All entries for June 2019

June 27, 2019

"And then it just clicked

A bit more of the general "philosophy of programming" today, based on a quote I found on the brilliant "C FAQ", currently here and hopefully there to stay. The quote is from Q 18.9b, on learning resources and says:

A word of warning: there is some excellent code out there to learn from, but there is plenty of truly bletcherous code, too. If you find yourself perusing some code which is scintillatingly clear and which accomplishes its task as easily as it ought to (if not more so), do learn everything you can from that code. But if you come across some code that is unmanageably confusing, that seems to be operating with ten bandaged thumbs and boxing gloves on, please do not imagine that that's the way it has to be; if nothing else, walk away from such code having learned only that you're not going to commit any such atrocities yourself.

It's a very good idea to read other people's code when learning - either completely in the wild, or in the form of snippets on sites like Stack Overflow. But always keep in mind that there is some truly terrible code out there, even in commercial packages. It's easy to fall into the trap of thinking that your problem is just "soooo hard" that it just can't be done elegantly, or readably, or even conforming to standards, at all, and mostly that just isn't the case.

Obviously, different people will find different things to be readable, clear, elegant etc. I have an Undergrad degree including Maths, and I rather like the shorthand notation of sums and sets and implication. To some people though, the symbols are simply "all Greek" (pun thoroughly intended). Writing things in a way everybody will find clear is thus often a losing battle. But there is one very very important thing to avoid at all possible costs : the anti-click.

The Click

The 'click' is that feeling of clarity when you jump from grasping the parts of the thing to understanding the whole. I get it a lot with things like Anagram word puzzles, or even song intro quizzes (the kind where you're meant to guess the title). One moment you're seeing a jumble of letters, trying to hold all dozen in your head, and the next you can 'see' the word it must be. Similarly, one moment you're following along the notes and words and the next the key lyric pops into your head and the song is obvious. Optical illusions do it too - and once you've seen it you struggle to "un-see" it again.

This is the 'click' and it's a real asset that you can develop with practice, by reading plenty of code, and writing plenty of code, until you can 'get the gist' of the thing easily.

Symptoms and Diagnosis

It also comes up a lot in debugging - you just 'get the hang' of the way an error pops up, and know what must have happened. That's why reading issue trackers or mailing lists can feel so confusing - the people answering the questions seem to have some mysterious knack for guessing what's wrong from the most un-intuitive errors.

For example, writing in C you may use a function like 'sqrt', and get a 'undefined symbol' error from the linker, which is saying that it can't work out what that function is. So, being logical, you go back and check that you have absolutely definitely included the "math.h" header, which absolutely definitely contains a sqrt function. What did you do wrong? Well probably you forgot to compile using the '-lm' flag, which means "link against the maths library", because that library contains a lot of compiled code (the code isn't in the math.h file). This error can seem very weird, but actually, once you know the cause, it's "obvious".

We had a go at writing a catalogue of programming bugs a while ago, which tried to sort of encapsulate the 'symptoms' of a bug (available here, PDF download). Any bugs, errors or omissions please let us know (rse {@} Once you see enough bugs, you'll probably start to 'click' and 'just know' what to look for.

The Anti-Click

I mentioned optical illusions up there, and how you can't seem to "unsee" them. Sometimes code has this same sort of thing - an illusory apparent action or cause which is actually not real. This can be awkward and dangerous, because you, and others, will struggle to "unsee" it. It's hard to give an example that isn't really contrived, so I shall fall back onto a classic bit of C: pointer declarations.

In C, you declare pointers using a '*', such as `int * p;`. This is fine. But what about `int * p, q;`? Is q a pointer? No, it's not. Some people argue that the "proper style" will prevent this anti-click, that is, writing that as `int *p, q` and associating closely the * and the p. This is surprisingly hotly debated (e.g. hereand here) with some really tempting anti-clicks (such as here- do read the answers, as the OP there is wrong) but ultimately does need careful thought. You're probably best using whatever you personally find clearest, and changing that only after consideration.

The golden rule - DO NOT write misleading code, docs etc etc. Make it wordy if you have to, but it's not worth the hassle of an obvious, yet wrong, interpretation. As a last resort, just put in a comment explaining what this does not mean, or does not do.

And the flip side - NEVER trust the click - always verify. Always step through line by line and be sure you're right!

Click Immunity

One last thing - there are people for whom some things just never do 'click'. It's very hard to describe, but easy to spot. It's sort of like trying to explain computers to that one relative or quadratic equations to somebody who can't do maths. They're clearly not stupid, but they just don't seem to 'get it'. You explain one thing, like how to print, and it works, but now they need to print from a different program and isn't it just obvious that you do the same thing?

Some people seem to have a knack even beyond that - they don't just "not get it", it's worse! Bug reports display this sometimes - somebody who always gives a lot of information but somehow never includes the vital pieces. They'll post a 100MB log file, but forget to mention which OS. They'll explain exactly what commands they ran but omit some vital parameter.

There's two sides to this - dealing with people who don't click, and dealing when you can't click.

Hell is Other People

Usually you only have one real option to deal with other people who don't get it - guide them through it. Mostly, it just takes longer, not happens never. You probably want to try explaining things different ways, because what feels neat and obvious to you isn't to them. The Socratic style is handy - ask them what they're trying to do, or what they feel they should do, rather than telling.

I just don't GET IT

I expect everybody, sooner or later, finds something that just doesn't click right. You don't get it - it's unintuitive, your gut feeling is always wrong etc. So what do you do? Treat yourself the same as you would somebody else - read different explanations until you find one that fits you. Ask yourself "what am I trying to achieve". Ask yourself "when I ask this question, what might somebody need to answer it" - and if in doubt, ask them! Stop assuming anything, and walk through every step of the problem.

