3-D equations.
5 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.
30 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).
30 nHIS Number of timesteps between the writing fields
into history file.
0 nQCK Number of timesteps between the writing fields
into quicksave file.
F LuvSponge Turning OFF sponge on horizontal momentum.
F LtracerSponge(01) Turning OFF sponge on tracer 01: temp
F LtracerSponge(02) Turning OFF sponge on tracer 02: salt
1.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
5.0000E-06 Akk_bak Background vertical mixing coefficient (m2/s)
for turbulent energy.
5.0000E-06 Akp_bak Background vertical mixing coefficient (m2/s)
for turbulent generic statistical field.
3.000 gls_p GLS stability exponent.
1.500 gls_m GLS turbulent kinetic energy exponent.
-1.000 gls_n GLS turbulent length scale exponent.
7.6000E-06 gls_Kmin GLS minimum value of turbulent kinetic energy.
1.0000E-12 gls_Pmin GLS minimum value of dissipation.
5.4770E-01 gls_cmu0 GLS stability coefficient.
1.4400E+00 gls_c1 GLS shear production coefficient.
1.9200E+00 gls_c2 GLS dissipation coefficient.
-4.0000E-01 gls_c3m GLS stable buoyancy production coefficient.
1.0000E+00 gls_c3p GLS unstable buoyancy production coefficient.
1.0000E+00 gls_sigk GLS constant Schmidt number for TKE.
1.3000E+00 gls_sigp GLS constant Schmidt number for PSI.
1400.000 charnok_alpha Charnok factor for Zos calculation.
0.500 zos_hsig_alpha Factor for Zos calculation using Hsig(Awave).
0.250 sz_alpha Factor for Wave dissipation surface tke flux .
100.000 crgban_cw Factor for Craig/Banner surface tke flux.
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).
2.0000E-02 Zos Surface roughness (m).
1.0000E+01 blk_ZQ Height (m) of surface air humidity measurement.
1.0000E+01 blk_ZT Height (m) of surface air temperature measurement.
1.0000E+01 blk_ZW Height (m) of surface winds measurement.
1.0000E-01 Dcrit Minimum depth for wetting and drying (m).
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
0.0000E+00 theta_s S-coordinate surface control parameter.
1.0000E-01 theta_b S-coordinate bottom control parameter.
100.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1025.000 rho0 Mean density (kg/m3) for Boussinesq approximation.
5844.000 dstart Time-stamp assigned to model initialization (days).
20000101.00 time_ref Reference time for units attribute (yyyymmdd.dd)
0.0000E+00 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
0.0000E+00 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
9.0000E+01 Tnudg_SSS Nudging/relaxation time scale (days)
for sea surface salinity.
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.
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).
F LuvSrc Turning OFF momentum point Sources/Sinks.
F LwSrc Turning OFF volume influx point Sources/Sinks.
F LtracerSrc(01) Turning OFF point Sources/Sinks on tracer 01: temp
F LtracerSrc(02) Turning OFF point Sources/Sinks on tracer 02: salt
F LsshCLM Turning OFF processing of SSH climatology.
F Lm2CLM Turning OFF processing of 2D momentum climatology.
F Lm3CLM Turning OFF processing of 3D momentum climatology.
F LtracerCLM(01) Turning OFF processing of climatology tracer 01: temp
F LtracerCLM(02) Turning OFF processing of climatology tracer 02: salt
F LnudgeM2CLM Turning OFF nudging of 2D momentum climatology.
F LnudgeM3CLM Turning OFF nudging of 3D momentum climatology.
F LnudgeTCLM(01) Turning OFF nudging of climatology tracer 01: temp
F LnudgeTCLM(02) Turning OFF nudging of climatology tracer 02: salt

T Hout(idFsur) Write out free-surface.
T Hout(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: SE_rst.nc
Output History File: SE_his.nc
Input Grid File: ../../../easygrid_v2/SE_Asia_grd.nc
Input Nonlinear Initial File: ../../../easygrid_v2/SE_ASIA2_ini.nc
Input Forcing File 01: ../../../Documents/nesting/matlab/forcing/utest.nc
Input Forcing File 02: ../../../Documents/nesting/matlab/forcing/vtest.nc
Input Forcing File 03: ../../../Documents/nesting/matlab/forcing/ptest.nc
Input Forcing File 04: ../../../Documents/nesting/matlab/forcing/SE_Tair_era.nc
Input Forcing File 05: ../../../Documents/nesting/matlab/forcing/SE_Qair_era.nc
Input Forcing File 06: ../../../Documents/nesting/matlab/forcing/SE_lwrad_era.nc
Input Forcing File 07: ../../../Documents/nesting/matlab/forcing/SE_rain_era.nc

