Right OS choice for Opteron System - Redhat

This is a discussion on Right OS choice for Opteron System - Redhat ; Hi, I'm building a system to do some serious number crunching. The manufacturer of the software I use has suggested using dual Opteron Processors (64 bit) for the system. The only RedHat OS I see that supports the Opteron is ...

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Thread: Right OS choice for Opteron System

  1. Right OS choice for Opteron System

    Hi,

    I'm building a system to do some serious number crunching. The
    manufacturer of the software I use has suggested using dual Opteron
    Processors (64 bit) for the system. The only RedHat OS I see that
    supports the Opteron is the RedHat Enterprise software. We've never
    ordered a 64 bit machine before so this is new ground and I don't want
    to spend the cash if we won't get any performance out of it.

    Will these processors work with RedHat 9 or Fedora to their full
    capability or would we need to purchase RedHat Enterprise? Also I've
    never used anything but the free OS, is the enterprise software fully
    compatible with software that works on RH 8 & 9?

    Also does anyone have any other hardware suggestions? We have about
    $2000 to spend, but we are also going to need scsi drives for the
    system so that takes at least $500 out of the starting money.

    Any thoughts would greatly be appreciated.

  2. Re: Right OS choice for Opteron System

    Melissa wrote:
    > Hi,
    >
    > I'm building a system to do some serious number crunching. The
    > manufacturer of the software I use has suggested using dual Opteron
    > Processors (64 bit) for the system. The only RedHat OS I see that
    > supports the Opteron is the RedHat Enterprise software. We've never
    > ordered a 64 bit machine before so this is new ground and I don't want
    > to spend the cash if we won't get any performance out of it.
    >
    > Will these processors work with RedHat 9 or Fedora to their full
    > capability or would we need to purchase RedHat Enterprise? Also I've
    > never used anything but the free OS, is the enterprise software fully
    > compatible with software that works on RH 8 & 9?


    SuSE Linux Enterprise Server 8 and the new SuSE Linux 9.1
    Professional both support Opterons.

    > Also does anyone have any other hardware suggestions? We have about
    > $2000 to spend, but we are also going to need scsi drives for the
    > system so that takes at least $500 out of the starting money.
    >
    > Any thoughts would greatly be appreciated.


    If you can get a dual opteron with SCSI drives fully
    outfitted for less than $2K I'll be surprised...


  3. Re: Right OS choice for Opteron System

    delpayne@yahoo.com (Melissa) wrote in message news:<373b68c7.0405171044.5f896bdf@posting.google.com>...
    > Hi,
    >
    > I'm building a system to do some serious number crunching. The
    > manufacturer of the software I use has suggested using dual Opteron
    > Processors (64 bit) for the system. The only RedHat OS I see that
    > supports the Opteron is the RedHat Enterprise software. We've never
    > ordered a 64 bit machine before so this is new ground and I don't want
    > to spend the cash if we won't get any performance out of it.
    >
    > Will these processors work with RedHat 9 or Fedora to their full
    > capability or would we need to purchase RedHat Enterprise? Also I've
    > never used anything but the free OS, is the enterprise software fully
    > compatible with software that works on RH 8 & 9?
    >
    > Also does anyone have any other hardware suggestions? We have about
    > $2000 to spend, but we are also going to need scsi drives for the
    > system so that takes at least $500 out of the starting money.
    >
    > Any thoughts would greatly be appreciated.


    Melissa:

    I'm guessing that this is probably going to be herisy in this group,
    but unless you want some of the enterprise requirements that generally
    justify ES, then I wouldn't recommend using it. You could certainly
    use on of the other distros, like fedora, or RH 9, but another option
    is SuSE. SuSE is a well respected OS that has both free and "in the
    box" distros. I know that the recent shift in RH's software model has
    made us switch distros for some of the servers that used to run redhat
    to either suse or freeBSD/openBSD. The mix of RHES for "mission
    critical" servers and clusers of S/F/O on the other servers has worked
    well for us.


    The following article may be of some interest:

    http://www.osnews.com/story.php?news_id=6223



    Hope that helps,
    Nicholas

  4. Re: Right OS choice for Opteron System

    In article <373b68c7.0405171044.5f896bdf@posting.google.com>, Melissa wrote:
    >
    > I'm building a system to do some serious number crunching. The
    > manufacturer of the software I use has suggested using dual Opteron
    > Processors (64 bit) for the system. The only RedHat OS I see that
    > supports the Opteron is the RedHat Enterprise software. We've never
    > ordered a 64 bit machine before so this is new ground and I don't want
    > to spend the cash if we won't get any performance out of it.
    >
    > Will these processors work with RedHat 9 or Fedora to their full
    > capability or would we need to purchase RedHat Enterprise? Also I've
    > never used anything but the free OS, is the enterprise software fully
    > compatible with software that works on RH 8 & 9?


    RHEL3 is basically RH9 with more testing and a more solid kernel. I've
    got 6 dual Opteron systems here running RHEL3 WS that I got with an
    academic discount. There's also RHPW, which is basically RHEL with less
    support (and thus cheaper).

