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__TOC__
Back to the beginning: [[GotCloud]]
Back to the beginning: [[GotCloud]]
Back to [[GotCloud: Amazon]]
If you have access to your own cluster, your task will be much simpler.
If you have access to your own cluster, your task will be much simpler.
Install the Pipeline software (links at [[GotCloud]])
Install the GotCloud software ([[GotCloud: Source Releases]])
and run it as descibed on the same pages.
and run it as described on the same pages.
For those who are not so lucky to have access to a cluster, Amazon Web Services (AWS) provides an alternative.
For those who are not so lucky to have access to a cluster, Amazon Web Services (AWS) provides an alternative.
You may run the pipeline software on a cluster created in AWS.
You may run the gotcloud software on a cluster created in AWS.
One tool that makes the creation of a cluster of AMIs (Amazon Machine Instances) is
One tool that makes the creation of a cluster of AMIs (Amazon Machine Instances) is
'''StarCluster''' (see http://star.mit.edu/cluster/).
'''StarCluster''' (see http://star.mit.edu/cluster/).
The following shows an example of how you might use ''StarCluster'' to create
The following shows an example of how you might use ''StarCluster'' to create an AWS cluster and set it up to run GotCloud.
There are many details setting up starcluster and this is ''not'' intended to explain all
There are many details setting up starcluster and this is ''not'' intended to explain all
of the many variations you might choose, but should provide you a working example.
of the many variations you might choose, but should provide you a working example.
* Install the ec2 tools package (ec2-api-tools for Ubuntu) on your machine (optional)
== Getting Started With StarCluster ==
* Install and configure starcluster on your machine (required)
StarCluster provides lots of documentation (http://star.mit.edu/cluster/) which will provide more information on it than we have here.
* Create an EBS volume based on the GotCloud snapshot
* Configure StarCluster to use the volume just created
To install and setup StarCluster for the first time, you can follow the QuickStart instructions: http://star.mit.edu/cluster/docs/latest/quickstart.html
* Create an AWS cluster
* Includes installation instructions
* Create storage for your sequence data and make it available for the software
** See http://star.mit.edu/cluster/docs/latest/installation.html for more detailed StarCluster installation instructions if the QuickStart instructions are not enought (especially if running on Windows)
* Run the Pipeline software
* Includes setting up a basic StarCluster configuration file
** You will need your AWS Credentials to setup the configuration file
*** If you need help setting up your AWS credentials, see: [[AWS Credentials]]
You can skip actually starting the cluster in the QuickStart instructions if you want.
''' Troubleshooting: ''' When I tried this, the <code>starcluster start mycluster</code> step failed similar to:
* http://star.mit.edu/cluster/mlarchives/2425.html
* So I followed the suggestions there and at https://github.com/jtriley/StarCluster/issues/455:
*# <pre>$ sudo pip uninstall boto</pre>
*# <pre>$ sudo easy_install boto==2.32.0</pre>
*#* I was having trouble with pip install, but found that easy_install worked
* I had to force terminate mycluster after a failed start:
** <pre> starcluster terminate -f mycluster</pre>
* Then I was able to successfully start my cluster
''' Don't forget to terminate your cluster:'''
starcluster terminate mycluster
== StarCluster and GotCloud ==
=== StarCluster Config Settings ===
By default, StarCluster expects a configuration file in ~/.starcluster/config.
* StarCluster will create a model file for you
Ensure your StarCluster configuration file is set for your usage.
* General AWS Settings:
[aws info]
aws_access_key_id = #your aws access key id here
aws_secret_access_key = #your secret aws access key here
aws_user_id = #your 12-digit aws user id here
* You should have set these in [[#Getting Started With StarCluster|Getting Started With StarCluster]] above (quickstart guide and AWS Credentials) .
