PROBLEMS RUNNING ESTUARY SEDIMENT TEST

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jande023
Posts: 29
Joined: Tue Oct 16, 2012 8:55 pm
Location: Old Dominion Universiy

PROBLEMS RUNNING ESTUARY SEDIMENT TEST

#1 Post by jande023 » Sun Dec 30, 2012 8:09 pm

Have Upwelling Test up and running in serial mode on Linux with gfortran. Created new directory in Projects folder, EstuarySedment, and copied into it: build.bash from successful upwelling run, estuary_test.h, ocean_estuary_test.in, sediment_estuary_test.in, and varinfo.dat. Then modified build script to:

Export ROMS_APPLICATIOIN=ESTUARY_TEST
Export MY_PROJECT_DIR${MY_ROOT_DIR)/Projects/EstuarySediment

Build appears to configure properly and creates: oceanS
I try to execute oceans with the command:

./oceans < ocean_estuary_test.in sediment_estuary_test.in > sedimentTest.out

Run quickly fails with sedimentTest.out as follows:

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

Doesn’t seem to make any difference if I set the path in ocean_estuary_test.in to the ROMS External source directory or the copy of varinfo.dat in my project directory,

VARNAME = ROMS/External/varinfo.dat, OR VARNAME = varinfo.dat,

I get the same error.

Any recommendations to fix and any other obvious flaws with my set-up so far?

csherwood
Posts: 38
Joined: Fri Apr 02, 2004 4:46 pm
Location: USGS, Woods Hole, USA

Re: PROBLEMS RUNNING ESTUARY SEDIMENT TEST

#2 Post by csherwood » Mon Dec 31, 2012 7:07 pm

I see a couple things that are either typos or mistakes.

The executable is oceanS (note uppercase S). The input file you should be piping to that is
ocean_estuary_test.in, not sediment_estuary_test.in (that file should be specified in ocean_estuary_test.in).

Unless you have reason to change it, best to leave varinfo.dat where it is, and in the .in file, use the full path name, e.g.:

VARNAME = /fullpathtoromssourcecode/ROMS/External/varinfo.dat

If that doesn't work, post your build.bash file and a ls of what you have in your project directory.
Chris Sherwood, USGS
1 508 457 2269

jande023
Posts: 29
Joined: Tue Oct 16, 2012 8:55 pm
Location: Old Dominion Universiy

Re: PROBLEMS RUNNING ESTUARY SEDIMENT TEST

#3 Post by jande023 » Tue Jan 01, 2013 7:17 pm

Chris,
Sincerely appreciate the quick reply and assistance. The typos you identified oceans versus oceanS were errors in my posting versus my actual code. I reset the ocean_estuary_test.in pointer to varinfo.dat as follows:

VARNAME = ${HOME}/ROMS/trunk/ROMS/External/varinfo.dat

Then I re-ran: ./oceans < ocean_estuary_test.in > sedimentTest.out and got the same unable to open varinfo.dat error.

Below is the ls from my project directory (Projects/EstuarySediment):

Build
build.bash
oceanS
ocean_estuary_test.in
sediment_estuary_test.in
estuary_test.h

Note, I was unable to upload my build script—cycled “upload in progress” for over 30 minutes, so I stopped and tried again and finally gave up and copied txt below. thanks again for your assistance.

John

#!/bin/bash
#
# svn $Id: build.bash 585 2012-01-03 18:44:28Z arango $
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# Copyright (c) 2002-2012 The ROMS/TOMS Group :::
# Licensed under a MIT/X style license :::
# See License_ROMS.txt :::
#::::::::::::::::::::::::::::::::::::::::::::::::::::: Hernan G. Arango :::
# :::
# ROMS/TOMS Compiling Script :::
# :::
# Script to compile an user application where the application-specific :::
# files are kept separate from the ROMS source code. :::
# :::
# Q: How/why does this script work? :::
# :::
# A: The ROMS makefile configures user-defined options with a set of :::
# flags such as ROMS_APPLICATION. Browse the makefile to see these. :::
# If an option in the makefile uses the syntax ?= in setting the :::
# default, this means that make will check whether an environment :::
# variable by that name is set in the shell that calls make. If so :::
# the environment variable value overrides the default (and the :::
# user need not maintain separate makefiles, or frequently edit :::
# the makefile, to run separate applications). :::
# :::
# Usage: :::
# :::
# ./build.bash [options] :::
# :::
# Options: :::
# :::
# -j [N] Compile in parallel using N CPUs :::
# omit argument for all available CPUs :::
# -noclean Do not clean already compiled objects :::
# :::
# Notice that sometimes the parallel compilation fail to find MPI :::
# include file "mpif.h". :::
# :::
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

