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PostPosted: Fri Mar 25, 2016 1:40 am 
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Joined: Tue Mar 01, 2016 1:38 am
Posts: 45
Location: the Ocean University of China
I am a first time user to install and run ROMS, when I attempt to compile the Upwelling case, I meet this and don't know what's going wrong.I set the build.bash just as the Tutorial(https://www.myroms.org/wiki/ROMS_UNSW2008),I have installed the intel compiler and use ifort. could you mind tell me how to deal with it ?


mod_netcdf.f90(19): error #7013: This module file was not generated by any release of this compiler. [NETCDF]
USE netcdf
----------^
mod_netcdf.f90(109): error #6592: This symbol must be a defined parameter, an enumerator, or an argument of an inquiry function that evaluates to a compile-time constant. [NF90_REAL]
integer, parameter :: NF_FOUT = nf90_real
--------------------------------------^
mod_netcdf.f90(110): error #6592: This symbol must be a defined parameter, an enumerator, or an argument of an inquiry function that evaluates to a compile-time constant. [NF90_DOUBLE]
integer, parameter :: NF_FRST = nf90_double
--------------------------------------^
mod_netcdf.f90(111): error #6592: This symbol must be a defined parameter, an enumerator, or an argument of an inquiry function that evaluates to a compile-time constant. [NF90_DOUBLE]
integer, parameter :: NF_TYPE = nf90_double
--------------------------------------^
mod_netcdf.f90(117): error #6592: This symbol must be a defined parameter, an enumerator, or an argument of an inquiry function that evaluates to a compile-time constant. [NF90_64BIT_OFFSET]
integer :: CMODE = nf90_64bit_offset ! NetCDF 64-bit offset format
-------------------------^
mod_netcdf.f90(117): error #6973: This is not a valid initialization expression. [NF90_64BIT_OFFSET]
integer :: CMODE = nf90_64bit_offset ! NetCDF 64-bit offset format
-------------------------^
mod_netcdf.f90(109): error #6404: This name does not have a type, and must have an explicit type. [NF90_REAL]
integer, parameter :: NF_FOUT = nf90_real
--------------------------------------^
mod_netcdf.f90(110): error #6404: This name does not have a type, and must have an explicit type. [NF90_DOUBLE]
integer, parameter :: NF_FRST = nf90_double
--------------------------------------^
mod_netcdf.f90(117): error #6404: This name does not have a type, and must have an explicit type. [NF90_64BIT_OFFSET]
integer :: CMODE = nf90_64bit_offset ! NetCDF 64-bit offset format
-------------------------^
mod_netcdf.f90(212): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQUIRE]
status=nf90_inquire(ncid, n_dim, n_var, n_gatt, rec_id)
---------------^
mod_netcdf.f90(214): error #6404: This name does not have a type, and must have an explicit type. [NF90_NOERR]
IF ((status.eq.nf90_noerr).and.(n_dim.le.Mdims)) THEN
-----------------------^
mod_netcdf.f90(221): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQUIRE_DIMENSION]
status=nf90_inquire_dimension(ncid, dim_id(i), &
-------------------^
mod_netcdf.f90(706): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQUIRE]
status=nf90_inquire(my_ncid, n_dim, n_var, n_gatt, rec_id)
---------------^
mod_netcdf.f90(715): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQUIRE_VARIABLE]
status=nf90_inquire_variable(my_ncid, var_id(i), &
-------------------^
mod_netcdf.f90(721): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQ_ATTNAME]
status=nf90_inq_attname(my_ncid, var_id(i), j, &
-----------------------^
mod_netcdf.f90(809): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQUIRE_DIMENSION]
status=nf90_inquire_dimension(my_ncid, var_Dids(i), &
---------------------^
mod_netcdf.f90(825): error #6632: Keyword arguments are invalid without an explicit interface. [XTYPE]
& xtype = my_Atype, &
------------------------------------------------^
mod_netcdf.f90(826): error #6632: Keyword arguments are invalid without an explicit interface. [LEN]
& len = my_Alen)
------------------------------------------------^
mod_netcdf.f90(823): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQUIRE_ATTRIBUTE]
status=nf90_inquire_attribute(my_ncid, my_id, &
-------------------------^
mod_netcdf.f90(829): error #6404: This name does not have a type, and must have an explicit type. [NF90_INT]
& (my_Atype.eq.NF90_INT)) THEN
-------------------------------------^
mod_netcdf.f90(830): error #6404: This name does not have a type, and must have an explicit type. [NF90_GET_ATT]
status=nf90_get_att(my_ncid, my_id, &
-----------------------------^
mod_netcdf.f90(844): error #6404: This name does not have a type, and must have an explicit type. [NF90_FLOAT]
& ((my_Atype.eq.NF90_FLOAT ).or. &
-------------------------------------------^
mod_netcdf.f90(859): error #6404: This name does not have a type, and must have an explicit type. [NF90_CHAR]
ELSE IF (my_Atype.eq.NF90_CHAR) THEN
-----------------------------------------^
mod_netcdf.f90(982): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQ_VARID]
status=nf90_inq_varid(ncid, TRIM(myVarName), VarID)
---------------^
mod_netcdf.f90(1066): error #6632: Keyword arguments are invalid without an explicit interface. [NAME]
& name = my_Vname, &
-------------------------------------^
mod_netcdf.f90(1067): error #6632: Keyword arguments are invalid without an explicit interface. [NATTS]
& nAtts = my_natts)
-------------------------------------^
mod_netcdf.f90(1065): error #6404: This name does not have a type, and must have an explicit type. [NF90_INQUIRE_VARIABLE]
status=nf90_inquire_variable(my_ncid, varid, &
---------------^
mod_netcdf.f90(4515): catastrophic error: Too many errors, exiting
compilation aborted for mod_netcdf.f90 (code 1)
make: *** [/root/Projects/upwelling/Build/mod_netcdf.o] 错误 1
[root@centos upwelling]#


