Commit c773b9fc authored by Pierre Cazenave's avatar Pierre Cazenave
Browse files

Add the Estuary example and set up files.

parent 4a39af50
This diff is collapsed.
This diff is collapsed.
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run/run/fvcom: No such file or directory
real 0m3.591s
user 0m0.757s
sys 0m1.822s
=== begin of FVCOM section
Mon Jan 12 10:16:36 GMT 2015
medusa4
medusa4
medusa4
medusa4
medusa4
medusa4
medusa4
medusa4
medusa5
medusa5
medusa5
medusa5
medusa5
medusa5
medusa5
medusa5
medusa6
medusa6
medusa6
medusa6
medusa6
medusa6
medusa6
medusa6
medusa7
medusa7
medusa7
medusa7
medusa7
medusa7
medusa7
medusa7
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run
working directory : /home_nfs/pica
4 32
running fvcom ...
/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run
#!/bin/bash
#PBS -l select=4:ncpus=8:mpiprocs=8
#PBS -l place=scatter
#PBS -N FVCOM.32.HP
echo "=== begin of FVCOM section"
date
cat $PBS_NODEFILE
NNODES=`cat $PBS_NODEFILE | uniq | wc -l`
NTASKS=`cat $PBS_NODEFILE | wc -l`
echo $PBS_NODEFILE $NTASKS $NNODES > $HOME/run.log
cp $PBS_NODEFILE $HOME
CFILE=/tmp/mpd2.console_bench_$PBS_JOBID
source /opt/intel/fce/10.1.012/bin/ifortvars.sh
source /opt/intel/cce/10.1.012/bin/iccvars.sh
source /opt/mpi/mpibull2-1.3.5-4.t/share/setenv_mpibull2.sh
source /opt/intel/idbe/10.1.012/bin/idbvars.sh
export IDB_HOME=/opt/intel/idbe/10.1.012/bin/
mpibull2-devices -d=ibmr_gen2
export NUM_RDMA_BUFFER=0
export MPIBULL2_USE_POSTAL=0
ulimit -Ss unlimited
PF=`date +%y%m%d-%H%M%S`
RUNDIR=/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run
EXE=${RUNDIR}/run/fvcom
CASENAME=tst
#WDIR=${DATA}-${PF}-${NTASKS}
WDIR=`pwd`
cd $RUNDIR
pwd
echo "working directory : $WDIR"
driver=`mpibull2-devices -c | grep "driver" | cut -d":" -f2 | sed "s, ,,"`
if [ "x$driver" != "xibmr_gen2" ]
then
echo "driver = |${driver}|"
echo "Cannot set comm driver to ibmr_gen2!"
exit
fi
export LD_PRELOAD=/home_nfs/bench/libaffinity/arch/mpibull2-1.3.5/lib/libmpiaffinity.so
export LD_LIBRARY_PATH=/home_nfs/pica/src/UK-FVCOM/FVCOM/PML/src/FVCOM_source/libs/install/lib/:$LD_LIBRARY_PATH
if [ "8" == "8" ]
then
export MPI_SETAFFINITY=rank
else
export MPI_SETAFFINITY=topo:scatter,L2
fi
export MKL_SERIAL=yes
export OMP_NUM_THREADS=1
# following two lines needed for core dumping
export decfort_dump_flag=y
ulimit -c unlimited
export F_UFMTENDIAN=77,78
touch logs/info
date >> logs/info
env >> logs/info
ulimit -a >> logs/info
cat $PBS_NODEFILE >> logs/info
mpibull2-devices -c > logs/mpi.device
echo "$NNODES $NTASKS"
echo "running fvcom ..."