parallel=0
clean=0

while [ $# -gt 0 ]
do
case "$1" in
-j )
shift
parallel=1
test=`echo $1 | grep -P '^\d+$'`
if [ "$test" != "" ]; then
NCPUS="-j $1"
shift
else
NCPUS="-j"
fi
;;

-noclean )
shift
clean=0
;;

* )
echo ""
echo "$0 : Unknown option [ $1 ]"
echo ""
echo "Available Options:"
echo ""
echo "-j [N] Compile in parallel using N CPUs"
echo " omit argument for all avaliable CPUs"
echo "-noclean Do not clean already compiled objects"
echo ""
exit 1
;;
esac
done

# Set the CPP option defining the particular application. This will
# determine the name of the ".h" header file with the application
# CPP definitions.

export ROMS_APPLICATION=ESTUARY_TEST

# Set a local environmental variable to define the path to the directories
# where all this project's files are kept.


export MY_ROOT_DIR=${HOME}/ROMS
export MY_PROJECT_DIR=${MY_ROOT_DIR}/Projects/EstuarySediment

# The path to the user's local current ROMS source code.
#
# If using svn locally, this would be the user's Working Copy Path (WCPATH).
# Note that one advantage of maintaining your source code locally with svn
# is that when working simultaneously on multiple machines (e.g. a local
# workstation, a local cluster and a remote supercomputer) you can checkout
# the latest release and always get an up-to-date customized source on each
# machine. This script is designed to more easily allow for differing paths
# to the code and inputs on differing machines.

#export MY_ROMS_SRC=${MY_ROOT_DIR}/branches/arango
export MY_ROMS_SRC=${MY_ROOT_DIR}/trunk

# Set path of the directory containing makefile configuration (*.mk) files.
# The user has the option to specify a customized version of these files
# in a different directory than the one distributed with the source code,
# ${MY_ROMS_SRC}/Compilers. If this is the case, the you need to keep
# these configurations files up-to-date.

export COMPILERS=${MY_ROMS_SRC}/Compilers
#export COMPILERS=${MY_ROOT_DIR}/Compilers

# Set tunable CPP options.
#
# Sometimes it is desirable to activate one or more CPP options to run
# different variants of the same application without modifying its header
# file. If this is the case, specify each options here using the -D syntax.
# Notice also that you need to use shell's quoting syntax to enclose the
# definition. Both single or double quotes work. For example,
#
#export MY_CPP_FLAGS="-DAVERAGES"
#export MY_CPP_FLAGS="${MY_CPP_FLAGS} -DDEBUGGING"
#
# can be used to write time-averaged fields. Notice that you can have as
# many definitions as you want by appending values.

#export MY_CPP_FLAGS="-D"

# Other user defined environmental variables. See the ROMS makefile for
# details on other options the user might want to set here. Be sure to
# leave the switches meant to be off set to an empty string or commented
# out. Any string value (including off) will evaluate to TRUE in
# conditional if-statements.