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PostPosted: Fri Mar 25, 2016 1:42 am 
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Joined: Tue Mar 01, 2016 1:38 am
Posts: 45
Location: the Ocean University of China
I Customize the Build Script like that:

#export USE_MPI=on # distributed-memory parallelism
#export USE_MPIF90=on # compile with mpif90 script
#export which_MPI=mpich # compile with MPICH library
#export which_MPI=mpich2 # compile with MPICH2 library
#export which_MPI=openmpi # compile with OpenMPI library

#export USE_OpenMP=on # shared-memory parallelism


export FORT=ifort
#export FORT=gfortran
#export FORT=pgi

#export USE_DEBUG=on # use Fortran debugging flags
export USE_LARGE=on # activate 64-bit compilation
#export USE_NETCDF4=on # compile with NetCDF-4 library
#export USE_PARALLEL_IO=on # Parallel I/O with Netcdf-4/HDF5

export USE_MY_LIBS=on # use my library paths below


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PostPosted: Fri Mar 25, 2016 5:45 am 
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Joined: Wed Jul 02, 2003 5:29 pm
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Location: IMS/UAF, USA
You probably don't need USE_LARGE and you should be using USE_NETCDF4. However:
Quote:
mod_netcdf.f90(19): error #7013: This module file was not generated by any release of this compiler. [NETCDF]
USE netcdf
You need to have netcdf-fortran compiled with the same compiler you are using to build ROMS - the exact same version is most likely to be successful.


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PostPosted: Sun Mar 27, 2016 1:33 pm 
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Joined: Tue Mar 01, 2016 1:38 am
Posts: 45
Location: the Ocean University of China
Thank you very much Kate,I reinstalled my Netcdf, the executable oceanS file is created successfully. But when I was going to run ROMS, another error happened :

[root@centos upwelling]# ./oceanS < ocean_upwelling.in

Model Input Parameters: ROMS/TOMS version 3.7
Monday - March 28, 2016 - 5:28:07 AM
-----------------------------------------------------------------------------

MOD_NCPARAM - Unable to open variable information file:
ROMS/External/varinfo.dat
Default file is located in source directory.


