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| >>> Cluster template settings are valid | | >>> Cluster template settings are valid |
| >>> Starting cluster... | | >>> Starting cluster... |
− | >>> Launching a 3-node cluster...
| + | [lines deleted] |
− | >>> Creating security group @sc-myseq-example...
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− | Reservation:r-c3b4f6f0
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− | >>> Waiting for cluster to come up... (updating every 30s)
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− | >>> Waiting for all nodes to be in a 'running' state...
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− | 3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Waiting for SSH to come up on all nodes...
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− | 3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Waiting for cluster to come up took 1.282 mins
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− | >>> The master node is ec2-50-112-230-67.us-west-2.compute.amazonaws.com
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− | >>> Setting up the cluster...
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− | >>> Configuring hostnames...
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− | 3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Creating cluster user: None (uid: 1001, gid: 1001)
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− | 3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Configuring scratch space for user(s): sgeadmin
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− | 3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Configuring /etc/hosts on each node
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− | 3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Starting NFS server on master
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− | >>> Configuring NFS exports path(s):
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− | /home
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− | >>> Mounting all NFS export path(s) on 2 worker node(s)
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− | 2/2 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Setting up NFS took 0.096 mins
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− | >>> Configuring passwordless ssh for root
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− | >>> Configuring passwordless ssh for sgeadmin
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− | >>> Shutting down threads...
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− | 20/20 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Configuring SGE...
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− | >>> Configuring NFS exports path(s):
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− | /opt/sge6
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− | >>> Mounting all NFS export path(s) on 2 worker node(s)
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− | 2/2 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Setting up NFS took 0.048 mins
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− | >>> Installing Sun Grid Engine...
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− | 2/2 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Creating SGE parallel environment 'orte'
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− | 3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Adding parallel environment 'orte' to queue 'all.q'
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− | >>> Shutting down threads...
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− | 20/20 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Running plugin createusers
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− | >>> Creating 2 cluster users
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− | 3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Configuring passwordless ssh for 2 cluster users
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− | 2/2 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Configuring scratch space for user(s): mktrost, tpg
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− | 3/3 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%
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− | >>> Tarring all SSH keys for cluster users...
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− | >>> Copying cluster users SSH keys to: /tmp/myseq-example-us-west-2.tar.gz
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− | /tmp/myseq-example-us-west-2.tar.gz 100% |||||||||||| Time: 00:00:00 0.00 B/s
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− | >>> Configuring cluster took 1.583 mins
| |
− | >>> Starting cluster took 2.895 mins
| |
− | | |
− | The cluster is now ready to use. To login to the master node
| |
− | as root, run:
| |
− | | |
− | $ starcluster sshmaster myseq-example | |
− | | |
− | 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> | | </code> |
| | | |
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| Software Tools for Academics and Researchers (STAR) | | Software Tools for Academics and Researchers (STAR) |
| [lines deleted] | | [lines deleted] |
− | | + | |
| # Install Pipeline software just like says in | | # Install Pipeline software just like says in |
| '''mkdir debs''' | | '''mkdir debs''' |
Line 197: |
Line 110: |
| '''wget ftp://share.sph.umich.edu/biopipe/current-umake.deb''' | | '''wget ftp://share.sph.umich.edu/biopipe/current-umake.deb''' |
| [lines deleted] | | [lines deleted] |
− | | + | |
− | '''dpkg -i debs/current-align*.deb debs/current-umake*amd64.deb''' | + | '''dpkg -i debs/current-align*.deb debs/current-umake*.deb''' |
| [lines deleted] | | [lines deleted] |
| </code> | | </code> |