Tile partition information for Grid 01: 0258x0221x0030 tiling: 001x001

tile Istr Iend Jstr Jend Npts

Number of tracers: 2
0 1 258 1 221 1710540

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 259.50 0.50 221.50 RHO-points

0 0.00 259.00 0.50 221.50 U-points

0 0.50 259.50 0.00 221.00 V-points

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

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

zeta 1 Closed Closed Closed Closed

ubar 1 Closed Closed Closed Closed

vbar 1 Closed Closed Closed Closed

u 1 Closed Closed Closed Closed

v 1 Closed Closed Closed Closed

temp 1 Closed Closed Closed Closed

salt 1 Closed Closed Closed Closed

tke 1 Closed Closed Closed Closed

Activated C-preprocessing Options:

SE2 SE Asia
ANA_BSFLUX Analytical kinematic bottom salinity flux.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_SRFLUX Analytical kinematic shortwave radiation flux.
ANA_SSFLUX Analytical kinematic surface salinity flux.
ASSUMED_SHAPE Using assumed-shape arrays.
BULK_FLUXES Surface bulk fluxes parameterization.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
GLS_MIXING Generic Length-Scale turbulence closure.
LIMIT_BSTRESS Limit bottom stress to maintain bottom velocity direction.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
LIMIT_BSTRESS Limit bottom stress to maintain bottom velocity direction.
MASKING Land/Sea masking.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
N2S2_HORAVG Horizontal smoothing of buoyancy and shear.
OUT_DOUBLE Double precision output fields in NetCDF files.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
K_GSCHEME Third-order upstream advection of TKE fields.
RI_SPLINES Parabolic Spline Reconstruction for Richardson Number.
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SPLINES_VDIFF Parabolic Spline Reconstruction for Vertical Diffusion.
SPLINES_VVISC Parabolic Spline Reconstruction for Vertical Viscosity.
TS_U3HADVECTION Third-order upstream horizontal advection of tracers.
TS_C4VADVECTION Fourth-order centered vertical advection 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.
VAR_RHO_2D Variable density barotropic mode.
WET_DRY Wetting and drying activated.

Process Information:

Thread # 0 (pid= 61980) is active.

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

Vertical S-coordinate System, Grid 01:

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

30 0.0000000 0.0000000 0.000 0.000 0.000 0.000
29 -0.0333333 -0.0011675 -0.128 -1.725 -6.319 -9.585
28 -0.0666667 -0.0046693 -0.257 -3.567 -18.842 -31.790
27 -0.1000000 -0.0105031 -0.386 -5.525 -37.563 -66.601
26 -0.1333333 -0.0186649 -0.516 -7.600 -62.470 -113.997
25 -0.1666667 -0.0291493 -0.646 -9.791 -93.550 -173.950
24 -0.2000000 -0.0419494 -0.776 -12.097 -130.784 -246.421
23 -0.2333333 -0.0570566 -0.906 -14.519 -174.150 -331.364
22 -0.2666667 -0.0744609 -1.037 -17.056 -223.620 -428.725
21 -0.3000000 -0.0941507 -1.168 -19.708 -279.164 -538.442
20 -0.3333333 -0.1161130 -1.300 -22.472 -340.748 -660.443
19 -0.3666667 -0.1403332 -1.432 -25.350 -408.332 -794.651
18 -0.4000000 -0.1667954 -1.564 -28.340 -481.874 -940.979
17 -0.4333333 -0.1954820 -1.697 -31.441 -561.329 -1099.333
16 -0.4666667 -0.2263742 -1.830 -34.652 -646.644 -1269.609
15 -0.5000000 -0.2594516 -1.963 -37.973 -737.768 -1451.699
14 -0.5333333 -0.2946926 -2.097 -41.401 -834.641 -1645.485
13 -0.5666667 -0.3320740 -2.231 -44.937 -937.202 -1850.842
12 -0.6000000 -0.3715715 -2.365 -48.579 -1045.387 -2067.639
11 -0.6333333 -0.4131593 -2.499 -52.325 -1159.128 -2295.736
10 -0.6666667 -0.4568104 -2.634 -56.174 -1278.352 -2534.987
9 -0.7000000 -0.5024966 -2.770 -60.125 -1402.984 -2785.239
8 -0.7333333 -0.5501882 -2.905 -64.176 -1532.946 -3046.333
7 -0.7666667 -0.5998546 -3.041 -68.326 -1668.156 -3318.103
6 -0.8000000 -0.6514640 -3.177 -72.573 -1808.530 -3600.376
5 -0.8333333 -0.7049834 -3.314 -76.916 -1953.980 -3892.975
4 -0.8666667 -0.7603786 -3.450 -81.352 -2104.415 -4195.714
3 -0.9000000 -0.8176145 -3.587 -85.881 -2259.741 -4508.404
2 -0.9333333 -0.8766550 -3.725 -90.499 -2419.864 -4830.850
1 -0.9666667 -0.9374628 -3.862 -95.206 -2584.684 -5162.850
0 -1.0000000 -1.0000000 -4.000 -100.000 -2754.099 -5504.199

