Model indicates infinite grid size, but pm, pn are non-zero

[wjschulz]

Using a grid file created from scratch in matlab, am attempting to run a straight channel with an embayment along the northern shore, and only the east boundary open (forced by M2 tide.) The model blows up prior to run, indicating that "DXMax (and DYmax, and max volume) = Infinity, with Courant numbers = 0. I've checked that pm, pn are non-zero. (These are written into 'grid.nc' during execution of the create_grids.m, which calls c_grid, uvp_masks.m and write_mask.m from the repository.) I cannot find where to ensure max grid size is computed by or inputted to the model. Appreciate any help!


-----------------------------------------------------------------------------------------------

Model Input Parameters: ROMS/TOMS version 3.5
Sunday - June 10, 2012 - 2:32:11 PM
-----------------------------------------------------------------------------

POTOMAC

Operating system : Linux
CPU/hardware : x86_64
Compiler system : ifort
Compiler command : /usr/local/openmpi/openmpi-1.4.3/x86_64/ib/intel2011/bin/mpif90
Compiler flags : -heap-arrays -fp-model precise -ip -O3 -free -free -free

Input Script : ./External/ocean.in

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 564M

Local Root : /usr/local/roms
Header Dir : /home/schulz/Projects/MRIVER
Header file : potomac.h
Analytical Dir: /home/schulz/Projects/MRIVER/Functionals

Resolution, Grid 01: 0498x0198x005, Parallel Nodes: 8, Tiling: 002x004


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

401 ntimes Number of timesteps for 3-D equations.
20.000 dt Timestep size (s) for 3-D equations.
45 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.
3600 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).
10 nHIS Number of timesteps between the writing fields
into history file.
1.0000E-05 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
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.
2.6500E-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 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.
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.
0.000 dstart Time-stamp assigned to model initialization (days).
0.000 tide_start Reference time origin for tidal forcing (days).
0.00 time_ref Reference time for units attribute (yyyymmdd.dd)
5.0000E-01 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
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.
3.0000E+01 obcfac Factor between passive and active
open boundary conditions.
5.000 T0 Background potential temperature (C) constant.
35.000 S0 Background salinity (PSU) constant.
1.000 gamma2 Slipperiness variable: free-slip (1.0) or
no-slip (-1.0).
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(idDano) Write out density anomaly.

Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Input Grid File: Forcing/grid.nc
Input Nonlinear Initial File: Initial/init.nc
Input Forcing File 01: Forcing/frc_surface.nc
Input Forcing File 02: Forcing/frc_tides.nc
Input Boundary File: Boundary/boundary.nc

Tile partition information for Grid 01: 0498x0198x0005 tiling: 002x004

tile Istr Iend Jstr Jend Npts

0 1 249 1 49 61005
1 250 498 1 49 61005
2 1 249 50 99 62250
3 250 498 50 99 62250
4 1 249 100 149 62250
5 250 498 100 149 62250
6 1 249 150 198 61005
7 250 498 150 198 61005

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 249.50 0.50 49.50 RHO-points
1 249.50 498.50 0.50 49.50 RHO-points
2 0.50 249.50 49.50 99.50 RHO-points
3 249.50 498.50 49.50 99.50 RHO-points
4 0.50 249.50 99.50 149.50 RHO-points
5 249.50 498.50 99.50 149.50 RHO-points
6 0.50 249.50 149.50 198.50 RHO-points
7 249.50 498.50 149.50 198.50 RHO-points

0 1.00 249.50 0.50 49.50 U-points
1 249.50 498.00 0.50 49.50 U-points
2 1.00 249.50 49.50 99.50 U-points
3 249.50 498.00 49.50 99.50 U-points
4 1.00 249.50 99.50 149.50 U-points
5 249.50 498.00 99.50 149.50 U-points
6 1.00 249.50 149.50 198.50 U-points
7 249.50 498.00 149.50 198.50 U-points

0 0.50 249.50 1.00 49.50 V-points
1 249.50 498.50 1.00 49.50 V-points
2 0.50 249.50 49.50 99.50 V-points
3 249.50 498.50 49.50 99.50 V-points
4 0.50 249.50 99.50 149.50 V-points
5 249.50 498.50 99.50 149.50 V-points
6 0.50 249.50 149.50 198.00 V-points
7 249.50 498.50 149.50 198.00 V-points

Maximum halo size in XI and ETA directions:

HaloSizeI(1) = 522
HaloSizeJ(1) = 124
TileSide(1) = 255
TileSize(1) = 14280


Activated C-preprocessing Options:

