[Bioclusters] Problems with gridEngine on OS X

Chris Dagdigian dag at sonsorol.org
Thu Apr 21 19:14:42 EDT 2005

Hi Randy,

First off I should tell you that the Grid Engine GUI tool is next to 
useless. I can't think of any serious SGE admin or end user(s) who find 
it useful (the interface is too inflexible and dated). It badly needs to 
be updated.

You can manage and use SGE faster via the commandline tools than you can 
via the GUI.

The *only* benefit the qmon X11 interface has is that sometimes it 
allows you to quickly change relatively obscure queue or policy 
configuration parameters that can sometimes be a pain to find and edit 
via the commandline methods. The gui has "plain english" explanations of 
settings while the config file has parameter names that may not be as 

So my first advice to you is to forget about qmon entirely unless you 
have an actual desire/need for it! No need to stress over what is really 
not that great of an admin or user interface.

I routinly build Grid Engine from source on Mac OS X and Mac OS X server 
(we built on Tiger last week just for the heck of it...) and I also use 
the binaries from the Grid Engine site. I've never had the odd Motif 
related issues that you mention and I've never had to edit or even think 
about resource files.

The biggest thing back in the day was realizing the following:

o you need Apple X11 installed (well of course...)
o you ALSO need the Apple X11 SDK .pkg installed
o motif can come from anywhere really

Both of these can be found on the Apple DevTools CDROM -- the biggie is 
the "X11 SDK" package -- that is what made everything click for me. You 
can only find the X11 SDK on the devTools CDROM.

If you tell me what platform you are using I can try sending you a 
precompiled qmon binary -- maybe that would work.

Your qconf errors on SGE 6 have nothing to do with qmon. SGE in general 
is extremely sensitive to issues of hostnames and forward/reverse DNS. 
There was not enough info in your last email for me to guess what is 
actually happening though.


zauhar wrote:

> Hi Folks,
> I am spending way too much time trying to get gridEngine up and running 
> on our OS X boxes. I started with version 5.3 (because I thought it 
> would be more "stable") and was able to get things working via command 
> line. However, despite a lot of effort I could not get qmon to work, and 
> given the complexity of the commands I really wanted it to work. My aim 
> is to make it available to everyone in our group, including students.
> I tried to google every relevant piece of information I could (including 
> messages on this list). The error message I cannot eradicate is
> Warning: Cannot find callback list in XtAddCallBack
> (appearing dozens of times) which precedes the creation of a mangled 
> GUI. I cannot determine if this is an issue of the Qmon resource file 
> not being located (I copied it to every bloody place I could imagine, 
> followed by endless tinkering with the various path environment 
> variables that motif uses). My only minuscule success was to set the 
> environment variable XBMLANGPATH to point at the PIXMAPS directory under 
> $SGE_ROOT/qmon , which produced a reasonable-looking GUI but did not 
> eliminate the XtAddCallBack messages; and said GUI did not work. I am no 
> expert on motif (I have learned more than I ever expected to know at 
> this point) and cannot go much further.
> SO, I decided to move up to version 6.0! I installed it remotely on our 
> network server (named "galapagos"). All seemed to go well. I added my 
> office machine ("cabriolet") as an admin host, and then tried again to 
> run qmon. It didn't work (in fact just terminated abruptly). When I 
> tried to run qconf on my office machine, I got this message:
> [cabriolet-usip-edu:/var/db/netinfo] zauhar# qconf -sh
> error: commlib error: access denied (client IP resolved to host name 
> "cabriolet.usip.edu". This is not identical to clients host name "ca)
> ERROR: unable to contact qmaster using port 9902 on host 
> "galapagos.usip.edu"
> Huh? The business about the host name resolution looks incredibly peculiar.
> Sorry for the clueless character of this message, but think how superior 
> you will feel if you can show me what an ass I am. :-)
> Thanks in advance,
> Randy
> Randy J. Zauhar, PhD
> Assoc. Prof. of Biochemistry
> Director, Graduate Program in Bioinformatics
> Dept. of Chemistry & Biochemistry
> University of the Sciences in Philadelphia
> 600 S. 43rd Street
> Philadelphia, PA 19104
> Phone: (215)596-8691
> FAX: (215)596-8543
> E-mail: r.zauhar at usip.edu
> Web: http://tonga.usip.edu/zauhar
> Discussion after watching Disney's "Lilo & Stitch":
> DAD: "But why did the space aliens speak English, as opposed to French, 
> or Swahili? And why did the one alien speak English with an Eastern 
> European accent? I don't get it."
> CATHERINE (age 7): "That's 'cause you don't have a good cartoon brain."
> ------------------------------------------------------------------------
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

Chris Dagdigian, <dag at sonsorol.org>
BioTeam  - Independent life science IT & informatics consulting
Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E iChat/AIM: bioteamdag  Web: http://bioteam.net

More information about the Bioclusters mailing list