[Bioclusters] Which Sun Grid Engine?

Michael James Michael.James at csiro.au
Thu Aug 17 02:21:20 EDT 2006

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,

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.

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