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Running a GBrowse2 render farm
GBrowse 2 can be configured to use one or more "render slave" daemons. A render slave is a small Perl process that runs in the background, processing requests to render GBrowse tracks. By distributing several render slaves across one or more computers, you can spread out the work of generating GBrowse pages, thereby achieving improved performance. A slave can be attached to a particular track, a particular set of tracks, or to all tracks. In addition, you may assign multiple slaves to tracks, in which case the load will be distributed across each slave in a round-robin fashion.
Configuration of a render slave is minimal. All the datasource-specific information is stored in the central GBrowse script (known as the "master" GBrowse) and sent across the wire to the render slave. Configuration of the master GBrowse is also quite simple, and requires just an extra line or two in its configuration files.
The main limitations on render slaves is that a slave needs access to the database underlying any track that it is asked to render. If you run slaves on multiple hosts, then each host must have access to the relevant databases. For relational database backends, such as MySQL, you will need to grant access permissions for each host. For file-based database backends, such as the BerkeleyDB and in-memory databases, the database files must be replicated among the hosts, or else mounted on a common filesystem such as NFS. An additional limitation is that all plugins and uploaded files will be rendered on the master, and cannot be offloaded to render slaves.
Figures 1 through 4 illustrate common render slave configurations. In each of these configurations, we assume that your data source has three underlying databases: a "scaffold" database that contains basic chromosome information and the DNA sequence, for use by any plugins running on the master, and two "annotation" databases that contain feature tracks.
Figure 1 illustrates a simple case in which the master and slave processes are all running on the same machine and all databases are locally accessible. This configuration makes sense on a multiprocessor or multicore system that can take advantage of parallel processes. The only special configuration needed for this arrangement is to activate GBrowse's renderfarm support (as described in Initial Setup and to launch one or more slave processes at machine startup time.
Figure 2 illustrates a master server and two slave servers, all located on the same LAN. Each server runs a single GBrowse slave process; however it is possible to launch multiple processes for a possible performance boost. The three databases are located on a single NFS-mounted volume, so that the master server and the two slave servers have direct access to them. The host for this volume could be the master server, one of the slave servers, or a dedicated NFS server somewhere on the LAN.
Figure 3 illustrates almost the same configuration as the previous one, except that instead of an NFS-mounted filesystem, the databases reside on a relational database (e.g. MySQL) server which is accessed via the network.
Figure 4 illustrates a case in which the master and slave servers do not share databases. In this case, each machine has access to a private local database file or relational database server.
Which configuration is best for you depends on your needs. For small renderfarms, a shared disk or database server is easy and effective. For large renderfarms, you may encounter resource contention as the slave servers all attempt to access the same files. In this case, it makes more sense to give each slave its own database copy.
Many other configurations are possible, including distributing the work across the Internet. However, there is no particular authentication or authorization mechanism built into the slaves, so it is recommended that they be run on a protected LAN.
To set up a GBrowse renderfarm, you will need to install and configure slaves on each physical server you plan to use, arrange for the slaves to launch at boot time, and configure the master server to use the slaves.
Installing the GBrowse Slave Software
The GBrowse render slave is a small perl script named gbrowse_slave. Most of its functionality is contained in various Perl modules that are part of the GBrowse core distribution. On the master server, when you install GBrowse using ./Build install, gbrowse_slave will be installed automatically to Perl's default binary directory, usually /usr/local/bin. For the master, no additional software installation is needed.
% cd Generic-Genome-Browser % perl Build.PL % ./Build test (optional) % sudo ./Build install_slave
The last step, which should be performed as root, will install the required Perl libraries, manual pages and gbrowse_slave script, as well as the init support scripts needed to launch gbrowse_slave at startup time. Running the tests is optional, but it does ensure that all prerequisites are installed and working properly. The slave requires all the same prerequisites as the master server, including Bio::Perl, GD, CGI::Session, JSON, etc. However, an Apache server is not needed to run a slave.