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

Primary Secondary Accumulated to Current Step

1 0.0119306869089341 0.2000000000000000 0.0119306869089341 0.2000000000000000
2 0.0475049776008205 0.1976138626182131 0.0594356645097547 0.3976138626182131
3 0.1047629417620785 0.1881128670980491 0.1641986062718331 0.5857267297162622
4 0.1760826281731955 0.1671602787456334 0.3402812344450286 0.7528870084618955
5 0.2416469636634478 0.1319437531109943 0.5819281981084765 0.8848307615728898
6 0.2602974116474964 0.0836143603783047 0.8422256097559728 0.9684451219511945
7 0.1577743902440273 0.0315548780488054 1.0000000000000000 0.9999999999999999

ndtfast, nfast = 5 7 nfast/ndtfast = 1.40000

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

1.000000000000 1.084198606272 0.542099303136 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.00000

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

Minimum X-grid spacing, DXmin = 1.50000000E+01 km
Maximum X-grid spacing, DXmax = 1.50000333E+01 km
Minimum Y-grid spacing, DYmin = 1.50000000E+01 km
Maximum Y-grid spacing, DYmax = 1.55908600E+01 km
Minimum Z-grid spacing, DZmin = 1.28384748E-01 m
Maximum Z-grid spacing, DZmax = 3.41348659E+02 m

Minimum barotropic Courant Number = 1.94485509E-02
Maximum barotropic Courant Number = 6.57079840E-01
Maximum Coriolis Courant Number = 9.20089964E-03


NLM: GET_STATE - Read state initial conditions, t = 5844 00:00:00
(Grid 01, File: SE_ASIA2_ini.nc, Rec=0001, Index=1)
- free-surface
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- vertically integrated u-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- vertically integrated v-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- u-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- v-momentum component
(Min = 0.00000000E+00 Max = 0.00000000E+00)
- potential temperature
(Min = 9.00000000E+00 Max = 9.00000000E+00)
- salinity
(Min = 3.00000000E+01 Max = 3.00000000E+01)
GET_2DFLD - surface u-wind component, t = 5844 00:00:00
(Rec=0000001, Index=1, File: utest.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = -1.22636754E+01 Max = 4.81609346E+00)
GET_2DFLD - surface v-wind component, t = 5844 00:00:00
(Rec=0000001, Index=1, File: vtest.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = -1.21289526E+01 Max = 3.68782660E+00)
GET_2DFLD - surface air pressure, t = 5844 00:00:00
(Rec=0000001, Index=1, File: ptest.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = 1.01185653E+01 Max = 1.03030460E+01)
GET_2DFLD - surface air temperature, t = 5844 00:00:00
(Rec=0000001, Index=1, File: SE_Tair_era.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = 2.56414107E+03 Max = 2.08692103E+04)
GET_2DFLD - surface air relative humidity, t = 5844 00:00:00
(Rec=0000001, Index=1, File: SE_Qair_era.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = 5.00000000E+01 Max = 5.00000000E+01)
GET_2DFLD - net longwave radiation flux, t = 5843 22:30:00
(Rec=0000001, Index=1, File: SE_lwrad_era.nc)
(Tmin= 5843.9375 Tmax= 5874.9375)
(Min = 6.78818394E-07 Max = 7.42758226E-07)
GET_2DFLD - rain fall rate, t = 5843 22:30:00
(Rec=0000001, Index=1, File: SE_rain_era.nc)
(Tmin= 5843.9375 Tmax= 5874.9375)
(Min = -2.73776874E+00 Max = -1.20218290E+00)

Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 9.496374E-01 (Beckmann and Haidvogel)
rx1 = 3.049303E+01 (Haney)

Initial basin volumes: TotVolume = 1.3989106538E+16 m3
MinVolume = 3.4621784284E+07 m3
MaxVolume = 7.6841808058E+10 m3
Max/Min = 2.2194641220E+03

