[Tfug] Seeking general storage and CPU/mobo advice for updating my work machine

[Harry McGregor]

Hi,

Here is my advice (and yes, I am going to top-post instead of inline or
bottom post...).

Storage, I would look at Raid10 (lvm on top, or luks and lvm) with SSD
for the primary system storage.

240-250GB SSDs can be had for under $70 for OK drives, and about $100
for the higher end.  I would use two (or four) drives in raid10, and
yes, I mean raid10.  Linux raid10 will stripe the reads, and with the
low latency of SSDs, that works REALLY well.  SSD lifespan has been
GREATLY overblown as a big issue, field experience shows that it's not
an issue.

For bulk storage, I like HGST drives the best, and I would look at 3TB
or 4TB drives in Raid1 (if you don't need much space) or Raid6 if you
need a ton of space.  I don't consider Raid5 as viable any more due to
issues with drive failure during rebuild, etc.

For CPUs, I really base this more on memory.  With large amounts of
memory, I really prefer to have ECC memory.  AMD supports ECC on the FX
line (as long as the MB supports it).  Intel will only let you do ECC on
Xeon processors (workstation/server grade).  So will 8 3GHz+ modern
cores be enough for what your doing?

-Harry



On 4/15/15, 2:21 PM, John Gruenenfelder wrote:
>
> Hey TFUG,
>
> I sent this two weeks ago and didn't get any response.  I wasn't sure
> if maybe nobody knew, if it was tl;dr, or the list was having issues. 
> So, I'm resending it just in case.  Thanks in advance.
>
> --
> --John Gruenenfelder    Systems Manager, MKS Imaging Technology, LLC.
> Try Weasel Reader for PalmOS  --  http://weaselreader.org
> "This is the most fun I've had without being drenched in the blood
> of my enemies!"
>         --Sam of Sam & Max
>
> ---------- Forwarded message ----------
> From: "John Gruenenfelder" <jetpackjohn at gmail.com
> <mailto:jetpackjohn at gmail.com>>
> Date: Apr 2, 2015 4:45 AM
> Subject: Seeking general storage and CPU/mobo advice for updating my
> work machine
> To: "Tucson Free UNIX Group" <tfug at tfug.org <mailto:tfug at tfug.org>>
> Cc:
>
> Hi TFUG,
>
> It is starting to look like I'll finally get to upgrade my work
> server/workstation machine.  To give you some idea of its age, it
> contains an
> Athlon 64 X2 4400+ CPU, and that chip is plugged into one of those lovely
> early 64bit motherboards that would accept 4 GB of RAM but only allow
> access
> to 3.5 GB.
>
> As for the machine's purpose, it's mostly general purpose.  It is used
> by a
> fairly small number of users, primarily myself and my boss followed by
> a few
> who use it much less often.  As time has progressed and the machine has
> "become" slower, it sees less data processing and more data storing. 
> We run
> MATLAB and IDL on it occasionally, some data visualization (this is all
> astronomy stuff, BTW), and when I'm actually in the office it's the
> machine I
> do all of my dev work on.
>
> The machine, in name, has existed now for, oh, maybe 16 or 17 years? 
> After
> switching to Debian many years ago, the "upgrade" path has always been to
> build the replacement and then copy over the contents of the old
> drives, OS,
> data, and all.  Linux is so nice in that way where it can boot up on
> sometimes
> radically different hardware after the transfer and chances are there
> will be
> only minor issues, if any.  This new computer will be, if I'm counting
> right,
> the 5th incarnation.
>
>
> Anyway, it's time to reinvent the machine once more.  I can handle
> most of the
> requirements and whatnot myself, but I would very much appreciate the
> group's
> advice on a couple of topics:
>
>
> 1) Storage
>
> Disk space is cheap and we have a lot of data so the new machine was
> always
> going to have a lot of storage.  The present incarnation has roughly
> 900 GB
> altogether, split among several logical volumes.  Actually, it has
> twice that,
> but the volumes sit atop a (Linux kernel) RAID-1 array.
>
> The problem: once you go SSD, you don't want to go back.  I was painfully
> reminded of this today when a) I began a long overdue system update,
> b) the
> bi-hourly snapshot system triggered, and c) my boss came in and wanted to
> recreate for me an error he is having with a large program that uses a
> large
> data file.  Boy did that take forever...
>
> Obviously, using SSDs for all data would be insanely expensive, and
> given the
> numerous years that will undoubtedly pass before another machine rebuild,
> longevity is a concern.  I was thinking about the feasibility of using
> a SSD
> for the OS and possibly /home (on this system, I keep /home relatively
> small
> to "encourage" users to think about where they dump their bulk data).  It
> would be trivial to move /var/log onto one of the giant magnetic
