[Beowulf] Re: energy costs and poor grad students

Mark Kosmowski mark.kosmowski at gmail.com
Wed Jul 2 11:19:42 EDT 2008


On 7/2/08, Joe Landman <landman at scalableinformatics.com> wrote:
> Hi Mark
>
> Mark Kosmowski wrote:
> > I'm in the US.  I'm almost, but not quite ready for production runs -
> > still learning the software / computational theory.  I'm the first
> > person in the research group (physical chemistry) to try to learn
> > plane wave methods of solid state calculation as opposed to isolated
> > atom-centered approximations and periodic atom centered calculations.
> >
>
> Heh... my research group in grad school went through that transition in the
> mid 90s.  Went from an LCAO-type simulation to CP like methods.  We needed a
> t3e to run those (then).
>
> Love to compare notes and see which code you are using someday.
> On-list/off-list is fine.

Right now I'm using CPMD.  This is the first package I've looked at
and wrestled with the 32-bit limitations of memory allocation prior to
the debut of the Opterons.  I was at the cusp of buying UltraSparc
hardware at student pricing to go forward when the Opterons were
released to market, so I decided to go with the PC hardware I was
already familiar with.

We're comparing calculations to inelastic neutron scattering
experiments and it looks like abinit or quantum espresso might be a
better choice for this to do vibrational analysis at q-space other
than the gamma point.  Speaking of, I only have an eighth of a clue
about understanding k-points (and, by extension, q-space).  If anyone
can suggest some reading for this topic that even a part-time
chemistry student can understand it would be greatly appreciated.

>
> > It is turning out that the package I have spent the most time learning
> > is perhaps not the best one for what we are doing.  For a variety of
> > reasons, many of which more off-topic than tac nukes and energy
> > efficient washing machines ;) , I'm doing my studies part-time while
> > working full-time in industry.
> >
>
> More power to ya!  I did mine that way too ... the writing was the hardest
> part.  Just don't lose focus, or stop believing you can do it. When the
> light starts getting visible at the end of the process, it is quite
> satisfying.
>
> I have other words to describe this, but they require a beer lever to get
> them out of me ...

I make mead on occaision - if you're ever in central NY (Syracuse -
Rome - Utica area)...

Speaking of satisfaction, I did teach myself enough Fortran to add to
the CPMD code to give an output format natively readable by aClimax
(used to calculate harmonics from fundamental frequencies for INS).
This is/will be included in the recently/soon to be released version
of CPMD.  Heck, there's one or two pages of dissertation right there.
:)

>
> > I think I have come to a compromise that can keep me in business.
> > Until I have a better understanding of the software and am ready for
> > production runs, I'll stick to a small system that can be run on one
> > node and leave the other two powered down.  I've also applied for an
> > adjunt instructor position at a local college for some extra cash and
> > good experience.  When I'm ready for production runs I can either just
> > bite the bullet and pay the electricity bill or seek computer time
> > elsewhere.
> >
>
> Give us a shout when you want to try the time on a shared resource. Some
> folks here may be able to make good suggestions.  RGB is a physics guy at
> Duke, doing lots of simulations, and might know of resources. Others here
> might as well.
>
> Joe
>
>

Sounds good.  The big thing is getting a bit better understanding of
the theory, especially DFT dispersion correction to account for
hydrogen bonding.  I'm thinking that I will learn about DFT dispersion
correction with CPMD to at least get a reasonable understanding and
then consider learning one of the other packages to do q-space
calculations.

