[Beowulf] [EXTERNAL] Re: Deskside clusters

Lux, Jim (US 7140) james.p.lux at jpl.nasa.gov
Tue Aug 24 21:18:49 UTC 2021

One potential *problem* with desk side clusters is that while they can be self-administered, if not carefully done, you can run afoul of a variety of "cybersecurity" requirements.
 At least for me at NASA/JPL, there is an ever increasing paperwork burden - it's not that keeping it safe is an issue - if your desktop machine talks to a headnode on an isolated network, then there's not much chance of a threat.  It's that there is a LONG list of potential things (NIST 800-53) that you have to address, even if only to say "Not Applicable".  And unfortunately, it's not a one-and-done analysis and report, every year, you have to re-evaluate and receive "authorization to operate".  

If you're using an institutionally provided cluster, some other poor soul has had to deal with all that.

OTOH, if you're not in an environment that's bound by regulation so tightly - yeah, the "private cluster" gets you out from institutional requirements for fire protection analysis, system administration, software inventories, you name the things that the "IT group" wants to do.

In some ways, the "naming" of the deskside box is important.  You might want to give it a "benign" sounding description - "supercomputer" is probably a bad choice. There are a lot of "instrument controllers" around that are PCs with a GPIB interface that never gets used.

And as Doug pointed out, sometimes your grant funding may drive towards "buy equipment" as opposed to "buy services via chargeback".  Grantors sometimes like something tangible they can touch, and in the "end of year we didn't spend our equipment budget frenzy" maybe a deskside cluster is a good investment.  I don't know enough about, say, NIH grants, to know if they'd rather you buy a small cluster for the lab, or another LN2 dewar, or a -80C freezer (the latter two, I understand, are a popular item to absorb unspent capital lab equipment budgets in some labs).  So you get that Limulus, slap that "Property of NIH" inventory tag on it, and everyone's happy - you can do your genome matching without hassling for an account on the big iron at the computer center, etc.

All that said, it is a "niche" market, and probably one that isn't going to make anyone a kajillionaire, nor is it a volume that's big enough to interest the big players (Dell, HP) in offering something.  

Based on the list traffic, though, there are fewer and fewer people doing "roll your own" clusters (which, realistically, is only viable for smaller clusters a few dozen nodes perhaps?) - so there *is* a niche for assembly and support.

On 8/24/21, 1:33 PM, "Beowulf on behalf of Lux, Jim (US 7140) via Beowulf" <beowulf-bounces at beowulf.org on behalf of beowulf at beowulf.org> wrote:

    Yes, indeed.. I didn't call out Limulus, because it was mentioned earlier in the thread.

    And another reason why you might want your own.
    Every so often, the notice from JPL's HPC goes out to the users - "Halo/Gattaca/clustername will not be available because it is reserved for Mars {Year}"  While Mars landings at JPL are a *big deal*, not everyone is working on them (in fact, by that time, most of the Martians are now working on something else), and you want to get your work done.  I suspect other institutional clusters have similar "the 800 pound (363 kg) gorilla has requested" scenarios.

    On 8/24/21, 11:34 AM, "Douglas Eadline" <deadline at eadline.org> wrote:


        You are describing a lot of the design pathway for Limulus
        clusters. The local (non-data center) power, heat, noise are all
        minimized while performance is maximized.

        A well decked out system is often less than $10K and
        are on par with a fat multi-core workstations.
        (and there are reasons a clustered approach performs better)

        Another use case is where there is no available research data center
        hardware because there is no specialized sysadmins/space/budget.
        (Many smaller colleges and universities fall into this
        group). Plus, often times, dropping something into a data center
        means an additional cost to the researchers budget.