#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

# There are several MPI libraries available. Here, we set the desired
# "mpif90" script to use during compilation. This only works if the make
# configuration file (say, Linux-pgi.mk) in the "Compilers" directory
# has the following definition for FC (Fortran Compiler) in the USE_MPI
# section:
#
# FC := mpif90
#
# that is, "mpif90" defined without any path. Notice that the path
# where the MPI library is installed is computer dependent. Recall
# that you still need to use the appropriate "mpirun" to execute.

if [ -n "${USE_MPIF90:+1}" ]; then
case "$FORT" in
ifort )
if [ "${which_MPI}" = "mpich" ]; then
export PATH=/opt/intelsoft/mpich/bin:$PATH
elif [ "${which_MPI}" = "mpich2" ]; then
export PATH=/opt/intelsoft/mpich2/bin:$PATH
elif [ "${which_MPI}" = "openmpi" ]; then
export PATH=/opt/intelsoft/openmpi/bin:$PATH
fi
;;

pgi )
if [ "${which_MPI}" = "mpich" ]; then
export PATH=/opt/pgisoft/mpich/bin:$PATH
elif [ "${which_MPI}" = "mpich2" ]; then
export PATH=/opt/pgisoft/mpich2/bin:$PATH
elif [ "${which_MPI}" = "openmpi" ]; then
export PATH=/opt/pgisoft/openmpi/bin:$PATH
fi
;;

gfortran )
if [ "${which_MPI}" = "mpich2" ]; then
export PATH=/opt/gfortransoft/mpich2/bin:$PATH
elif [ "${which_MPI}" = "openmpi" ]; then
export PATH=/opt/gfortransoft/openmpi/bin:$PATH
fi
;;

esac
fi

# If the USE_MY_LIBS is activated above, the path of the libraries
# required by ROMS can be set here using environmental variables
# which take precedence to the values specified in the make macro
# definitions file (Compilers/*.mk). For most applications, only
# the location of the NetCDF library is needed during compilation.
#:wg

# Notice that when the USE_NETCDF4 macro is activated, we need the
# serial or parallel version of the NetCDF-4/HDF5 library. The
# configuration script NC_CONFIG (available since NetCDF 4.0.1)
# is used to set up all the required libraries according to the
# installed options (openDAP, netCDF4/HDF5 file format). The
# parallel library uses the MPI-I/O layer (usually available
# in MPICH2 and OpenMPI) requiring compiling with the selected
# MPI library.
#
# In ROMS distributed-memory applications, you may use either the
# serial or parallel version of the NetCDF-4/HDF5 library. The
# parallel version is required when parallel I/O is activated
# (ROMS cpp option PARALLEL_IO and HDF5).
#
# However, in serial or shared-memory ROMS applications, we need
# to use the serial version of the NetCDF-4/HDF5 to avoid conflicts
# with the compiler. We cannot activate MPI constructs in serial
# or shared-memory ROMS code. Hybrid parallelism is not possible.
#
# Recall also that the MPI library comes in several flavors:
# MPICH, MPICH2, OpenMPI, etc.

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=/opt/intelsoft/serial/netcdf4/bin/nc-config
export NETCDF_INCDIR=/opt/intelsoft/serial/netcdf4/include
fi
else
export NETCDF_INCDIR=${HOME}/netcdf/include
export NETCDF_LIBDIR=${HOME}/netcdf/lib
fi
;;

pgi )
export ESMF_OS=Linux
export ESMF_COMPILER=pgi
export ESMF_BOPT=O
export ESMF_ABI=64
export ESMF_COMM=mpich
export ESMF_SITE=default

