Teaching basic lab skills
for research computing

Workshop at GeoSim (Potsdam)

I had never taught a Software Carpentry workshop before (though I have taught an Advanced Scientific Programming in Python many times), so when the hosts for this one asked if I would be willing to do a full-week workshop, I said they were crazy ;) They convinced me to do it, but I said in that case I could only do that if I can recycle the materials I use for our summer school. They agreed, and I managed to convince a buddy in Berlin to help me with tutoring.

There were 28 students from Geophysics with a very diverse background in programming. Most did not know Python and several had only ever used Windows with GUIs. Given that, we soon figured out that the classic lecture-plus-exercises paradigm wasn't going to work, so we switched to a completely live-coding based approach. We would talk about tests while writing them for my own project, about Git while using it on a real paper, and so on. Based on the feedback we got at the end, it worked well.

But in retrospect we won't do something like that again: performing non-stop from 9:00 in the morning to 6:30 in the afternoon, getting questions that made me question my own knowledge of Python (see below), improvising a live session on Python with MPI on clusters (of which I have zero experience) and resorted to teaching them how do you go about looking for libraries and docs in the SciPy ecosystem was exhausting. The feedback from the students was very positive, though, so it was a learning experience on both sides.

Footnote: I was explaining the difference between passing by-value and by-reference and Python approach to this issue as compared to Matlab and to functional languages, But then someone came up with this example:

>>> def mult1(x):
...     x = x*2
...     return x
>>> def mult2(x):
...     x = [x*2]*2
...     return x
>>> y = mult1([1, 2, 3])
>>> z = mult2([1, 2, 3])
>>> print y
[1, 2, 3, 1, 2, 3]
>>> y[2] = 10
>>> print y
[1, 2, 10, 1, 2, 3]
>>> print z
[[1, 2, 3, 1, 2, 3], [1, 2, 3, 1, 2, 3]]
>>> z[0][2] = 10
>>> print z
[[1, 2, 10, 1, 2, 3], [1, 2, 10, 1, 2, 3]]

I told to the students that in the case of mult1 the return value bound to the name y has no "memory" of the fact that it has been created by concatenating two lists, so when you set y[2] the result is what you would expect. And then the student came up with the function mult2 and told me that it seems like in this case the return value bound to z is actually "remembering" that it came from concatenating two lists, as seen when you try to set z[0][2] and then you get also z[1][2] changed. A colleague told me he would interpret the results this way:

z >>>>>>>> [ . , . ]
             v   v
             v   v
             v   v
             >>>>>>>>>>> [1, 2, 3, 4, 5, 6]

z does not remember that it came from two lists. If it did, then setting z[0][2] would also change z[0][5], but it doesn't. But z[0] and z[1] point to the same object.

I also don't think that mutability is important here. (It influences what operations can be performed, but not the identity of objects).

>>> a = mult2((1,2,3))
>>> a
[(1, 2, 3, 1, 2, 3), (1, 2, 3, 1, 2, 3)]
>>> a[0] is a[1]

If anyone has a better explanation, please do share.

Dialogue & Discussion

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