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PostPosted: Sun Mar 27, 2016 1:39 pm 
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Location: IMS/UAF, USA
You have the varinfo.dat file, but you don't have it in:
Quote:
ROMS/External/varinfo.dat
which is where you said it is in the ocean_upwelling.in file.


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PostPosted: Sun Mar 27, 2016 2:23 pm 
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Posts: 45
Location: the Ocean University of China
I changed the path in ocean_upwelling.in , tried it agian, lt looks like a success but a failure,oh.....

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00001440)


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

0 0 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: ocean_his.nc
./oceanS: symbol lookup error: ./oceanS: undefined symbol: netcdf_mp_nf90_create_


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PostPosted: Sun Mar 27, 2016 2:26 pm 
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[root@centos upwelling]# ./oceanS < ocean_upwelling.in

Model Input Parameters: ROMS/TOMS version 3.7
Monday - March 28, 2016 - 6:15:09 AM
-----------------------------------------------------------------------------

Wind-Driven Upwelling/Downwelling over a Periodic Channel

Operating system : Linux
CPU/hardware : x86_64
Compiler system : ifort
Compiler command : /opt/intel/compilers_and_libraries_2016.2.181/linux/bin/intel64/ifort
Compiler flags : -heap-arrays -fp-model precise -ip -O3 -free -free -free

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 783

Local Root : /root/MyDir
Header Dir : /root/Projects/upwelling
Header file : upwelling.h
Analytical Dir: /root/Projects/upwelling

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.
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
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 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: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc
Output Diagnostics File: ocean_dia.nc

Tile partition information for Grid 01: 0041x0080x0016 tiling: 001x001

tile Istr Iend Jstr Jend Npts

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

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.
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_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= 23466) 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

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 0.0335513677379153-0.0022367614257356 0.4026337758325831
13 0.0060106451121704 0.0334078920475245 0.0037738836864348 0.4360416678801076
14 0.0079087469427945 0.0332075372104522 0.0116826306292293 0.4692492050905598
15 0.0099910761708920 0.0329439123123590 0.0216737068001213 0.5021931174029188
16 0.0122483446563884 0.0326108764399960 0.0339220514565097 0.5348039938429148
17 0.0146692120341107 0.0322025982847830 0.0485912634906204 0.5670065921276978
18 0.0172400033810439 0.0317136245503127 0.0658312668716643 0.5987202166780105
19 0.0199444086685725 0.0311389577709445 0.0857756755402368 0.6298591744489550
20 0.0227631639997064 0.0304741441486588 0.1085388395399432 0.6603333185976138
21 0.0256737146312911 0.0297153720153352 0.1342125541712342 0.6900486906129490
22 0.0286498597812016 0.0288595815276255 0.1628624139524359 0.7189082721405746
23 0.0316613792205220 0.0279045862015855 0.1945237931729578 0.7468128583421600
24 0.0346736416507075 0.0268492068942347 0.2291974348236653 0.7736620652363948
25 0.0376471948657328 0.0256934188392112 0.2668446296893981 0.7993554840756060
26 0.0405373376992232 0.0244385123436867 0.3073819673886213 0.8237939964192927
27 0.0432936737565710 0.0230872677537126 0.3506756411451924 0.8468812641730054
28 0.0458596469320356 0.0216441452951603 0.3965352880772280 0.8685254094681656
29 0.0481720587108284 0.0201154903974257 0.4447073467880565 0.8886408998655914
30 0.0501605672561820 0.0185097551070648 0.4948679140442384 0.9071506549726561
31 0.0517471682814030 0.0168377361985254 0.5466150823256415 0.9239883911711815
32 0.0528456577069106 0.0151128305891453 0.5994607400325521 0.9391012217603267
33 0.0533610761022577 0.0133513086655816 0.6528218161348098 0.9524525304259084
34 0.0531891349131379 0.0115726061288397 0.7060109510479478 0.9640251365547481
35 0.0522156244733761 0.0097996349650684 0.7582265755213239 0.9738247715198165
36 0.0503158038019030 0.0080591141492892 0.8085423793232269 0.9818838856691057
37 0.0473537721847153 0.0063819206892258 0.8558961515079423 0.9882658063583315
38 0.0431818225418188 0.0048034616164019 0.8990779740497611 0.9930692679747334
39 0.0376397765791564 0.0033640675316746 0.9367177506289175 0.9964333355064080
40 0.0305543017255206 0.0021094083123694 0.9672720523544381 0.9985427438187774
41 0.0217382098544504 0.0010909315881854 0.9890102622088885 0.9996336754069628
42 0.0109897377911118 0.0003663245930371 1.0000000000000004 0.9999999999999999