> drives, and
> /tmp could be handled similarly or be mounted as a tmpfs.
>
> On the other hand, this machine will be on 24/7 and will have *way*
> more than
> the 3.5 GB of RAM the current machine does.  This means that the disk
> cache
> will be very large and, given the expected workload, should remain in
> memory
> for long periods of time.  After a short time, this should give most users
> SSD-like I/O performance when running programs from /usr and using data
> residing in /usr and /home.
>
> Which way would you go and why?
>
> Oh, and a related sub-topic... currently, the configuration is
> root-on-LVM-on-RAID1 which has been working quite nicely for a number of
> years.  Should I stick with RAID1 or move up the ladder?  At home on my
> personal server I have root-on-LVM-on-LUKS_crypto-on-RAID5.  When I
> finally
> get the money and wherewithal to upgrade my home server I'll switch it to
> RAID6.  With ever larger drives and the desire to not lose 50% of the
> total
> space to RAID1, should I move up to RAID6?  Provided, of course, that the
> final configuration has a sufficient number of drives for the desired RAID
> level.
>
>
> 2) Processor & motherboard
>
> The only real requirement that has been passed down to me, other than
> a rough
> upper limit on funds, is that the new machine should have strong parallel
> processing capabilities.  Multiple cores is a given, but there's also the
> possibility of multiple multi-core CPUs.  This parallel processing will be
> used for useful data processing, of course, but the primary use will be
> developing that code and running smaller jobs.  Larger jobs with more data
> would be moved off to larger clusters.
>
> It has been some time since I last had to do this.  Personal
> computers, on my
> own tight budget, yes, but now I have been given a high enough cap
> that I can
> look at more options.
>
> And great googley moogley!  Just a cursory glance on Newegg was enough
> for a
> good scare.  From $200 to $1000 there are CPUs of every conceivable
> combination of speed, number of cores, core name, and socket type.  I'm
> definitely in over my head here, it seems.
>
> Multiple physical CPUs would appear to require a "server" motherboard
> and a
> Xeon CPU.  There is only one 8-core desktop-class CPU, so going that route
> would mean either a 4- or 6-core CPU.  Server-class CPUs have a much
> larger
> spread and 4 to 8 cores seems feasible.  I did notice also that the
> server-class Xeon chips tend to have significantly lower wattage than
> similar
> desktop-class CPUs.
>
> At the same time, however, I can't simply pick a maximum price point,
> let's
> say $800, and pick the best available CPU.  At any given price you can
> adjust
> the sliders for frequency, number of cores, etc. and still have several
> choices for "best".
>
> With the rather vague usage scenario I've given above, how would you
> proceed?
> Fancy and fast six-core "desktop" CPU, or a fancier Xeon (maybe two?)
> eight-core CPU?  And then there's the offerings from AMD, though that
> seems to
> be rather less to sort through... and then the choice of motherboard...
> Ugh...
>
> Any available chip will be able to handle the "usual" tasks we're
> likely to
> throw at it: regular desktop applications/usage, sharing data among remote
> users, the small amount of web and mail traffic, etc.  Are Intel and
> AMD once
> again at parity with regards to running mathematical jobs?  I remember
> a few
> years back that AMD's highly anticipated Bulldozer core was being
> routinely
> crushed by Intel's then-available cores in raw integer and floating
> point math
> tasks.  Is one markedly better than the other these days?
>
> Are there any current CPU models that the community at large are flocking
> towards?  A model considered a good buy or particularly reliable, that
> sort of
> thing?
>
> Oh, and though it would seem like an entirely logical direction to
> move in, we
> are not currently doing any general purpose GPU type work.  I want to keep
> that avenue open, but whatever I put together now doesn't need to
> accomodate,
> for example, four giant power hungry video cards.  Just adding that in
> case it
> helps narrow the list at all.
>
>
> So many more variables to juggle.  Brain, ceasing to function... 
> Having seen
> that the landscape is far more vast than I was expecting, I would greatly
> appreciate any advice.
>
>
> --
> --John Gruenenfelder    Systems Manager, MKS Imaging Technology, LLC.
> My various (fun) projects  --  https://bach.as.arizona.edu/~johng
> <https://bach.as.arizona.edu/%7Ejohng>
> "This is the most fun I've had without being drenched in the blood
> of my enemies!"
>         --Sam of Sam & Max
>
>
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