GBROWSE_AWS_BALANCER(1p) | User Contributed Perl Documentation | GBROWSE_AWS_BALANCER(1p) |
gbrowse_aws_balancer.pl - Load balance GBrowse using Amazon Web Service instances
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
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.
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.
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 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:
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.
The options in this sections configure the master GBrowse instance. Three options are recognized:
The external IP that the balancer script finds can be seen in a log message when verbosity is 2 or higher.
The options in this section apply to the render slaves launched by the balancer.
data_snapshots = snap-12345 snap-abcdef
The gbrowse_sync_aws_slave.pl script will automatically maintain this option for you.
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.
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.
{ "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.
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.
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.
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_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.
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
VM::EC2, VM::EC2::Staging::Manager
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.
2018-10-03 | perl v5.26.2 |