From 07aeb8147716b25e823f275a41581bbc7a1b7093 Mon Sep 17 00:00:00 2001
From: Chris Hines <chris.hines@monash.edu>
Date: Fri, 3 Jul 2015 03:19:11 +0000
Subject: [PATCH] missing bits from the mbp_roles
---
.../files/get_node.py | 193 ++++++++++++++++++
.../files/mbp_node | 6 +
roles/jasons_ssh_ca/tasks/main.yml | 2 +
3 files changed, 201 insertions(+)
create mode 100644 roles/MonashBioinformaticsPlatform_node_allocation/files/get_node.py
create mode 100755 roles/MonashBioinformaticsPlatform_node_allocation/files/mbp_node
diff --git a/roles/MonashBioinformaticsPlatform_node_allocation/files/get_node.py b/roles/MonashBioinformaticsPlatform_node_allocation/files/get_node.py
new file mode 100644
index 00000000..e181f0f2
--- /dev/null
+++ b/roles/MonashBioinformaticsPlatform_node_allocation/files/get_node.py
@@ -0,0 +1,193 @@
+#!/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()
diff --git a/roles/MonashBioinformaticsPlatform_node_allocation/files/mbp_node b/roles/MonashBioinformaticsPlatform_node_allocation/files/mbp_node
new file mode 100755
index 00000000..024d535f
--- /dev/null
+++ b/roles/MonashBioinformaticsPlatform_node_allocation/files/mbp_node
@@ -0,0 +1,6 @@
+#!/bin/bash
+mpbctrl='/home/hines/mbp_script/get_node.py'
+node=$( $mbpctrl $1 )
+if [[ $node ]]; then
+ ssh -t $node tmux attach-session
+fi
diff --git a/roles/jasons_ssh_ca/tasks/main.yml b/roles/jasons_ssh_ca/tasks/main.yml
index 1823b183..9f71db4d 100644
--- a/roles/jasons_ssh_ca/tasks/main.yml
+++ b/roles/jasons_ssh_ca/tasks/main.yml
@@ -1,4 +1,6 @@
---
+- 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
--
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