Provided by: gbrowse_2.56+dfsg-10build1_all 
NAME
gbrowse_aws_balancer.pl - Load balance GBrowse using Amazon Web Service instances
SYNOPSIS
Launch the balancer in the foreground
% gbrowse_aws_balancer.pl --conf /etc/gbrowse2/aws_balancer.conf \
--access_key XYZZY \
--secret_key Plugh
Launch the balancer in the background as a daemon:
% gbrowse_aws_balancer.pl --background \
--conf /etc/gbrowse2/aws_balancer.conf \
--access_key XYZZY \
--secret_key Plugh \
--logfile /var/log/gbrowse/aws_balancer.log \
--pidfile /var/run/aws_balancer.pid \
--user nobody
Kill a running balancer daemon:
% gbrowse_aws_balancer.pl --kill \
--conf /etc/gbrowse2/aws_balancer.conf \
--access_key XYZZY \
--secret_key Plugh \
--logfile /var/log/gbrowse/aws_balancer.log \
--pidfile /var/run/aws_balancer.pid \
--user nobody
Use the init script:
% sudo /etc/init.d/gbrowse-aws-balancer start
% sudo /etc/init.d/gbrowse-aws-balancer restart
% sudo /etc/init.d/gbrowse-aws-balancer stop
% sudo /etc/init.d/gbrowse-aws-balancer status
Synchronize the master with the slave image:
% sudo gbrowse_sync_aws_slave.pl -c /etc/gbrowse2/aws_balancer.conf
syncing data....done
data stored in snapshot(s) snap-12345
updated conf file, previous version in /etc/gbrowse2/aws_balancer.conf.bak
DESCRIPTION
This script launches a process that monitors the load on the local GBrowse instance. If
the load exceeds certain predefined levels, then it uses Amazon web services to launch one
or more GBrowse slave instances. The work of rendering tracks is then handed off to these
instances, reducing the load on the local instance. Slave instances are implemented using
Amazon's spot instance mechanism, which allows you to run EC2 instances at a fraction of
the price of a standard on-demand instance.
Load balancing is most convenient to run in conjunction with a GBrowse instance running
within the Amazon Web Service EC2 cloud, but it can also be used to supplement an instance
running on local hardware. The sections below describe the configuration needed for these
two scenarios.
Note that this script requires you to have an Amazon Web Services account, and for the
VM::EC2 Perl module to be installed on the machine that is running this script.
COMMAND-LINE OPTIONS
Options can be abbreviated. For example, you can use -a for --access_key:
--access_key EC2 access key
--secret_key EC2 secret key
--conf Path to balancer configuration file
--pidfile Path to file that holds daemon process ID
--logfile Path to file that records log messages
--user User to run daemon under (script must be
started as root)
--verbosity Logging verbosity. 0=least, 3=most.
--background Go into the background and run as daemon.
--kill Kill a previously-launched daemon. Must provide
the same --pidfile argument as used when
the daemon was started.
--ssh_key Enable ssh login on the slave(s) using the specified
AWS ssh keypair. Login will only be available
from the host this script is run on.
PREREQUISITES
1. You must have the Perl modules VM::EC2 (v1.21 or later), and
Parse::Apache::ServerStatus installed on the machine you intend to run the balancer on.
The balancer must run on the same machine that GBrowse is running on. To install these
modules, run:
perl -MCPAN -e 'install VM::EC2; install Parse::Apache::ServerStatus'
2. You must have an account on Amazon Web Services and must be familiar with using the AWS
Console to launch and terminate EC2 instances. If you run GBrowse on local hardware, then
you will need to provide the script with your access key and secret access key when
launching it. It may be safer to create and use an IAM user (Identity and Access
Management) who has more limited privileges. See CONFIGURATION below for some suggestions.
3. GBrowse must be running under Apache.
4. Apache must be configured to enable the mod_status module and to allow password-less
requests to this module from localhost
(http://httpd.apache.org/docs/2.2/mod/mod_status.html). This is the recommended
configuration:
<IfModule mod_status.c>
ExtendedStatus on
<Location /server-status>
SetHandler server-status
Order deny,allow
Deny from all
Allow from 127.0.0.1 ::1
</Location> </IfModule>
5. If you are running GBrowse on local hardware, the local hardware must be connected to
the Internet or have a Virtual Private Cloud (VPC) connection to Amazon.
