Date:         Tue, 26 Aug 2003 10:48:50 +0100
Reply-To:     Real SAS User <sasuser@GUILDENSTERN.DYNDNS.ORG>
Sender:       "SAS(r) Discussion" <SAS-L@LISTSERV.UGA.EDU>
From:         Real SAS User <sasuser@GUILDENSTERN.DYNDNS.ORG>
Subject:      Re: Debian Linux partition
In-Reply-To:  <Pine.GSO.4.05.10308250935590.11246-100000@paladin>
Content-Type: text/plain; charset=us-ascii

on Mon, Aug 25, 2003 at 09:41:50AM -0400, Kevin Roland Viel (kviel@EMORY.EDU) wrote:
> Greetings,
>
> I am attempting to install Debian Linux on a 60 gig drive at home.  I
> was wondering if I should not have a partition for SAS, if I am ever
> able to get SAS for Linux.  I ask this with the utmost ignorance for
> what I am really doing, but I learned to swim by being thrown off a
> dock.
>
> The reason I wonder about a partition is because I read a paragraph on
> the /var partition into which logs (not SAS) reside.
>
> The reason I need Linux is for genomics software, such as PHRAP, and,
> further, enlightment :).

Googling for "linux partitioning" will provide you with some good
references for general guidelines in the top few results.  You might
even feel lucky.

SAS doesn't _need_ a dedicated partition, though a partition can be
useful for rationalizing space, or allowing yourself to recover
gracefully in an out-of-disk situation.  You'd benefit more from
dedicated spindles or RAID 0, and Linux software RAID is as fast or
faster than hardware these days, plus you can't beat the price.


I'd recommend giving yourself either:

  - A generous /var partition, in which you allocate saswork (say, in
    /var/tmp).   Depending on what else you plan on putting on the
    system, 1.5 - 2 GiB is baseline, so several GiB on top of that if
    you need. it.

  - A very generous /home partition.  You would need to allocate at most
    ~10 GiB to system partitions (/, /boot, /tmp, /usr, /var, and swap).
    I'll assume that 50 GiB would take you a while to fill.  Allocate
    saswork within your home directory.  This is probably the most
    straightforward and flexible option.  You risk running yourself out
    of space on your /home directory, but you will probably be able to
    find  your system administrator should you need to clean things up.
    Even calling him late nights at home if necessary ;-)

  - Cut down on /home a bit and give yourself a fat data partition
    someplace.  Note that this gives you the advantage that when you do
    fill up your SAS data space, you still can function over the rest of
    your system.  The disadvantage is that you're going to slice up your
    available storage that much more, so you'll have to decide between
    oggs or SAS datasets.

  - Buy a 2nd HD, chuck it in on your second IDE controller, and have
    a lot less disk contention to worry about.  Make it SCSI and enjoy
    even more happiness (yes, for a price).

  - Note that Debian doesn't clean out your /var/tmp as it
    does /tmp at boot.  Or apt-get install tmpreaper and configure
    appropriately.  I'd also cron a run of the SAS cleanwork utility at
    least daily (more often wouldn't hurt, and may well help).


I'd also strongly advise you run 'hdparm' to test and tune your drives
to optimal performance.  This can make a _huge_ difference for SAS
performance:

    http://linux.oreillynet.com/pub/a/linux/2000/06/29/hdparm.html


If you feel inclined to continue messign around with your partitioning,
I'd also recommend using lvm, the logical volume manager, as it allows
on-the-fly partition resizing and administration.

--
Charming man. I wish I had a daughter so I could forbid her to marry one...