pwd
LF=logs/$CASENAME.$NNODES.$NTASKS.log
time mpirun -np $NTASKS $EXE --casename $CASENAME --dbg=0 | tee $LF
for node in `cat $PBS_NODEFILE | uniq ` ; do ssh $node "rm -f $CFILE" ; done
#!/bin/bash
#PBS -l select=__NODES__:ncpus=8:mpiprocs=__TPN__
#PBS -l place=scatter
#PBS -N FVCOM.__TASKS__.__POPMOD__
echo "=== begin of FVCOM section"
date
cat $PBS_NODEFILE
NNODES=`cat $PBS_NODEFILE | uniq | wc -l`
NTASKS=`cat $PBS_NODEFILE | wc -l`
echo $PBS_NODEFILE $NTASKS $NNODES > $HOME/run.log
cp $PBS_NODEFILE $HOME
CFILE=/tmp/mpd2.console_bench_$PBS_JOBID
source /opt/intel/fce/10.1.012/bin/ifortvars.sh
source /opt/intel/cce/10.1.012/bin/iccvars.sh
source /opt/mpi/mpibull2-1.3.5-4.t/share/setenv_mpibull2.sh
source /opt/intel/idbe/10.1.012/bin/idbvars.sh
export IDB_HOME=/opt/intel/idbe/10.1.012/bin/
mpibull2-devices -d=ibmr_gen2
export NUM_RDMA_BUFFER=0
export MPIBULL2_USE_POSTAL=0
ulimit -Ss unlimited
PF=`date +%y%m%d-%H%M%S`
RUNDIR=/home_nfs/pica/models/FVCOM/fvcom-examples/Estuary/run
EXE=${RUNDIR}/run/fvcom
CASENAME=tst
#WDIR=${DATA}-${PF}-${NTASKS}
WDIR=`pwd`
cd $RUNDIR
pwd
echo "working directory : $WDIR"
driver=`mpibull2-devices -c | grep "driver" | cut -d":" -f2 | sed "s, ,,"`
if [ "x$driver" != "xibmr_gen2" ]
then
echo "driver = |${driver}|"
echo "Cannot set comm driver to ibmr_gen2!"
exit
fi
export LD_PRELOAD=/home_nfs/bench/libaffinity/arch/mpibull2-1.3.5/lib/libmpiaffinity.so
export LD_LIBRARY_PATH=/home_nfs/pica/src/UK-FVCOM/FVCOM/PML/src/FVCOM_source/libs/install/lib/:$LD_LIBRARY_PATH
if [ "__TPN__" == "8" ]
then
export MPI_SETAFFINITY=rank
else
export MPI_SETAFFINITY=topo:scatter,L2
fi
export MKL_SERIAL=yes
export OMP_NUM_THREADS=1
# following two lines needed for core dumping
export decfort_dump_flag=y
ulimit -c unlimited
export F_UFMTENDIAN=77,78
touch logs/info
date >> logs/info
env >> logs/info
ulimit -a >> logs/info
cat $PBS_NODEFILE >> logs/info
mpibull2-devices -c > logs/mpi.device
echo "$NNODES $NTASKS"
echo "running fvcom ..."
pwd
LF=logs/$CASENAME.$NNODES.$NTASKS.log
time mpirun -np $NTASKS $EXE --casename $CASENAME --dbg=0 | tee $LF
for node in `cat $PBS_NODEFILE | uniq ` ; do ssh $node "rm -f $CFILE" ; done
#!/usr/bin/env bash
# Script to generate a .pbs file and launch the job.
TPN=8
PROCS=$1
NODES=$(($PROCS/$TPN))
TEMPLATE=$2
PBS=estuary.p$PROCS.n$NODES.pbs
sed "s,__NODES__,$NODES,g;s,__TPN__,$TPN,g;s,__POPMOD__,HP,g;s,__TASKS__,$PROCS,g" $TEMPLATE > $PBS
qsub -qworkq $PBS
!================================================================!
_______ _ _ _______ _______ _______ ______ _____
(_______)(_) (_)(_______)(_______)(_______)(_____ \ (_____)
_____ _ _ _ _ _ _ _ _ _____) ) _ __ _
| ___) | | | || | | | | || ||_|| |(_____ ( | |/ /| |
| | \ \ / / | |_____ | |___| || | | | _____) )_| /_| |
|_| \___/ \______) \_____/ |_| |_|(______/(_)\_____/
-- Beta Release
!================================================================!
! !
!========DOMAIN DECOMPOSITION USING: METIS 4.0.1 ================!
!======Copyright 1998, Regents of University of Minnesota========!
! !
