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StarCluster (view source)

Revision as of 12:56, 29 October 2012

4,807 bytes added ,  12:56, 29 October 2012
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'''Create Your Cluster'''
 
'''Create Your Cluster'''
    +
<code>
 +
  '''starcluster start -c myexample myseq-example'''
 +
  StarCluster - (http://web.mit.edu/starcluster) (v. 0.93.3)
 +
  Software Tools for Academics and Researchers (STAR)
 +
  Please submit bug reports to starcluster@mit.edu
 +
 +
  >>> Validating cluster template settings...
 +
  >>> Cluster template settings are valid
 +
  >>> Starting cluster...
 +
  >>> Launching a 3-node cluster...
 +
  >>> Creating security group @sc-myseq-example...
 +
  Reservation:r-c3b4f6f0
 +
  >>> Waiting for cluster to come up... (updating every 30s)
 +
  >>> Waiting for all nodes to be in a 'running' state...
 +
  3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Waiting for SSH to come up on all nodes...
 +
  3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Waiting for cluster to come up took 1.282 mins
 +
  >>> The master node is ec2-50-112-230-67.us-west-2.compute.amazonaws.com
 +
  >>> Setting up the cluster...
 +
  >>> Configuring hostnames...
 +
  3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Creating cluster user: None (uid: 1001, gid: 1001)
 +
  3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Configuring scratch space for user(s): sgeadmin
 +
  3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Configuring /etc/hosts on each node
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  3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Starting NFS server on master
 +
  >>> Configuring NFS exports path(s):
 +
  /home
 +
  >>> Mounting all NFS export path(s) on 2 worker node(s)
 +
  2/2 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Setting up NFS took 0.096 mins
 +
  >>> Configuring passwordless ssh for root
 +
  >>> Configuring passwordless ssh for sgeadmin
 +
  >>> Shutting down threads...
 +
  20/20 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Configuring SGE...
 +
  >>> Configuring NFS exports path(s):
 +
  /opt/sge6
 +
  >>> Mounting all NFS export path(s) on 2 worker node(s)
 +
  2/2 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Setting up NFS took 0.048 mins
 +
  >>> Installing Sun Grid Engine...
 +
  2/2 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Creating SGE parallel environment 'orte'
 +
  3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Adding parallel environment 'orte' to queue 'all.q'
 +
  >>> Shutting down threads...
 +
  20/20 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Running plugin createusers
 +
  >>> Creating 2 cluster users
 +
  3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Configuring passwordless ssh for 2 cluster users
 +
  2/2 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Configuring scratch space for user(s): mktrost, tpg
 +
  3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100% 
 +
  >>> Tarring all SSH keys for cluster users...
 +
  >>> Copying cluster users SSH keys to: /tmp/myseq-example-us-west-2.tar.gz
 +
  /tmp/myseq-example-us-west-2.tar.gz 100% |||||||||||| Time: 00:00:00  0.00 B/s
 +
  >>> Configuring cluster took 1.583 mins
 +
  >>> Starting cluster took 2.895 mins
   −
'''Login to Master Node'''
+
  The cluster is now ready to use. To login to the master node
 +
  as root, run:
    +
      $ starcluster sshmaster myseq-example
   −
'''What Did This Cost?'''
+
  If you're having issues with the cluster you can reboot the
 +
  instances and completely reconfigure the cluster from
 +
  scratch using:
 +
 
 +
      $ starcluster restart myseq-example
 +
 
 +
  When you're finished using the cluster and wish to terminate
 +
  it and stop paying for service:
 +
 
 +
      $ starcluster terminate myseq-example
 +
 
 +
  Alternatively, if the cluster uses EBS instances, you can
 +
  use the 'stop' command to shutdown all nodes and put them
 +
  into a 'stopped' state preserving the EBS volumes backing
 +
  the nodes:
 +
 
 +
      $ starcluster stop myseq-example
 +
 
 +
  WARNING: Any data stored in ephemeral storage (usually /mnt)
 +
  will be lost!
 +
 
 +
  You can activate a 'stopped' cluster by passing the -x
 +
  option to the 'start' command:
 +
 
 +
      $ starcluster start -x myseq-example
 +
 
 +
  This will start all 'stopped' nodes and reconfigure the
 +
  cluster.
 +
</code>
 +
 
 +
 
 +
'''Set Up Master Node, Login as root'''
 +
 
 +
<code>
 +
  '''starcluster sshmaster myseq-example'''
 +
  StarCluster - (http://web.mit.edu/starcluster) (v. 0.93.3)
 +
  Software Tools for Academics and Researchers (STAR)
 +
    [lines deleted]
 +
 
 +
  #  Install Pipeline software just like says in
 +
  '''mkdir debs'''
 +
  '''cd debs'''
 +
  '''wget ftp://share.sph.umich.edu/biopipe/current-align.deb'''
 +
    [lines deleted]
 +
  '''wget ftp://share.sph.umich.edu/biopipe/current-umake.deb'''
 +
    [lines deleted]
 +
 
 +
  '''dpkg -i debs/current-align*.deb debs/current-umake*amd64.deb'''
 +
    [lines deleted]
 +
</code>
Terry Gliedt
283

edits

Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/5688"

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