POTOMAC POTOMAC
ADD_FSOBC Adding tidal elevation to proccesed OBC data.
ANA_BTFLUX Analytical kinematic bottom temperature flux.
ANA_M2OBC Analytical 2D momentum boundary conditions.
ANA_STFLUX Analytical kinematic surface temperature flux.
ASSUMED_SHAPE Using assumed-shape arrays.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
EAST_FSCHAPMAN Eastern edge, free-surface, Chapman condition.
EAST_M2FLATHER Eastern edge, 2D momentum, Flather condition.
EAST_M3RADIATION Eastern edge, 3D momentum, radiation condition.
EAST_TRADIATION Eastern edge, tracers, radiation condition.
GLS_MIXING Generic Length-Scale turbulence closure.
INLINE_2DIO Processing 3D IO level by level to reduce memory needs.
KANTHA_CLAYSON Kantha and Clayson stability function formulation.
MASKING Land/Sea masking.
MPI MPI distributed-memory configuration.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
NORTHERN_WALL Wall boundary at Northern edge.
N2S2_HORAVG Horizontal smoothing of buoyancy and shear.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
K_GSCHEME Third-order upstream advection of TKE fields.
RADIATION_2D Use tangential phase speed in radiation conditions.
RAMP_TIDES Ramping tidal forcing for one day.
!RST_SINGLE Double precision fields in restart NetCDF file.
SOLVE3D Solving 3D Primitive Equations.
SOUTHERN_WALL Wall boundary at Southern edge.
SPLINES Conservative parabolic spline reconstruction.
SSH_TIDES Add tidal elevation to SSH climatology.
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.
UV_TIDES Add tidal currents to 2D momentum climatologies.
VAR_RHO_2D Variable density barotropic mode.
WESTERN_WALL Wall boundary at Western edge.

Process Information:

Node # 0 (pid= 27652) is active.
Node # 7 (pid= 27659) is active.
Node # 4 (pid= 27656) is active.
Node # 2 (pid= 27654) is active.
Node # 5 (pid= 27657) is active.
Node # 6 (pid= 27658) is active.
Node # 3 (pid= 27655) is active.
Node # 1 (pid= 27653) 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 -0.0260168 -0.100 -0.100 -0.438 -0.776
3 -0.4000000 -0.1356491 -0.200 -0.200 -1.964 -3.727
2 -0.6000000 -0.3746809 -0.300 -0.300 -5.171 -10.042
1 -0.8000000 -0.6041494 -0.400 -0.400 -8.254 -16.109
0 -1.0000000 -1.0000000 -0.500 -0.500 -13.501 -26.502

