add script to run all standalone turbulence generator files on one node

runall_pbs_in_turb.p

+
+### Standard Output
+#PBS -N runall_turb
+#PBS -o ./pbs_out/runall_turb.out
+### Standard Error
+#PBS -e ./pbs_out/runall_turb.err
+#PBS -W umask=0003
+### Maximum wallclock time format HOURS:MINUTES:SECONDS
+#PBS -l walltime=3:00:00
+#PBS -l nodes=1:ppn=20
+### Queue name
+#PBS -q windq
+
+
+echo "----------------------------------------------------------------------"
+echo "activate python environment wetb_py3"
+source /home/python/miniconda3/bin/activate wetb_py3
+echo "CHECK 2x IF wetb_py3 IS ACTIVE, IF NOT TRY AGAIN"
+CMD="from distutils.sysconfig import get_python_lib;print (get_python_lib().find('/usr/lib/python'))"
+ACTIVATED=`python -c "$CMD"`
+if [ $ACTIVATED -eq 0 ]; then source /home/python/miniconda3/bin/activate wetb_py3;fi
+ACTIVATED=`python -c "$CMD"`
+if [ $ACTIVATED -eq 0 ]; then source /home/python/miniconda3/bin/activate wetb_py3;fi
+
+echo "----------------------------------------------------------------------"
+cd /scratch/$USER/$PBS_JOBID/
+echo 'current working directory:'
+pwd
+
+echo "create CPU directories on the scratch disk"
+mkdir -p /scratch/$USER/$PBS_JOBID/simid/
+#mkdir -p /scratch/$USER/$PBS_JOBID/turb/
+#mkdir -p /scratch/$USER/$PBS_JOBID/turb_meand/
+#mkdir -p /scratch/$USER/$PBS_JOBID/turb_micro/
+#mkdir -p /scratch/$USER/$PBS_JOBID/0/
+#mkdir -p /scratch/$USER/$PBS_JOBID/1/
+#mkdir -p /scratch/$USER/$PBS_JOBID/2/
+#mkdir -p /scratch/$USER/$PBS_JOBID/3/
+#mkdir -p /scratch/$USER/$PBS_JOBID/4/
+#mkdir -p /scratch/$USER/$PBS_JOBID/5/
+#mkdir -p /scratch/$USER/$PBS_JOBID/6/
+#mkdir -p /scratch/$USER/$PBS_JOBID/7/
+#mkdir -p /scratch/$USER/$PBS_JOBID/8/
+#mkdir -p /scratch/$USER/$PBS_JOBID/9/
+#mkdir -p /scratch/$USER/$PBS_JOBID/10/
+#mkdir -p /scratch/$USER/$PBS_JOBID/11/
+#mkdir -p /scratch/$USER/$PBS_JOBID/12/
+#mkdir -p /scratch/$USER/$PBS_JOBID/13/
+#mkdir -p /scratch/$USER/$PBS_JOBID/14/
+#mkdir -p /scratch/$USER/$PBS_JOBID/15/
+#mkdir -p /scratch/$USER/$PBS_JOBID/16/
+#mkdir -p /scratch/$USER/$PBS_JOBID/17/
+#mkdir -p /scratch/$USER/$PBS_JOBID/18/
+#mkdir -p /scratch/$USER/$PBS_JOBID/19/
+
+cp -r $PBS_O_WORKDIR/pbs_in_turb /scratch/$USER/$PBS_JOBID/simid/
+
+echo "----------------------------------------------------------------------"
+cd /scratch/$USER/$PBS_JOBID/simid
+echo 'current working directory:'
+pwd
+echo "START RUNNING JOBS IN find+xargs MODE"
+winefix
+# run all the PBS *.p files in find+xargs mode
+export LAUNCH_PBS_MODE=false
+/home/MET/sysalt/bin/find pbs_in_turb/turb/ -type f -name '*.p' | sort -z
+
+echo "number of files to be launched: "`find pbs_in_turb/turb/ -type f | wc -l`
+/home/MET/sysalt/bin/find pbs_in_turb/turb/ -type f -name '*.p' -print0 | sort -z | /home/MET/sysalt/bin/xargs -0 -I{} --process-slot-var=CPU_NR -n 1 -P 20 sh {}
+echo "END OF JOBS IN find+xargs MODE"
+
+echo "----------------------------------------------------------------------"
+echo 'total scratch disk usage:'
+du -hs /scratch/$USER/$PBS_JOBID/
+
+
+echo "----------------------------------------------------------------------"
+# in case wine has crashed, kill any remaining wine servers
+# caution: ALL the users wineservers will die on this node!
+echo "following wineservers are still running:"
+ps -u $USER -U $USER | grep wineserver
+killall -u $USER wineserver
+exit