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00003600)

GET_2DFLD - surface u-wind component, t = 5844 12:00:00
(Rec=0000002, Index=2, File: utest.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = -1.19747591E+01 Max = 3.37829314E+00)
GET_2DFLD - surface v-wind component, t = 5844 12:00:00
(Rec=0000002, Index=2, File: vtest.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = -1.27883484E+01 Max = 2.67607881E+00)
GET_2DFLD - surface air pressure, t = 5844 12:00:00
(Rec=0000002, Index=2, File: ptest.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = 1.01103045E+01 Max = 1.02726652E+01)
GET_2DFLD - surface air temperature, t = 5844 12:00:00
(Rec=0000002, Index=2, File: SE_Tair_era.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = 3.66556213E+03 Max = 2.04005658E+04)
GET_2DFLD - surface air relative humidity, t = 5844 12:00:00
(Rec=0000002, Index=2, File: SE_Qair_era.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = 5.00000000E+01 Max = 5.00000000E+01)
GET_2DFLD - net longwave radiation flux, t = 5844 10:30:00
(Rec=0000002, Index=2, File: SE_lwrad_era.nc)
(Tmin= 5843.9375 Tmax= 5874.9375)
(Min = -3.83092890E-08 Max = 6.42174955E-07)
GET_2DFLD - rain fall rate, t = 5844 10:30:00
(Rec=0000002, Index=2, File: SE_rain_era.nc)
(Tmin= 5843.9375 Tmax= 5874.9375)
(Min = -3.03388892E+03 Max = -2.52202799E+03)

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

0 5844 00:00:00 0.000000E+00 1.508919E+04 1.508919E+04 1.455726E+16
(000,000,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: SE_his.nc
WRT_HIS - wrote history fields (Index=1,1) in record = 0000001
1 5844 00:02:30 2.761005E+01 1.572569E+04 1.575330E+04 1.398958E+16
(104,113,30) 1.410010E+01 1.268761E+01 0.000000E+00 1.898574E+03
DIAG speed trouble 1898.5744590090233
DIAG speed ijk 1509.5531256078064 103 113 30 1

Blowing-up: Saving latest model state into RESTART file

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

Elapsed CPU time (seconds):

Thread # 0 CPU: 121.579
Total: 121.579

Nonlinear ocean model elapsed time profile, Grid: 01

Allocation and array initialization .............. 13.727 (11.2906 %)
Ocean state initialization ....................... 2.178 ( 1.7912 %)
Reading of input data ............................ 8.801 ( 7.2387 %)
Processing of input data ......................... 0.102 ( 0.0839 %)
Computation of vertical boundary conditions ...... 0.075 ( 0.0617 %)
Computation of global information integrals ...... 4.167 ( 3.4277 %)
Writing of output data ........................... 3.613 ( 2.9721 %)
Model 2D kernel .................................. 5.005 ( 4.1169 %)
2D/3D coupling, vertical metrics ................. 3.077 ( 2.5305 %)
Omega vertical velocity .......................... 1.427 ( 1.1735 %)
Equation of state for seawater ................... 7.637 ( 6.2814 %)
Atmosphere-Ocean bulk flux parameterization ...... 0.697 ( 0.5732 %)
GLS vertical mixing parameterization ............. 26.115 (21.4800 %)
3D equations right-side terms .................... 5.254 ( 4.3217 %)
3D equations predictor step ...................... 9.365 ( 7.7025 %)
Pressure gradient ................................ 5.271 ( 4.3356 %)
Corrector time-step for 3D momentum .............. 7.315 ( 6.0166 %)
Corrector time-step for tracers .................. 8.237 ( 6.7748 %)
Total: 112.062 92.1725

All percentages are with respect to total time = 121.579


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_srflux.h
ROMS/Functionals/ana_stflux.h

User avatar
kate
Posts: 4088
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: blowing up: Diag Speed Trouble

#2 Unread post by kate »

DIAG speed ijk 1509.5531256078064 103 113 30 1
It is at least telling you to look at point (i,j,k) = (103,113,30)
GET_2DFLD - surface air pressure, t = 5844 00:00:00
(Rec=0000001, Index=1, File: ptest.nc)
(Tmin= 5844.0000 Tmax= 5875.0000)
(Min = 1.01185653E+01 Max = 1.03030460E+01)
What units is your pressure in? ROMS wants something around 1000. Maybe you're using my varinfo.dat for converting from Pascals to millibars? Better check your Qair and Tair too.

Post Reply