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


Basin information for Grid 01:

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

Initial basin volumes: TotVolume = 3.8843755884E+11 m3
MinVolume = 8.4521383562E+05 m3
MaxVolume = 2.5612332106E+07 m3
Max/Min = 3.0302783777E+01

NL ROMS/TOMS: started time-stepping: (Grid: 01 TimeSteps: 00000001 - 00001440)


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

0 0 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: ocean_his.nc
./oceanS: symbol lookup error: ./oceanS: undefined symbol: netcdf_mp_nf90_create_


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PostPosted: Mon Mar 28, 2016 12:59 am 
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Did you get a warning like that at the compile/linking phase too? It's probably missing the -lnetcdff in the link command.


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PostPosted: Tue Apr 05, 2016 12:49 pm 
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hello kate
In order to avoid building C and fortran libraries respectively, I installed netcdf in version before 4.2 and run the upwelling case successfullly. With the purpose of getting the Cross-section plots,I installed a binary distribution of NCL6.1.2, which compiled against NETCDF-4.2. So I reinstalled netcdf in version 4.2.

[root@centox upwelling]# nf-config --all

This netCDF-Fortran 4.2 has been built with the following features:

--cc -> icc
--cflags -> -I/usr/local/include -I/usr/local/include
--libs -> -L/usr/local/lib -L/usr/local/lib -lnetcdf -lnetcdf

--fc -> ifort
--fflags -> -O3 -xHost -ip -no-prec-div -static-intel -I/usr/local/include
--flibs -> -L/usr/local/lib -lnetcdff -L/usr/local/lib -lnetcdf -lnetcdf
--has-f90 -> yes

--has-nc2 -> yes
--has-nc4 -> yes

--prefix -> /usr/local
--includedir-> /usr/local/include
--version -> netCDF-Fortran 4.2

[root@centox upwelling]# nc-config --all

This netCDF 4.2 has been built with the following features:

--cc -> icc
--cflags -> -I/usr/local/include -I/usr/local/include
--libs -> -L/usr/local/lib -lnetcdf

--cxx -> @CXX@
--has-c++ -> @HAS_CXX@

--fc -> @FC@
--fflags -> @FFLAGS@ @MOD_FLAG@/usr/local/include
--flibs -> -L/usr/local/lib @NC_FLIBS@
--has-f77 -> @HAS_F77@
--has-f90 -> @HAS_F90@

--has-dap -> yes
--has-nc2 -> yes
--has-nc4 -> yes
--has-hdf5 -> yes
--has-hdf4 -> no
--has-pnetcdf-> no
--has-szlib ->

