NETCDF PROBLEM WHEN RUNNING MODEL

[javadi]

Dear users
I have faced an error when running upwelling_test case which is related to Netcdf. Here are the details of this error.
Please help me with your interesting comments.

Wind-Driven Upwelling/Downwelling over a Periodic Channel

Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /usr/bin/gfortran
Compiler flags : -frepack-arrays -O3 -ffast-math -O3 -ffast-math -

GIT Root URL : https://github.com/kshedstrom/roms.git
GIT Revision : kate_svn commit 45632fb01be13aae698d6c1fa99a666bfc3b4d19
Git Status : The working tree is DIRTY with 1 changes

SVN Root URL :
SVN Revision :

Local Root : /home/javadbabagoli/Documents/roms
Header Dir : /home/javadbabagoli/Documents/Test
Header file : upwelling.h
Analytical Dir : /home/javadbabagoli/Documents/Test

Resolution, Grid 01: 41x80x16, Parallel Threads: 1, Tiling: 1x1


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

1440 ntimes Number of timesteps for 3-D equations.
300.000 dt Timestep size (s) for 3-D equations.
30 ndtfast Number of timesteps for 2-D equations between
each 3D timestep.
1 ERstr Starting ensemble/perturbation run number.
1 ERend Ending ensemble/perturbation run number.
0 nrrec Number of restart records to read from disk.
T LcycleRST Switch to recycle time-records in restart file.
288 nRST Number of timesteps between the writing of data
into restart fields.
1 ninfo Number of timesteps between print of information
to standard output.
T ldefout Switch to create a new output NetCDF file(s).
72 nHIS Number of timesteps between the writing fields
into history file.
0 nQCK Number of timesteps between the writing fields
into quicksave file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
72 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
1 ntsDIA Starting timestep for the accumulation of output
time-averaged diagnostics data.
72 nDIA Number of timesteps between the writing of
time-averaged data into diagnostics file.
0.0000E+00 nl_tnu2(01) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 01: temp
0.0000E+00 nl_tnu2(02) NLM Horizontal, harmonic mixing coefficient
(m2/s) for tracer 02: salt
5.0000E+00 nl_visc2 NLM Horizontal, harmonic mixing coefficient
(m2/s) for momentum.
F LuvSponge Turning OFF sponge on horizontal momentum.
F LtracerSponge(01) Turning OFF sponge on tracer 01: temp
F LtracerSponge(02) Turning OFF sponge on tracer 02: salt
1.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
1.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
1.0000E-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
2.0000E-02 Zob Bottom roughness (m).
2 Vtransform S-coordinate transformation equation.
4 Vstretching S-coordinate stretching function.
3.0000E+00 theta_s S-coordinate surface control parameter.
0.0000E+00 theta_b S-coordinate bottom control parameter.
25.000 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).
0.00 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.
1027.000 R0 Background density (kg/m3) used in linear Equation
of State.
1.7000E-04 Tcoef Thermal expansion coefficient (1/Celsius).
0.0000E+00 Scoef Saline contraction coefficient (1/PSU).
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
T Hout(idStr) Write out strain.
T Hout(id3dPV) Write out potential vorticity.
T Hout(id3dPVK) Write out k component of potential vorticity.
T Hout(id3dPVJ) Write out j component of potential vorticity.
T Hout(id3dPVI) Write out i component of potential vorticity.

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

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

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

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

Output/Input Files:

Output Restart File: roms_rst.nc
Output History File: roms_his.nc
Output Averages File: roms_avg.nc
Output Diagnostics File: roms_dia.nc
ROMS I/O variables Metadata File: varinfo.dat

Tile partition information for Grid 01: 41x80x16 tiling: 1x1

tile Istr Iend Jstr Jend Npts

Number of tracers: 2
0 1 41 1 80 52480

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

tile Xmin Xmax Ymin Ymax grid

0 -1.50 42.50 0.50 81.50 RHO-points

0 -2.00 42.00 0.50 81.50 U-points

0 -1.50 42.50 0.00 81.00 V-points

Tracer Advection Scheme: NLM
========================

Variable Grid Horizontal Vertical
--------- ---- ------------ ------------

temp 1 Upstream3 Centered4

salt 1 Upstream3 Centered4

Akima4 Fourth-order Akima advection
Centered2 Second-order centered differences advection
Centered4 Fourth-order centered differences advection
HSIMT Third High-order Spatial Inteporlation at Middle Time Advection with TVD limiter
MPDATA Multidimensional Positive Definite Advection Algorithm, recursive method
Splines Conservative Parabolic Splines Reconstruction Advection (only vertical; not recommended)
Split_U3 Split third-order Upstream Advection
Upstream3 Third-order Upstream-biased Advection (only horizontal)


