| Line 91: |
Line 91: |
| | >>> 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...
| |
| − | 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
| |
| − | 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
| |
| − | | |
| − | 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> |
| | | | |
| Line 189: |
Line 102: |
| | 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> |