export ARPACK_LIBDIR=/opt/pgisoft/serial/ARPACK
if [ -n "${USE_MPI:+1}" ]; then
if [ "${which_MPI}" = "mpich" ]; then
export ESMF_DIR=/opt/pgisoft/mpich/esmf
export MCT_INCDIR=/opt/pgisoft/mpich/mct/include
export MCT_LIBDIR=/opt/pgisoft/mpich/mct/lib
export PARPACK_LIBDIR=/opt/pgisoft/mpich/PARPACK
elif [ "${which_MPI}" = "mpich2" ]; then
export ESMF_DIR=/opt/pgisoft/mpich2/esmf
export MCT_INCDIR=/opt/pgisoft/mpich2/mct/include
export MCT_LIBDIR=/opt/pgisoft/mpich2/mct/lib
export PARPACK_LIBDIR=/opt/pgisoft/mpich2/PARPACK
elif [ "${which_MPI}" = "openmpi" ]; then
export ESMF_DIR=/opt/pgisoft/openmpi/esmf
export MCT_INCDIR=/opt/pgisoft/openmpi/mct/include
export MCT_LIBDIR=/opt/pgisoft/openmpi/mct/lib
export PARPACK_LIBDIR=/opt/pgisoft/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/pgisoft/mpich/netcdf4/bin/nc-config
export NETCDF_INCDIR=/opt/pgisoft/mpich/netcdf4/include
elif [ "${which_MPI}" = "mpich2" ]; then
export NC_CONFIG=/opt/pgisoft/mpich2/netcdf4/bin/nc-config
export NETCDF_INCDIR=/opt/pgisoft/mpich2/netcdf4/include
elif [ "${which_MPI}" = "openmpi" ]; then
export NC_CONFIG=/opt/pgisoft/openmpi/netcdf4/bin/nc-config
export NETCDF_INCDIR=/opt/pgisoft/openmpi/netcdf4/include
fi
else
export NC_CONFIG=/opt/pgisoft/serial/netcdf4/bin/nc-config
export NETCDF_INCDIR=/opt/pgisoft/serial/netcdf4/include
fi
else
export NETCDF_INCDIR=/opt/pgisoft/serial/netcdf3/include
export NETCDF_LIBDIR=/opt/pgisoft/serial/netcdf3/lib
fi
;;

gfortran )
export ESMF_OS=Linux
export ESMF_COMPILER=gfortran
export ESMF_BOPT=O
export ESMF_ABI=64
export ESMF_COMM=mpich
export ESMF_SITE=default

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

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

esac
fi

# The rest of this script sets the path to the users header file and
# analytical source files, if any. See the templates in User/Functionals.
#
# If applicable, use the MY_ANALYTICAL_DIR directory to place your
# customized biology model header file (like fennel.h, nemuro.h, ecosim.h,
# etc).

export MY_HEADER_DIR=${MY_PROJECT_DIR}

export MY_ANALYTICAL_DIR=${MY_PROJECT_DIR}

# Put the binary to execute in the following directory.

export BINDIR=${MY_PROJECT_DIR}

# Put the f90 files in a project specific Build directory to avoid conflict
# with other projects.

export SCRATCH_DIR=${MY_PROJECT_DIR}/Build

# Go to the users source directory to compile. The options set above will
# pick up the application-specific code from the appropriate place.

cd ${MY_ROMS_SRC}

# Remove build directory.

if [ $clean -eq 1 ]; then
make clean
fi

# Compile (the binary will go to BINDIR set above).

if [ $parallel -eq 1 ]; then
make $NCPUS
else
make
fi

csherwood
Posts: 38
Joined: Fri Apr 02, 2004 4:46 pm
Location: USGS, Woods Hole, USA

Re: PROBLEMS RUNNING ESTUARY SEDIMENT TEST

#4 Post by csherwood » Tue Jan 01, 2013 11:04 pm

John,

I did an svn update (just to make sure we were working on the same code) and copied the build.bash, .in and .h files to a project dir, modified build.bash, and built the estuary test case.

Putting this in the .in file:

VARNAME = ${HOME}/src/my_roms/ROMS/External/varinfo.dat

does not work for me either. But if I replace ${HOME} with the actual path, it works fine. Check your syntax and make sure it is there from the project directory:

ls /home/csherwood/src/my_roms/ROMS/External/varinfo.dat

If any of your files have been on a Windows system, make sure they they have not gotten extra <CR><LF> added to the end.
Chris Sherwood, USGS
1 508 457 2269

jande023
Posts: 29
Joined: Tue Oct 16, 2012 8:55 pm
Location: Old Dominion Universiy

Re: PROBLEMS RUNNING ESTUARY SEDIMENT TEST

#5 Post by jande023 » Wed Jan 02, 2013 1:25 am

Chris,

I use the Linux editor vim, so don't think I have introduced any unwanted <CR><LF> but this is good to know for future reference. Ran pwd for the ROMS/External directory and put in full path returned:

/afs/lions.odu.edu/home/j/jande023/ROMS/trunk/ROMS/External/varinfo.dat

also tried

~/ROMS/trunk/ROMS/External/varinfo.dat

Couldn't locate in either case, so I reverted back to the way I had successfully set up the Upwelling test case with:

VARNAME = varinfo.dat and varinfo.dat in my EstuarySediment project directory.

