missing bits from the mbp_roles

roles/MonashBioinformaticsPlatform_node_allocation/files/get_node.py

+#!/usr/bin/python
+import subprocess
+import sys
+
+def getTime():
+    print "How long do you think you need this computer for?"
+    print "If you need the computer for 2 days and 12 hours please enter as 2-12 or 2-12:00:00"
+    time=sys.stdin.readline().strip()
+    try:
+        (days,hours)=time.split('-')
+    except:
+        days=0
+        hours=time
+    try:
+        (hours,minues) = time.split(':')
+    except:
+        pass
+    return (days,hours)
+
+def getNCPUs():
+    print "How many CPUs would you like?"
+    cpus=None
+    while cpus==None:
+        cpustr=sys.stdin.readline().strip()
+        try:
+            cpus=int(cpustr)
+        except:
+            print "Sorry I can't interpret %s as a number"%cpustr
+            print "How many CPUs would you like?"
+
+    return cpus
+
+def getRAM():
+    print "How much RAM would you like (press enter for the default)?"
+    ramstr= sys.stdin.readline().strip()
+    while ramstr!=None and ramstr!="":
+            try:
+                ram=int(ramstr)
+                return ram
+            except:
+                print "Sorry I can't interpret %s as a number"%ramstr
+                print "How much RAM would you like?"
+                ramstr= sys.stdin.readline()
+    return None
+
+def subjob(time,cpus,ram):
+    if ram==None:
+        ram=cpus*2000
+    import subprocess
+    scriptpath='/home/chines'
+    p=subprocess.Popen(['sbatch','--time=%s-%s'%(time[0],time[1]),'--nodes=1','--mincpu=%s'%cpus,'--mem=%s'%ram,'%s/mbpjob.sh'%scriptpath],stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+    (stdout,stderr)=p.communicate()
+    import re
+    m=re.match('Submitted batch job (?P<jobid>[0-9]+)',stdout)
+    if m:
+        return m.groupdict()['jobid']
+
+def isState(jobid,state='RUNNING'):
+    import re
+    p=subprocess.Popen(['scontrol','show','job','-d',jobid],stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+    (stdout,stderr)=p.communicate()
+    jobidre=re.compile('JobId=(?P<jobid>[0-9]+)\s')
+    statere=re.compile('^\s+JobState=(?P<state>\S+)\s')
+    currentjobid=None
+    for l in stdout.splitlines():
+        m=jobidre.match(l)
+        if m:
+            currentjobid=m.groupdict()['jobid']
+        m=statere.match(l)
+        if m:
+            if m.groupdict()['state']==state:
+                if jobid==currentjobid:
+                    return True
+            else:
+                if jobid==currentjobid:
+                    return False
+    return False
+
+def waitjob(jobid):
+    import time
+    while True:
+        if isState(jobid,'RUNNING'):
+            return
+        else:
+            print "job %s not running"%jobid
+            time.sleep(1)
+
+def listJobs():
+    import re
+    r=[]
+    user = subprocess.check_output(['whoami'])
+    jobs = subprocess.check_output(['squeue','-u',user,'-h','-o','"%i %L %j %c"'])
+    jobre=re.compile("(?P<jobid>(?P<jobidNumber>[0-9]+)) (?P<time>\S+ (?P<jobname>\S+) (?P<cpus>[0-9]+))$"
+    for l in jobs.splitlines():
+        m=jobidre.search(l)
+        if m:
+            r.append(m.groupdict())
+    return r
+
+def getNode(jobid):
+    import re
+    stdout=subprocess.check_output(['scontrol','show','job','-d',jobid])
+    for l in stdout.splitlines():
+        m=re.search('^\s+Nodes=(?P<nodelist>\S+)\s',l)
+        if m:
+            nodes=m.groupdict()['nodelist'].split(',')
+            return nodes[0]
+
+def createJob(*args,**kwargs):
+    time=getTime()
+    #cpus=getNCPUs()
+    cpus=1
+    #ram=getRAM()
+    ram=None
+    subjob(time,cpus,ram)
+
+def selectJob(jobidlist):
+    if len(jobidlist)==1:
+        return jobidlist[0]['jobid']
+    else:
+        print "Please select a job (or press enter to cancel)"
+        i=1
+        print "\tJob name\tNum CPUs\tRemaining Time"
+        for j in jobidlist:
+            print "%s\t%s\t%s\t%s"%(i,j['jobname'],j['numcpus'],j['time'])
+        try:
+            jobnum=int(sys.stdin.readline().strip())
+            if (jobnum>0 and jobnum<=jobidlist):
+                return jobidlist[jobnum-1]['jobid']
+        except:
+            pass
+    return None
+
+
+def connect(*args,**kwargs):
+    jobidlist=listJobs()
+    jobid=selectJob(jobidlist)
+    if jobid!=None:
+        waitjob(jobid)
+        node=getNode(jobid)
+        print node
+
+def stop(*args,**kwargs):
+    jobidlist=listJobs()
+    jobid=selectJob(jobidlist)
+    if jobid!=None:
+        stopjob(jobid)
+
+
+
+def main():
+    import argparse
+    parser = argparse.ArgumentParser()
+    subparser = parser.add_subparsers()
+
+    start = subparser.add_parser('start', help='alloate a node to the user')
+    start.set_defaults(func=createJob)
+
+    connect = subparser.add_parser('connect')
+    start.set_defaults(func=connect)
+
+    stop = subparser.add_parser('stop')
+    start.set_defaults(func=stop)
+        
+    args = parser.parse_args()
+    args.func(args)
+
+try:
+    jobidlist=listJobs()
+    if len(jobidlist)>1:
+        print "cancel all jobs here"
+    jobidlist=listJobs()
+    if len(jobidlist)==0:
+        time=getTime()
+        #cpus=getNCPUs()
+        cpus=1
+        #ram=getRAM()
+        ram=None
+        subjob(time,cpus,ram)
+    jobidlist=listJobs()
+    if len(jobidlist)==1:
+        jobid=jobidlist[0]
+        waitjob(jobid)
+        node=getNode(jobid)
+        print node
+        sys.exit(0)
+except Exception as e:
+    print e
+    import traceback
+    print traceback.format_exc()
+    sys.exit(1)
+
+main()

roles/MonashBioinformaticsPlatform_node_allocation/files/mbp_node

+#!/bin/bash 
+mpbctrl='/home/hines/mbp_script/get_node.py'
+node=$( $mbpctrl $1 )
+if [[ $node ]]; then
+    ssh -t $node tmux attach-session
+fi

roles/jasons_ssh_ca/tasks/main.yml

 ---
+- include_vars: "{{ ansible_os_family }}_{{ ansible_architecture }}.yml"
+
 - name: copy ca cert
   copy: src=server_ca.pub dest=/etc/ssh/server_ca.pub owner=root group=root mode=644
   sudo: true