[Bioclusters] Which Sun Grid Engine?

Rayson Ho raysonlogin at yahoo.com
Sun Aug 20 23:14:13 EDT 2006

Sorry for the late reply, been busy with all those sailing related

Chris wrote about the free download of N1 GE:

You will need to register to download Sun's "Solaris Enterprise
System", then you will get access to the SGE download page with links
to the zip files... one of the zip files has ACRo in it.

ACRo is a powerful accounting tool, but often it is not needed for
clusters with just a few users... you can use qacct, and there are a
number of accounting scripts posted on the mailing list:

BTW, SGE 6 still has support for SGE 5.x type of queues. In SGE 6, you
have "cluster queue", which can span multiple execution hosts. And if
you want SGE 5.x kind of queue (ie. per host queue), it is now called
"queue instance".


--- Bernard Li <bli at bcgsc.ca> wrote:
> I haven't tried the ARCo (accounting) stuff, but it sounds great and
> I'm sure it's great in practise.  I don't have the exact link, but
> perhaps Rayson can point you at the correct direction :)
> It's free (not open source) but there is no problem integrating with
> the open source version of Grid Engine.
> Have you looked at mpiBLAST?  I think Joe Landman has some
> integration scripts for SGE to make it even easier to use.
> Regarding SGE 5 & 6's definition of what a "queue" is - actually the
> way it is defined in 6 is the more "popular" defintion as you
> allocate resources (nodes) to it, whereas previously in 5, each node
> has its own queue, which is somewhat "strange" to traditional
> clustering.  For instance our cluster is still 5.x based and our
> users submit jobs to Projects, however when we migrate to 6, they
> will be submitting to queues.
> Cheers,
> Bernard
> -----Original Message-----
> From: Michael James [mailto:Michael.James at csiro.au]
> Sent: Wed 16/08/2006 23:21
> To: HPC in Bioinformatics; Bernard Li
> Subject: Re: [Bioclusters] Which Sun Grid Engine?
> On Thu, 17 Aug 2006 03:04 pm, Bernard Li wrote:
> > You can get official support from Sun
> > if you purchase Sun N1 Grid Engine.
> > "Sun Grid Engine" is the open source version.
> > As far as I know they are working off the same tree,
> > and even some previously proprietary things
> > like Windows execution hosts,
> > accounting are now freely downloadable (not open source though).   
> "Official Support" phooey.
> "Windows execution hosts" even more phooey.
> However  "Accounting"  Oh yes please!
> I lost hair and sleep over that confounded "accounting" file.
> Eventually restored sanity with a perl script
>  that put the entries in order by month
>  and weeded out the half that were dead jobs
>  with no resource usage attached ...
> > The users at gridengine.sunsource.net mailing
> > is extremely high traffic, so you usually get
> > pretty good support for questions.  
> Thanks, I'll have a look.
> > In terms of upgrade -
> > I suppose they have some upgrade scripts,
> > but 5.x is fundamentally different from 6...  
> Our cluster is simple enough (66 identical nodes)
>  that we can re-build that from scratch.
> More difficult is any adjustment to the calling scripts,
>  the batchblast script that cuts a concatenated fasta file
>  into single sequences, and issues the qsub -t  command
> And then there's grocking the underlying paradigm;
>  in sge5.3 the queue is something that describes a computing resource
>  in sge6 (I believe) a queue characterises a job.
> So in 6 you submit a job to a queue ("urgent", "batch", etc)
>  whereupon it takes on that queue's characteristics.
> In 5 it was the job of the scheduling system to decide
>  which computing resource (also called a queue)
>  should process a given job
>  based solely on the flags in the qsub command.
> Thanks again,
> michaelj
> -- 
> Michael James                         michael.james at csiro.au
> System Administrator                    voice:  02 6246 5040
> CSIRO Bioinformatics Facility             fax:  02 6246 5166
> No matter how much you pay for software,
>  you always get less than you hoped.
> Unless you pay nothing, then you get more.
> > _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

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