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

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

zeta 1 Periodic Closed Periodic Closed

ubar 1 Periodic Closed Periodic Closed

vbar 1 Periodic Closed Periodic Closed

u 1 Periodic Closed Periodic Closed

v 1 Periodic Closed Periodic Closed

temp 1 Periodic Closed Periodic Closed

salt 1 Periodic Closed Periodic Closed

Activated C-preprocessing Options:

UPWELLING Wind-Driven Upwelling/Downwelling over a Periodic Channel
ANA_BSFLUX Analytical kinematic bottom salinity flux
ANA_BTFLUX Analytical kinematic bottom temperature flux
ANA_GRID Analytical grid set-up
ANA_INITIAL Analytical initial conditions
ANA_SMFLUX Analytical kinematic surface momentum flux
ANA_SSFLUX Analytical kinematic surface salinity flux
ANA_STFLUX Analytical kinematic surface temperature flux
ANA_VMIX Analytical vertical mixing coefficients
ASSUMED_SHAPE Using assumed-shape arrays
AVERAGES Writing out time-averaged nonlinear model fields
DIAGNOSTICS_TS Computing and writing tracer diagnostic terms
DIAGNOSTICS_UV Computing and writing momentum diagnostic terms
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002)
DOUBLE_PRECISION Double precision arithmetic numerical kernel
MIX_S_TS Mixing of tracers along constant S-surfaces
MIX_S_UV Mixing of momentum along constant S-surfaces
NONLINEAR Nonlinear Model
!NONLIN_EOS Linear Equation of State for seawater
POWER_LAW Power-law shape time-averaging barotropic filter
PROFILE Time profiling activated
!RST_SINGLE Double precision fields in restart NetCDF file
SALINITY Using salinity
SOLVE3D Solving 3D Primitive Equations
SPLINES_VDIFF Parabolic Spline Reconstruction for Vertical Diffusion
SPLINES_VVISC Parabolic Spline Reconstruction for Vertical Viscosity
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_LDRAG Linear bottom stress
UV_VIS2 Harmonic mixing of momentum
VAR_RHO_2D Variable density barotropic mode

Process Information:

Thread # 0 (pid= 17814) is active.

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

ANA_GRID - x-location of PSI-points: x_psi
(Grid = 01, Min = 0.00000000E+00 Max = 4.00000000E+04)
ANA_GRID - y-location of PSI-points: y_psi
(Grid = 01, Min = 0.00000000E+00 Max = 8.00000000E+04)
ANA_GRID - x-location of RHO-points: x_rho
(Grid = 01, Min = 5.00000000E+02 Max = 4.05000000E+04)
ANA_GRID - y-location of RHO-points: y_rho
(Grid = 01, Min = -5.00000000E+02 Max = 8.05000000E+04)
ANA_GRID - x-location of U-points: x_u
(Grid = 01, Min = 0.00000000E+00 Max = 4.00000000E+04)
ANA_GRID - y-location of U-points: y_u
(Grid = 01, Min = -5.00000000E+02 Max = 8.05000000E+04)
ANA_GRID - x-location of V-points: x_v
(Grid = 01, Min = 5.00000000E+02 Max = 4.05000000E+04)
ANA_GRID - y-location of V-points: y_v
(Grid = 01, Min = 0.00000000E+00 Max = 8.00000000E+04)
ANA_GRID - reciprocal XI-grid spacing: pm
(Grid = 01, Min = 1.00000000E-03 Max = 1.00000000E-03)
ANA_GRID - reciprocal ETA-grid spacing: pn
(Grid = 01, Min = 1.00000000E-03 Max = 1.00000000E-03)
ANA_GRID - angle between XI-axis and EAST: angler
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_GRID - Coriolis parameter at RHO-points: f
(Grid = 01, Min = -8.26000000E-05 Max = -8.26000000E-05)
ANA_GRID - bathymetry at RHO-points: h
(Grid = 01, Min = 2.52004887E+01 Max = 1.50000000E+02)

