I think a lot of people use FSL on Ubuntu. Maybe you could add it to the
wiki? The default SGE install works for Ubuntu.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Andrew Janke
Sent: Wednesday, May 20, 2009 6:08 PM
To: [log in to unmask]
Subject: Re: [FSL] FSL in SGE - questions
> Dear SGE experts in the list,
> I am setting up an FSL SGE cluster.
> 1) how to set the numbre of cores in each machine in grid ? I am using
> mainly the queue long, but by default it uses 1 "thread"
This is set via the configuration for each queue. So for example for the
all.q:
$ qconf -sq all.q
You will see a line like this:
slots
1,[murdoch.lclust=8],[ben.lclust=4],[bill.lclust=4], \
[donald.lclust=4]
This means that the default for new hosts is 1 slot and for the named
hosts, the numbers as set individually. (murdoch has 8 for example).
You can then change this like this:
$ qconf -mq all.q
> 2) what is the best(=fastest but reasonably secure?) way to share data
> between nodes ?NFS ? SMB ? Something else ?
I'm with Evi, NFS on a local gigabit subnet running jumbo frames with
a switch that can handle such things. I like the HP 2824 for this bit
it is a bit overkill when you can get something like a Linksys SR2024
for (usually) less than half the price.
Also when I say NFS, I really mean AutoFS as it is far more fault tolerant.
I have often thought about writing a quick "howto" for SGE + NFS + FSL
+ Ubuntu/Linux in general but in past there was not much feedback
regarding a need for this.
If others are interested I can post some example configs and others
can comment and/or add to it.
--
Andrew Janke
([log in to unmask] || http://a.janke.googlepages.com/)
Canberra->Australia +61 (402) 700 883
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