Now get a different error: At line 434 of file inp_par.f90 Fortran runtime error: No such file or directory. Not sure where inp_par.f90 is to investigate further. Next step is to svn relevant files; but, I fear that's not the issue. My output file, sedimentTest.out, is copied below, showing where the run terminates.


Model Input Parameters: ROMS/TOMS version 3.6
Tuesday - January 1, 2013 - 8:19:08 PM
-----------------------------------------------------------------------------

Suspended Sediment Test in an Estuary

Operating system : Linux
CPU/hardware : x86_64
Compiler system : gfortran
Compiler command : /usr/bin/gfortran
Compiler flags : -frepack-arrays -O3 -ffast-math -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none

SVN Root URL : https://www.myroms.org/svn/src/trunk
SVN Revision : 634M

Local Root : /afs/lions.odu.edu/home/j/jande023/ROMS/trunk
Header Dir : /afs/lions.odu.edu/home/j/jande023/ROMS/Projects/EstuarySediment
Header file : estuary_test.h
Analytical Dir: /afs/lions.odu.edu/home/j/jande023/ROMS/Projects/EstuarySediment

Resolution, Grid 01: 0200x0003x020, Parallel Threads: 1, Tiling: 001x001


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

28800 ntimes Number of timesteps for 3-D equations.
30.000 dt Timestep size (s) for 3-D equations.
20 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.
2880 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).
120 nHIS Number of timesteps between the writing fields
into history file.
1 ntsAVG Starting timestep for the accumulation of output
time-averaged data.
1440 nAVG Number of timesteps between the writing of
time-averaged data into averages file.
5.0000E-06 Akt_bak(01) Background vertical mixing coefficient (m2/s)
for tracer 01: temp
5.0000E-06 Akt_bak(02) Background vertical mixing coefficient (m2/s)
for tracer 02: salt
5.0000E-05 Akv_bak Background vertical mixing coefficient (m2/s)
for momentum.
5.0000E-06 Akk_bak Background vertical mixing coefficient (m2/s)
for turbulent energy.
5.0000E-06 Akp_bak Background vertical mixing coefficient (m2/s)
for turbulent generic statistical field.
3.000 gls_p GLS stability exponent.
1.500 gls_m GLS turbulent kinetic energy exponent.
-1.000 gls_n GLS turbulent length scale exponent.
7.6000E-06 gls_Kmin GLS minimum value of turbulent kinetic energy.
1.0000E-12 gls_Pmin GLS minimum value of dissipation.
5.4770E-01 gls_cmu0 GLS stability coefficient.
1.4400E+00 gls_c1 GLS shear production coefficient.
1.9200E+00 gls_c2 GLS dissipation coefficient.
-4.0000E-01 gls_c3m GLS stable buoyancy production coefficient.
1.0000E+00 gls_c3p GLS unstable buoyancy production coefficient.
1.0000E+00 gls_sigk GLS constant Schmidt number for TKE.
1.3000E+00 gls_sigp GLS constant Schmidt number for PSI.
1400.000 charnok_alpha Charnok factor for Zos calculation.
0.500 zos_hsig_alpha Factor for Zos calculation using Hsig(Awave).
0.250 sz_alpha Factor for Wave dissipation surface tke flux .
100.000 crgban_cw Factor for Craig/Banner surface tke flux.
3.0000E-04 rdrg Linear bottom drag coefficient (m/s).
3.0000E-03 rdrg2 Quadratic bottom drag coefficient.
5.0000E-03 Zob Bottom roughness (m).
5.0000E-03 Zos Surface roughness (m).
1 Vtransform S-coordinate transformation equation.
1 Vstretching S-coordinate stretching function.
1.0000E+00 theta_s S-coordinate surface control parameter.
1.0000E+00 theta_b S-coordinate bottom control parameter.
1.000 Tcline S-coordinate surface/bottom layer width (m) used
in vertical coordinate stretching.
1028.000 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)
1.2500E-01 Tnudg(01) Nudging/relaxation time scale (days)
for tracer 01: temp
1.2500E-01 Tnudg(02) Nudging/relaxation time scale (days)
for tracer 02: salt
1.0000E-03 Znudg Nudging/relaxation time scale (days)
for free-surface.
1.0000E-03 M2nudg Nudging/relaxation time scale (days)
for 2D momentum.
1.0000E-03 M3nudg Nudging/relaxation time scale (days)
for 3D momentum.
1.0000E+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.
10.000 T0 Background potential temperature (C) constant.
30.000 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).
7.6000E-04 Scoef Saline contraction coefficient (1/PSU).
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 Hout(idUbms) Write out bottom U-momentum stress.
T Hout(idVbms) Write out bottom V-momentum stress.
T Hout(idBott) Write out bottom property 01: grain_diameter
T Hout(idBott) Write out bottom property 02: grain_density
T Hout(idBott) Write out bottom property 03: settling_vel
T Hout(idBott) Write out bottom property 04: erosion_stress
T Hout(idBott) Write out bottom property 05: ripple_length
T Hout(idBott) Write out bottom property 06: ripple_height
T Hout(idBott) Write out bottom property 07: bed_wave_amp
T Hout(idBott) Write out bottom property 08: Zo_def
T Hout(idBott) Write out bottom property 09: Zo_app
T Hout(idVvis) Write out vertical viscosity: AKv.
T Hout(idSdif) Write out vertical diffusion: AKt(isalt).
T Hout(idMtke) Write out turbulent kinetic energy.
T Hout(idMtls) Write out turbulent generic length-scale.

