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Rosetta wrapper submits and waits properly. Now need to check for exp…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,140 @@ | ||
| #!/usr/bin/env python | ||
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| import pickle | ||
| import datetime | ||
| import shutil | ||
| import optparse | ||
| from sys import * | ||
| import os,sys,re | ||
| from optparse import OptionParser | ||
| import glob | ||
| import subprocess | ||
| from os import system | ||
| import linecache | ||
| import time | ||
| import string | ||
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| #========================= | ||
| def setupParserOptions(): | ||
| parser = optparse.OptionParser() | ||
| parser.set_usage("This program will wait for a rosetta refinement to finish on AWS.") | ||
| parser.add_option("--instanceIDlist",dest="instanceID",type="string",metavar="FILE", | ||
| help="Instance ID list (pickle dump)") | ||
| parser.add_option("--instanceIPlist",dest="instanceIP",type="string",metavar="FILE", | ||
| help="Instance IP list (pickle dump)") | ||
| parser.add_option("--volIDlist",dest="volID",type="string",metavar="FILE", | ||
| help="Volume ID list (pickle dump)") | ||
| parser.add_option("--numModels",dest="numModels",type="int",metavar="INT", | ||
| help="Total number of models in rosetta run") | ||
| parser.add_option("--numPerInstance",dest="numPerInstance",type="int",metavar="Number", | ||
| help="Number of models per instance requested") | ||
| parser.add_option("--outdir",dest='outdir',type="string",metavar='FILE', | ||
| help='Output directory') | ||
| options,args = parser.parse_args() | ||
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| if len(args) > 0: | ||
| parser.error("Unknown commandline options: " +str(args)) | ||
| if len(sys.argv) <= 2: | ||
| parser.print_help() | ||
| sys.exit() | ||
| params={} | ||
| for i in parser.option_list: | ||
| if isinstance(i.dest,str): | ||
| params[i.dest] = getattr(options,i.dest) | ||
| return params | ||
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| #================================================ | ||
| if __name__ == "__main__": | ||
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| params=setupParserOptions() | ||
| startTime=datetime.datetime.utcnow() | ||
| startday=now.day | ||
| starthr=now.hour | ||
| startmin=now.minute | ||
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| keypair=subprocess.Popen('echo $KEYPAIR_PATH',shell=True, stdout=subprocess.PIPE).stdout.read().strip() | ||
| time.sleep(60) | ||
| loadMin=5 | ||
| #Read in pickle files | ||
| with open (params['instanceIP'], 'rb') as fp: | ||
| instanceIPlist = pickle.load(fp) | ||
| with open (params['volID'], 'rb') as fp: | ||
| volIDlist = pickle.load(fp) | ||
| with open (params['instanceID'], 'rb') as fp: | ||
| instanceIDlist = pickle.load(fp) | ||
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| l='%s/rosetta.out' %(params['outdir']) | ||
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| cmd="echo 'Starting to check status of Rosetta refinement at %sUTC' >> %s" %(startTime.strftime('%Y-%m-%dT%H:%M:00'),l) | ||
| subprocess.Popen(cmd,shell=True).wait() | ||
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| os.makedirs('%s/output' %(params['outdir'])) | ||
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| counter=0 | ||
| instanceCounter=1 | ||
| while counter < len(instanceIPlist): | ||
| isdone=0 | ||
| while isdone == 0: | ||
| #If cloudwatch has load < 5% BUT there aren't finished PDBs yet, job crashed. Terminate. | ||
| currentTime=datetime.datetime.utcnow() | ||
| if os.path.exists('%s/cloudwatchtmp.log'%(params['outdir'])): | ||
| os.remove('%s/cloudwatchtmp.log'%(params['outdir'])) | ||
| cmd='aws cloudwatch get-metric-statistics --metric-name CPUUtilization --start-time %s --period 300 --namespace AWS/EC2 --statistics Average --dimensions Name=InstanceId,Value=%s --end-time %s > %s/cloudwatchtmp.log' %(startTime.strftime('%Y-%m-%dT%H:%M:00'),instanceIDlist[counter],currentTime.strftime('%Y-%m-%dT%H:%M:00'),params['outdir']) | ||
| subprocess.Popen(cmd,shell=True).wait() | ||
| o1=open('%s/cloudwatchtmp.log'%(params['outdir']),'r') | ||
| for line in o1: | ||
| if len(line.split())>0: | ||
| if line.split()[0] == '"Average":': | ||
| load=float(line.split()[1][:-1]) | ||
| cmd="echo 'Current load on instance %i is %f at %sUTC' >> %s" %(counter+1,load,currentTime.strftime('%Y-%m-%dT%H:%M:00'),l) | ||
| subprocess.Popen(cmd,shell=True).wait() | ||
| if load < loadMin: | ||
| #Download all pdb files, take note if you didn't download enough files consdiering number of models requested | ||
| isdone=1 | ||
| cmd='echo "--------> Instance %i finished at %sUTC" >> %s' %(counter+1,currentTime.strftime('%Y-%m-%dT%H:%M:00'),l) | ||
| subprocess.Popen(cmd,shell=True).wait() | ||
| currCounter=1 | ||
| while currCounter <= params['numPerInstance']: | ||
| cmd='scp -q -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -i %s ubuntu@%s:~/S_%i_0001.pdb %s/output/S_%i_0001.pdb' %(keypair,instanceIPlist[counter],currCounter,params['outdir'],instanceCounter) | ||
| subprocess.Popen(cmd,shell=True).wait() | ||
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| cmd='scp -q -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -i %s ubuntu@%s:~/score_%i.sc %s/output/S_%i_0001_score.sc' %(keypair,instanceIPlist[counter],currCounter,params['outdir'],instanceCounter) | ||
| subprocess.Popen(cmd,shell=True).wait() | ||
| instanceCounter=instanceCounter+1 | ||
| currCounter=currCounter+1 | ||
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| cmd='aws ec2 terminate-instances --instance-ids %s > %s/tmp4949585940.txt' %(instanceIDlist[counter],params['outdir']) | ||
| subprocess.Popen(cmd,shell=True).wait() | ||
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| o1.close() | ||
| os.remove('%s/cloudwatchtmp.log'%(params['outdir'])) | ||
| time.sleep(60) | ||
| counter=counter+1 | ||
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| cmd='echo "Rosetta refinement finished. Shutting down instances %s" >> %s' %(currentTime.strftime('%Y-%m-%dT%H:%M:00'),l) | ||
| subprocess.Popen(cmd,shell=True).wait() | ||
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| counter=0 | ||
| while counter < len(instanceIPlist): | ||
| isdone=0 | ||
| while isdone == 0: | ||
| status=subprocess.Popen('aws ec2 describe-instances --instance-ids %s --query "Reservations[*].Instances[*].{State:State}" | grep Name'%(instanceIDlist[counter]),shell=True, stdout=subprocess.PIPE).stdout.read().strip().split()[-1].split('"')[1] | ||
| if status == 'terminated': | ||
| isdone=1 | ||
| time.sleep(10) | ||
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| cmd='aws ec2 delete-volume --volume-id %s > %s/tmp4949585940.txt' %(volIDlist[counter],params['outdir']) | ||
| subprocess.Popen(cmd,shell=True).wait() | ||
| counter=counter+1 | ||
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| #now=datetime.datetime.now() | ||
| #finday=now.day | ||
| #finhr=now.hour | ||
| #finmin=now.minute | ||
| #if finday != startday: | ||
| # finhr=finhr+24 | ||
| #deltaHr=finhr-starthr | ||
| #if finmin > startmin: | ||
| # deltaHr=deltaHr+1 | ||
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