--prefix -> /usr/local
--includedir-> /usr/local/include
--version -> netCDF 4.2
I Customize the Build Script like that:

export FORT=ifort
#export FORT=gfortran
#export FORT=pgi

#export USE_DEBUG=on # use Fortran debugging flags
#export USE_LARGE=on # activate 64-bit compilation
export USE_NETCDF4=on # compile with NetCDF-4 library
#export USE_PARALLEL_IO=on # Parallel I/O with Netcdf-4/HDF5

export USE_MY_LIBS=on # use my library paths below


if [ -n "${USE_MY_LIBS:+1}" ]; then
case "$FORT" in
ifort )
export ESMF_OS=Linux
export ESMF_COMPILER=ifort
export ESMF_BOPT=O
export ESMF_ABI=64
export ESMF_COMM=mpich
export ESMF_SITE=default

export ARPACK_LIBDIR=/opt/intelsoft/serial/ARPACK
if [ -n "${USE_MPI:+1}" ]; then
if [ "${which_MPI}" = "mpich" ]; then
export ESMF_DIR=/opt/intelsoft/mpich/esmf
export MCT_INCDIR=/opt/intelsoft/mpich/mct/include
export MCT_LIBDIR=/opt/intelsoft/mpich/mct/lib
export PARPACK_LIBDIR=/opt/intelsoft/mpich/PARPACK
elif [ "${which_MPI}" = "mpich2" ]; then
export ESMF_DIR=/opt/intelsoft/mpich2/esmf
export MCT_INCDIR=/opt/intelsoft/mpich2/mct/include
export MCT_LIBDIR=/opt/intelsoft/mpich2/mct/lib
export PARPACK_LIBDIR=/opt/intelsoft/mpich2/PARPACK
elif [ "${which_MPI}" = "openmpi" ]; then
export ESMF_DIR=/opt/intelsoft/openmpi/esmf
export MCT_INCDIR=/opt/intelsoft/openmpi/mct/include
export MCT_LIBDIR=/opt/intelsoft/openmpi/mct/lib
export PARPACK_LIBDIR=/opt/intelsoft/openmpi/PARPACK
fi
fi

if [ -n "${USE_NETCDF4:+1}" ]; then
if [ -n "${USE_PARALLEL_IO:+1}" ] && [ -n "${USE_MPI:+1}" ]; then
if [ "${which_MPI}" = "mpich" ]; then
export NC_CONFIG=/opt/intelsoft/mpich/netcdf4/bin/nc-config
export NETCDF_INCDIR=/opt/intelsoft/mpich/netcdf4/include
elif [ "${which_MPI}" = "mpich2" ]; then
export NC_CONFIG=/opt/intelsoft/mpich2/netcdf4/bin/nc-config
export NETCDF_INCDIR=/opt/intelsoft/mpich2/netcdf4/include
elif [ "${which_MPI}" = "openmpi" ]; then
export NC_CONFIG=/opt/intelsoft/openmpi/netcdf4/bin/nc-config
export NETCDF_INCDIR=/opt/intelsoft/openmpi/netcdf4/include
fi
else
export NC_CONFIG=/usr/local/bin/nc-config
export NETCDF_INCDIR=/usr/local/include
fi
else
export NETCDF_INCDIR=/usr/local/include
export NETCDF_LIBDIR=/usr/local/lib
fi
;;



I got error like this

ifort: error #10005: unable to open argument file 'NC_FLIBS@'
make: *** [/root/Projects/upwelling/oceanS] 错误 1


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PostPosted: Tue Apr 05, 2016 4:32 pm 
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Quote:
--flibs -> -L/usr/local/lib @NC_FLIBS@
You can either fix your nc-config script or invoke your nf-config script instead during the ROMS build.


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PostPosted: Fri Apr 19, 2019 8:00 pm 
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kate wrote:
Did you get a warning like that at the compile/linking phase too? It's probably missing the -lnetcdff in the link command.

