Please help !!
I was found the problem about the compiler in ROMS.
I was trying to compile ROMS on my Linux computer. At first I used compiler (gfortran) and it had an error message " This module file was not generated by any release of this compiler".
I will show you about my code to compiler:
[roms@localhost gulfthailand]$ ./oceanS < gulfthailand.in
Model Input Parameters: ROMS/TOMS version 3.6
Tuesday - April 29, 2014 - 12:46:16 PM
-----------------------------------------------------------------------------
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 -I/usr/local/mct/include -fno-bounds-check -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none
SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 655
Local Root : /home/roms/main/roms
Header Dir : /home/roms/main/roms/projects/gulfthailand
Header file : gulfthailand.h
Analytical Dir: /home/roms/main/roms/projects/gulfthailand
Resolution, Grid 01: 0041x0080x016, Parallel Threads: 1, Tiling: 001x001
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.
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.
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
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).
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 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 momentun acceleration.
T Dout(M2pgrd) Write out 2D momentum pressure gradient.
T Dout(M2fcor) Write out 2D momentum Coriolis force.
T Dout(M2hadv) Write out 2D momentum horizontal advection.
T Dout(M2xadv) Write out 2D momentum horizontal X-advection.
T Dout(M2yadv) Write out 2D momentum horizontal Y-advection.
T Dout(M2hvis) Write out 2D momentum horizontal viscosity.
T Dout(M2xvis) Write out 2D momentum horizontal X-viscosity.
T Dout(M2yvis) Write out 2D momentum horizontal Y-viscosity.
T Dout(M2sstr) Write out 2D momentum surface stress.
T Dout(M2bstr) Write out 2D momentum bottom stress.
T Dout(M3rate) Write out 3D momentun acceleration.
T Dout(M3pgrd) Write out 3D momentum pressure gradient.
T Dout(M3fcor) Write out 3D momentum Coriolis force.
T Dout(M3hadv) Write out 3D momentum horizontal advection.
T Dout(M3xadv) Write out 3D momentum horizontal X-advection.
T Dout(M3yadv) Write out 3D momentum horizontal Y-advection.
T Dout(M3vadv) Write out 3D momentum vertical advection.
T Dout(M3hvis) Write out 3D momentum horizontal viscosity.
T Dout(M3xvis) Write out 3D momentum horizontal X-viscosity.
T Dout(M3yvis) Write out 3D momentum horizontal Y-viscosity.
T Dout(M3vvis) Write out 3D momentum vertical viscosity.
T Dout(iTrate) Write out rate of change of tracer 01: temp
T Dout(iTrate) Write out rate of change of tracer 02: salt
T Dout(iThadv) Write out horizontal advection, tracer 01: temp
T Dout(iThadv) Write out horizontal advection, tracer 02: salt
T Dout(iTxadv) Write out horizontal X-advection, tracer 01: temp
T Dout(iTxadv) Write out horizontal X-advection, tracer 02: salt
T Dout(iTyadv) Write out horizontal Y-advection, tracer 01: temp
T Dout(iTyadv) Write out horizontal Y-advection, tracer 02: salt
T Dout(iTvadv) Write out vertical advection, tracer 01: temp
T Dout(iTvadv) Write out vertical advection, tracer 02: salt
T Dout(iThdif) Write out horizontal diffusion, tracer 01: temp
T Dout(iThdif) Write out horizontal diffusion, tracer 02: salt
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 01: temp
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 02: salt
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 01: temp
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 02: salt
T Dout(iTvdif) Write out vertical diffusion, tracer 01: temp
T Dout(iTvdif) Write out vertical diffusion, tracer 02: salt
Output/Input Files:
Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc
Output Diagnostics File: ocean_dia.nc
READ_PHYPAR - could not find input file: ocean_grd.nc
Elapsed CPU time (seconds):
ROMS/TOMS - Output NetCDF summary for Grid 01:
ROMS/TOMS - I/O error ............... exit_flag: 4
ERROR: I/O related problem.
[roms@localhost gulfthailand]$ ./oceanS < gulfthailand.in
Model Input Parameters: ROMS/TOMS version 3.6
Wednesday - April 30, 2014 - 11:59:43 AM
-----------------------------------------------------------------------------
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 -I/usr/local/mct/include -fno-bounds-check -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none
SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 655
Local Root : /home/roms/main/roms
Header Dir : /home/roms/main/roms/projects/gulfthailand
Header file : gulfthailand.h
Analytical Dir: /home/roms/main/roms/projects/gulfthailand
Resolution, Grid 01: 0512x0060x030, Parallel Threads: 1, Tiling: 001x001
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.
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.
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
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).
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 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 momentun acceleration.
T Dout(M2pgrd) Write out 2D momentum pressure gradient.
T Dout(M2fcor) Write out 2D momentum Coriolis force.
T Dout(M2hadv) Write out 2D momentum horizontal advection.
T Dout(M2xadv) Write out 2D momentum horizontal X-advection.
T Dout(M2yadv) Write out 2D momentum horizontal Y-advection.
T Dout(M2hvis) Write out 2D momentum horizontal viscosity.
T Dout(M2xvis) Write out 2D momentum horizontal X-viscosity.
T Dout(M2yvis) Write out 2D momentum horizontal Y-viscosity.
T Dout(M2sstr) Write out 2D momentum surface stress.
T Dout(M2bstr) Write out 2D momentum bottom stress.
T Dout(M3rate) Write out 3D momentun acceleration.
T Dout(M3pgrd) Write out 3D momentum pressure gradient.
T Dout(M3fcor) Write out 3D momentum Coriolis force.
T Dout(M3hadv) Write out 3D momentum horizontal advection.
T Dout(M3xadv) Write out 3D momentum horizontal X-advection.