* GotCloud Cluster Definition
** You may want to create a new cluster section for running GotCloud (or you can use smallcluster) in your configuration file: <code>~/.starcluster/config</code>
** You can call it anything you want, for example, <pre>gccluster</pre>
** Example:
**: <pre>[cluster gccluster] KEYNAME = mykey CLUSTER_SIZE = 4 CLUSTER_USER = sgeadmin CLUSTER_SHELL = bash MASTER_IMAGE_ID = ami-6ae65e02 NODE_IMAGE_ID = ami-3393a45a NODE_INSTANCE_TYPE = m3.large</pre>
*** Set <code>KEYNAME</code> to the key you want to use
*** Set <code>CLUSTER_SIZE</code> to the number of nodes you want to start up (this may be different than 4)
*** Set <code>CLUSTER_USER</code> to add additional users, like <code>sgeadmin</code>
*** Set <code>CLUSTER_SHELL</code> to define the shell you want to use, like <code>bash</code>
*** Set <code>MASTER_IMAGE_ID</code> to the latest GotCloud AMI, see: [[GotCloud: AMIs]]
**** Contains GotCloud, the reference, and the demo files in the /home/ubuntu/ directory that will be visible on all nodes in the cluster
**** Has a 30G volume, but only 6G available
*** Set <code>NODE_IMAGE_ID</code> to a StarCluster <code>ubuntu x86_64</code> AMI
**** Since each node does not need its own 30G volume containing GotCloud, the reference, and the demo files, we use a separate image for the nodes.
*** The nodes can just access the master's copy of GotCloud, the reference, and the Amazon demo
*** Set <code>NODE_INSTANCE_TYPE</code> to the type of instances you want to start in your cluster
**** See http://aws.amazon.com/ec2/pricing/ for instance descriptions and prices
**** We do not recommend running GotCloud on machines with less than 4MB of memory
** The <code>CLUSTER_SIZE</code> * CPUs in <code>NODE_INSTANCE_TYPE</code> = the number of jobs you can run concurrently in GotCloud
* Define Data Volumes
** By default, the GotCloud AMI contains about 5G of extra space that you can use
*** /home/ubuntu/ directory is visible from all machines
**** Use /home/ubuntu/ for the output directory if it is <5G
**** This directory will be deleted when you terminate the AMI
** Create your Own Volumes and attach them to the GotCloud cluster
*** '''Instructions TBD'''
=== Starting the Cluster ===
# Start the cluster:
#* <pre>starcluster start -c gccluster mycluster</pre>
#** Alternatively, if you can the default template at the start of the configuration file in the <code>[global]</code> section to gccluster: <code>DEFAULT_TEMPLATE=gccluster</code>, you can run:
#*** <pre>starcluster start mycluster</pre>
#* It will take a few minutes for the cluster to start
=== Copying Data to/from the Cluster ===
Copy data onto the cluster (command run from your local machine)
starcluster put /path/to/local/file/or/dir /remote/path/
Pull the data from the cluster onto your local machine (command run from your local machine)
starcluster get /path/to/remote/file/or/dir /local/path/
'''Reminder, if you write your output to /home/ubuntu/, it will be deleted when you terminate the cluster'''
=== Running GotCloud on StarCluster ===
* If you have not already, logon to the cluster as ubuntu:
** <pre>starcluster sshmaster -u ubuntu mycluster</pre>
*** Type <code>yes</code> if the terminal asks if you want to continue connecting
* When running GotCloud:
** Set the cluster/batch type in either configuration or on the command line:
*** In Configuration:
***: <pre>BATCH_TYPE = sgei</pre>
*** On the command-line:
***: <pre>--batchtype sgei</pre>
** Set the number of jobs to run:
**: <pre>--numjobs #</pre>
*** Replace number with the number of concurrent jobs you want to run (probably <code>CLUSTER_SIZE</code> * CPUs in <code>NODE_INSTANCE_TYPE</code>)