    On the free side, Fedora Core 1 for x86_64 has been out for a while,
    and FC2 for x86_64 comes out today. By all reports, they're quite solid.
    I'd look hard at FC2.

    > Also does anyone have any other hardware suggestions? We have about
    > $2000 to spend, but we are also going to need scsi drives for the
    > system so that takes at least $500 out of the starting money.


    Why do you "need" SCSI drives? I've found that lots of times when
    folks "need" SCSI, they actually don't. If you can afford it, I'd
    certainly go with the Opterons -- they're damn nice chips.

    --
    Joshua Baker-LePain
    Department of Biomedical Engineering
    Duke University

  5. Re: Right OS choice for Opteron System

    Thanks for the thought. I'll look into SUSE, the software we use has
    full support for SUSE so that might be the way to go. I'm not that
    familiar with distro's other than RedHat and Knoppix so I hadn't
    considered it.

    Newegg has some good prices on opteron and I'm thinking I can pick the
    two processors up for about $1000, scsi HD for $500 and that would
    leave me another $500 to play with. It will be close, but I should be
    able to get in the price range or pretty close to it.

    Thanks for the help!

    Melissa

  6. Re: Right OS choice for Opteron System

    > Why do you "need" SCSI drives? I've found that lots of times when
    > folks "need" SCSI, they actually don't. If you can afford it, I'd
    > certainly go with the Opterons -- they're damn nice chips.


    Unfortunatly the program uses an obscene amount of scratch space and
    writes to a drive constantly while it does it's figuring. Faster HD
    access definitly seems to speed up the calcuations. Though we're
    talking about taking calculation that currently take 14 days on a dual
    processor (each 2ghz) machine down to 12 days.

    I'd really like to knock a couple of days off of that with the new
    system.

  7. Re: Right OS choice for Opteron System

    In article <373b68c7.0405190437.5e2a8167@posting.google.com>, Melissa wrote:
    >> Why do you "need" SCSI drives? I've found that lots of times when
    >> folks "need" SCSI, they actually don't. If you can afford it, I'd
    >> certainly go with the Opterons -- they're damn nice chips.

    >
    > Unfortunatly the program uses an obscene amount of scratch space and
    > writes to a drive constantly while it does it's figuring. Faster HD
    > access definitly seems to speed up the calcuations. Though we're
    > talking about taking calculation that currently take 14 days on a dual
    > processor (each 2ghz) machine down to 12 days.
    >
    > I'd really like to knock a couple of days off of that with the new
    > system.


    First, as an aside, how much scratch spare are we talking? If you
    could utilize a RAMdisk for it, that'd *really* speed things up.

    But I'm guessing it's more space than would be feasible in RAM. Before
    you commit to SCSI (and I assume you're talking about a high-end 15K RPM
    drive), look at buying a couple (or more) of IDE disks and doing software
    RAID0. You'll end up with more space and it'll likely be faster than a
    single disk SCSI solution. Of course, be sure to religously back up
    any valuable data on the RAID0 -- one disk goes and the whole array goes.

    --
    Joshua Baker-LePain
    Department of Biomedical Engineering
    Duke University

  8. Re: Right OS choice for Opteron System

    In article , P Gentry wrote:
    > delpayne@yahoo.com (Melissa) wrote in message news:<373b68c7.0405190437.5e2a8167@posting.google.com>...
    >>

    > From what you've said so far, I'm not so sure that dual Opteron's will
    > be that much better than more established smp mobos. I'm not sure


    IMO, the Opteron situation *has* had the time to stabilize. The
    starting situation this time was actually pretty decent (in stark
    contrast to the Athlon MP launch), and it's gotten vastly better
    since then.

    > that anyone has seen these things working with "commodity" boxes
    > enough to know how to optimize them really. If the software maker
    > suggests dual Opterons, get them to tell you what sort of setup they
    > suggest and provide numbers that back up their claim of what sort of
    > improvement you should expect.


    Agreed -- the best benchmark is always your own code.

    > Right now I think everyone is just hoping that Opterons will deliver
    > what Itaniums promised. And as with any new chip design, you can't
    > really optimize for it before compilers catch up to take advantage of
    > the new/extended instruction set/processing.


    There are compiler suites out there now that work quite well
    with AMD64. Here are some benchmarks I did with a commercial FEM app
    (LS-DYNA) that show just how much the Opteron kicks butt (for this app,
    of course):

    http://www.duke.edu/~jlb17/bench-results.pdf

    > That said, Fedora Core 2 is just out yesterday that "promises" better
    > utilization of dual Opterons, but where are the proven mobos? Tyan
    > Tigers are the only ones I've seen that consistently get a thumbs up.


    Erm, only recently have the Tigers been getting good marks. The first
    few BIOS revisions were real rough, from what I hear. The Rioworks
    boards have always done quite well -- my systems have the HDAMA board in
    them and have consistently worked well.