        > I've been looking at "small scale" clusters for a long time (2000?)  and
        > talked a lot with the folks from Orion, as well as on this list.
        > They fit in a "hard to market to" niche.
        > My own workflow tends to have use cases that are a big "off-nominal" - one
        > is the rapid iteration of a computational model while experimenting - That
        > is, I have a python code that generates input to Numerical
        > Electromagnetics Code (NEC), I run the model over a range of parameters,
        > then look at the output to see if I'm getting what what I want. If not, I
        > change the code (which essentially changes the antenna design), rerun the
        > models, and see if it worked.  I'd love an iteration time of "a minute or
        > two" for the computation, maybe a minute or two to plot the outputs
        > (fiddling with the plot ranges, etc.).  For reference, for a radio
        > astronomy array on the far side of the Moon, I was running 144 cases, each
        > at 380 frequencies: to run 1 case takes 30 seconds, so farming it out to
        > 12 processors gave me a 6 minute run time, which is in the right range.
        > Another model of interaction of antnenas on a spacecraft runs about 15
        > seconds/case; and a third is about 120 seconds/case.
        > To get "interactive development", then, I want the "cycle time" to be 10
        > minutes - 30 minutes of thinking about how to change the design and
        > altering the code to generate the new design, make a couple test runs to
        > find the equivalent of "syntax errors", and then turn it loose - get a cup
        > of coffee, answer a few emails, come back and see the results.  I could
        > iterate maybe a half dozen shots a day, which is pretty productive.
        > (Compared to straight up sequential - 144 runs at 30 seconds is more than
        > an hour - and that triggers a different working cadence that devolves to
        > sort of one shot a day) - The "10 minute" turnaround is also compatible
        > with my job, which, unfortunately, has things other than computing -
        > meetings, budgets, schedules.  At 10 minute runs, I can carve out a few
        > hours and get into that "flow state" on the technical problem, before
        > being disrupted by "a person from Porlock."
        > So this is, I think, a classic example of  "I want local control" - sure,
        > you might have access to a 1000 or more node cluster, but you're going to
        > have to figure out how to use its batch management system (SLURM and PBS
        > are two I've used) - and that's a bit different than "self managed 100%
        > access". Or, AWS kinds of solutions for EP problems.   There's something
        > very satisfying about getting an idea and not having to "ok, now I have to
        > log in to the remote cluster with TFA, set up the tunnel, move my data,
        > get the job spun up, get the data back" - especially for iterative
        > development.  I did do that using JPLs and TACCs clusters, and "moving
        > data" proved to be a barrier - the other thing was the "iterative code
        > development" in between runs - Most institutional clusters discourage
        > interactive development on the cluster (even if you're only sucking up one
        > core).   If the tools were a bit more "transparent" and there were "shared
        > disk" capabilities, this might be more attractive, and while everyone is
        > exceedingly helpful, there are still barriers to making it "run it on my
        > desktop"
        > Another use case that I wind up designing for is the "HPC in places
        > without good communications and limited infrastructure" -  The notional
        > use case might be an archaeological expedition wanting to use HPC to
        > process ground penetrating radar data or something like that.   (or, given
        > that I work at JPL, you have a need for HPC on the surface of Mars) - So
        > sending your data to a remote cluster isn't really an option.  And here,
        > the "speedup" you need might well be a factor of 10-20 over a single
        > computer, something doable in a "portable" configuration (check it as
        > luggage, for instance). Just as for my antenna modeling problems, turning