> >
> > Thanks for the encouragement,
> >
> > Mark E. Kosmowski
> >
> > On 7/1/08, ariel sabiguero yawelak <asabigue at fing.edu.uy> wrote:
> >
> > > Well Mark, don't give up!
> > > I am not sure which one is your application domain, but if you require
> 24x7
> > > computation, then you should not be hosting that at home.
> > > On the other hand, if you are not doing real computation and you just
> have a
> > > testbed at home, maybe for debugging your parallel applications or
> something
> > > similar, you might be interested in a virtualized solution. Several
> years
> > > ago, I used to "debug" some neural networks at home, but training
> sessions
> > > (up to two weeks of training) happened at the university.
> > > I would suggest to do something like that.
> > > You can always scale-down your problem in several phases and save the
> > > complete data-set / problem for THE RUN.
> > >
> > > You are not being a heretic there, but suffering energy costs ;-)
> > > In more places that you may believe, useful computing nodes are being
> > > replaced just because of energy costs. Even in some application domains
> you
> > > can even loose computational power if you move from 4 nodes into a
> single
> > > quad-core (i.e. memory bandwidth problems). I know it is very nice to be
> > > able to do everything at home.. but maybe before dropping your studies
> or
> > > working overtime to pay the electricity bill, you might want to
> reconsider
> > > the fact of collapsing your phisical deploy into a single virtualized
> > > cluster. (or just dispatch several threads/processes in a single
> system).
> > > If you collapse into a single system you have only 1 mainboard, one HDD,
> one
> > > power source, one processor (physically speaking), .... and you can
> achieve
> > > almost the performance of 4 systems in one, consuming the power of....
> well
> > > maybe even less than a single one. I don't want to go into discussions
> about
> > > performance gain/loose due to the variation of the hardware
> architecture.
> > > Invest some bucks (if you haven't done that yet) in a good power source.
> > > Efficiency of OEM unbranded power sources is realy pathetic. may be
> 45-50%
> > > efficiency, while a good power source might be 75-80% efficient. Use the
> > > energy for computing, not for heating your house.
> > > What I mean is that you could consider just collapsing a complete
> "small"
> > > cluster into single system. If your application is CPU-bound and not I/O
> > > bound, VMware Server could be an option, as it is free software
> > > (unfortunately not open, even tough some patches can be done on the
> > > drivers). I think it is not possible to publish benchmarking data about
> > > VMware, but I can tell you that in long timescales, the performance you
> get
> > > in the host OS is similar than the one of the guest OS. There are a lot
> of
> > > problems related to jitter, from crazy clocks to delays, but if your
> > > application is not sensitive to that, then you are Ok.
> > > Maybe this is not a solution, but you can provide more information
> regarding
> > > your problem before quitting...
> > >
> > > my 2 cents....
> > >
> > > ariel
> > >
> > > Mark Kosmowski escribió:
> > >
> > >
> > > > At some point there a cost-benefit analysis needs to be performed.  If
> > > > my cluster at peak usage only uses 4 Gb RAM per CPU (I live in
> > > > single-core land still and do not yet differentiate between CPU and
> > > > core) and my nodes all have 16 Gb per CPU then I am wasting RAM
> > > > resources and would be better off buying new machines and physically
> > > > transferring the RAM to and from them or running more jobs each
> > > > distributed across fewer CPUs.  Or saving on my electricity bill and
> > > > powering down some nodes.
> > > >
> > > > As heretical as this last sounds, I'm tempted to throw in the towel on
> > > > my PhD studies because I can no longer afford the power to run my
> > > > three node cluster at home.  Energy costs may end up being the straw
> > > > that breaks this camel's back.
> > > >
> > > > Mark E. Kosmowski
> > > >
> > > >
> > > >
> > > >
> > > > > From: "Jon Aquilina" <eagles051387 at gmail.com>
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > > > > not sure if this applies to all kinds of senarios that clusters are
> used
> > > > >
> > > >
> > > in
> > >
> > > >
> > > > > but isnt the more ram you have the better?
> > > > >
> > > > > On 6/30/08, Vincent Diepeveen <diep at xs4all.nl> wrote:
> > > > >
> > > > >
> > > > >
> > > > > > Toon,
> > > > > >
> > > > > > Can you drop a line on how important RAM is for weather
> forecasting in
> > > > > > latest type of calculations you're performing?
> > > > > >
> > > > > > Thanks,
> > > > > > Vincent
> > > > > >
> > > > > >
> > > > > > On Jun 30, 2008, at 8:20 PM, Toon Moene wrote:
> > > > > >
> > > > > > Jim Lux wrote:
> > > > > >
> > > > > >
> > > > > >