** Otherwise, run GotCloud as you normally would.
To login to a specific non-master node, do:
starcluster sshnode -u ubuntu mycluster node001
=== Monitoring Cluster Usage ===
* Monitor jobs in the queue
** <pre>qstat</pre>
** This will show you how the currently running jobs and how they are spread across the nodes in your cluster
**:[[File:Qstat.png|800px]]
*** state descriptions:
**** <code>qw</code> : queued and waiting (not yet assigned to a node)
**** <code>r</code> : running
* View Sun Grid Engine Load
** <pre>qhost</pre>
**:[[File:Qhost.png|600px]]
*** ARCH : architecture
*** NCPU : number of CPUs
*** LOAD : current load
*** MEMTOT : total memory
*** MEMUSE : memory in use
*** SWAPTO : swap space
*** SWAPUS : swap space in use
* View the average load per node using:
** <pre>qstat -f</pre>
**:[[File:Qstatf.png|650px]]
*** <code>load_avg</code> field contains the load average for each node
=== Terminate the Cluster ===
# Reminder, check if you need to copy any data off of the cluster that will be deleted upon termination
#* [[#Copying Data to/from the Cluster|Copying Data to/from the Cluster]]
# Terminate the cluster
#* <pre>starcluster terminate mycluster</pre>
== Run GotCloud Demo Using StarCluster ==
#Create a new cluster section in your configuration file: <code>~/.starcluster/config</code>
#* Add the following to the end of the configuration file:
#*: <pre>[cluster gccluster] KEYNAME = mykey CLUSTER_SIZE = 4 CLUSTER_USER = sgeadmin CLUSTER_SHELL = bash MASTER_IMAGE_ID = ami-6ae65e02 NODE_IMAGE_ID = ami-3393a45a NODE_INSTANCE_TYPE = m3.large</pre>
# Start the cluster:
#* <pre>starcluster start -c gccluster mycluster</pre>
#** Alternatively, if you can the default template at the start of the configuration file in the <code>[global]</code> section to gccluster: <code>DEFAULT_TEMPLATE=gccluster</code>, you can run:
#*** <pre>starcluster start mycluster</pre>
#* It will take a few minutes for the cluster to start
# Logon to the cluster as ubuntu:
#* <pre>starcluster sshmaster -u ubuntu mycluster</pre>
#** Type <code>yes</code> if the terminal asks if you want to continue connecting
{{GotCloud: Amazon Demo Setup|hdr=====}}
==== Run GotCloud SnpCall Demo ====
# Run GotCloud snpcall
#* <pre>gotcloud snpcall --conf example/test.conf --outdir output --numjobs 8 --batchtype sgei</pre>
#** The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found
#** There is enough space in /home/ubuntu to put the Demo output
#*** /home/ubuntu is visible from all nodes in the cluster
#** This will take a few minutes to run.
#** GotCloud first generates a makefile, and then runs the makefile
#** After a while GotCloud snpcall will print some messages to the screen. This is expected and ok.
# See [[#Monitoring Cluster Usage|Monitoring Cluster Usage]] if you are interested in monitoring the cluster usage as GotCloud runs
# When complete, GotCloud snpcall will indicate success/failure
#* Look at the snpcall results, see: [[GotCloud:_Amazon_Demo#Examining_SnpCall_Output|GotCloud: Amazon Demo -> Examining SnpCall Output]]
==== Run GotCloud Indel Demo ====
# Run GotCloud indel
#* <pre>gotcloud indel --conf example/test.conf --outdir output --numjobs 8 --batchtype sgei</pre>
#** The ubuntu user is setup to have the gotcloud program and tools in its path, so you can just type the program name and it will be found
#** There is enough space in /home/ubuntu to put the Demo output
#*** /home/ubuntu is visible from all nodes in the cluster
#** This will take a few minutes to run.