Running the Render Slave Daemon
The slave usually runs as a daemon, listening on a designated server port and logging its output to a log file. You may run it by hand using an invocation like the following:
/usr/local/bin/gbrowse_slave --verbose=3 --log=`pwd`/slave.log --pid=`pwd`/slave.pid --port=8100
This will launch the slave with maximum (level 3) verbosity, write its output to the file slave.log, leave its process ID in the file named slave.pid and listen for incoming connections on port 8100. If it launches successfully, the slave.log and slave.pid files will be created in the current directory and the log file will contain lines like the following:
[Thu Jan 22 17:58:45 2009] [info] [pid=8128] GBrowse render slave starting on port 8100 [Thu Jan 22 17:58:45 2009] [debug] [pid=8128] Waiting for connection...
To kill the server, run the following command:
% /usr/local/bin/gbrowse_slave -k --pid=`pwd`/slave.pid
A more convenient way to start and stop the slave is using its init script, which was installed during ./Build install_slave. This init script is located in /etc/init.d/gbrowse-slave, and works on a variety of Linux distributions (it has not yet been tested on MacOSX - please edit this if you are able to confirm that it works or doesn't). The script will not work with Windows as it requires the bash shell.
- To start the slave
sudo /etc/init.d/gbrowse-slave start
If successful, you will see a message that three slave renderers have been started on ports 8101, 8102 and 8103. The slaves will log their activities to /var/log/gbrowse/gbrowse_slave, and write their process IDs to /var/run/gbrowse/
- To stop the slave
sudo /etc/init.d/gbrowse-slave stop
The number of slave servers to launch, the network ports they listen on, and the location of their log and pid files are controlled by a defaults file located in /etc/default/gbrowse-slave. This file looks like this:
#!/bin/sh DAEMON=/usr/local/bin/gbrowse_slave USER=www-data PRELOAD=/etc/gbrowse2/slave_preload.conf RUNDIR=/var/run/gbrowse LOGDIR=/var/log/gbrowse PORT="8101 8102 8103" VERBOSITY=3 NICE=0
Adjust this file as needed to meet your preferences. DAEMON gives the path to the gbrowse_slave script. USER indicates which user account to run under. If you run the slave daemon on the same machine used by the master, then this should be set to the same user as the one the Apache daemon uses, as they share directories. PRELOAD, an optional argument, gives the path to a file of in-memory databases for the render slave to load at startup time. RUNDIR and LOGDIR indicate the directories containing the slave's PID and log files, respectively. PORT is a space-delimited list of ports to listen on. The init script will launch one slave for each port. VERBOSITY controls the verbosity of the log file, and ranges from 0 (fatal errors only) to 3 (verbose informational logging). Lastly, NICE sets the daemon nice level, and ranges from 0 (normal priority) to 20 (very low priority). Adjust this if you find that slave processes are interfering with other processes on the machine.
To arrange for the init script to run at system boot time, simply create a symbolic link from the script to the appropriate /etc/rc.* directory. For example, if the machine usually runs at runlevel 2 (which you can determine using the runlevel command), then run the following commands:
% cd /etc/rc2.d % sudo ln -s ../init.d/gbrowse-slave S99gbrowse-slave
You may prefer to use your distribution's GUI for configuring startup services.
Once the slaves are configured and running, you need to tell the master GBrowse server about them. There are two configuration options that control this: renderfarm and remote renderer.
The renderfarm option is placed in the [GENERAL] section of either the main GBrowse.conf configuration file, or the [GENERAL] section of one or more datasource-specific configuration files. Set this option to a true value (non-zero) to activate slave rendering support:
[GENERAL] ...other options... renderfarm = 1 ...
It is safe to set renderfarm to 1 even for a datasource that does not use slaves. It is most often used as a convenient way to disable remote rendering during debugging and troubleshooting.