Vertical S-coordinate System, Grid 01:

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

16 0.0000000 0.0000000 0.000 0.000 0.000 0.000
15 -0.0625000 -0.0019442 -0.809 -0.806 -1.348 -1.589
14 -0.1250000 -0.0078455 -1.668 -1.661 -2.966 -3.687
13 -0.1875000 -0.0179119 -2.580 -2.568 -4.867 -6.321
12 -0.2500000 -0.0324983 -3.549 -3.531 -7.077 -9.535
11 -0.3125000 -0.0521190 -4.581 -4.558 -9.630 -13.397
10 -0.3750000 -0.0774659 -5.686 -5.656 -12.573 -17.996
9 -0.4375000 -0.1094327 -6.875 -6.837 -15.967 -23.445
8 -0.5000000 -0.1491465 -8.162 -8.114 -19.889 -29.890
7 -0.5625000 -0.1980075 -9.564 -9.506 -24.435 -37.512
6 -0.6250000 -0.2577387 -11.104 -11.034 -29.721 -46.531
5 -0.6875000 -0.3304460 -12.808 -12.724 -35.892 -57.218
4 -0.7500000 -0.4186931 -14.709 -14.609 -43.121 -69.903
3 -0.8125000 -0.5255915 -16.846 -16.726 -51.622 -84.987
2 -0.8750000 -0.6549105 -19.266 -19.124 -61.651 -102.953
1 -0.9375000 -0.8112096 -22.028 -21.859 -73.518 -124.388
0 -1.0000000 -1.0000000 -25.200 -25.000 -87.600 -150.000

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

Primary Secondary Accumulated to Current Step

1-0.0008094437383769 0.0333333333333333-0.0008094437383769 0.0333333333333333
2-0.0014053566728197 0.0333603147912792-0.0022148004111966 0.0666936481246126
3-0.0017877524645903 0.0334071600137066-0.0040025528757869 0.1001008081383191
4-0.0019566842408176 0.0334667517625262-0.0059592371166046 0.1335675599008453
5-0.0019122901320372 0.0335319745705535-0.0078715272486418 0.1670995344713988
6-0.0016548570247459 0.0335957175749547-0.0095263842733877 0.2006952520463536
7-0.0011849025289723 0.0336508794757796-0.0107112868023600 0.2343461315221331
8-0.0005032751608631 0.0336903762267453-0.0112145619632232 0.2680365077488784
9 0.0003887272597151 0.0337071520654408-0.0108258347035081 0.3017436598143192
10 0.0014892209965583 0.0336941944901169-0.0093366137069498 0.3354378543044362
11 0.0027955815694920 0.0336445537902317-0.0065410321374578 0.3690824080946679
12 0.0043042707117221 0.0335513677379153-0.0022367614257357 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864347 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708920 0.0329439123123590 0.0216737068001212 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565096 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906203 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716642 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402367 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399431 0.6603333185976138
21 0.0256737146312910 0.0297153720153352 0.1342125541712341 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524357 0.7189082721405746
23 0.0316613792205220 0.0279045862015855 0.1945237931729577 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236651 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893979 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886211 0.8237939964192927
27 0.0432936737565711 0.0230872677537126 0.3506756411451922 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772278 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880562 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442381 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256412 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325517 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348094 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479473 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213234 0.9738247715198165
36 0.0503158038019031 0.0080591141492892 0.8085423793232265 0.9818838856691057
37 0.0473537721847153 0.0063819206892258 0.8558961515079418 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497606 0.9930692679747335
39 0.0376397765791564 0.0033640675316746 0.9367177506289170 0.9964333355064081
40 0.0305543017255206 0.0021094083123694 0.9672720523544377 0.9985427438187775
41 0.0217382098544505 0.0010909315881854 0.9890102622088881 0.9996336754069629
42 0.0109897377911119 0.0003663245930371 1.0000000000000000 1.0000000000000000

ndtfast, nfast = 30 42 nfast/ndtfast = 1.40000

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

1.000000000000 1.047601458608 0.523800729304 1.000000000000 1.000000000000

Power filter parameters, Fgamma, gamma = 0.28400 0.18933

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

Minimum X-grid spacing, DXmin = 1.00000000E+00 km
Maximum X-grid spacing, DXmax = 1.00000000E+00 km
Minimum Y-grid spacing, DYmin = 1.00000000E+00 km
Maximum Y-grid spacing, DYmax = 1.00000000E+00 km
Minimum Z-grid spacing, DZmin = 8.08965824E-01 m
Maximum Z-grid spacing, DZmax = 2.56123321E+01 m

