Difference between revisions of "WormBase Infrastructure"

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* a pool of redundant database servers running AceDB and MySQL
 
* a pool of redundant database servers running AceDB and MySQL
 
* a caching/load balancing server that distributes requests to the server pool, aggressively caching responses
 
* a caching/load balancing server that distributes requests to the server pool, aggressively caching responses
 +
* major services are either served on dedicated hosts (GBrowse) or as VirtualHosts on specific servers (wiki, blog, forums)
  
 
== Servers-at-a-glance  ==
 
== Servers-at-a-glance  ==

Revision as of 18:18, 4 May 2010

The WormBase Infrastructure

This document describes the WormBase infrastructure including hardware and software configuration.

Document conventions

Commands that require super-user privileges are prefaced with "sudo" or a "$" prompt. If the system is configured correctly, you should not need to be a root user in order to update the site.

*** Potential stumbling blocks are indented and hilighted with a
 *** preceeding triple asterisk.  Yikes!
 

General network topology

The network topology of the WormBase site looks like this:

                   REQUEST
                      |                                (Non-accelerated / non-cached reqeuests)
                      |---------------------------------------------------------------------------
                      |                              |             |             |             |
                      |                              |             |             |             |
            |---------|---------|                    |             |             |             |
            |         |         |                    |             |             |             |
            |         |         |                    |             |             |             |
            |        \/         |                    |             |             |             |
            |       squid       |                    |             |             |             |
            |         |         | www (fe)           |             |             |             |
            |        \/         |                    |             |             |             |
            |   load balancer   |                    |             |             |             |
            |         |         |                    |             |             |             |
            |---------|---------|                    |             |             |             |
                      |                              |             |             |             |
                      |                              |             |             |             |
       |------------------------------|              |             |             |             |
       |              |               |              \/            \/            \/            \/
 |-----------|  |-----------|  |-----------|    |-----------| |-----------| |-----------| |-----------|
 |     |     |  |     |     |  |           |    |           | |           | |           | |           |
 |   httpd   |  |   httpd   |  |   httpd   |    |   httpd   | | httpd/ace | |  biomart  | |  future   |
 |    unc    |  |    vab    |  |  crestone |    |   blast   | | aceserver | |           | |           |
 -------------  -------------  -------------    ------------- ------------- ------------- -------------

The WormBase infrastructure is composed of:

  • a pool of partially redundant web servers running GBrowse, each with all required GBrowse databases
  • a pool of partially redundant web servers running the web application
  • a pool of redundant database servers running AceDB and MySQL
  • a caching/load balancing server that distributes requests to the server pool, aggressively caching responses
  • major services are either served on dedicated hosts (GBrowse) or as VirtualHosts on specific servers (wiki, blog, forums)

Servers-at-a-glance

Cold Spring Harbor

primary name aliases/other FQDNs tasks ports* mysqld server ID
fe.wormbase.org www.wormbase.org
  • primary front end Squid caching server
  • balances load to back end servers
80 -
fe2.wormbase.org -
unc.wormbase.org

brie6.cshl.edu, stein.cshl.edu

  • serves up most AceDB-based pages at WormBase
  • hosts wormbase and wormbook mailing lists
  • hosts WormBook (not accelerated by fe.wormbase.org)
  • hosts steinlab.cshl.edu (not accelerated by fe.wormbase.org)

ssh: 22

httpd: 80 (WormBook)
httpd: 8080

7
be1 8
vab.wormbase.org
  • serves Genome Browser pages for WormBase
httpd: 8080 2
gene.wormbase.org httpd: 8080
3
blast.wormbase.org
  • provides blast and blat searches for WormBase

ssh: 22

httpd: 8080

4
aceserver.cshl.org
  • provides support for AQL, WB query language, and cisortho

httpd: 80

sgifaceserver: 2005

mysqld: 3306

5
biomart.wormbase.org
  • hosts the WormBase implementation of BioMart
80 (?)
dev.wormbase.org

brie3.cshl.edu

  • hosts the WormBase FTP site

ftp: 21

ssh: 22

httpd: 80

1 (master)
crestone.cshl.org
  • secondary WormBase development machine
  • hosts the WormBaseWiki
httpd: 8080 6

OICR

Production Nodes (GBrowse)

primary name aliases/other FQDNs tasks ports* services
wb-www1.oicr.on.ca GBrowse master server

ssh: 22

httpd: 80

apache, mysql, gbrowse


wb-www2.oicr.on.ca GBrowse slave server

ssh: 22

httpd: 80

apache, mysql, gbrowse


wb-www3-warm.oicr.on.ca GBrowse slave server

ssh: 22

httpd: 80

apache, mysql, gbrowse

Development servers

primary name aliases/other FQDNs tasks ports* services
dev.wormbase.org wb-dev.oicr.on.ca
  • primary WormBase development machine

ssh: 22

httpd: 80

apache, mysql, gbrowse

'* Firewall exceptions in boldface'

Production nodes

"Production nodes" or "live servers" are the servers that provide all the functionality at www.wormbase.org.

fe.wormbase.org

This server acts as a proxy for the entire WormBase site fielding requests for www.wormbase.org on port 80 using the reverse-proxy caching server "squid". Each request is filtered through a simple load balancing script which rewrites the URL and sends the request to an appropriate back end server. Returned results are cached in memory and/or on disk before being returned to the client to accelerate subsequent requests. Internally, this server is also known as fe.wormbase.org (for "front end"). fe.wormbase.org is configured as a redundant RAID in case of catastrophic disk failure.