&NML_CASE
CASE_TITLE = 'IDEAL ESTUARY CASE'
TIMEZONE = 'none',
DATE_FORMAT = 'YMD'
START_DATE = 'seconds=0.0'
END_DATE = 'days=3.0'
/
&NML_STARTUP
STARTUP_TYPE = 'coldstart' ,
STARTUP_FILE = 'none' ,
STARTUP_UV_TYPE = 'default' ,
STARTUP_TURB_TYPE = 'default' ,
STARTUP_TS_TYPE = 'constant' ,
STARTUP_T_VALS = 15.0 ,
STARTUP_S_VALS = 35.0 ,
STARTUP_DMAX = -10.00000
/
&NML_IO
INPUT_DIR = '../tstinp' ,
OUTPUT_DIR = './' ,
IREPORT = 40,
VISIT_ALL_VARS = F,
WAIT_FOR_VISIT = F,
USE_MPI_IO_MODE = F
/
&NML_INTEGRATION
EXTSTEP_SECONDS = 5.00 ,
ISPLIT = 10,
IRAMP = 500 ,
MIN_DEPTH = 0.05000000E+00,
STATIC_SSH_ADJ = 0.0000000E+00
/
&NML_RESTART
RST_ON = F,
RST_FIRST_OUT = 'cycle = 0' ,
RST_OUT_INTERVAL = 'cycle = 200' ,
RST_OUTPUT_STACK = 0
/
&NML_NETCDF
NC_ON = T,
NC_FIRST_OUT = 'seconds=0.0',
NC_OUT_INTERVAL = 'seconds=3600.' ,
NC_OUTPUT_STACK = 0,
NC_GRID_METRICS = F,
NC_VELOCITY = T,
NC_SALT_TEMP = T,
NC_TURBULENCE = T,
NC_AVERAGE_VEL = T,
NC_VERTICAL_VEL = T,
NC_WIND_VEL = F,
NC_WIND_STRESS = F,
NC_EVAP_PRECIP = F,
NC_SURFACE_HEAT = F,
NC_GROUNDWATER = F
/
&NML_NETCDF_AV
NCAV_ON = F,
NCAV_FIRST_OUT = 'none' ,
NCAV_OUT_INTERVAL = 'none' ,
NCAV_OUTPUT_STACK = 0,
NCAV_SUBDOMAIN_FILES = ,
NCAV_GRID_METRICS = F,
NCAV_FILE_DATE = F,
NCAV_VELOCITY = F,
NCAV_SALT_TEMP = F,
NCAV_TURBULENCE = F,
NCAV_AVERAGE_VEL = F,
NCAV_VERTICAL_VEL = F,
NCAV_WIND_VEL = F,
NCAV_WIND_STRESS = F,
NCAV_EVAP_PRECIP = F,
NCAV_SURFACE_HEAT = F,
NCAV_GROUNDWATER = F,
NCAV_BIO = F,
NCAV_WQM = F,
NCAV_VORTICITY = F
/
&NML_SURFACE_FORCING
wIND_ON = F,
WIND_TYPE = 'stress' ,
WIND_FILE = 'wrf_for.nc' ,
WIND_KIND = 'variable' ,
WIND_X = 0.0000000E+00,
WIND_Y = 0.0000000E+00,
HEATING_ON = F,
HEATING_TYPE = 'flux' ,
HEATING_KIND = 'variable' ,
HEATING_FILE = 'wrf_for.nc' ,
HEATING_LONGWAVE_LENGTHSCALE = 6.3 ,
HEATING_LONGWAVE_PERCTAGE = 0.78000000 ,
HEATING_SHORTWAVE_LENGTHSCALE = 1.4000000 ,
HEATING_RADIATION = 0.0000000E+00,
HEATING_NETFLUX = 0.0000000E+00,
PRECIPITATION_ON = F,
PRECIPITATION_KIND = 'variable' ,
PRECIPITATION_FILE = 'wrf_for.nc' ,
PRECIPITATION_PRC = 0.0000000E+00,
PRECIPITATION_EVP = 0.0000000E+00,
AIRPRESSURE_ON = F,
AIRPRESSURE_KIND = 'none' ,
AIRPRESSURE_FILE = 'none' ,
AIRPRESSURE_VALUE = 0.0000000E+00
/
&NML_PHYSICS
HORIZONTAL_MIXING_TYPE = 'closure' ,
HORIZONTAL_MIXING_FILE = 'none' ,