Time Splitting Weights: ndtfast = 45 nfast = 63

Primary Secondary Accumulated to Current Step

1-0.0005234147293094 0.0222222222222222-0.0005234147293094 0.0222222222222222
2-0.0009714664692682 0.0222338536606513-0.0014948811985777 0.0444560758828736
3-0.0013441562052106 0.0222554418044128-0.0028390374037882 0.0667115176872864
4-0.0016414877689917 0.0222853119423064-0.0044805251727799 0.0889968296295928
5-0.0018634711234351 0.0223217894482840-0.0063439962962150 0.1113186190778769
6-0.0020101269605588 0.0223631999176937-0.0083541232567738 0.1336818189955705
7-0.0020814926135807 0.0224078694057061-0.0104356158703545 0.1560896884012766
8-0.0020776292827024 0.0224541247971190-0.0125132451530569 0.1785438131983956
9-0.0019986305746722 0.0225002943367346-0.0145118757277291 0.2010441075351302
10-0.0018446323561274 0.0225447083495051-0.0163565080838566 0.2235888158846354
11-0.0016158239207149 0.0225857001796413-0.0179723320045715 0.2461745160642766
12-0.0013124604699909 0.0226216073778794-0.0192847924745624 0.2687961234421560
13-0.0009348769080999 0.0226507731661014-0.0202196693826623 0.2914468966082574
14-0.0004835029502319 0.0226715482085036-0.0207031723328942 0.3141184448167610
15 0.0000411204551404 0.0226822927185088-0.0206620518777537 0.3368007375352697
16 0.0006383233902467 0.0226813789306168-0.0200237284875071 0.3594821164658865
17 0.0013072879182242 0.0226671939663891-0.0187164405692829 0.3821493104322756
18 0.0020470277195447 0.0226381431237619-0.0166694128497381 0.4047874535560374
19 0.0028563664146621 0.0225926536188831-0.0138130464350760 0.4273801071749205
20 0.0037339145728811 0.0225291788096684-0.0100791318621949 0.4499092859845888
21 0.0046780454074473 0.0224462029302710-0.0054010864547475 0.4723554889148598
22 0.0056868691568581 0.0223422463656611 0.0002857827021106 0.4946977352805209
23 0.0067582061523945 0.0222158714955087 0.0070439888545051 0.5169136067760296
24 0.0078895585718746 0.0220656891365666 0.0149335474263797 0.5389792959125962
25 0.0090780808796274 0.0218903656127471 0.0240116283060071 0.5608696615253433
26 0.0103205489526884 0.0216886304820887 0.0343321772586955 0.5825582920074320
27 0.0116133278932156 0.0214592849498068 0.0459455051519111 0.6040175769572388
28 0.0129523385271270 0.0212012109966242 0.0588978436790381 0.6252187879538630
29 0.0143330225889594 0.0209133812515769 0.0732308662679975 0.6461321692054399
30 0.0157503065929473 0.0205948696384890 0.0889811728609449 0.6667270388439289
31 0.0171985643903243 0.0202448628253123 0.1061797372512691 0.6869719016692413
32 0.0186715784128440 0.0198626725055274 0.1248513156641131 0.7068345741747686
33 0.0201624996025234 0.0194477485407975 0.1450138152666365 0.7262823227155660
34 0.0216638060276065 0.0189996929940748 0.1666776212942430 0.7452820157096408
35 0.0231672601847493 0.0185182750823502 0.1898448814789924 0.7638002907919910
36 0.0246638649874256 0.0180034470782446 0.2145087464664180 0.7818037378702356
37 0.0261438184405543 0.0174553611896352 0.2406525649069723 0.7992590990598708
38 0.0275964670013474 0.0168743874465117 0.2682490319083198 0.8161334865063825
39 0.0290102576263795 0.0162611326242596 0.2972592895346993 0.8323946191306421
40 0.0303726885048774 0.0156164602325623 0.3276319780395767 0.8480110793632043
41 0.0316702584782326 0.0149415115991205 0.3593022365178093 0.8629525909623248
42 0.0328884151457325 0.0142377280773820 0.3921906516635418 0.8771903190397068
43 0.0340115016565149 0.0135068744074769 0.4262021533200568 0.8906971934471837
44 0.0350227021877421 0.0127510632595543 0.4612248555077989 0.9034482567067380
45 0.0359039861089966 0.0119727809887156 0.4971288416167955 0.9154210376954536
46 0.0366360508328980 0.0111749146307379 0.5337648924496935 0.9265959523261915
47 0.0371982633519407 0.0103607801677846 0.5709631558016341 0.9369567324939762
48 0.0375686004615529 0.0095341520932970 0.6085317562631870 0.9464908845872732
49 0.0377235876693763 0.0086992943052625 0.6462553439325633 0.9551901788925357
50 0.0376382367907677 0.0078609923570542 0.6838935807233311 0.9630511712495898
51 0.0372859822305206 0.0070245870950371 0.7211795629538517 0.9700757583446269
52 0.0366386159508082 0.0061960097121366 0.7578181789046599 0.9762717680567635
53 0.0356662211253486 0.0053818182465631 0.7934844000300084 0.9816535863033267
54 0.0343371044797891 0.0045892355548887 0.8278215045097975 0.9862428218582153
55 0.0326177273183132 0.0038261887886712 0.8604392318281108 0.9900690106468865
56 0.0304726352364682 0.0031013504038198 0.8909118670645790 0.9931703610507062
57 0.0278643865202132 0.0024241807318983 0.9187762535847923 0.9955945417826044
58 0.0247534792311892 0.0018049721425602 0.9435297328159815 0.9973995139251646
59 0.0210982769782096 0.0012548948263115 0.9646280097941911 0.9986544087514762
60 0.0168549333749721 0.0007860442267958 0.9814829431691632 0.9994404529782719
61 0.0119773151839916 0.0004114901517964 0.9934602583531548 0.9998519431300683
62 0.0064169241467539 0.0001453275921521 0.9998771824999086 0.9999972707222204
63 0.0001228175000916 0.0000027292777798 1.0000000000000002 1.0000000000000002

ndtfast, nfast = 45 63 nfast/ndtfast = 1.40000

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

1.000000000000 1.036028576182 0.518014288091 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.22089

Minimum X-grid spacing, DXmin = 1.00000000E-01 km
Maximum X-grid spacing, DXmax = Infinity km
Minimum Y-grid spacing, DYmin = 1.00000000E-01 km
Maximum Y-grid spacing, DYmax = Infinity km
Minimum Z-grid spacing, DZmin = 1.00000000E-01 m
Maximum Z-grid spacing, DZmax = 1.03927543E+01 m

Minimum barotropic Courant Number = 0.00000000E+00
Maximum barotropic Courant Number = 0.00000000E+00
Maximum Coriolis Courant Number = 0.00000000E+00


