[Beowulf] [EXTERNAL] Re: Rant on why HPC isn't as easy as I'd like it to be. [EXT]

Stu Midgley sdm900 at gmail.com
Wed Sep 22 07:01:10 UTC 2021

We actually help people use our commercial HPCaaS (dug.com/hpcaas) and work
with them to get great performance on our platform.  With a little help,
they get way better performance and save money compared with the public

Interestingly, it is the bioinformatics groups that benefit the most.  We
get their workflows running really well, using all threads on a node,
making good use of the IO (our all flash VAST system helps a lot)... and
they get a LOT of data and work done.

@Tim - we even provide the HPC for Imperial College's Masters in Advanced

Supporting the users goes a long way.


On Wed, Sep 22, 2021 at 4:57 AM Lux, Jim (US 7140) via Beowulf <
beowulf at beowulf.org> wrote:

> This is interesting, because the figure of merit is “time to first answer”
> – that’s much like my iterative antenna modeling task – The cost of the
> computing is negligible compared to the cost of the engineer(s) waiting for
> the results.
> Running the AWS calculator, a EC instance is $74/month when used 2hrs/day,
> so let’s call that about $1/hr. With an engineer billing out at $100/hr,
> spinning up 50 instances isn’t all that unreasonable.
> *From: *Beowulf <beowulf-bounces at beowulf.org> on behalf of Tim Cutts <
> tjrc at sanger.ac.uk>
> *Date: *Tuesday, September 21, 2021 at 5:02 AM
> *To: *John Hearns <hearnsj at gmail.com>
> *Cc: *"beowulf at beowulf.org" <beowulf at beowulf.org>
> *Subject: *[EXTERNAL] Re: [Beowulf] Rant on why HPC isn't as easy as I'd
> like it to be. [EXT]
> I think that’s exactly the situation we’ve been in for a long time,
> especially in life sciences, and it’s becoming more entrenched.  My
> experience is that the average user of our scientific computing systems has
> been becoming less technically savvy for many years now.
> The presence of the cloud makes that more acute, in particular because it
> makes it easy for the user to effectively throw more hardware at the
> problem, which reduces the incentive to make their code particularly fast
> or efficient.  Cost is the only brake on it, and in many cases I’m finding
> the PI doesn’t actually care about that.  They care that a result is being
> obtained (and it’s time to first result they care about, not time to
> complete all the analysis), and so they typically don’t have much time for
> those of us who are telling them they need to invest in time up front
> developing and optimising efficient code.
> And cost is not necessarily the brake I thought it was going to be
> anyway.  One recent project we’ve done on AWS has impressed me a great
> deal.  It’s not terribly CPU efficient, and would doubtless, with
> sufficient effort, run much more efficiently on premise.  But it’s
> extremely elastic in its nature, and so a good fit for the cloud.   Once a
> week, the project has to completely re-analyse the 600,000+ COVID genomes
> we’e sequenced so far, looking for new branches in the phylogenetic tree,
> and to complete that analysis inside 8 hours.   Initial attempts to naively
> convert the HPC implementation to run on AWS looked as though they were
> going to be very expensive (~$50k per weekly run).  But a fundamental
> reworking of the entire workflow to make it as cloud native as possible, by
> which I mean almost exclusively serverless, has succeeded beyond what I
> expected.  The total cost is <$5,000 a month, and because there is
> essentially no statically configured infrastructure at all, the security is
> fairly easy to be comfortable about.  And all of that was done with no
> detailed thinking about whether the actual algorithms running in the
> containers are at all optimised in a traditional HPC sense.  It’s just not
> needed for this particular piece of work.  Did it need software developers
> with hardcore knowledge of performance optimisation?  No.  Was it rapid to
> develop and deploy?  Yes.  Is the performance fast enough for UK national
> COVID variant surveillance?  Yes.  Is it cost effective?  Yes.  Sold!  The
> one thing it did need was knowledgeable cloud architects, but the cloud
> providers can and do help with that.
> Tim
> --
> Tim Cutts
> Head of Scientific Computing
> Wellcome Sanger Institute
> On 21 Sep 2021, at 12:24, John Hearns <hearnsj at gmail.com> wrote:
> Some points well made here. I have seen in the past job scripts passed on
> from graduate student to graduate student - the case I am thinking on was
> an Abaqus script for 8 core systems, being run on a new 32 core system. Why
> WOULD a graduate student question a script given to them - which works.
> They should be getting on with their science. I guess this is where
> Research Software Engineers come in.
> Another point I would make is about modern processor architectures, for
> instance AMD Rome/Milan. You can have different Numa Per Socket options,
> which affect performance. We set the preferred IO path - which I have seen
> myself to have an effect on latency of MPI messages. IF you are not
> concerned about your hardware layout you would just go ahead and run,
> missing  a lot of performance.
> I am now going to be controversial and common that over in Julia land the
> pattern seems to be these days people develop on their own laptops, or
> maybe local GPU systems. There is a lot of microbenchmarking going on. But
> there seems to be not a lot of thought given to CPU pinning or shat happens
> with hyperthreading. I guess topics like that are part of HPC 'Black Magic'
> - though I would imagine the low latency crowd are hot on them.
> I often introduce people to the excellent lstopo/hwloc utilities which
> show the layout of a system. Most people are pleasantly surprised to find
> this.
> -- The Wellcome Sanger Institute is operated by Genome Research Limited, a
> charity registered in England with number 1021457 and a company registered
> in England with number 2742969, whose registered office is 215 Euston Road,
> London, NW1 2BE.
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Dr Stuart Midgley
sdm900 at gmail.com
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