        > an "overnight" computation into a "10-20 minute"  computation would change
        > the workflow dramatically.
        > Another market is "learn how to cluster" - for which the RPi clusters work
        > (or "packs" of Beagleboards) - they're fun, and in a classroom
        > environment, I think they are an excellent cost effective solution to
        > learning all the facets of "bringing up a cluster from scratch", but I'm
        > not convinced they provide a good "MIPS/Watt" or "MIPS/liter" metric - in
        > terms of convenience.  That is, rather than a cluster of 10 RPis, you
        > might be better off just buying a faster desktop machine.
        > Let's talk design desirements/constraints
        > I've had a chance to use some "clusters in a box" over the last decades,
        > and I'd suggest that while power is one constraint, another is noise.
        > Just the other day, I was in a lab and someone commented that "those
        > computers are amazingly fast, but you really need to put them in another
        > room". Yes, all those 1U and 2U rack mounted boxes with tiny fans
        > screaming is just not "office compatible"   And that kind of brings up
        > another interesting constraint for "deskside" computing - heat.  Sure you
        > can plug in 1500W of computers (or even 3000W if you have two circuits),
        > but can you live in your office with a 1500W space heater?
        > Interestingly, for *my* workflow, that's probably ok - *my* computation
        > has a 10-30% duty cycle - think for 30 minutes, compute for 5-10.  But
        > still, your office mate will appreciate if you keep the sound level down
        > to 50dBA.
        > GPUs - some codes can use them, some can't.  They tend, though, to be
        > noisy (all that air flow for cooling). I don't know that GPU manufacturers
        > spend a lot of time on this.  Sure, I've seen charts and specs that claim
        > <50 dBA. But I think they're gaming the measurement, counting on the user
        > to be a gamer wearing headphones or with a big sound system.  I will say,
        > for instance, that the PS/4 positively roars when spun up unless you’ve
        > got external forced ventilation to keep the inlet air temp low.
        > Looking at GSA guidelines for office space - if it's "deskside" it's got
        > to fit in the 50-80 square foot cubicle or your shared part of a 120
        > square foot office.
        > Then one needs to figure out the "refresh cycle time" for buying hardware
        > - This has been a topic on this list forever - you have 2 years of
        > computation to do: do you buy N nodes today at speed X, or do you wait a
        > year, buy N/2 nodes at speed 4X, and finish your computation at the same
        > time.
        > Fancy desktop PCs with monitors, etc. come in at under $5k, including
        > burdens and installation, but not including monthly service charges (in an
        > institutional environment).  If you look at "purchase limits" there's some
        > thresholds (usually around $10k, then increasing in factors of 10 or 100
        > steps) for approvals.  So a $100k deskside box is going to be a tough
        > sell.
        > On 8/24/21, 6:07 AM, "Beowulf on behalf of Douglas Eadline"
        > <beowulf-bounces at beowulf.org on behalf of deadline at eadline.org> wrote:
        >     Jonathan
        >     It is a real cluster, available in 4 and 8 node versions.
        >     The design if for non-data center use. That is, local
        >     office, lab, home where power, cooling, and noise
        >     are important. More info here:
        >     https://urldefense.us/v3/__https://www.limulus-computing.com__;!!PvBDto6Hs4WbVuu7!f3kkkCuq3GKO288fxeGGHi3i-bsSY5P83PKu_svOVUISu7dkNygQtSvIpxHkE0XDpKU4fOA$
        >     https://urldefense.us/v3/__https://www.limulus-computing.com/Limulus-Manual__;!!PvBDto6Hs4WbVuu7!f3kkkCuq3GKO288fxeGGHi3i-bsSY5P83PKu_svOVUISu7dkNygQtSvIpxHkE0XD7eWwVuM$
        >     --
        >     Doug
        >     > Hi Doug,
        >     >
        >     > Not to derail the discussion, but a quick question you say desk
        > side
        >     > cluster is it a single machine that will run a vm cluster?
        >     >
        >     > Regards,
        >     > Jonathan