Place the remote renderer option into datasource-specific [TRACK] sections to enable remote rendering for that track. Here is a simple example:
# in a datasource-specific config file, such as yeast_renderfarm.conf [Genes] feature = gene database = volvox_annotations remote renderer = http://slavehost1.example.org:8101 glyph = gene bgcolor = yellow key = Protein-coding genes [tRNAs] feature = tRNA database = volvox_annotations remote renderer = http://slavehost2.example.org:8101 glyph = generic bgcolor = lightgray height = 6 key = tRNAs
This defines two tracks named Genes and tRNAs respectively. The Genes track fetches features of type "gene" from the database "volvox_annotations". This database is defined in a configuration stanza named [volvox_annotations:database] as usual. The rendering task is passed off to the render slave running on port 8101 on the host slavehost1.example.org. The rest of the stanza is as usual, and contains options for selecting the glyph, color, height and key of the rendered feature.
The tRNAs track is similar, except that it uses the render slave running on port 8101 of slavehost2.example.org.
The format of the remote renderer option is a space-delimited list of one or more slave addresses. Slaves are addressed using ordinary HTTP URLs. The hostname and port number parts of the URL are significant. The path part of the URL (e.g. /path/to/index.html) is not needed and is ignored if present. If you list multiple render slaves, then requests will be distributed across them in a round-robin fashion. For example:
remote renderer = http://slavehost1.example.org:8101 http://slavehost1.example.org:8102 http://slavehost2.example.org:8101
This will distribute requests across the two slave processes running on slavehost1 at ports 8101 and 8102, and across the slave running on slavehost2 port 8101. If one of the slave servers goes down, the master will note this and mark it temporarily unavailable for use. This provides a simple failover facility.
Note that the database named "volvox_annotations" must be available to the two slave servers. If it is a file-based database, such as one created using the "memory" adaptor of Bio::DB::SeqFeature::Store or Bio::DB::GFF, then the directory the database is located in must be available to the slave server at the path indicated in the [volvox_annotations:database] stanza. If the database is available on a network-connected relational database server, then the slave must have access privileges and the RDBMS hostname, username and password credentials indicated in the database configuration stanza must be appropriate for the slave.
Using [TRACK DEFAULTS]
In many cases you will wish to use the [TRACK DEFAULTS] stanza to assign a set of slaves to all tracks by default:
[TRACK DEFAULTS] remote renderer = http://localhost:8101 http://localhost:8102 http://slavehost1:8101 http://slavehost2:8101 database = volvox_annotations
This make two slaves running on the local machine and two additional slaves running on slavehost1 and slavehost2 the defaults. It also makes "volvox_annotations" the default database for all tracks. If you wish you can override the choice of slaves for individual tracks by placing "remote renderer" option in those tracks' stanzas. Use a value of "none" or "local" to turn off slave rendering for a particular track:
[TRANSL] remote renderer = none global feature = 1 glyph = translation database = chromosomes
The slave_preload.conf file
If you are relying on in-memory databases, you may wish to have them preloaded at slave startup time. This avoids the overhead of parsing and storing the in-memory database with each slave request. Note that preloading databases is usually unnecessary for relational databases, as the overhead for creating and tearing down a network connection to the database server is usually minimal.
The slave_preload.conf file is located in the gbrowse configuration directory, typically /etc/gbrowse2. It consists of a series of database stanzas that follow the same format as the stanzas in the data source configuration file. For example:
[yeast12:database] db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor memory -dir /var/www/gbrowse2/databases/yeast_chr1+2 [scaffolds:database] db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor memory -dir /var/www/gbrowse2/databases/yeast_scaffolds
You can name the stanzas the same as you name them in the data source configuration file ([yeast12:database]) or leave off the :database part ([yeast12]). In fact, the stanza name isn't significant; the slave uses the db_adaptor and db_args options to match up preloaded databases with the database in the request, so you can name the stanzas [db1], [db2], or whatever you like.
You are encouraged to experiment with preloading databases or not to see whether performance improves on your system.
Slaves write diagnostic messages to a log file usually located in /var/log/gbrowse/gbrowse_slave. Error messages will be written to this location. During troubleshooting you may wish to increase VERBOSITY option in the /etc/default/gbrowse-slave file to its maximum level of 3.