-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathjob_OR_refinement_newEM_cytoplasm.sh
executable file
·133 lines (112 loc) · 4.67 KB
/
job_OR_refinement_newEM_cytoplasm.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
#!/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=84
#'
# 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_cytoplasm.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_842_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