Minimum barotropic Courant Number = 2.22358627E-01
Maximum barotropic Courant Number = 5.42494240E-01
Maximum Coriolis Courant Number = 2.47800000E-02

ANA_INITIAL - vertically integrated u-momentum component: ubar
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - vertically integrated v-momentum component: vbar
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - free-surface: zeta
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - u-momentum component: u
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - v-momentum component: v
(Grid = 01, Min = 0.00000000E+00 Max = 0.00000000E+00)
ANA_INITIAL - potential temperature: temp
(Grid = 01, Min = 1.45204834E+01 Max = 2.19365219E+01)
ANA_INITIAL - salinity: salt
(Grid = 01, Min = 3.50000000E+01 Max = 3.50000000E+01)

Basin information for Grid 01:

Maximum grid stiffness ratios: rx0 = 6.931666E-02 (Beckmann and Haidvogel)
rx1 = 8.661243E-01 (Haney)

Initial domain volumes: TotVolume = 3.8843755884E+11 m3
MinCellVol = 8.4521383562E+05 m3
MaxCellVol = 2.5612332106E+07 m3
Max/Min = 3.0302783777E+01

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 000000000001 - 000000001440)


TIME-STEP YYYY-MM-DD hh:mm:ss.ss KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME
C => (i,j,k) Cu Cv Cw Max Speed

0 0001-01-01 00:00:00.00 0.000000E+00 6.585677E+02 6.585677E+02 3.884376E+11
(00,00,00) 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00
DEF_HIS - creating history file, Grid 01: roms_his.nc
Found Error: ** Line: 8222 Source: ROMS/Modules/mod_netcdf.F, netcdf_create

NETCDF_CREATE - unable to create output NetCDF file:
roms_his.nc
call from: ROMS/Utility/def_his.F
NetCDF: Malformed URL
Found Error: 03 Line: 105 Source: ROMS/Utility/def_his.F

DEF_HIS - unable to create history NetCDF file: roms_his.nc
Found Error: 03 Line: 151 Source: ROMS/Nonlinear/output.F
Found Error: 03 Line: 600 Source: ROMS/Nonlinear/main3d.F
Found Error: 03 Line: 303 Source: ROMS/Drivers/nl_ocean.h

Elapsed CPU time (seconds):

Thread # 0 CPU: 0.085
Total: 0.085

Nonlinear ocean model elapsed time profile, Grid: 01

Allocation and array initialization .............. 0.068 (79.9226 %)
Ocean state initialization ....................... 0.009 (11.0992 %)
Reading of input data ............................ 0.000 ( 0.0106 %)
Processing of input data ......................... 0.000 ( 0.0577 %)
Processing of output time averaged data .......... 0.000 ( 0.0930 %)
Computation of vertical boundary conditions ...... 0.000 ( 0.0459 %)
Computation of global information integrals ...... 0.001 ( 1.2135 %)
2D/3D coupling, vertical metrics ................. 0.002 ( 2.7424 %)
Omega vertical velocity .......................... 0.001 ( 1.1758 %)
Equation of state for seawater ................... 0.001 ( 1.5478 %)
Total: 0.083 97.9085

Unique code regions profiled ..................... 0.083 97.9085 %
Residual, non-profiled code ...................... 0.002 2.0915 %


All percentages are with respect to total time = 0.085


>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

Dynamic and Automatic memory (MB) usage for Grid 01: 41x80x16 tiling: 1x1

tile Dynamic Automatic USAGE

0 77.16 3.87 81.04

TOTAL 77.16 3.87 81.04

<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

ROMS/TOMS - Output NetCDF summary for Grid 01:

Analytical header files used:

