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job_OR_refinement_newEM_nucleoplasm.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=8 ## Should be an "EVEN number" or 1
#NSLOTS=1 ## Should be an "EVEN number" or 1
SGE_TASK_ID=861
#'
# load MPI modules
#module load openmpi-1.6-nodlopen
#module load sali-libraries
#mpirun -V
export IMP=setup_environment.sh
#MODELING_SCRIPT=modeling_outer_ring_refinement.py
#MODELING_SCRIPT=modeling_outer_ring_refinement82.py
#MODELING_SCRIPT=modeling_outer_ring_refinement82_n133n120.py
MODELING_SCRIPT=modeling_outer_ring_refinement82_n133n120_newEM_nucleoplasm.py
SAXS_FILE=SAXS.dat
XL_FILE=XL.csv
#RMF_FILE=../data_npc/Outer_ring_rmfs/OuterRing_0.rmf3
#RMF_FILE=../data_npc/Outer_ring_rmfs/OuterRing_refine1.rmf3
#RMF_FILE=../data_npc/Outer_ring_rmfs/OuterRing_refine2.rmf3
RMF_FILE=../data_npc/Outer_ring_rmfs/OR_846_0_best_newEM.rmf3
RMF_FRAME=0
EM2D_FILE=../data/em2d/2.pgm
EM2D_WEIGHT=10000.0
# Parameters
if [ -z $1 ]; then
REPEAT="5000"
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)
i=$(expr $SGE_TASK_ID)
DIR=modeling$i
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
cd ..
fi
# done
hostname
date
#exit -1
################################################################################
#cd $OUTPUT
#process_output.py -f modeling2/output/stat.0.out -s ISDCrossLinkMS_Distance_interrb_13-State:0-127:Cul5_80:EloC-1-1-1.0_DSS ISDCrossLinkMS_Score_interrb_13-State:0-127:Cul5_80:EloC-1-1-1.0_DSS ISDCrossLinkMS_PriorSig_Score_DSS ISDCrossLinkMS_Sigma_1_DSS
#process_output.py -f modeling2/output/stat.1.out -s ISDCrossLinkMS_Distance_interrb_13-State:0-127:Cul5_80:EloC-1-1-1.0_DSS ISDCrossLinkMS_Score_interrb_13-State:0-127:Cul5_80:EloC-1-1-1.0_DSS ISDCrossLinkMS_PriorSig_Score_DSS ISDCrossLinkMS_Sigma_1_DSS
#process_output.py -f modeling2/output/stat.0.out -n 1
#process_output.py -f modeling2/output/stat.0.out -p
################################################################################
### searching for correlationo of the pdb file with rmf file / output log file
################################################################################
#process_output.py -f modeling2/output/stat.0.out -s SimplifiedModel_Total_Score_None ISDCrossLinkMS_Data_Score_scEDC ElectronMicroscopy2D_None Stopwatch_None_delta_seconds rmf_file rmf_frame_index
#process_output.py -f modeling2/output/stat.0.out -s SimplifiedModel_Total_Score_None ISDCrossLinkMS_Data_Score_scEDC ElectronMicroscopy2D_None Stopwatch_None_delta_seconds
#process_output.py -f modeling2/pre-EM2D_output/stat.0.out -s SimplifiedModel_Total_Score_None ISDCrossLinkMS_Data_Score_scEDC Stopwatch_None_delta_seconds
#process_output.py -f modeling2/output/stat.0.out -s SimplifiedModel_Total_Score_None rmf_file rmf_frame_index | grep 103.147
#rmf_slice 29.rmf3 n82_r29_f1445.rmf3 -f 1445 -s 1000000
#em2d_single_score model.0.pdb -r 20 -s 3.23 -n 400 -c *.pgm