Added .sh and .pbs files

Author: evanmason

prepare_run_eddy_DT10.sh

@@ -0,0 +1,59 @@
+#!/bin/bash
+
+ROOT_DIR="/work/sentinel3/pva_axp/Eddy_Tracking/"
+#DATA_DIR="${ROOT_DIR}/data/sla/DT10/"
+DATA_DIR="${ROOT_DIR}/data/sla/DT10/test/"
+INSTALL_DIR="${ROOT_DIR}/process"
+yaml_template="eddy_tracker_configuration_DT10.yaml"
+
+echo "Looking at data file in ${DATA_DIR}"
+echo "Template yaml configuration file is: ${yaml_template}"
+# Prepare the list of yaml files
+i=0
+for file in $(ls ${DATA_DIR}); do
+    i=$(($i+1))
+    filename=$(basename ${file})
+    datestr=${file:31:8}
+    outyaml="${INSTALL_DIR}/production/sh/eddy_tracker_configuration_${datestr}.yaml"
+    echo "Preparing yaml file for date ${datestr}: ${outyaml}"
+    sed "s/XXXXXXXX/${datestr}/g" ${yaml_template} > ${outyaml}
+    outsh="production/sh/eddy_job_${i}.sh"
+    cmd="python -u ${INSTALL_DIR}/make_eddy_track_AVISO.py ${outyaml}"
+    echo "#!/bin/bash" > ${outsh}
+    echo "${cmd}" >> ${outsh}
+    #echo "echo ${outyaml}" >> ${outsh}
+    chmod u+x ${outsh}
+done
+
+echo "Found ${i} files: preparing array of ${i} jobs"
+
+# Prepare  the PBS script
+
+cat > run_eddy.pbs << EOF 
+
+#!/bin/bash
+#PBS -N pbs_eddy
+#PBS -J 1-${i}
+#PBS -l select=1:ncpus=1:mem=16000mb 
+#PBS -l walltime=24:00:00
+#PBS -m bea
+#PBS -M [email protected]
+
+# repertoire d execution
+module load python/2.7.5
+cd /work/sentinel3/pva_axp/Eddy_Tracking/process
+
+/work/sentinel3/pva_axp/Eddy_Tracking/process/production/sh/eddy_job_\${PBS_ARRAY_INDEX}.sh
+
+EOF
+
+echo "wrote run_eddy.pbs".
+echo "Run command: qsub run_eddy.pbs"
+
+
+    
+
+
+
+
+ 

prepare_run_eddy_DT14.sh

@@ -0,0 +1,58 @@
+#!/bin/bash
+
+ROOT_DIR="/work/sentinel3/pva_axp/Eddy_Tracking/"
+DATA_DIR="${ROOT_DIR}/data/sla/2006/"
+INSTALL_DIR="${ROOT_DIR}/process"
+yaml_template="eddy_tracker_configuration.yaml"
+
+echo "Looking at data file in ${DATA_DIR}"
+echo "Template yaml configuration file is: ${yaml_template}"
+# Prepare the list of yaml files
+i=0
+for file in $(ls ${DATA_DIR}); do
+    i=$(($i+1))
+    filename=$(basename ${file})
+    datestr=${file:24:8}
+    outyaml="${INSTALL_DIR}/production/sh/eddy_tracker_configuration_${datestr}.yaml"
+    echo "Preparing yaml file for date ${datestr}: ${outyaml}"
+    sed "s/XXXXXXXX/${datestr}/g" ${yaml_template} > ${outyaml}
+    outsh="production/sh/eddy_job_${i}.sh"
+    cmd="python -u ${INSTALL_DIR}/make_eddy_track_AVISO.py ${outyaml}"
+    echo "#!/bin/bash" > ${outsh}
+    echo "${cmd}" >> ${outsh}
+    #echo "echo ${outyaml}" >> ${outsh}
+    chmod u+x ${outsh}
+done
+
+echo "Found ${i} files: preparing array of ${i} jobs"
+
+# Prepare  the PBS script
+
+cat > run_eddy.pbs << EOF 
+
+#!/bin/bash
+#PBS -N pbs_eddy
+#PBS -J 1-${i}
+#PBS -l select=1:ncpus=1:mem=16000mb 
+#PBS -l walltime=24:00:00
+#PBS -m bea
+#PBS -M [email protected]
+
+# repertoire d execution
+module load python/2.7.5
+cd /work/sentinel3/pva_axp/Eddy_Tracking/process
+
+/work/sentinel3/pva_axp/Eddy_Tracking/process/production/sh/eddy_job_\${PBS_ARRAY_INDEX}.sh
+
+EOF
+
+echo "wrote run_eddy.pbs".
+echo "Run command: qsub run_eddy.pbs"
+
+
+    
+
+
+
+
+ 

run_eddy.pbs

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+
+#!/bin/bash
+#PBS -N pbs_eddy
+#PBS -J 1-3
+#PBS -l select=1:ncpus=1:mem=16000mb 
+#PBS -l walltime=2:00:00
+#PBS -m bea
+#PBS -M [email protected]
+
+# repertoire d execution
+module load python/2.7.5
+cd /work/sentinel3/pva_axp/Eddy_Tracking/process
+
+/work/sentinel3/pva_axp/Eddy_Tracking/process/production/sh/eddy_job_${PBS_ARRAY_INDEX}.sh
+