reconstruct/run_in_order.sh at master · MatthiasHerrmann/reconstruct · GitHub

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
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
#!/bin/bash

source /beegfs/work/workspace/ws/fr_mh595-conda-0/conda/etc/profile.d/conda.sh
conda activate binenv

REPEATS=100 ### Change to 100 for Normal or 250 for Chem

execute () {    ######## Make sure to change filename in first sed command to 'chem_runall_binac.sh' or just 'runall_binac.sh'

    sed '/reconstruct.py/s/$/'"$STRING"'/' chem_runall_binac.sh > .run_$RESPREFIX.sh
    JOBID=$(qsub -q short -t 1-$REPEATS .run_$RESPREFIX.sh | sed -r 's/^[^0-9]*([0-9]+).*$/\1/')
    echo "Current Task: $JOBID : $STRING"
    echo "$JOBID : $STRING" >> results.txt
}

######IF sed is not used:    JOBID=$(qsub -q short -t 1-$REPEATS runall_binac.sh "$STRING"| sed -r 's/^[^0-9]*([0-9]+).*$/\1/')

report () {
    echo "$STRING" >> results.txt
    python reconstruct.py report --resprefix $RESPREFIX >> results.txt
}

reportchem () {
    echo "$STRING" >> results.txt
    python reconstruct.py reportchem --resprefix $RESPREFIX >> results.txt
}

pass () {
    echo "Passing on: $RESPREFIX"
}


echo "Start: $(date)"
## Parameter Optimization
CIPSELECTOR=2
for PARETO in 'greedy' 'default'; do
    for NORMALIZATION in 0 1; do
        for CIPK in 10; do
            for DECOMPRADIUS in 1 2; do
                for CONTEXTSIZE in 1 2; do
                    for MINCOUNT in 1 2; do
                        for SIZELIMITER in 0 1; do
                            RESPREFIX="$CIPSELECTOR-$CIPK-$CONTEXTSIZE-$MINCOUNT-$SIZELIMITER-$NORMALIZATION-$DECOMPRADIUS-$PARETO"
                            STRING=" --cipselector_option $CIPSELECTOR --pareto_option $PARETO --cipselector_k $CIPK --context_size $CONTEXTSIZE --min_count $MINCOUNT --graph_size_limiter $SIZELIMITER --use_normalization $NORMALIZATION --max_decompose_radius $DECOMPRADIUS --resprefix $RESPREFIX"
#####                            report ##  Replace this with report/execute... HANDLE WITH CARE
                        done
                    done
                done
            done
        done
    done
done
## Chemset Comparison
CIPSELECTOR=2
for PARETOOPTION in 'default' 'greedy'; do
for CONTEXTSIZE in 1 2; do
    for CIPK in 5 10 15 20; do
        RESPREFIX="res_CHEMCOMPARE_pareto-$PARETOOPTION-cipsel-$CIPSELECTOR-cipK-$CIPK-contextsize-$CONTEXTSIZE"
        STRING=" --pareto_option $PARETOOPTION --core_sizes 0 1 2 3 --context_size $CONTEXTSIZE --cipselector_option $CIPSELECTOR --cipselector_k $CIPK --resprefix $RESPREFIX"
#        reportchem
    done
done
done

## Artificial Comparison
CIPSELECTOR=2
CIPK=10
for PARETOOPTION in 'default' 'greedy'; do
for CONTEXTSIZE in 1 2; do
    RESPREFIX="res_cipsel-$CIPSELECTOR-cipk-$CIPK-pareto-$PARETOOPTION-coresizes-012-contextsize-$CONTEXTSIZE"
    STRING=" --cipselector_option $CIPSELECTOR --cipselector_k $CIPK --pareto_option $PARETOOPTION --core_sizes 0 1 2 --context_size $CONTEXTSIZE --resprefix $RESPREFIX"
#    report
    RESPREFIX="res_cipsel-$CIPSELECTOR-cipk-$CIPK-pareto-$PARETOOPTION-coresizes-01-contextsize-$CONTEXTSIZE"
    STRING=" --cipselector_option $CIPSELECTOR --cipselector_k $CIPK --pareto_option $PARETOOPTION --core_sizes 0 1 --context_size $CONTEXTSIZE --resprefix $RESPREFIX"
#    report
    RESPREFIX="res_cipsel-$CIPSELECTOR-cipk-$CIPK-pareto-$PARETOOPTION-coresizes-0-contextsize-$CONTEXTSIZE"
    STRING=" --cipselector_option $CIPSELECTOR --cipselector_k $CIPK --pareto_option $PARETOOPTION --core_sizes 0 --context_size $CONTEXTSIZE --resprefix $RESPREFIX"
#    report
done
done

