[Bioclusters] Problems with gridEngine on OS X

Thu Apr 21 23:40:51 EDT 2005

Rayson, Chris,

Here is one problem solved - I can now at least run qconf from the  
command line of my office machine (cabriolet) communicating with the  
server (galapagos).

The host name for cabriolet on galapagos is fully qualified as  
"cabriolet.usip.edu" - at least that is how it appears in the machines  
entry of my netinfo database.

However, the command 'hostname' executed on cabriolet reported

cabriolet-usip-edu.local

(This is a default, I did not configure this.)

Explicitly setting the hostname of cabriolet -

hostname cabriolet.usip.edu

- makes everything work. This was NOT a problem in sge5.3.

Randy

On Apr 21, 2005, at 8:23 PM, Rayson Ho wrote:

> --- Chris Dagdigian <dag at sonsorol.org> wrote:
>> 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.
>
> Chris: I've heard that the PBS GUI is even worst :)
>
> Randy: You can take a look at the mail archive for host name resolution
> issues:
> http://gridengine.sunsource.net
>
> Rayson
>
>
>
>
>
>
>>
>> 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
>>
>> familiar
>>
>> 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.
>>
>>
>> Regards,
>> Chris
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 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
>> _______________________________________________
>> Bioclusters maillist  -  Bioclusters at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/bioclusters
>>
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>
>

Randy J. Zauhar, PhD
Assoc. Prof. of Biochemistry
Director, Graduate Program in Bioinformatics
University of the Sciences in Philadelphia
Dept. of Chemistry & Biochemistry
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