Hello Kate,

I am facing the same problem, when I running oceanS for upwelling case:
Code:
oceanS: symbol lookup error: oceanS: undefined symbol: __netcdf_MOD_nf90_create

During compile/linking phase, I did have two warning message said:
Code:
/usr/bin/ld: warning: libhdf5_hl.so.100, needed by /opt/junk/netcdf4/lib/libnetcdf.so, may conflict with libhdf5_hl.so.8
/usr/bin/ld: warning: libhdf5.so.103, needed by /opt/junk/netcdf4/lib/libnetcdf.so, may conflict with libhdf5.so.8

I tried to set LD_LIBRARY_PATH equals to the folder with libhdf5_hl.so.100 and libhdf5.so.103. But the warning still there.
Thanks for your help!

Best regards
Yifan


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PostPosted: Fri Apr 19, 2019 8:29 pm 
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My hdf libraries are a few years old but are version 10.0.x, but that probably has nothing to do with this at all. Do you get a linking error from NetCDF rather than HDF?


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PostPosted: Fri Apr 19, 2019 9:00 pm 
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kate wrote:
My hdf libraries are a few years old but are version 10.0.x, but that probably has nothing to do with this at all. Do you get a linking error from NetCDF rather than HDF?

Thanks for your reply, Kate!
When I run oceanS, I did get a error message about netcdf:
Code:
oceanS: error while loading shared libraries: libnetcdf.so.15: cannot open shared object file: No such file or directory

And I tried to solve this by set up the LD_LIBRARY_PATH environment:
Code:
export LD_LIBARRY_PATH=${LD_LIBARAY_PATH}:/opt/junk/netcdf4/lib

After doing this, I rerun the oceanS and got the current error.

Another possible information may be useful is that I hacked nf-config a little bit, since the whole netcdf folder has been moved and the nf-config point to old path. I edited nf-config to point to right folder. Before I edit the nf-config, I got error:
Code:
/usr/bin/ld: cannot find -lnetcdff
   collect2: ld returned 1 exit status
   make: *** [/home/ywang/roms/Projects/Upwelling/oceanS] Error 1

What I edited in nf-config is highlighted below:


prefix=/opt/junk/netcdff
exec_prefix=${prefix}
libdir=${exec_prefix}/lib
includedir=${prefix}/include

cc="gcc"
fc="gfortran"
cflags=" -I${includedir} -I/opt/netcdf4/include"
fflags="-I${includedir}"
has_dap="yes"
has_nc2="yes"
has_nc4="yes"
has_f90="no"
has_f03="yes"
#flibs="-L${libdir} -lnetcdff -L/opt/junk/netcdf4/lib -lnetcdf -lnetcdf -lhdf5_hl -lhdf5 -lsz -lcurl -lm "
flibs="-L${libdir} -lnetcdff -L/opt/junk/netcdf4/lib -lnetcdf -lnetcdf -lhdf5_hl -lhdf5 -lsz -lcurl "


The reason I remove the '-lm' from flibs is that I guess it may related with matlab, while I found the library file libhdf5_hl.so.8, causing conflict, comes from a matlab library folder.... Actually I have no idea what -lm is.

Thanks for your help!

Best regards
Yifan


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PostPosted: Fri Apr 19, 2019 9:41 pm 
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-lm is a math library, not matlab.

Maybe try putting your junk directory at the front of LD_LIBRARY_PATH instead.


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PostPosted: Mon Apr 22, 2019 2:09 pm 
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kate wrote:
-lm is a math library, not matlab.

Maybe try putting your junk directory at the front of LD_LIBRARY_PATH instead.


Thank you Kate,

It seems the warning messages didn't bother me anymore.
I found I didn't add the netcdf-fortran library folder into LD_LIBRARY_PATH, so I put netcdf and netcdf-fortran library folders at the front of LD_LIBRARY_PATH in .bash_profile and re-compile the build.bash. The oceanS came out with the same warning messages. However, the good thing is that there is no problem of running oceanS right. now. Thank you!

Best regards
Yifan


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