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

Output/Input Files:

Output Restart File: ocean_rst.nc
Output History File: ocean_his.nc
Output Averages File: ocean_avg.nc

Tile partition information for Grid 01: 0200x0003x0020 tiling: 001x001

tile Istr Iend Jstr Jend Npts

0 1 200 1 3 12000

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

tile Xmin Xmax Ymin Ymax grid

0 0.50 201.50 0.50 3.50 RHO-points

0 0.00 201.00 0.50 3.50 U-points

0 0.50 201.50 0.00 3.00 V-points

csherwood
Posts: 38
Joined: Fri Apr 02, 2004 4:46 pm
Location: USGS, Woods Hole, USA

Re: PROBLEMS RUNNING ESTUARY SEDIMENT TEST

#6 Post by csherwood » Wed Jan 02, 2013 2:07 am

It is weird that putting the full path name in did not fix the problem.

The .f90 files are in the ./Build directory: they are made when the C pre-processor program is run on the .F files, and are a good place to look to see what code is actually included after all of the #ifdef commands are resolved.

Have you changed the path of the sediment_estuary_test.in file specified in your ocean_estuary_test.in file? It starts out as /ROMS/External, but you should remove the path prefix to that it points to the local version.
Chris Sherwood, USGS
1 508 457 2269

jande023
Posts: 29
Joined: Tue Oct 16, 2012 8:55 pm
Location: Old Dominion Universiy

Re: PROBLEMS RUNNING ESTUARY SEDIMENT TEST

#7 Post by jande023 » Wed Jan 02, 2013 2:05 pm

Good news Chris,

Had not specified location of sediment_estuary_test.in in ocean_estuary_test.in and doing so appearred to fix the problem. Did not change the path on the remaining files in the "External" folder as shown below:

APARNAM = ROMS/External/s4dvar.in
SPOSNAM = ROMS/External/stations.in
FPOSNAM = ROMS/External/floats.in
BPARNAM = ROMS/External/bio_Fennel.in
SPARNAM = sediment_estuary_test.in
USRNAME = ROMS/External/MyFile.dat

Run appears to complete "ROMS/TOMS: DONE... Wednesday - January 2, 2013 - 8:00 15 A
and created .nc files. Guess I need to plot to see if the run was actually successful?

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