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job_MLPs.sh
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#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -r n
#$ -j y
#$ -l mem_free=4G
#$ -l arch=linux-x64
##$ -l netapp=5G,scratch=5G
##$ -l netappsali=5G
##$ -l scrapp=500G
##$ -l scrapp2=500G
#$ -l h_rt=335:59:59
#$ -R y
#$ -V
##$ -q lab.q
#$ -l hostname="i*" #-- anything based on Intel cores
##$ -l hostname="!opt*" #-- anything but opt*
##$ -m e #-- uncomment to get email when the job finishes
#$ -pe ompi 6
##$ -t 1
#$ -t 1-20 #-- specify the number of tasks
#$ -N npc_IR
#########################################
#: '#lyre usage : nohup ./job_test.sh 20000 output > job_test.log &
#NSLOTS=20 ## Should be an "EVEN number" or 1
NSLOTS=4 ## Should be an "EVEN number" or 1
SGE_TASK_ID=9191
#'
# load MPI modules
#module load openmpi-1.6-nodlopen
#module load sali-libraries
#mpirun -V
export IMP=setup_environment.sh
MODELING_SCRIPT=modeling_MLPs.py
SAXS_FILE=SAXS.dat
XL_FILE=XL.csv
RMF_FRAME=0
EM2D_FILE=../data/em2d/2.pgm
EM2D_WEIGHT=10000.0
# Parameters
if [ -z $1 ]; then
#REPEAT="10000"
REPEAT="1000"
else
REPEAT="$1"
fi
echo "number of REPEATs = $REPEAT"
if [ -z $2 ]; then
OUTPUT="output"
else
OUTPUT="$2"
fi
echo "OUTPUT foler = $OUTPUT"
echo "SGE_TASK_ID = $SGE_TASK_ID"
echo "JOB_ID = $JOB_ID"
echo "NSLOTS = $NSLOTS"
# write hostname and starting time
hostname
date
let "SLEEP_TIME=$SGE_TASK_ID*2"
#sleep $SLEEP_TIME
PWD_PARENT=$(pwd)
for (( INDEX=2100; INDEX <= 2120; INDEX++ )); do
# write hostname and starting time
echo "INDEX = $INDEX"
hostname
date
DIR=modeling${INDEX}
RMF_FILE=../prefilter/${INDEX}kmeans_10_1/all_models.9/0_1spoke.rmf3
rm -rf $DIR
if [ ! -d $DIR ]; then
mkdir $DIR
cp -pr template/$MODELING_SCRIPT $DIR
#cp -pr template/em2d_nup82.py $DIR
#cp -pr template/representation_nup82.py $DIR
#cp -pr template/crosslinking_nup82.py $DIR
fi
sleep 1
cd $DIR
PWD=$(pwd)
echo $PWD_PARENT : $PWD
if [ $PWD_PARENT != $PWD ]; then
# run the job
#echo "mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT"
#mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT
#mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -sym False -r $REPEAT -out $OUTPUT -refine True -w 50.0 -x ../data/$XL_FILE
#echo "mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT -em2d $EM2D_FILE -weight $EM2D_WEIGHT"
#mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT -em2d $EM2D_FILE -weight $EM2D_WEIGHT
echo "mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT -rmf $RMF_FILE -rmf_n $RMF_FRAME"
mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT -rmf $RMF_FILE -rmf_n $RMF_FRAME > $DIR.log
cd ..
fi
# done
hostname
date
done
for (( INDEX=2200; INDEX <= 2220; INDEX++ )); do
# write hostname and starting time
echo "INDEX = $INDEX"
hostname
date
DIR=modeling${INDEX}
RMF_FILE=../prefilter/${INDEX}kmeans_10_1/all_models.9/0_1spoke.rmf3
rm -rf $DIR
if [ ! -d $DIR ]; then
mkdir $DIR
cp -pr template/$MODELING_SCRIPT $DIR
#cp -pr template/em2d_nup82.py $DIR
#cp -pr template/representation_nup82.py $DIR
#cp -pr template/crosslinking_nup82.py $DIR
fi
sleep 1
cd $DIR
PWD=$(pwd)
echo $PWD_PARENT : $PWD
if [ $PWD_PARENT != $PWD ]; then
# run the job
#echo "mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT"
#mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT
#mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -sym False -r $REPEAT -out $OUTPUT -refine True -w 50.0 -x ../data/$XL_FILE
#echo "mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT -em2d $EM2D_FILE -weight $EM2D_WEIGHT"
#mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT -em2d $EM2D_FILE -weight $EM2D_WEIGHT
echo "mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT -rmf $RMF_FILE -rmf_n $RMF_FRAME"
mpirun -np $NSLOTS $IMP python ./$MODELING_SCRIPT -r $REPEAT -out $OUTPUT -rmf $RMF_FILE -rmf_n $RMF_FRAME > $DIR.log
cd ..
fi
# done
hostname
date
done