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February 4th, 2016

09:21 am: Flu!
Feeling so ill this morning that I could barely get out of bed, I reluctantly conceded that there was no way in hell I was even going to be able to make it out of the house, let alone into the office, and emailed in sick.

After trying and failing to find a thermometer, not that one was really necessary, I realised I'd got all the symptoms of classic flu and settled in to spend the next 24 hours alseep.


February 3rd, 2016

08:10 pm: Spiralling downwards
Despite not starting at 6am, like some of the others, today — actually I'm shamelessly retconning this from the weekend — was a real slog. I sat in with the rest of the gang as they ran through a CLE update, with the usual range of unexpected glitches.

As the day wore on, I felt increasingly tired and unwell. By the time we'd reached what should've been the end, I realised that I was very febrile and my body temperature was skyrocketing. But just as I'd accepted that and was working to put my post-upgrade tunings in prior to going home, we discovered an particular unfortunate oversight that required an extra hour of work; something I managed to do despite feeling worse by the second.

With the work finally done, I managed to catch the bus home, snuggling into my down jacket as if conditions were arctic and not unexpected warm for the time of year. When I got back, I texted my sister who advice her standard aggressive cocktail of antipyretics, and collapsed into bed, all the while dreading the morrow...

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January 30th, 2016

11:37 am: Sixteenth parkrun
Not the best run in the world this week, with a distinctly sluggish 21:07. Although, on balance, I'm not quite as disappointed as I might be: going was very slippery across the playing fields and despite shaking off last weekend's sore throat, something about the last week has left me feeling deeply exhausted in a way that might just excuse today's poor athletic performance...

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January 29th, 2016

07:39 am: Breaking in the shoes
After going at things a bit more heavily yesterday, a gentle bouldering session to start breaking in the new shoes. As expected they're very tight but they're also very precise and very positive, especially on overhangs. And as an added benefit, my Tenayas now feel like a comfy pair of slippers in comparison...


January 28th, 2016

08:05 pm: Topology-aware scheduling on the Cray XC40
Just finished an interesting and surprisingly simple bit of work to enable topology-aware scheduling on the Cray XC40. The system is supposed to be placement neutral, but experimental evidence has shown that certain real-world models suffer a 10-15 per cent degradation in performance when they span multiple electrical groups.

The Aries interconnect on the XC uses a hierarchical dragonfly topology. At the very lowest level are blades, which communicate with each other using the Aries ASIC. At the next level, every blade in a chassis can communicate with every other blade via the backplane. Further up the hierarchy, chassis are linked together in groups of six via a copper cables which run in two dimensions to create an electrical group. Finally, at the highest level, every electrical group contains multiple fibre optic links to every other electrical group.

The dragonfly topology is designed to ensure that every node is a minimum of four hops from every other. The routing algorithms, however, don't necessarily use the minimum-cost route: in the event of congestion in the network, it will randomly select another node in the system to use as a virtual root and then re-route traffic via this to find a new route to the destination. This means that routing between runs of an application is non-deterministic because it depends on traffic elsewhere in the interconnect; offering potential for varied performance, especially when individual tasks in an application are placed relatively distant from each other.

Fortunately, PBS Pro provides a means to address this: placement sets. These use arbitrary labels which can be added to each node — or vnode in the case of the Cray — and which can be used to apply best-fit guidelines to the allocation of nodes within the system. Best of all the steps required to enable this are trivial, and can be enabled as follows:

  1. create custom resources for each required placement element, e.g. blade, chassis, electrical
  2. tag each node or vnode in system with its resource, e.g. "set node cray_100 resources_available.electrical = g0", "set node cray_400 resources_available.electrical = g1" and so on until everything is labelled appropriately
  3. define a set of node sorts key in the server e.g. "set server node_sort_key = electrical". Multiple keys can be specified using commas, e.g. "set server node_sort_key = \"blade,chassis,electrical\"", with the smallest group first
  4. enable placement rules with "set server node_group_enable = true"

With placement enabled, PBS will attempt to assign the application to the first set that matches; if a particular set cannot be matched, PBS will move on to the next constraint until it finally reaches the implicit universal set which matches the entire system. This means that placement is treated as a preference rather than a hard scheduling rule.

It is possible for users to require a particular resource using the -l place=group=<resource> option to qsub, e.g. qsub -l place=group=electrical myjob.sh. Unlike a server placement set, a user-specified placement imposes a hard constraint on the job, preventing it from being started until the resource requirement can be satisfied — importantly it doesn't require a specific resource to be available, only that all nodes assigned to job share the same resource.

The performance of placement sets can be determined by post-processing the PBS accounting data. Simply extract the exec_nodes field — or exec_vnodes in the case of the Cray — and match the allocated hosts to their corresponding hardware groups. Examine a sample of data from before the change and a similar sample from after. If everything is working as expected — and the workload is mixed relative to size of the placement set — it should be possible to a clear decrease in the numbers of jobs spanning placement sets.

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January 26th, 2016

09:38 pm: Annihilation
On the advice of Dr S, I've been reading Jeff VanderMeer's delightfully wonderful Southern Reach Trilogy. Annihilation unfolds from the perspective of an unnamed biologist who has been sent into Area X, a zone of the southern US cut off from the rest of the world by a strange barrier.