# See [[#Monitoring Cluster Usage|Monitoring Cluster Usage]] if you are interested in monitoring the cluster usage as GotCloud runs
# When complete, GotCloud indel will indicate success/failure
#* Look at the indel results, see: [[GotCloud:_Amazon_Demo#Examining_Indel_Output|GotCloud: Amazon Demo -> Examining Indel Output]]
==== Terminate the Demo Cluster ====
# Exit out of your master node
#* <pre>exit</pre>
# Terminate the cluster
#* Since this is just a demo, we don't have to worry about the data getting deleted upon termination
#* <pre>starcluster terminate mycluster</pre>
#** Answer <code>y</code> to the questions <code>Terminate EBS cluster mycluster (y/n)? </code>
== Old Instructions==
'''StarCluster Configuration Example'''
'''StarCluster Configuration Example'''
AWS_USER_ID=199998888709
AWS_USER_ID=199998888709
AWS_REGION_NAME = us-west-2 # Choose your own region
AWS_REGION_NAME = us-east-1 # Choose your own region
AWS_REGION_HOST = ec2.us-west-2.amazonaws.com
AWS_REGION_HOST = ec2.us-east-1.amazonaws.com
AWS_S3_HOST = s3-us-west-2.amazonaws.com
AWS_S3_HOST = s3-us-east-1.amazonaws.com
###########################
###########################
## EC2 Keypairs
## EC2 Keypairs
###########################
###########################
[key <font color='green'>west2_starcluster</font>]
[key <font color='green'>east1_starcluster</font>]
KEY_LOCATION = ~/.ssh/AWS/west2_starcluster_key.rsa # Same region
KEY_LOCATION = ~/.ssh/AWS/east1_starcluster_key.rsa # Same region
###########################################
###########################################
## Define Cluster
## Define Cluster
## starcluster start -c west2_starcluster nameichose4cluster
## starcluster start -c east1_starcluster nameichose4cluster
###########################################
###########################################
[cluster <font color='red'>myexample</font>] # Name of this cluster definition
[cluster <font color='red'>myexample</font>] # Name of this cluster definition
KEYNAME = <font color='green'>west2_starcluster</font> # Name of keys I need
KEYNAME = <font color='green'>east1_starcluster</font> # Name of keys I need
CLUSTER_SIZE = 4 # Number of nodes
CLUSTER_SIZE = 4 # Number of nodes
CLUSTER_SHELL = bash
CLUSTER_SHELL = bash
# Choose the base AMI using starcluster listpublic
# Choose the base AMI using starcluster listpublic
# (http://star.mit.edu/cluster/docs/0.93.3/faq.html)
# (http://star.mit.edu/cluster/docs/0.93.3/faq.html)
NODE_IMAGE_ID = ami-c6bd30f6
NODE_IMAGE_ID = ami-765b3e1f
AVAILABILITY_ZONE = us-west-2a # Region again!
AVAILABILITY_ZONE = us-east-1 # Region again!
NODE_INSTANCE_TYPE = m1.medium # 4G memory should work for Pipeline
NODE_INSTANCE_TYPE = m1.medium # 4G memory is the minimum for GotCloud
VOLUMES = gotcloud, mydata
VOLUMES = <font color='orange'>gotcloud</font>, <font color='blue'>mydata</font>
[volume mydata]
[volume <font color='blue'>mydata</font>]
VOLUME_ID = vol-6e729657
VOLUME_ID = vol-6e729657
MOUNT_PATH = /mydata
MOUNT_PATH = /mydata
[volume gotcloud]
[volume <font color='orange'>gotcloud</font>]
VOLUME_ID = vol-56071570
VOLUME_ID = vol-56071570
MOUNT_PATH = /gotcloud
MOUNT_PATH = /gotcloud
<code>
<code>
'''starcluster start -c <font color='red'>westcluster</font> myseq-example'''
'''starcluster start -c <font color='red'>myexample</font> myseq-example'''
StarCluster - (http://web.mit.edu/starcluster) (v. 0.93.3)
StarCluster - (http://web.mit.edu/starcluster) (v. 0.93.3)
Software Tools for Academics and Researchers (STAR)
Software Tools for Academics and Researchers (STAR)
>>> Cluster template settings are valid
>>> Cluster template settings are valid
>>> Starting cluster...
>>> Starting cluster...
[lines deleted]
>>> Mounting EBS volume vol-32273514 on /gotcloud...
>>> Mounting EBS volume vol-36788522 on /mydata...
[lines deleted]
[lines deleted]
</code>
</code>
When this completes, you are ready to run the GotCloud software on your data.
Make sure you have defined and mounted volumes for your sequence data and the
output steps of the aligner and umake.
These volumes (as well as /gotcloud) should be available on each node.
<code>
<code>
[lines deleted]
[lines deleted]
'''mkdir debs'''
'''df -h'''
'''ssh node001 df -h'''
'''wget ftp://share.sph.umich.edu/biopipe/current-umake.deb'''
</code>
</code>
If your data is visible on each node, you're ready to run the software as described
in [[GotCloud]].