THE CONFIGURATION FILE
The balancer requires a configuration file, ordinarily named aws_balancer.conf and located
in the GBrowse configuration directory (e.g. /etc/gbrowse2). The configuration file has
three sections:
[LOAD TABLE]
This section describes the number of slave instances to launch for different load levels.
It consists of a three-column space-delimited table with the following columns:
<requests/sec> <min instances> <max instances>
For example, the first few rows of the default table reads:
0.1 0 1
0.5 0 2
1.0 1 3
2.0 2 4
This is read as meaning that when the number of requests per second on the GBrowse server
is greater than 0.1 but less than 0.5, run at least 0 slave servers but no more than 1
slave server. When the number of requests is between 0.5 and 1.0, run between 0 and 2
slave instances. When the rate is between 1.0 and 2.0, run at least 1 slave instance, but
no more than 3. Load levels below the lowest value on the table (0.1 in this case) will
run no slave servers, while levels above the highest value on the table (2.0) will launch
the minimum and maximum number of slaves for that load value (between 2 and 4 in this
case).
The reason for having a range of instance counts for each load range is to avoid
unecessarily launching and killing slaves repeatedly when the load fluctuates around the
boundary. You may wish to tune the values in this table to maximize the performance of
your GBrowse installation.
Note that the server load includes both GBrowse requests and all other requests on the web
server. If this is a problem, you may wish to run GBrowse on a separate Apache port or
virtual host.
[MASTER]
The options in this sections configure the master GBrowse instance. Three options are
recognized:
external_ip (optional)
This controls the externally-visible IP address of the GBrowse master, which is needed
by the firewall rule for master/slave communications. This option can usually be left
blank: when the master is running on EC2, then the IP address is known; when the
master is running on a local machine, the externally-visible IP address is looked up
using a web service. It is only in the rare case that this lookup is incorrect that
you will need to configure this option yourself.
The external IP that the balancer script finds can be seen in a log message when
verbosity is 2 or higher.
poll_interval (required)
This is the interval, in minutes, that the balancer script will periodically check the
Apache load and adjust the number of slave instances. The suggested value is 0.5 (30s
intervals).
server_status_url (required)
This is the URL to call to fetch the server load from Apache's server_status module.
[SLAVE]
The options in this section apply to the render slaves launched by the balancer.
instance_type (required)
This is the EC2 instance type. Faster instances give better performance. High-IO
instances give the best performance, but cost more.
spot_bid (required)
This is the maximum, in US dollars, that you are willing to pay per hour to run a
slave spot instance. Typically you will pay less than the bid price. If the spot price
increases beyond the maximum bid, then the spot instances will be terminated and the
balancer will wait until the spot price decreases below the maximum bid before
launching additional slaves.
ports (required)
This is a space-delimited list of TCP port numbers on which the render slaves should
listen for incoming render requests from the master. Generally it is only necessary to
listen on a single port; multiple ports were supported for performance reasons in
earlier single-threaded versions of the slave.
region (required for local masters)
The Amazon region in which to launch slaves. When the master is running in EC2, this
is automatically chosen to be the same as the master's region and can be left blank.
image_id (required for local masters)
This is the ID of the AMI that will be used to launch slaves. The correct value will
be filled in when you run the gbrowse_sync_aws_slave.pl. You can leave this value
blank if the GBrowse master is being run within an EC2 instance, in which case the
slave will be launched using the same AMI that was used to launch the master.
data_snapshots (required for local masters)
Before launching the slave, attach EBS volumes created from one or more volume
snapshots listed in this option. Multiple snapshots can be attached by providing a
space-delimited list:
data_snapshots = snap-12345 snap-abcdef
The gbrowse_sync_aws_slave.pl script will automatically maintain this option for you.
availability_zone (optional)
This option will force the slave into the named availability zone. If not specified,
an availability zone in the current region will be chosen at random.
subnet (optional)
If you are in a VPC environment, then this option will force the slave into the named
subnet. Ordinarily the balancer script will launch slaves into non-VPC instances if
the master is running on local hardware or a non-VPC EC2 instance. The balancer will
launch slaves into the same VPC subnet as the master if the master is running on a VPC
instance.
security_group (optional)
This specifies the security group to assign the slaves to. If not specified, a
properly-configured security group will be created as needed and destroyed when the
balancer script exits. If you choose to manage the security group manually, be sure to
configure the firewall ingress rule to allow access to the slave port(s) (see the
"ports" option) from the master's group or IP address.