ROMS/Functionals/ana_btflux.h
/home/javadbabagoli/Documents/Test/ana_grid.h
/home/javadbabagoli/Documents/Test/ana_initial.h
ROMS/Functionals/ana_smflux.h
ROMS/Functionals/ana_stflux.h
ROMS/Functionals/ana_vmix.h
Found Error: 03 Line: 423 Source: ROMS/Utility/close_io.F

ROMS/TOMS - Output error ............ exit_flag: 3


ERROR: Abnormal termination: NetCDF OUTPUT.
REASON: NetCDF: Malformed URL

[robertson]

It doesn't really agree with the error you're getting but are you absolutely sure you have write permissions to the directory you're writing the history file to?

[javadi]

Dear Robertson
Thank you o much for your response.

I usually use the trunk to run the model and I ran my test case without any problem. However, I try to add ice in my model; thus, I add kate branch to my system. I download from git when using clone. After that, I have faced this error. I use the same method to run kate branch and trunk.
When it comes to directory, I am not sure about it because I have faced this error when compiling.

svn: E155007: '/home/javadbabagoli/Documents/roms' is not a working copy

and also, when I compile the model, I enter with root but I ran the model without using root because I have faced this error


mpirun has detected an attempt to run as root.

Running as root is *strongly* discouraged as any mistake (e.g., in
defining TMPDIR) or bug can result in catastrophic damage to the OS
file system, leaving your system in an unusable state.

We strongly suggest that you run mpirun as a non-root user.

You can override this protection by adding the --allow-run-as-root option
to the cmd line or by setting two environment variables in the following way:
the variable OMPI_ALLOW_RUN_AS_ROOT=1 to indicate the desire to override this
protection, and OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1 to confirm the choice and
add one more layer of certainty that you want to do so.
We reiterate our advice against doing so - please proceed at your own risk.

[robertson]

That svn error should not stop compilation and the command that is failing is only used for informational purposes. Compiling (and running) ROMS as root is never a good idea. It's also quite likely that somewhere along the line you made a directory that is owned by root and that is probably what isn't allowing you to create files.

In the directory where you're planning to have your ROMS output (not as root) try running 'touch junk' and see if you get a permission error.

Also, I don't see how compiling with root would make that svn error go away.

[javadi]

Dear Robertson
When it comes to compiling without root, I have faced some permission errors. However, when I run ‘touch junk’, a file junk is made in my output directory without errors.
The error when compiling without root:

svn: E155007: '/home/javadbabagoli/Documents/roms' is not a working copy
svn: E155007: '/home/javadbabagoli/Documents/roms' is not a working copy
rm -f -r core *.ipo /home/javadbabagoli/Documents/Test/Build_roms /home/javadbabagoli/make_macros.mk
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/convolve.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/set_avg2_mod.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/def_avg.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/get_bounds.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/set_tides.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/dateclock.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/mod_floats.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/obc_adjust_mod.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/close_io.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/ini_lanczos.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/mod_ocean.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/set_3dfldr.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/sum_imp.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/NN_corstep.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/set_3dfldr.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/abort.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/dotproduct.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/wvelocity.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/conv_bry2d.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/round.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/ccsm_flux_mod.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/def_station.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/nf_fread2d.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/get_ngfldr.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/bc_3d.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/shapiro_mod.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/step3d_t_mod.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/nf_fwrite4d.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/def_impulse.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/extract_sta.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/mod_nesting.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/congrad.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/mod_coupling.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/checkvars.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/checkvars.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/set_avg_mod.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/exchange_3d.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/nf_fread4d.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/analytical.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/mod_fourdvar.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/wrt_rst.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/abort.f90': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/state_copy_mod.mod': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/mod_kinds.o': Permission denied
rm: cannot remove '/home/javadbabagoli/Documents/Test/Build_roms/strings.f90': Permission denied

[robertson]

Since you executed the build script as root, the Build_roms directory is owned by root so user javadbabagoli does not have permission to remove it. Manually remove (rm -rf Build_roms) the Build_roms directory as root. Then run the build script (as javadbabagoli) again. If you still get permission errors then it's likely that your "Test" directory is also owned by root.

[javadi]

Dear Robertson

Yes. Your opinion is completely right.

Thank you so much for your help