> > > > > > > Yep.  And for good reason.  Even a big DoD job is still tiny in
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > Nvidia's
> > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > >
> > > > > > > > scale of operations. We face this all the time with NASA work.
> > > > > > > >  Semiconductor manufacturers have no real reason to produce
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > special purpose
> > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > > > or customized versions of their products for space use,
> because
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > they can
> > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > > > sell all they can make to the consumer market. More than once,
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > I've had a
> > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > > > phone call along the lines of this:
> > > > > > > > "Jim: I'm interested in your new ABC321 part."
> > > > > > > > "Rep: Great. I'll just send the NDA over and we can talk about
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > it."
> > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > > > "Jim: Great, you have my email and my fax # is..."
> > > > > > > > "Rep: By the way, what sort of volume are you going to be
> using?"
> > > > > > > > "Jim: Oh, 10-12.."
> > > > > > > > "Rep: thousand per week, excellent..."
> > > > > > > > "Jim: No, a dozen pieces, total, lifetime buy, or at best
> maybe
> > > > > > > >
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > every
> > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > > > year."
> > > > > > > > "Rep: Oh...<dial tone>"
> > > > > > > > {Well, to be fair, it's not that bad, they don't hang up on
> you..
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > Since about a year, it's been clear to me that weather
> forecasting
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > (i.e.,
> > >
> > > >
> > > > >
> > > > > >
> > > > > > > running a more or less sophisticated atmospheric model to
> provide
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > weather
> > >
> > > >
> > > > >
> > > > > >
> > > > > > > predictions) is going to be "mainstream" in the sense that every
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > business
> > >
> > > >
> > > > >
> > > > > >
> > > > > > > that needs such forecasts for its operations can simply run them
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > in-house.
> > >
> > > >
> > > > >
> > > > > >
> > > > > > > Case in point:  I bought a $1100 HP box (the obvious target
> group
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > being
> > >
> > > >
> > > > >
> > > > > >
> > > > > > > teenage downloaders) which performs the HIRLAM limited area
> model
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > *on the
> > >
> > > >
> > > > >
> > > > > >
> > > > > > > grid that we used until October 2006* in December last year.
> > > > > > >
> > > > > > > It's about twice as slow as our then-operational 50-CPU Sun Fire
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > 15K.
> > >
> > > >
> > > > >
> > > > > >
> > > > > > > I wonder what effect this will have on CPU developments ...
> > > > > > >
> > > > > > > --
> > > > > > > Toon Moene - e-mail: toon at moene.indiv.nluug.nl - phone: +31 346
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > 214290
> > >
> > > >
> > > > >
> > > > > >
> > > > > > > Saturnushof 14, 3738 XG  Maartensdijk, The Netherlands
> > > > > > > At home: http://moene.indiv.nluug.nl/~toon/
> > > > > > > Progress of GNU Fortran:
> > > > > > >
> > > > > >
> > > > >
> > > >
> > > http://gcc.gnu.org/ml/gcc/2008-01/msg00009.html
> > >
> > > >
> > > > >
> > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > _______________________________________________
> > > > > > Beowulf mailing list, Beowulf at beowulf.org
> > > > > > To change your subscription (digest mode or unsubscribe) visit
> > > > > > http://www.beowulf.org/mailman/listinfo/beowulf
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > --
> > > > > Jonathan Aquilina
> > > > >
> > > > >
> > > > >
> > > > _______________________________________________
> > > > Beowulf mailing list, Beowulf at beowulf.org
> > > > To change your subscription (digest mode or unsubscribe) visit
> > > >
> > > http://www.beowulf.org/mailman/listinfo/beowulf
> > >
> > > >
> > > >
> > > >
> > >
> >
> > _______________________________________________
> > Beowulf mailing list, Beowulf at beowulf.org
> > To change your subscription (digest mode or unsubscribe) visit
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> >
>
>
> --
> Joseph Landman, Ph.D
> Founder and CEO
> Scalable Informatics LLC,
> email: landman at scalableinformatics.com
> web  : http://www.scalableinformatics.com
>       http://jackrabbit.scalableinformatics.com
> phone: +1 734 786 8423
> fax  : +1 866 888 3112
> cell : +1 734 612 4615
>

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