CONFIGURING AWS CREDENTIALS
To work, the balancer script must be able to make spot instance requests and to monitor
and terminate instances. To perform these operations the script must have access to the
appropriate AWS credentials (access key and secret key) on the command line or as
environment variables.
While the script does its best to shield the credentials from prying eyes, there is still
a chance that the credentials can be intercepted by another party with login access to the
machine that the master runs on and use the credentials to run up your AWS bill. For this
reason some people will prefer to create an EC2 account or role with limited access to AWS
resources.
1. Your personal EC2 credentials
You may provide the balancer script with --access_key and --secret_key command line
arguments using your personal EC2 credentials or set the environment variables
EC2_ACCESS_KEY and EC2_SECRET_KEY. If not provided, the script will interactively
prompt for one or both of these values.
This is the simplest method, but has the risk that if the credentials are intercepted
by a malicious third party, he or she gains access to all your EC2 resources.
2. The credentials of a restricted IAM account
You may use the Amazon AWS console to create an IAM (Identity Access and Management)
user with restricted permissions, and provide that user's credentials to the script on
the command line or with environment variables. The following IAM permission policy is
the minimum needed for the balancer script to work properly:
{
"Statement": [
{
"Sid": "BalancerPolicy",
"Action": [
"ec2:AuthorizeSecurityGroupEgress",
"ec2:AuthorizeSecurityGroupIngress",
"ec2:CreateSecurityGroup",
"ec2:DeleteSecurityGroup",
"ec2:DescribeAvailabilityZones",
"ec2:DescribeImageAttribute",
"ec2:DescribeImages",
"ec2:DescribeInstances",
"ec2:DescribeInstanceAttribute",
"ec2:DescribeInstanceStatus",
"ec2:DescribeSecurityGroups",
"ec2:DescribeVolumes",
"ec2:DescribeSnapshots",
"ec2:DescribeSpotInstanceRequests",
"ec2:RequestSpotInstances",
"ec2:CreateKeyPair",
"ec2:DescribeKeyPairs",
"ec2:DeleteKeyPair",
"ec2:RunInstances",
"ec2:TerminateInstances",
"ec2:CreateSnapshot",
"ec2:CreateVolume",
"ec2:CreateTags",
"ec2:DeleteTags"
],
"Effect": "Allow",
"Resource": [
"*"
]
}
]
}
Note that even with these restrictions, an unauthorized user with access to the
credentials could still launch a large number of spot instances or terminate bona fide
instances. This is just a fundamental limitation of the granularity of EC2's
permissions system.
3. Create an IAM role
If the master is running on an EC2 instance, then the most convenient way to pass
credentials is by assigning the instance an IAM role. The balancer script can then
obtain temporary credentials by making internal EC2 calls. The credentials do not need
to be provided on the command line or in environment variables, and are only valid for
short periods of time, limiting the effect of theft.
First, create an IAM role using the Amazon Console. Select IAM->Roles->Create New
Role, and give the role the name "GBrowseMaster" (or whatever you prefer).
Next, when prompted for the role type, select AWS Service Roles->Amazon EC2.
On the Select Role Permissions screen, choose "Custom Policy". Give the policy a name
like "GBrowseBalancer" and cut and paste into the Policy Document text field the
permission policy listed above in the instructions for creating a restriced IAM
account. Be sure to remove the whitespace before the beginning of the first curly
brace, or the console will complain about an invalid policy.