NLM: GET_STATE - Read state initial conditions, t = 30 00:00:00
(File: init.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 = 1.00000000E+01 Max = 1.00000000E+01)
GET_NGFLD - tidal period
(Min = 4.47141600E+04 Max = 4.47141600E+04)
GET_2DFLD - tidal elevation amplitude
(Min = 1.00000000E+00 Max = 1.00000000E+00)
GET_2DFLD - tidal elevation phase angle
(Min = 7.85398163E-01 Max = 7.85398163E-01)
GET_2DFLD - tidal current inclination angle
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - tidal current phase angle
(Min = 2.35619449E+00 Max = 2.35619449E+00)
GET_2DFLD - maximum tidal current, ellipse major axis
(Min = 5.00000000E-01 Max = 5.00000000E-01)
GET_2DFLD - minimum tidal current, ellipse minor axis
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_2DFLD - surface u-momentum stress, t = 30 00:00:00
(Rec=0002, Index=1, File: frc_surface.nc)
(Tmin= 0.0000 Tmax= 330.0000)
(Min = 4.87804878E-04 Max = 4.87804878E-04)
GET_2DFLD - surface v-momentum stress, t = 30 00:00:00
(Rec=0002, Index=1, File: frc_surface.nc)
(Tmin= 0.0000 Tmax= 330.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)
GET_NGFLD - free-surface eastern boundary condition, t = ***** **:**:**
(Rec=0200, Index=2, File: boundary.nc)
(Tmin= 0.0000 Tmax= 0.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)

Maximum grid stiffness ratios: rx0 = 3.692595E-01 (Beckmann and Haidvogel)
rx1 = 1.678067E+00 (Haney)


Initial basin volumes: TotVolume = Infinity m3
MinVolume = 1.0000000000E+20 m3
MaxVolume = Infinity m3
Max/Min = Infinity


NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00129601 - 00000401)

GET_2DFLD - surface u-momentum stress, t = 60 00:00:00
(Rec=0003, Index=2, File: frc_surface.nc)
(Tmin= 0.0000 Tmax= 330.0000)
(Min = 4.87804878E-04 Max = 4.87804878E-04)
GET_2DFLD - surface v-momentum stress, t = 60 00:00:00
(Rec=0003, Index=2, File: frc_surface.nc)
(Tmin= 0.0000 Tmax= 330.0000)
(Min = 0.00000000E+00 Max = 0.00000000E+00)

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

129600 30 00:00:00 NaN NaN NaN Infinity
(000,000,0) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00

Elapsed CPU time (seconds):

Node # 3 CPU: 0.455
Node # 7 CPU: 0.460
Node # 0 CPU: 0.440
Node # 4 CPU: 0.455
Node # 6 CPU: 0.452
Node # 2 CPU: 0.460
Node # 5 CPU: 0.452
Node # 1 CPU: 0.459
Total: 3.632

Nonlinear model elapsed time profile:

Allocation and array initialization .............. 0.234 ( 6.4409 %)
Ocean state initialization ....................... 0.068 ( 1.8716 %)
Reading of input data ............................ 0.660 (18.1669 %)
Processing of input data ......................... 0.003 ( 0.0826 %)
Computation of global information integrals ...... 0.032 ( 0.8808 %)
2D/3D coupling, vertical metrics ................. 0.056 ( 1.5414 %)
Omega vertical velocity .......................... 0.014 ( 0.3854 %)
Equation of state for seawater ................... 0.074 ( 2.0368 %)
Total: 1.141 31.4065

Nonlinear model message Passage profile:

Message Passage: 2D halo exchanges ............... 0.051 ( 1.4038 %)
Message Passage: 3D halo exchanges ............... 0.045 ( 1.2386 %)
Message Passage: 4D halo exchanges ............... 0.005 ( 0.1376 %)
Message Passage: data broadcast .................. 1.154 (31.7646 %)
Message Passage: data reduction .................. 0.012 ( 0.3302 %)
Message Passage: data scattering.................. 1.510 (41.5630 %)
Total: 2.777 76.4379

All percentages are with respect to total time = 3.632

ROMS/TOMS - Output NetCDF summary for Grid 01:

Analytical header files used:

ROMS/Functionals/ana_btflux.h
ROMS/Functionals/ana_m2obc.h
ROMS/Functionals/ana_stflux.h

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


MAIN: Abnormal termination: BLOWUP.

[wilkin]

You say you've checked that pm, pn are non-zero, but ROMS appears to insist otherwise.

Can you share your grid file through an http web service, ftp, google docs or whatever, so the community can take a look at it?

I suspect there is some issue with appropriate dimensions of the rho, u and v coordinates, or a netcdf FillValue or missingvalue.

John.

[wjschulz]

John - Thanks for the response. I went back and traced pn and pm inputs and found the problem - I was feeding incorrect dimensions for pn and pm in my matlab grid generation code. Seems to be working well now. Thanks again! - Bill