Walk away and do something else - give your brain time to work things through. Never stop asking questions and always learn from the answers. You don't need to 'click' to do something, you just need to watch for wrong intuition. Keep notes - add comments in your code for you to come back to.

Remember - intution is a skill like any other. It can be wrong. And while you might not have a talent for this thing, but with effort, you can make it work.

June 12, 2019

Datastructures – Linked lists part 2

Follow-up to Datastructures – Linked lists part 1 from Research Software Engineering at Warwick

This entry is back to the subject of linked lists. In the previous post on linked lists we described the idea of a linked list and how you created one. In this post I'm going to talk about how you remove items. The idea is pretty simple, to remove item "n" you want item "n-1" to believe that the item after it is now item "n+1" and you want item "n+1" to believe that the item before it is item "n-1". There are a few wrinkles to deal with if the item is at the start of the list (recall that this is usually called the `head` element) but mostly the idea is this simple. This is most easily shown by a code example recalling the definition of linked list items from part 1.

void remove_item(llitem *item, llitem *head)
    if (item->prev) {
    /*Item has an item before it in the list*/
    item->prev->next = item->next;
  } else {
    /*Item does not have an item before it. It is the head*/
    head = item->next;
    item->next->prev = NULL;

  if(item->next) {
    item->next->prev = item->prev;


SUBROUTINE remove_item(item, head)
  TYPE(llitem), POINTER, INTENT(INOUT) :: item !Item to be removed
  TYPE(llitem), POINTER, INTENT(INOUT) :: head !Head of linked list

  IF (ASSOCIATED(item%prev)) THEN
    !Item has an item before it in the list
    item%prev%next => item%next
    !Item does not have an item before it. It is the head
    head => item%next
    item%next%prev => NULL()

  IF (ASSOCIATED(item%next)) THEN
    item%next%prev => item%prev


END SUBROUTINE remove_item

This routine removes an item from a linked list and deals with changing the head of the list to match if needed. After the item is removed from the list it is deallocated. You might not want to do this automatically when an item is removed from a list (you can have multiple lists and freely move items between them) but you do have to do it when you are finished with the item or you will have a memory leak. One of the downsides of linked lists is that since they involve direct pointer operations in normal use memory leaks are a greater risk than in many data structures.

You can also see what's going on in a diagram showing how you remove both a "normal" and a "head" item from the linked list. In both cases links shown in green are new links and links shown in orange are links that are being deleted or changed.

Normal Linked List delete

Removing head element of a linked list

Hopefully the idea is quite clear between the code and the diagrams. If "item" is item "n" in the list then "n-1" is item->prev and "n+1" is item->next. Either or both of these items may not exist if "item" is either the start or the end of the list so you have to cope with these cases. So to update the next element of "n-1" you have to set "item->prev->next" which looks a bit odd but makes sense if you unpack it. Similarly the "prev" element of "n+1" is "item->next->prev".

You will notice that the links on the item being removed aren't touched and the code simply relies on that item being deleted immediately. In a system where you want to retain an item (perhaps to add it to another linked list) you'll probably want to nullify it's prev and next pointers after you remove it from the list.

That code will remove any item from the linked list that it is in. There is however a problem if you have multiple lists, each with it's own head element. Imagine that I tried to use that "remove_item" function where I passed it an element from one list but the head from a different list. So long as "item" isn't the first item of the list that it is in then nothing would go wrong but as soon as it is it would replace the head of the second list. This would cause real problems

  1. The list that "item" was in will become invalid. Because it's "head" element is never updated it will still point to the now deleted "item" and will sooner or later fail when you try to use it. It might, for a while, look as though "item" hasn't been deleted because of this
  2. The original list that you specified the "head" from will now be lost completely. The only reference that you have to a linked list is the head element so if anything happens to this the memory is lost forever. You have both lost data and caused a memory leak
  3. You have also moved data. The list that you specified the head from will now be a valid list, but it will be the list that "item" was originally part of, not the list that is meant to be there.

This type of error in a linked list thus causes memory leaks, segmentation faults and data corruption all in one nice package so you have to be careful to avoid it. You can program in safeguards to prevent doing things like this but they do slow down the operation of the linked list and require extra memory (as well as making rather harder some nice tricks that you can do with linked lists that I'm not going to talk about here) so many working linked list implementations don't bother. You can see graphically what's happening here too.

Error deleting an item in a linked list

Mostly linked lists in operation are stable and reliable but it is possible to get yourself into a bit of a tangle. But you can immediately see that this makes is a lot easier to remove an element from the middle of the linked list than if you had an array. If you had an array then you'd either have to flag that item as "invalid" somehow to know that you shouldn't use it anymore or failing that actually copy all of the elements in your array above the item being removed down to fill the gap. The first one adds complexity and means that you can't actually reduce your memory footprint when removing items (not quite true if you use an array of pointers to items but that's even more complicated) while the second is quite often very slow. This is especially true if you use a library that guarantees contiguity of the elements of your array after every delete operation when you are deleting multiple items (e.g. std::vector in C++. This behaviour is generally an advantage but here is a cost. You can get around it in other ways in C++ but other libraries are less flexible). The cost is managable if you delete many items and then pack the array up but packing after every deletion can be very costly.

The next entry in this section will describe adding items to a linked list which, as you might imagine, is quite similar to deletion but in reverse.

June 2019

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