The biologist's mission is the twelfth to be sent into the area by the Southern Reach Authority, the government agency responsible for investigating and containing the area. The mission, for experimental reasons which remain unclear, is made up of women: the biologist, the anthropologist, the surveyor, and the psychologist. The psychologist, armed with a series of phrases which can be used to trigger hypnotic states in the others, is in charge. None of the women have names; names were deemed unnecessary — maybe even hazardous — and were removed early in the group's training. They were supposed to have a linguist with them, but she dropped out when confronted with the prospect of crossing the boarder into Area X.

Reaching the base camp established by previous missions, the team discover an error in their map of the Area: a topographical anomaly which everyone bar the biologist insists is a tunnel; the biologist, our unreliable narrator, insists against all the evidence that it is a tower. Descending into the anomaly, the biologist finds a set of cryptic words written on the wall using a living fungus:

Where lies the strangling fruit that came from the hand of the sinner I shall bring forth the seeds of the dead...

The rest of the book focuses on the group's reaction to their experiences in the tower, especially as the biologist begin to realise that her encounter with the words is starting to change her. She investigates other aspects of the Area — strange flora and fauna, the lighthouse on the coast where one of the previous missions has come to particularly bloody end — but she keeps on finding herself drawn back to the mystery of the tower.

The mission has a dream-like quality, while Area has a logic all of its own that comes to infect the thinking of each mission sent to explore it. Some of the missions have returned. Some haven't. Some have returned horribly changed. There doesn't seem to be any rhyme or reason to it.

The book excels at an unpleasant, obsessive sense of horror, with the main characters fixated on something which they know is dangerous but which they can't quite seem to leave alone. In a lot of ways the biologist's obsession reminded me of the tower in Alastair Reynolds' superb gothic novella Diamond Dogs and its cast of characters willing to sacrifice almost anything to get to the secret at the heart of their mysterious spire.

As a standalone novel, Annihilation doesn't resolve anything; but it is not supposed to. Instead it's a beautifully written and delightfully unsettling scene-setter for events of the next novel in the trilogy...

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January 25th, 2016

07:58 pm: Manic Reading Project: looking back at 2015
We're into the last week of January — not quite sure how that happened! — and I've realised I haven't got round to talking about last year's reading. So, better late than never, here are a few thoughts on 2015's manic reading project starting with a few stats:

  • Number of books: 167
  • Number of authors: 58
  • Male to female ratio: 78 to 88
  • Genre split: 28 SF, 88 fantasy, 36 crime, 11 horror

On the qualitative front, high points included:

  • Emily St John Mandel's Station Eleven; every bit as good as everyone says
  • N.K. Jemisin's The Fifth Season; a superb start to what promises to be a really fascinating trilogy
  • Django Wexler's The Thousand Names and its sequels in the Shadow Campaigns series; one of my favourite discoveries of the year
  • Paul Cornell's The Witches of Lychford; note perfect and extremely enjoyable
  • Emma Newman's Planetfall; a wonderful combination of an unreliable narrator and an almost impossible to comprehend situation

Of the year's debuts, here are a few that really stood out and left me eager to see what their authors do next:

  • Genevieve Cogman's The Invisible Library; a fun, snarky steampunk fantasy that pushes all the right buttons
  • Peter Newman's The Vagrant; a intriguing world, an extremely accomplished narrative style, and a story in which only one member of the quartet of leading characters is able to speak — in part because one of them is a goat.
  • Fran Wilde's Updraft; a beautifully drawn world, a coming of age ritual, and the gradual discovery that the world isn't as simple and Manichaean as it seems

Dishonourable mentions? None! Because if you can't say anything nice, don't say anything at all. And because I'm not really sure I read anything truly awful last year. There were a couple of things that didn't suit my temperament, a couple of things where the author didn't quite manage to deliver on their initial premise, and one case where I felt that the writer had lost interest in series resulting in a very minor entry, but otherwise the quality was consistently pretty high.


January 24th, 2016

02:58 pm: Miura VS
Feeling in need of something to help with overhung problems which require serious heel work, I've picked up a new pair of La Sportivas at a solidly discounted price. I'd intended to try Katanas, but they didn't have any in my size, so I opted for a pair of Miura VSes instead:

Miura VS versus Tenaya Ra

They're a size smaller than my Tenayas although not quite as small as they look here: the Tenayas are old and thrashed, whereas the Miuras are new and aggressively down-turned in a way that shortens their apparent length.

I'm curious to see how I get on with them. I can't help feeling slightly intimidated: as though my current form isn't nearly good enough to justify quite such fancy shoes...


January 23rd, 2016

10:28 am: Fifteenth parkrun
An unexpectedly good one this morning with a solid time of 20:35 — my first PB since November — despite waking up with an unpleasantly sore throat and a mild feeling of malaise. I managed to miss M at the start — she told me she'd arrived late, which might well explain it — so, thinking I had no reason to wait around at the finish, I dashed off to get scanned and, feeling a bit grotty, skipped tea and hurried home.

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January 21st, 2016

08:10 pm: On being a stoic patient
Visiting the hygenist for a spot of dental work this afternoon I felt I had to appologise for last remnants of the epic bout of mouth ulcers I picked up over Christmas. When she took a look the hygenist winced, gave me the usual advice about getting them checked if they haven't healed after a few weeks, and said she'd do her best to avoid them.

I said that I got them all the time and wasn't too bothered, assuring her that they weren't all that bad and she shouldn't worry about it. Her reply? "There speaks someone who is used pain: any normal person with ulcers like that would be kicking up a terrible fuss..."

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