T Dout(M3yadv) Write out 3D momentum horizontal Y-advection.
T Dout(M3vadv) Write out 3D momentum vertical advection.
T Dout(M3hvis) Write out 3D momentum horizontal viscosity.
T Dout(M3xvis) Write out 3D momentum horizontal X-viscosity.
T Dout(M3yvis) Write out 3D momentum horizontal Y-viscosity.
T Dout(M3vvis) Write out 3D momentum vertical viscosity.
T Dout(iTrate) Write out rate of change of tracer 01: temp
T Dout(iTrate) Write out rate of change of tracer 02: salt
T Dout(iThadv) Write out horizontal advection, tracer 01: temp
T Dout(iThadv) Write out horizontal advection, tracer 02: salt
T Dout(iTxadv) Write out horizontal X-advection, tracer 01: temp
T Dout(iTxadv) Write out horizontal X-advection, tracer 02: salt
T Dout(iTyadv) Write out horizontal Y-advection, tracer 01: temp
T Dout(iTyadv) Write out horizontal Y-advection, tracer 02: salt
T Dout(iTvadv) Write out vertical advection, tracer 01: temp
T Dout(iTvadv) Write out vertical advection, tracer 02: salt
T Dout(iThdif) Write out horizontal diffusion, tracer 01: temp
T Dout(iThdif) Write out horizontal diffusion, tracer 02: salt
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 01: temp
T Dout(iTxdif) Write out horizontal X-diffusion, tracer 02: salt
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 01: temp
T Dout(iTydif) Write out horizontal Y-diffusion , tracer 02: salt
T Dout(iTvdif) Write out vertical diffusion, tracer 01: temp
T Dout(iTvdif) Write out vertical diffusion, tracer 02: salt
Output/Input Files:
Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc
Output Diagnostics File: ocean_dia.nc
Input Grid File: gulfthailand_grd.nc
Input Forcing File 01: gulfthailand_frc.nc
Tile partition information for Grid 01: 0512x0060x0030 tiling: 001x001
tile Istr Iend Jstr Jend Npts
0 1 512 1 60 921600
Tile minimum and maximum fractional grid coordinates:
(interior points only)
tile Xmin Xmax Ymin Ymax grid
0 -1.50 514.50 0.50 61.50 RHO-points
0 -2.00 514.00 0.50 61.50 U-points
0 -1.50 514.50 0.00 61.00 V-points
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:
GULFTHAILAND Wind-Driven Upwelling/Downwelling over a Periodic Channel
ANA_FSOBC Analytical free-surface boundary conditions.
ANA_INITIAL Analytical initial conditions.
ANA_M2OBC Analytical 2D momentum boundary conditions.
ANA_SSH Analytical sea surface height climatology.
ANA_SSS Analytical sea surface salinity.
ANA_SST Analytical SST and dQdSST.
ASSUMED_SHAPE Using assumed-shape arrays.
AVERAGES Writing out time-averaged nonlinear model fields.
CURVGRID Orthogonal curvilinear grid.
DIAGNOSTICS_TS Computing and writing tracer diagnostic terms.
DIAGNOSTICS_UV Computing and writing momentum diagnostic terms.
DJ_GRADPS Parabolic Splines density Jacobian (Shchepetkin, 2002).
DOUBLE_PRECISION Double precision arithmetic.
FSOBC_REDUCED Using free-surface data in reduced physics conditions
MASKING Land/Sea masking.
MIX_S_TS Mixing of tracers along constant S-surfaces.
MIX_S_UV Mixing of momentum along constant S-surfaces.
NONLINEAR Nonlinear Model.
NONLIN_EOS Nonlinear Equation of State for seawater.
POWER_LAW Power-law shape time-averaging barotropic filter.
PROFILE Time profiling activated .
!RST_SINGLE Double precision fields in restart NetCDF file.
SALINITY Using salinity.
SOLVE3D Solving 3D Primitive Equations.
SPLINES Conservative parabolic spline reconstruction.
SPHERICAL Spherical grid configuration.
TS_U3HADVECTION Third-order upstream 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_LDRAG Linear bottom stress.
UV_VIS2 Harmonic mixing of momentum.
VAR_RHO_2D Variable density barotropic mode.
Process Information:
Thread # 0 (pid= 21006) is active.
INITIAL: Configuring and initializing forward nonlinear model ...
NETCDF_CHECK_DIM - inconsistent size of dimension: xi_u 43 513
in file: gulfthailand_grd.nc
Elapsed CPU time (seconds):
Thread # 0 CPU: 0.447
Total: 0.447
Nonlinear model elapsed time profile:
Allocation and array initialization .............. 0.446 (99.7763 %)
Total: 0.446 99.7763
All percentages are with respect to total time = 0.447
ROMS/TOMS - Output NetCDF summary for Grid 01:
ROMS/TOMS - Input error ............. exit_flag: 2
ERROR: Abnormal termination: NetCDF INPUT.
REASON: No error
There are a number of errors in your configuration, and as Kate pointed out above, ROMS can often tell you what the problem is if you only look at the output. In this instance:
NETCDF_CHECK_DIM - inconsistent size of dimension: xi_u 43 513
in file: gulfthailand_grd.nc
Your grid (gulfthailand_grd.nc) size does not match the xi_u dimension specified in the input (*.in) file. (43 v 513)
More worrying is the fact that you say you have specified #ANA_GRID and also provided an input grid file.
(and also it seems you didn't #define ANA_GRID correctly during the model build as it's not shown in the compiler definitions echoed to the output file)
The purpose of #ANA_GRID is to analytically define an input grid, and not read in an actual grid file.
I would suggest you familiarise yourself with the fundamentals of creating a ROMS model. There is ample documentation available on the forum and the ROMS wiki.