        >     >
        >     > -----Original Message-----
        >     > From: Beowulf <beowulf-bounces at beowulf.org> On Behalf Of Douglas
        > Eadline
        >     > Sent: 23 August 2021 23:12
        >     > To: John Hearns <hearnsj at gmail.com>
        >     > Cc: Beowulf Mailing List <beowulf at beowulf.org>
        >     > Subject: Re: [Beowulf] List archives
        >     >
        >     > John,
        >     >
        >     > I think that was on twitter.
        >     >
        >     > In any case, I'm working with these processors right now.
        >     >
        >     > On the new Ryzens, the power usage is actually quite tunable.
        >     > There are three settings.
        >     >
        >     > 1) Package Power Tracking: The PPT threshold is the allowed socket
        > power
        >     > consumption permitted across the voltage rails supplying the
        > socket.
        >     >
        >     > 2) Thermal Design Current: The maximum current (TDC) (amps) that can
        > be
        >     > delivered by a specific motherboard's voltage regulator
        > configuration in
        >     > thermally-constrained scenarios.
        >     >
        >     > 3) Electrical Design Current: The maximum current (EDC) (amps) that
        > can be
        >     > delivered by a specific motherboard's voltage regulator
        > configuration in a
        >     > peak ("spike") condition for a short period of time.
        >     >
        >     > My goal is to tweak the 105W TDP R7-5800X so it draws power like
        > the
        >     > 65W-TDP R5-5600X
        >     >
        >     > This is desk-side cluster low power stuff.
        >     > I am using extension cable-plug for Limulus blades that have an
        > in-line
        >     > current meter (normally used for solar panels).
        >     > Now I can load them up and watch exactly how much current is being
        > pulled
        >     > across the 12V rails.
        >     >
        >     > If you need more info, let me know
        >     >
        >     > --
        >     > Doug
        >     >
        >     >> The Beowulf list archives seem to end in July 2021.
        >     >> I was looking for Doug Eadline's post on limiting AMD power and
        > the
        >     >> results on performance.
        >     >>
        >     >> John H
        >     >> _______________________________________________
        >     >> Beowulf mailing list, Beowulf at beowulf.org sponsored by Penguin
        >     >> Computing To change your subscription (digest mode or unsubscribe)
        >     >> visit
        >     >> https://urldefense.us/v3/__https://link.edgepilot.com/s/9c656d83/pBaaRl2iV0OmLHAXqkoDZQ?u=https:*__;Lw!!PvBDto6Hs4WbVuu7!f3kkkCuq3GKO288fxeGGHi3i-bsSY5P83PKu_svOVUISu7dkNygQtSvIpxHkE0XDvUGSdHI$
        >     >> /beowulf.org/cgi-bin/mailman/listinfo/beowulf
        >     >>
        >     >
        >     >
        >     > --
        >     > Doug
        >     >
        >     > _______________________________________________
        >     > Beowulf mailing list, Beowulf at beowulf.org sponsored by Penguin
        > Computing
        >     > To change your subscription (digest mode or unsubscribe) visit
        >     > https://urldefense.us/v3/__https://link.edgepilot.com/s/9c656d83/pBaaRl2iV0OmLHAXqkoDZQ?u=https:**Abeowulf.org*cgi-bin*mailman*listinfo*beowulf__;Ly8vLy8v!!PvBDto6Hs4WbVuu7!f3kkkCuq3GKO288fxeGGHi3i-bsSY5P83PKu_svOVUISu7dkNygQtSvIpxHkE0XDUP8JZUc$
        >     >
        >     --
        >     Doug
        >     _______________________________________________
        >     Beowulf mailing list, Beowulf at beowulf.org sponsored by Penguin
        > Computing
        >     To change your subscription (digest mode or unsubscribe) visit
        > https://urldefense.us/v3/__https://beowulf.org/cgi-bin/mailman/listinfo/beowulf__;!!PvBDto6Hs4WbVuu7!f3kkkCuq3GKO288fxeGGHi3i-bsSY5P83PKu_svOVUISu7dkNygQtSvIpxHkE0XDv6c1nNc$


    Beowulf mailing list, Beowulf at beowulf.org sponsored by Penguin Computing
    To change your subscription (digest mode or unsubscribe) visit https://urldefense.us/v3/__https://beowulf.org/cgi-bin/mailman/listinfo/beowulf__;!!PvBDto6Hs4WbVuu7!ecHWLYhc1jzzAUCLFQ4ytwxmbpUQLMlUimT-0_j2-2pXwettd-ICtaWd0ZFEAyswUQsd83c$ 

More information about the Beowulf mailing list