You only need to do this once. After this, whenever you launch an instance that will
run the GBrowse master (typically from a GBrowse AMI), specify the "GBrowseMaster" IAM
role name. This can be done from the AWS console's instance launch wizard, or by
passing the -p option to the ec2-run-instances command-line tool.
USING THE INIT SCRIPT
The gbrowse-aws-balancer init script can be used on Ubuntu and Debian-based systems to
simplify launching the balancer at boot time. It can be found in /etc/init.d by default,
and is called in the following manner:
start the service
% sudo /etc/init.d/gbrowse-aws-balancer start
stop the service
% sudo /etc/init.d/gbrowse-aws-balancer stop
stop and restart the service
% sudo /etc/init.d/gbrowse-aws-balancer restart
show the status of the service (running, stopped)
% sudo /etc/init.d/gbrowse-aws-balancer status
The various script options are all set in a single configuration file named
/etc/default/gbrowse-aws-balancer. The distribution contents of this file looks like this:
DAEMON=/usr/local/bin/gbrowse_aws_balancer.pl
USER=www-data
RUNDIR=/var/run/gbrowse
LOGDIR=/var/log/gbrowse
CONFFILE=/etc/gbrowse2/aws_balancer.conf
ACCESS_KEY=YOUR_EC2_ACCESS_KEY_HERE
SECRET_KEY=YOUR_EC2_SECRET_KEY_HERE
VERBOSITY=3
The variables in this file set the location of the balancer script, the location of its
configuration file, the verbosity to run with, and where to write the script's process ID
and log information. In addition, you can place your (or another authorized user's) EC2
access and secret key in this file. Please make sure that this file is only readable by
root.
DEBUGGING SLAVE PROBLEMS
If slaves are returning track renderinge errors, then there is likely an issue with data
synchronization. This typically happens when the data on the master differs from the data
on the slave, or path names are different on the two systems.
To debug this, launch the script with the -ssh_key option:
% gbrowse_aws_balancer.pl --conf /etc/gbrowse2/aws_balancer.conf \
--access_key XYZZY \
--secret_key Plugh \
--ssh_key John_Doe_default
You may then ssh into the slave using the specified ssh key and the username "admin". A
useful thing to do is to tail the slave log file:
ssh -i .ssh/John_Doe_default admin@54.280.19.203 \
tail -f /var/log/gbrowse/gbrowse_slave
Replace the IP number with the correct IP number of one of the running slaves, which you
can find in /etc/gbrowse2/renderfarm.conf.
THE GBROWSE_SYNC_AWS_SLAVE.PL SCRIPT
The gbrowse_sync_aws_script.pl script should be run on the master each time you add a new
database to an existing data source, or if you add a whole new data source. What it does
is to prepare a new Amazon EBS snapshot containing a copy of all the data needed for the
GBrowse slave to run. This snapshot is then attached to new slave instances.
After running, it updates the conf file with the current versions of the slave AMI and the
data snapshot.
% sudo gbrowse_sync_aws_script.pl --conf /etc/gbrowse2/aws_balancer.conf \
--mysql /var/lib/mysql \
--postgres /var/lib/postgresql
The --conf argument is required. The script will create a snapshot of the appropriate
size, mount it on a temporary staging instance, and rsync a copy of your gbrowse databases
directory (e.g. /var/lib/gbrowse2/databases) to the snapshot. If you have created mysql or
postgres databases, you must also give the paths to their database file directories, as
shown in the example.
Note that ALL your mysql and postgres data files located on the server will be copied; not
just those used for track display.
ENVIRONMENT VARIABLES
The following environment variables are used if the corresponding command line options are
not present:
EC2_ACCESS_KEY AWS EC2 access key
EC2_SECRET_KEY AWS EC2 secret key
SEE ALSO
VM::EC2, VM::EC2::Staging::Manager
AUTHOR
Lincoln Stein, lincoln.stein@gmail.com
Copyright (c) 2012 Ontario Institute for Cancer Research
This package and its accompanying libraries is free software; you can redistribute it
and/or modify it under the terms of the GPL (either version 1, or at your option, any
later version) or the Artistic License 2.0. Refer to LICENSE for the full license text.
In addition, please see DISCLAIMER.txt for disclaimers of warranty.