    --
    Joshua Baker-LePain
    Department of Biomedical Engineering
    Duke University

  9. Re: Right OS choice for Opteron System

    Thanks,

    Definitly good points. No one seems to be able to give me straight
    numbers on how much Opterons will help or if it would. The Gaussian
    tech support people have been really helpful in specing a system and
    basically they are just adding Opteron support and the support will be
    released very soon.

    Your points are really good and I'm leaning towards specing a system
    with a good mb, scsi hd for boot/scratch/swap and serial ata's for
    doing the mass storage needs and getting the fastest smb processors I
    can get my hands on.

    It's tought because the researcher won't have more money to upgrade
    the machine for 3+ years so I'm trying to get the best system I can.

    Lots of good responses and I'm definitly getting a wider view of the
    problem.

  10. Re: Right OS choice for Opteron System

    In article <373b68c7.0405200645.1f01a390@posting.google.com>, Melissa wrote:
    > Thanks,
    >
    > Definitly good points. No one seems to be able to give me straight
    > numbers on how much Opterons will help or if it would. The Gaussian
    > tech support people have been really helpful in specing a system and
    > basically they are just adding Opteron support and the support will be
    > released very soon.
    >
    > Your points are really good and I'm leaning towards specing a system
    > with a good mb, scsi hd for boot/scratch/swap and serial ata's for
    > doing the mass storage needs and getting the fastest smb processors I
    > can get my hands on.


    I would stick with SCSI for now - from everything I have read on the RHEL
    forums, people attempting to use SATA drives are currently only seeing
    ~IDE-level performance...

    Better would be to go for a SCSI RAID install, which will give the best
    optimization.

    > It's tought because the researcher won't have more money to upgrade
    > the machine for 3+ years so I'm trying to get the best system I can.
    >
    > Lots of good responses and I'm definitly getting a wider view of the
    > problem.


    Kevin

  11. Re: Right OS choice for Opteron System

    In article , Joshua Baker-LePain
    wrote:
    > In article <373b68c7.0405190437.5e2a8167@posting.google.com>, Melissa wrote:
    >>> Why do you "need" SCSI drives? I've found that lots of times when
    >>> folks "need" SCSI, they actually don't. If you can afford it, I'd
    >>> certainly go with the Opterons -- they're damn nice chips.

    >>
    >> Unfortunatly the program uses an obscene amount of scratch space and
    >> writes to a drive constantly while it does it's figuring. Faster HD
    >> access definitly seems to speed up the calcuations. Though we're
    >> talking about taking calculation that currently take 14 days on a dual
    >> processor (each 2ghz) machine down to 12 days.
    >>
    >> I'd really like to knock a couple of days off of that with the new
    >> system.

    >
    > First, as an aside, how much scratch spare are we talking? If you
    > could utilize a RAMdisk for it, that'd *really* speed things up.
    >
    > But I'm guessing it's more space than would be feasible in RAM. Before
    > you commit to SCSI (and I assume you're talking about a high-end 15K RPM
    > drive), look at buying a couple (or more) of IDE disks and doing software
    > RAID0. You'll end up with more space and it'll likely be faster than a
    > single disk SCSI solution. Of course, be sure to religously back up
    > any valuable data on the RAID0 -- one disk goes and the whole array goes.


    Well, if IDE / RAID is considered, it's not much more $$ to use hardware RAID
    (think of all the money saved with IDE vs SCSI disks), and it would probably be
    considerably faster than software RAID.

    Kevin

  12. Re: Right OS choice for Opteron System

    In article , Kevin Collins wrote:
    >
    > Well, if IDE / RAID is considered, it's not much more $$ to use hardware RAID
    > (think of all the money saved with IDE vs SCSI disks), and it would probably be
    > considerably faster than software RAID.


    Not necessariliy. Hardware RAID cards use their embedded (low power, slow)
    processor to do the RAID calculations. In software RAID, you're using the
    (obscenely fast, especially in comparison) system processor to do the RAID
    calculations. Even for RAID5 (the most computationally expensive common
    RAID level), I've seen benchmarks of software RAID beating a 3ware card (the
    best IDE hardware RAID card out there). For RAID0, since there's a minimal
    amount of computation, there's really not any sense in getting a hardware
    RAID card unless one needs the large number of ports. And even then I'd
    still use the card in JBOD mode and do the RAID in software.

    There's been a lot of discussion of this on the linux-raid list -- look
    at the archives there for more info and some numbers.

    --
    Joshua Baker-LePain
    Department of Biomedical Engineering
    Duke University

  13. Re: Right OS choice for Opteron System

    In article <373b68c7.0405200645.1f01a390@posting.google.com>, Melissa wrote:
    >
    > Your points are really good and I'm leaning towards specing a system
    > with a good mb, scsi hd for boot/scratch/swap and serial ata's for
    > doing the mass storage needs and getting the fastest smb processors I
    > can get my hands on.


    Be careful with SATA. There's support there for it, but only for certain
    chipsets. And I haven't looked too much, but it was my impression that SATA
    disks are SCSI-priced. Trust me -- you can get a lot of speed out of
    RAID0 IDE disks.

    --
    Joshua Baker-LePain
    Department of Biomedical Engineering
    Duke University

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