##########################


for KEEP in 12 30 60; do
    for CIPK in 50 100 250; do
        RESPREFIX="keep-$KEEP-cipk-$CIPK"
        STRING=" --keepgraphs $KEEP --cipselector_option 1 --cipselector_k $CIPK --resprefix $RESPREFIX"
#        report
    done
done


CIPSELECTOR=2
CIPK=10
## Pareto Comparison:
for PARETO in 'random' 'greedy' 'paretogreed' 'pareto_only' 'all' 'default'; do
    RESPREFIX="res_cipsel-$CIPSELECTOR-cipk-$CIPK-pareto-$PARETO"
    RESPREFIX="res_CHEM_cipsel-$CIPSELECTOR-cipk-$CIPK-pareto-$PARETO"
    RESPREFIX="res_MINCOUNT1_cipsel-$CIPSELECTOR-cipk-$CIPK-pareto-$PARETO"
    STRING=" --cipselector_option $CIPSELECTOR --cipselector_k $CIPK --pareto_option $PARETO --resprefix $RESPREFIX"
###    report
done


## Cipselector Comparison Graphs
KEEP=60
#CIP0
###for CIPK in 300 1500 3000 4500 6000 7500 9000; do # KEEP 30
###for CIPK in 100 900 2250 3750 5250 6750 8250; do
###for CIPK in 150 750 1500 2250 3000 3750 4500; do # KEEP 60
for CIPK in 50 450 1125 1875 2625 3375 4125; do
    RESPREFIX="res_keep-$KEEP-cipsel0-$CIPK"
    STRING=" --keepgraphs $KEEP --cipselector_option 0 --cipselector_k $CIPK --pareto_option 'greedy' --resprefix $RESPREFIX"
#    report
done
#CIP1
###for CIPK in 10 50 100 150 200 250 300; do # KEEP 30
###for CIPK in 50 30 75 125 175 225 275; do
###for CIPK in 5 25 50 75 100 125 150; do # KEEP 60
for CIPK in 1 15 38 63 88 113 138; do
    RESPREFIX="res_keep-$KEEP-cipsel1-$CIPK"
    STRING=" --keepgraphs $KEEP --cipselector_option 1 --cipselector_k $CIPK --pareto_option 'greedy' --resprefix $RESPREFIX"
#    report
done
#CIP2
###for CIPK in 10 20 30 40 50 60 70 80 90 100; do # KEEP 30
###for CIPK in 1 2 3 4 5 6 7 8 9; do
###for CIPK in 5 10 15 20 25 30 35 40 45 50; do # KEEP 60
for CIPK in 1 2 3 4 6 7 8 9; do
    RESPREFIX="res_keep-$KEEP-cipsel2-$CIPK"
    STRING=" --keepgraphs $KEEP --cipselector_option 2 --cipselector_k $CIPK --pareto_option 'greedy' --resprefix $RESPREFIX"
#    report
done


######### TESTING #########
RESPREFIX="res_TESTING"
STRING=" --cipselector_option 1 --cipselector_k 100 --pareto_option 'greedy' --resprefix $RESPREFIX"
#report # execute

### 24 Core Test ###
PARETOOPTION='greedy'
for CONTEXTSIZE in 1 2; do
    RESPREFIX="res_24core_CHEMCOMPARE_pareto-$PARETOOPTION-cipsel-2-cipK-10-contextsize-$CONTEXTSIZE"
    STRING=" --pareto_option $PARETOOPTION --core_sizes 0 1 2 3 --context_size $CONTEXTSIZE --cipselector_option 2 --cipselector_k 10 --resprefix $RESPREFIX"
#    reportchem
done