gridengine.info

Over at this link:

http://blog.bioteam.net/2010/02/07/grid-engine-6-2-on-mac-os-x/

... I've posted an article and accompanying 7 minute recorded screencast showing how to manually install SGE 6.2u5 on a Mac OS X Server system. The test system in the video was running 10.5.8 but the same methods are known to work on Snow Leopard systems as well.

Are you in the following situation?

1. /usr/bin/mail works perfectly from the command line
2. /usr/bin/mail configured as the SGE mailer produces no email
3. substituting a wrapper with extra logging also produces no logs or email

The only clue is in the spool logs:

09/10/2008 16:22:07|execd|xxx-fs01|E|mailer had timeout - killing
09/10/2008 16:22:07|execd|xxx-fs01|E|mailer exited with exit status= 1
09/10/2008 16:22:19|execd|xxx-fs01|E|mailer had timeout - killing
09/10/2008 16:22:19|execd|xxx-fs01|E|mailer exited with exit status= 1

Thanks to Valerio Luccio we have a workaround. The issue is apparently a conflict between one of the SGE supplied libraries that interferes with the mail MTA on OS X when SGE tries to invoke it. A trivial wrapper script that overrides the DYLD_LIBRARY_PATH environment variable is the fix:

#!/bin/sh
export DYLD_LIBRARY_PATH=/usr/lib
/usr/bin/mail -s "$2" $3

This solved a problem that had been bothering me for days, thanks Valerio - I owe you a beer if we ever end up at the same meeting or conference!

This is a follow-up post relating to the new Apple framework for starting, stopping and managing persistent daemons and services called "launchd". The issue of Grid Engine interoperability with the launchd framework has already been covered in a gridengine.info Wiki article.

The new news to report is that my coworker Bill Van Etten stumbled upon the SGE environment variable "SGE_ND" and realized that it could be useful for Apple launchd integration because launchd really hates daemons that fork off ASAP upon startup. By setting the "SGE_ND" variable to true, the daemons don't fork and can be better managed by launchd.

The new launchd scripts are discussed and available for download here:
http://blog.bioteam.net/2008/03/04/apple-os-x-105-launchd-scripts-for-grid-engine/

Feel free to use these scripts or simply refer to them when customizing your own. As always, feedback and comments would be appreciated. BioTeam remains committed to making sure SGE remains an excellent choice for use on OS X based systems.