Commit c773b9fc authored by Pierre Cazenave's avatar Pierre Cazenave

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
This diff is collapsed.
&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