fe.wormbase.org currently redirects the following requests (evaluated in this order):

URL host
/.*squid\/cachemgr\.cgi/ localhost
/.*\/gbrowse\/.*/ vab
/cisortho/ aceserver
/wiki/ crestone
* unc (brie6)

unc.wormbase.org (brie6)

Formerly the main www.wormbase.org server, unc.wormbase.org is a backend origin server running the entire WormBase site. It also serves the mailing lists archives, the RSS feeds, and access log statistics. unc also hosts a number of virtual hosts that do not pass through the proxy server on fe. Port 80 for unc.wormbase.org is open in the firewall.

vab.wormbase.org

vab answers requests on port 80 from fe.wormbase.org with httpd. Currently, vab.wormbase.org is only serving requests to the Genome Browser although it is capable of serving any request at WormBased. It hosts no virtual hosts. Port 80 for vab.wormbase.org is open in the firewall.

aceserver.cshl.org

aceserver is the publically accessible data mining server. Requests to aceserver.cshl.org do not pass through the proxy server on fe. Ports 80, 3360 (mysql), and 2005 (acedb) are open for aceserver.cshl.org.

aceserver.cshl.org also handles

   http://www.wormbase.org/db/searches/aql_query
   http://www.wormbase.org/db/searches/wb_query
   http://www.wormbase.org/cisortho/

blast.wormbase.org

BLAST and BLAT requests are handled by blast.wormbase.org. Requests for blast analyses at blast.wormbase.org do not pass through the proxy server on fe. blast.wormbase.org is also capable of handling requests load balancing requests but the redirector on fe.wormbase.org is not currently configured for this. Port 80 for blast.wormbase.org is open in the firewall.

biomart.wormbase.org

biomart.wormbase.org serves WormMart. Requests to biomart.wormbase.org do not pass through the proxy server on fe.

Development nodes

WormBase also maintains two development nodes.

dev.wormbase.org (brie3)

dev.wormbase.org is the current development server at WormBase. It maintains a CVS-checked out version of the source and database tarballs that is used to automatically push software and new databases onto the production nodes and mirror servers (described below). dev.wormbase.org also hosts the WormBase FTP site, aliased to ftp.wormbase.org.

crestone.cshl.org

crestone hosts the WormBase rearchitecture. Please don't junk it up with files -- disk space is at a premium!

Frozen release servers

freeze1 -- https://freeze1.wormbase.org:8333/

ws100.wormbase.org      143.48.220.44
ws110.wormbase.org      143.48.220.62
ws120.wormbase.org      143.48.220.46
ws130.wormbase.org      143.48.220.65



freeze2 -- https://freeze2.wormbase.org:8333/

ws140.wormbase.org      143.48.220.55
ws150.wormbase.org      143.48.220.66
ws160.wormbase.org      143.48.220.67


brie6 -- https://brie6.cshl.edu:8333/

 ws170.wormbase.org 143.48.220.208
 ws180.wormbase.org 143.48.220.69
 ws190.wormbase.org 143.48.220.192

be1.wormbase.org -- https://be1:8333/

 none currently

Typical request flow / infrastructure rationale

The WormBase infrastructure and design decisions are best understood by following requests through the system.

Static pages

First, consider a request for the home page, index.html. This request is recieved at www.wormbase.org by the squid server running on port 80. If this is the first request for the home page (unlikely!), squid passes the request to an instance of the load balancer script. This script rewrites the URL and sends it to one of the back end servers, unc or vab. The back end server returns the page to fe.wormbase.org which caches it in memory and on disk and returns it to the user. Subsequent requests are served directly from the cache, bypassing the back end servers altogether.

Dynamic pages

Consider a request for a typical gene page, unc-2. This request is recieved at www.wormbase.org by the squid server. Assuming that this is the first access of the unc-2 gene page during this release cycle, the load balancer sends the request to either unc.wormbase.org or vab.wormbase.org. The returned page is cached by the squid server and returned to the client.

It is important to note that the Gene page contains dynamically generate images. These images are now generated using absolute URLs. Thus, when a cached gene page is loaded, the client can correctly request the image from the appropriate back end server. For this to work correctly, the back end servers *must* be registered with DNS and have port 80 open in the firewall.

Special cases

  • POST requests

Because squid uses URLs as identifiers in the cache, any page view that results from a POST action will not be cached.

  • GBrowse (/db/seq/gbrowse)

Requests for Gbrowse (/db/seq/gbrowse) are not cached. Images created by gbrowse_img (such as those embedded on the Gene Summary and Clone pages) *are* cached as these can be considerably more "static" than individual GBrowse views. See the section "Access Control Lists" for additional details. Currently, requests for Gbrowse are handled exclusively by vab.wormbase.org.

  • Mailing list archives (/mailarch/)
  • RSS feeds (/rss/* and /private/manage_newsfeeds)
  • Access log statistics (/stats/)
  • The Feedback form (/db/misc/feedback)

These items are all handled directly by unc.wormbase.org (redirection is handled at the level of the redirector on fe.wormbase.org).

  • The Cache Manager CGI

The Cache Manager CGI is only available from fe.wormbase.org:81. Note you must be "on localhost" in order to use this statistics viewer.