HORIZONTAL_MIXING_KIND = 'constant' ,
HORIZONTAL_MIXING_COEFFICIENT = 0.2000000 ,
HORIZONTAL_PRANDTL_NUMBER = 1.00000000 ,
VERTICAL_MIXING_TYPE = 'closure' ,
VERTICAL_MIXING_COEFFICIENT = 1.0000E-04 ,
VERTICAL_PRANDTL_NUMBER = 1.000000 ,
BOTTOM_ROUGHNESS_TYPE = 'orig' ,
BOTTOM_ROUGHNESS_KIND = 'constant' ,
BOTTOM_ROUGHNESS_FILE = 'none' ,
BOTTOM_ROUGHNESS_LENGTHSCALE = 0.001 ,
BOTTOM_ROUGHNESS_MINIMUM = 0.0025 ,
CONVECTIVE_OVERTURNING = F,
SCALAR_POSITIVITY_CONTROL = T,
BAROTROPIC = F,
BAROCLINIC_PRESSURE_GRADIENT = 'sigma levels' ,
SEA_WATER_DENSITY_FUNCTION = 'dens2' ,
RECALCULATE_RHO_MEAN = F,
INTERVAL_RHO_MEAN = 'seconds= 1800.0' ,
TEMPERATURE_ACTIVE = T,
SALINITY_ACTIVE = T,
SURFACE_WAVE_MIXING = F,
WETTING_DRYING_ON = T,
ADCOR_ON = F
/
&NML_RIVER_TYPE
RIVER_NUMBER = 3,
RIVER_TS_SETTING = 'specified'
RIVER_INFLOW_LOCATION = 'edge'
RIVER_INFO_FILE = 'RIVERS_NAMELIST.nml'
RIVER_KIND = 'variable',
/
&NML_OPEN_BOUNDARY_CONTROL
OBC_ON = T,
OBC_NODE_LIST_FILE = 'tst_obc.dat' ,
OBC_ELEVATION_FORCING_ON = T,
OBC_ELEVATION_FILE = 'm2_only_1m.nc' ,
OBC_TS_TYPE = 3,
OBC_TEMP_NUDGING = F,
OBC_TEMP_FILE = 'none' ,
OBC_TEMP_NUDGING_TIMESCALE = 0.0000000E+00,
OBC_SALT_NUDGING = F,
OBC_SALT_FILE = 'none' ,
OBC_SALT_NUDGING_TIMESCALE = 0.0000000E+00,
OBC_MEANFLOW = F,
OBC_MEANFLOW_FILE = 'none' ,
OBC_LONGSHORE_FLOW_ON = F,
OBC_LONGSHORE_FLOW_FILE = 'none'
/
&NML_GRID_COORDINATES
GRID_FILE = tst_grd.dat ,
GRID_FILE_UNITS = 'meters' ,
PROJECTION_REFERENCE = 'proj=tmerc +datum=NAD83 +lon_0=-70d10 lat_0=42d50 k=.9999666666666667 x_0=900000 y_0=0'
SIGMA_LEVELS_FILE = 'sigma.dat' ,
DEPTH_FILE = 'tst_dep.dat' ,
CORIOLIS_FILE = 'tst_cor.dat' ,
SPONGE_FILE = 'tst_spg.dat'
/
&NML_GROUNDWATER
GROUNDWATER_ON = F,
GROUNDWATER_TEMP_ON = F,
GROUNDWATER_SALT_ON = F,
GROUNDWATER_KIND = 'none' ,
GROUNDWATER_FILE = 'none' ,
GROUNDWATER_FLOW = 0.0000000E+00,
GROUNDWATER_TEMP = 0.0000000E+00,
GROUNDWATER_SALT = 0.0000000E+00
/
&NML_LAG
LAG_PARTICLES_ON = F,
LAG_START_FILE = 'none' ,
LAG_OUT_FILE = 'none' ,
LAG_FIRST_OUT = 'none' ,
LAG_RESTART_FILE = 'none' ,
LAG_OUT_INTERVAL = 'none' ,
LAG_SCAL_CHOICE = 'none'
/
&NML_ADDITIONAL_MODELS
DATA_ASSIMILATION = F,
DATA_ASSIMILATION_FILE = 'none' ,
BIOLOGICAL_MODEL = F,
STARTUP_BIO_TYPE = 'observed'
SEDIMENT_MODEL = F,
