I wouldn't call the view optimistic. Rather I would call it the result of 2
years of observation while I wrote these kernels. If anything, I'm a bigger
pessimist than Ross. One of the biggest problems with GPU adoption right
now is the $h!+storm of half-a$$3d GPU LPU papers out there written by
computer scientists who port half an application to the GPU but possess zero
zip nada null low-level optimization talent and ultimately do little more
than provide warehouses of ammo for the GPUs are no better than CPUs crowd.
In any event, AMBER's performance is what happens when one both ports the
entire algorithm to the GPU and then ruthlessly optimizes it once it's
there. And that's currently the only way to illustrate exactly what GPUs
can do. The same issue is faced by game console programmers and they'd
likely agree with the above. Unfortunately, there aren't many of those
sorts in the sciences.
Scott
2011/9/13 Marek Maly <marek.maly.ujep.cz>
> Hello Scott,
> thanks for your optimistic view :))
> After this short discussion I think that the main problem
> (considering just single GPU jobs) will be probably "just"
> sufficient cooling ...
>
> Best wishes,
>
> Marek
>
>
> Dne Tue, 13 Sep 2011 20:15:27 +0200 Scott Le Grand <varelse2005.gmail.com>
> napsal/-a:
>
> > AMBER is designed to run the entire simulation in GPU-space. The CPU
> > acts
> > as a glorified foreman shouting out directions to the GPU as to which
> > tasks
> > it should run. If AMBER were rewritten from the ground up, that role
> > could
> > be removed entirely. The upshot is that for single-GPU runs, you could
> > probably stuff 8 GPUs into a single box and barely notice the difference.
> > And you could also use a cheap consumer CPU as well since it's mostly
> > sitting on its butt waiting on the GPU(s).
> >
> > The difference between using a 4 year-old $20 CPU and a current $1000+
> > CPU
> > in this situation is about 2-3%.
> >
> >
> >
> >
> > 2011/9/13 Marek Maly <marek.maly.ujep.cz>
> >
> >> Hi Ross,
> >>
> >> first of all thanks a lot for your complex answer !
> >> In fact I assume mainly independent single GPU jobs. So if I understood
> >> well, in such case there should not be problem considering below
> >> mentioned
> >> motherboard/CPU/4xGPU. Am I right ?
> >>
> >> Best wishes,
> >>
> >> Marek
> >>
> >>
> >>
> >>
> >> Dne Tue, 13 Sep 2011 18:53:34 +0200 Ross Walker <ross.rosswalker.co.uk>
> >> napsal/-a:
> >>
> >> > Hi Marek,
> >> >
> >> > I would say that the answer is, with caveats, not really. The reason
> >> for
> >> > this is not a core to GPU ratio argument per se but actually one of
> >> > memory
> >> > bandwidth. For a single socket motherboard there is no way that it can
> >> > drive
> >> > 4 PCI-E sockets flat out at x16 speed. Hence you are always going to
> >> get
> >> > contention. Typically I would say never go beyond 2 GPUs per node for
> >> a
> >> > single socket system. 4 GPUs per node is pushing it for a dual socket
> >> > system
> >> > even with the highest CPU FSB speed you can get so on a single socket
> >> > system
> >> > with a low end CPU it is definitely not going to cut it.
> >> >
> >> > Now if you only plan to run single GPU jobs. I.e. 4 independent jobs
> >> at
> >> > once
> >> > with reasonably large values for ntpr, ntwx etc then it is probably
> >> not
> >> > an
> >> > issue since the memory bandwidth only really comes into play at each
> >> > output
> >> > file or trajectory write for most types of calculations. However,
> >> trying
> >> > to
> >> > run in parallel where a single job spans GPUs it really all comes down
> >> > to a
> >> > combination of the aggregate memory bandwidth of the main CPU memory
> >> per
> >> > GPU
> >> > and the PCI-E bandwidth to each GPU when all are communicating flat
> >> out
> >> > at
> >> > the same time. You might be able to get speedup across 2 of the GPUs
> >> if
> >> > you
> >> > leave the other two idle. However, running two sets of dual GPU runs
> >> or
> >> > running a single 4 GPU run is likely to cause so much contention that
> >> see
> >> > little or no speedup.
> >> >
> >> > So it really comes down to a case of the type of jobs you want to run.
> >> >
> >> > I hope that helps.
> >> >
> >> > All the best
> >> > Ross
> >> >
> >> >> -----Original Message-----
> >> >> From: Marek Maly [mailto:marek.maly.ujep.cz]
> >> >> Sent: Tuesday, September 13, 2011 7:19 AM
> >> >> To: amber.ambermd.org
> >> >> Subject: [AMBER] Sufficient CPU cores/GPU ratio ?
> >> >>
> >> >> Hi all,
> >> >>
> >> >> just a very quick technical question. I would like to know if 4 core
> >> >> CPU
> >> >> "Intel Core i7-960" might be sufficient for
> >> >> 4 GPU machine (motherboard: Asus P6T7 WS SuperComputer - Intel X58
> >> ).
> >> >> I
> >> >> mean if ratio 1 CPU core/ 1 GPU might
> >> >> be here sufficient also considering some requirements (on CPU) for
> >> >> managing operating system etc.
> >> >>
> >> >> Thanks in advance for any relevant comment !
> >> >>
> >> >> Best wishes,
> >> >>
> >> >> Marek
> >> >>
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Received on Tue Sep 13 2011 - 13:00:05 PDT
