|
0
|
1 #!/bin/bash
|
|
|
2
|
|
|
3 # PIDs are not re-used until PID_MAX_DEFAULT is reached.
|
|
|
4
|
|
|
5 #requirement for the workflow
|
|
|
6 #source /home/galaxy-bitlab/galaxy/tools/proteindocking/scripts/ADT_VENV/bin/activate
|
|
|
7
|
|
|
8
|
|
|
9 # Reads a text file with commands to execute
|
|
|
10 if [ $# -lt 1 ]; then
|
|
|
11 echo " ==== ERROR ... ====."
|
|
|
12 echo ""
|
|
|
13 echo " usage: $0 <execution file> [max cores]"
|
|
|
14 echo ""
|
|
|
15 echo " MANDATORY <execution file>: a text file containing one command per line"
|
|
|
16 echo " OPTIONAL [max cores] : number of cores to use. Default is available cores minus one"
|
|
|
17 echo ""
|
|
|
18 exit -1
|
|
|
19 fi
|
|
|
20
|
|
|
21 input=$1
|
|
|
22 cores=$(grep -c ^processor /proc/cpuinfo)
|
|
|
23 cores=`expr $cores - 1`
|
|
|
24 current_jobs=0
|
|
|
25 pidArray=()
|
|
|
26 jobsArray=()
|
|
|
27 totalJobs=0
|
|
|
28 executedJobs=0
|
|
|
29 finishedJobs=0
|
|
|
30
|
|
|
31 if [ $# -eq 2 ]; then
|
|
|
32 cores=$2
|
|
|
33 fi
|
|
|
34
|
|
|
35 echo "Using $cores cores"
|
|
|
36
|
|
|
37
|
|
|
38 #initialize
|
|
|
39 for ((i=0 ; i < $cores ; i++))
|
|
|
40 do
|
|
|
41 pidArray[$i]=-1
|
|
|
42 done
|
|
|
43
|
|
|
44 # read execution guide and launch jobs
|
|
|
45 while IFS= read -r var
|
|
|
46 do
|
|
|
47
|
|
|
48 jobsArray[$totalJobs]=$var
|
|
|
49 #echo "${jobsArray[$totalJobs]}"
|
|
|
50 totalJobs=`expr $totalJobs + 1`
|
|
|
51
|
|
|
52 done < "$input"
|
|
|
53
|
|
|
54
|
|
|
55 # control them and only launch as many as specified
|
|
|
56 while [[ $executedJobs -lt $totalJobs || $finishedJobs -lt $totalJobs ]]; do
|
|
|
57
|
|
|
58 # Execute job
|
|
|
59
|
|
|
60 if [[ $current_jobs -lt $cores ]]; then
|
|
|
61
|
|
|
62 ${jobsArray[$executedJobs]} &
|
|
|
63 pid=$!
|
|
|
64 for ((i=0 ; i < $cores ; i++))
|
|
|
65 do
|
|
|
66
|
|
|
67
|
|
|
68 if [[ ${pidArray[$i]} -eq -1 && $executedJobs -lt $totalJobs ]]; then
|
|
|
69 pidArray[$i]=$pid
|
|
|
70 current_jobs=`expr $current_jobs + 1`
|
|
|
71 echo "PID: $pid JOBS: $current_jobs LAUNCHING: ${jobsArray[$executedJobs]}"
|
|
|
72 executedJobs=`expr $executedJobs + 1`
|
|
|
73 break
|
|
|
74 fi
|
|
|
75 done
|
|
|
76
|
|
|
77
|
|
|
78 fi
|
|
|
79
|
|
|
80 for ((i=0 ; i < $cores ; i++))
|
|
|
81 do
|
|
|
82 pid=${pidArray[$i]}
|
|
|
83 if [[ $pid -ne -1 ]]; then
|
|
|
84
|
|
|
85 ps -p $pid > /dev/null
|
|
|
86 if [[ $? == 1 ]]; then
|
|
|
87 current_jobs=`expr $current_jobs - 1`
|
|
|
88 finishedJobs=`expr $finishedJobs + 1`
|
|
|
89 echo "PID: $pid finished! Completed: $finishedJobs from total: $totalJobs"
|
|
|
90 pidArray[$i]=-1
|
|
|
91 fi
|
|
|
92
|
|
|
93 fi
|
|
|
94 done
|
|
|
95
|
|
|
96 sleep .01
|
|
|
97
|
|
|
98 done
|
|
|
99
|
|
|
100
|
|
|
101 #deactivate
|
|
|
102
|
|
|
103
|
|
|
104 #for job in `jobs -p`
|
|
|
105 #do
|
|
|
106 #echo $job
|
|
|
107 # wait $job
|
|
|
108 #done
|