SEDIMENT_MODEL_FILE = 'none' ,
ICING_MODEL = F,
ICING_FORCING_FILE = 'wrf_for.nc' ,
ICING_FORCING_KIND = 'variable' ,
ICING_AIR_TEMP = 0.0000000E+00,
ICING_WSPD = 0.0000000E+00,
ICE_MODEL = F,
ICE_FORCING_FILE = 'none' ,
ICE_FORCING_KIND = 'none' ,
ICE_SEA_LEVEL_PRESSURE = 0.0000000E+00,
ICE_AIR_TEMP = 0.0000000E+00,
ICE_SPEC_HUMIDITY = 0.0000000E+00,
ICE_SHORTWAVE = 0.0000000E+00,
ICE_CLOUD_COVER = 0.0000000E+00
/
&NML_PROBES
PROBES_ON = F,
PROBES_NUMBER = 0,
PROBES_FILE = 'none'
/
&NML_STATION_TIMESERIES
OUT_STATION_TIMESERIES_ON = F,
STATION_FILE = 'none' ,
LOCATION_TYPE = 'node',
OUT_ELEVATION = F,
OUT_VELOCITY_3D = F,
OUT_VELOCITY_2D = F,
OUT_WIND_VELOCITY = F,
OUT_SALT_TEMP = F,
OUT_INTERVAL = 'days= 0.0'
/
&NML_NCNEST
NCNEST_ON = F,
NCNEST_BLOCKSIZE = -1,
NCNEST_NODE_FILES = 'none'
/
&NML_NESTING
NESTING_ON = F,
NESTING_BLOCKSIZE = 120,
NESTING_FILE_NAME = 'node_nest.nc'
/
&NML_BOUNDSCHK
BOUNDSCHK_ON = F,
CHK_INTERVAL = 0,
VELOC_MAG_MAX = 0.0000000E+00,
ZETA_MAG_MAX = 0.0000000E+00,
TEMP_MAX = 0.0000000E+00,
TEMP_MIN = 0.0000000E+00,
SALT_MAX = 0.0000000E+00,
SALT_MIN = 0.0000000E+00
/
&NML_RIVER
RIVER_NAME = 'river1'
RIVER_FILE = 'River_data.nc'
RIVER_GRID_LOCATION = 1569,
RIVER_VERTICAL_DISTRIBUTION = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
/
&NML_RIVER
RIVER_NAME = 'river2'
RIVER_FILE = 'River_data.nc'
RIVER_GRID_LOCATION = 1567,
RIVER_VERTICAL_DISTRIBUTION = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
/
&NML_RIVER
RIVER_NAME = 'river3'
RIVER_FILE = 'River_data.nc'
RIVER_GRID_LOCATION = 1565,
RIVER_VERTICAL_DISTRIBUTION = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1
/
NUMBER OF SIGMA LEVELS = 11
SIGMA COORDINATE TYPE = UNIFORM
!SIGMA COORDINATE TYPE = GEOMETRIC
!SIGMA POWER= 2.0
!SIGMA COORDINATE TYPE = TANH
!DU = 1.0
!DL = 1.0
!SIGMA COORDINATE TYPE = GENERALIZED
DU = 1.0
DL = 1.0
MIN CONSTANT DEPTH = 5.9
KU = 5
KL = 4
ZKU = 4. 5. 3. 7. 9
ZKL = 5. 3. 7. 9
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
OBC Node Number = 25
1 1 1
2 2 1
3 3 1
4 4 1
5 5 1
6 6 1
7 7 1
8 8 1
9 9 1
10 10 1
11 11 1
12 12 1
13 13 1
14 14 1
15 15 1
16 16 1
17 17 1
18 18 1
19 19 1
20 20 1
21 21 1
22 22 1
23 23 1
24 24 1
25 25 1
Sponge Node Number = 2
51 100000. 0.01
12 80000. 0.002
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment