Do other PhD students do this too?

Send some results to your supervisor and then realise a few hours later that they are flawed and while the mistake is a minor one, you still feel like a bit of an idiot?

I do this *every* time it seems.


Enhanced by Zemanta

How slow is a fast computer?

Valgrind (Photo credit: Wikipedia)

I am working on a simulation environment for a NoC. The idea is that we can take a memory reference string – generated by Valgrind – and then test how long it will take to execute with different memory models for the NoC. It’s at an early stage and still quite crude.

The data set it is working with is of the order of 200GB, though that covers 18 threads of execution and so, very roughly speaking, it is 18 data sets of just over 10GB each. I have written some parallel Groovy/Java code to handle it and the code seems to work, though there is a lot of work to be done.

I am running it on the University of York’s compute server – a beast with 32 cores and a lot of memory. But it is slow, slow, slow. My current estimate is that it would take about 10 weeks to crunch a whole dataset. The code is slow because we have to synchronise the threads to model the inherent parallelism of the NoC. The whole thing is a demonstration – with a vengeance – of Amdahl’s Law.

Even in as long a project as a PhD I don’t have 10 weeks per dataset going free, so this is a problem!

A moment reached

Dougal and the Blue Cat
Dougal and the Blue Cat (Photo credit: Wikipedia)

I have just submitted my “qualifying dissertation” to the University of York.

Latterly I have been thinking of my PhD studies in terms of the film Dougal and the Blue Cat – I grew up at a bad time (the virtual collapse of cinema going in the 60s and 70s) and a bad place (in a civil war of varying intensity) and this was one of the few films I saw in my childhood (pre-13) in the cinema and it did have a profound impact!

In the film the Blue Cat has to undergo several trials on his route to kingship, rising in rank as he goes. I have just made my bid for the MSc stage (if the University fail me they may recommend I write up the literature review for a standard MSc). Next would come an MSc by Research, then an MPhil, then a PhD.

I don’t want any of them – except the last one of course – but it’s a decent guide to the amount of effort required, so this feels like a real milestone.

But it’s also the easiest part – I have to (assuming my dissertation is passed – my viva is in September) actually do some research and experimentation now!

Books about PhDs

I was wondering whether anyone has any recommendations for books about getting/doing a PhD. I am now reading The Unwritten Rules of PhD Research and it is very good, so I’d happily recommend it – it is one of those books that helps you see the underlying order in what appears to be the chaos going on around you.

For my domain of study Writing for Computer Science: The Art of effective Communication is also essential reading.

How to be a successful PhD student

Diagram of the gown, hood and bonnet used in g...
Diagram of the gown, hood and bonnet used in graduation/presentation ceremonies of Ph.Ds. (Photo credit: Wikipedia)

The answer is buy a soft backed note book.

Well, there is a bit of presumption going on here. I am not a successful PhD student as ultimately that is a binary thing: a successful PhD student is one who gets the doctorate. I have not even begun an experiment yet.

But I do feel like I am making progress like never before because of the soft-backed notebooks in my life.

To explain further I will use an analogy. When you are expecting your first child everyone says “it will change your life”. It is said so frequently it becomes boring and you think, every time you are told it – “as if I didn’t know”.

But when you have your first child you realise very quickly  just why everyone said that same thing to you – because it will change your life. They didn’t tell you enough of how deep and fundamental that change is.

So when you start your PhD everyone says “takes notes as you go along” and you think “of course”. But you don’t do it properly. You mix your notes up with everything else in this or that notebook and then months later you come back and think “what does that paper say again – these notes are a mess”.

And then you realise that you must have the notebook with you every time you read a paper and that notebook is your most important possession. And then you start to get it right…

End of term feeling

Christmas in the post-War United States
(Photo credit: Wikipedia)

Forty years ago about this time I had my nice-est ever educational experience when, to my complete surprise, I won the P3 Christmas story prize in Mrs MacManus’s class in Holy Child Primary School. I still remember the way disappointment at not coming third or second was turned into pure joy by actually winning, and being able to go home and tell my mother and show her the prize (some chocolate I think).

Twelve years later I remember the last Friday of my first (not very happy) term at Edinburgh University. I had no lectures to go to and a small amount of money to spend – my mother sent me a cheque which was enough to allow me to get more money from the bank, and that too was a care-free and happy day.

Today is another last Friday of term. I have just presented my literature review seminar to the real time systems group here at York and it was deemed more than acceptable, so I have made it through the first stage of the PhD process.

But care-free? Not really, because it is absolutely bucketing with rain outside (I am sitting in the library) and the BBC forecast is that this will go on all day. Even the 1km between here and my supervisor’s office on the eastern campus is going to see me absolutely drenched.

Cannot win them all.

Universities target plagiarism but maybe fraud should be the real worry

A simple graphic explaining the differences be...
A simple graphic explaining the differences between plagiarism and copyright issues (Photo credit: Wikipedia)

The first thing I had to do when I started work on my PhD course at York was to complete an online learning unit on plagiarism.

It was fairly tedious, as I had already had to sit through several hours worth of lectures at Birkbeck on the issue when preparing for my MSc project report.

Maybe plagiarism is the big issue with students – after all there are thousands of scientific papers out there and the temptation to “rip and paste” much be great for students struggling with deadlines.

In in my case I took no chances – this is the very first sentence of the report:

Multiprogramming computer systems face a fundamental problem of being able to run programs that, in sum, require more memory than is physically available (Tanenbaum, 2009, pp. 173 -174).

Is it over the top to cite for such a basic idea? Perhaps, but it didn’t harm anyone.

Yet it seems that plagiarism is not the real issue with researchers (and this presumably includes PhD students) – just 9.8% of biomedical paper retractions were for this reason. But 43.3% were for fraud.

And the proportion of crooked papers is rising – up by an order of magnitude between 1976 and 2007 – and that’s a rising proportion of a rising number too. But the better news is that this is an increase from 3 to 83 (out of 310,000 in 1976 and 868,000 in 2007).

Could I have fiddled my MSc report (I didn’t of course) – I suppose I could. Although I supplied all the software I used to conduct my experiments and plot their results (apart from some R used to draw pie charts and so on), I doubt that anyone would have had the time to actually replicate the results. Perhaps if my paper had broken new ground (as opposed to reconfirming some thirty year old findings that did not seem to have been validated for modern software before) then maybe somebody would have had to do that…