Gaël Varoquaux

Tue 23 December 2008


Tracking objects in scientific code

When I started working in my new field (data analysis of functional brain images), I was surprised to find in our data-analysis scripts what I thought was a very particular code smell: the numerical code is always doing a lot of filename and path manipulation, loading and saving data even in the core routines. I couldn’t picture what seemed wrong with this, but I was uncomfortable with it.

The good

Memory management

In the data-processing work I am currently doing, we deal with large objects, mostly huge numpy arrays, though sometimes some domain-specific data containers creep in. As a result, simple calculations take time (an SVD is 10 minutes), and I am always fighting with memory.

Saving to disk is a handy way of freeing memory. Moreover, with memmapping, reading only the relevant parts of pre-calculated arrays becomes very cheap.


When the simplest operation takes ten minutes, you want to save intermediate steps, to be able to resume calculations, or to inspect why the code crashed. And who knows, you might need this intermediate step.

The bad

The immediate apparent problem is that your code becomes riddled with path-management code. We often joke that once we have figured out the algorithm, the longest surviving piece of code is the path-related junk.

But, I believe this is only the tip of the iceberg, and that this code smell hints to deeper problems.

The ugly

Loss of scoping

When I started working on these problems, I was startled to encounter basic domain-specific algorithmic functions taking input and output data filenames. It took me a while to realize that the huge problem with this is that I loose scoping, or in other words naming locality. Let us pretend that I have a function ‘foo’ that does basic numerics on large numpy arrays, but to save memory it takes as a signature the name of the file where the input array is stored, and the name of the filename where the output array should be stored. So I have some code that looks like this:

def process_sessions(session_files):
    for session_file in session_files:
        foo(session_file, session_file + '.out')

Saving to files in the loop is a huge gain of memory;

Now I decide I want to add a parameter to foo, and vary this parameter, with, eg:

for param in params:
    process_sessions(session_files, param)

My code is hard to refactor, because I need to introduce modifications deep in all subroutines to make sure they do not save their outputs in the same file.

Suppose session_files are actually extracted from an upstream dataset, and now I want to apply my algorithm on a set of these upstream datasets, and in parallel. Once again I need to generate a score of new filenames and keep track of them. I can use temporary files, but I need to keep hold of this information too, and I loose most of my crash-resistance.

When you think it over, the way programming languages solve this problem elegantly, is by the rules connecting names to objects, and in particular scoping: a name corresponds to an object in a given function. Using files is equivalent to using globals, and we have to cook up our own scoping rules (which results in a lot of path-massaging code).

No history tracking

When I find a file on the disk, I do not really know how it has been generated. As a results, the crash-resistance is compromised. Moreover, when tweaking algorithms, we often try to rerun only the necessary parts of the algorithms, relying on the precomputed parts saved to the disk. We comment out code, or exercise different code paths. As a result we often end up in situations where the whole code does not actually run. And once again refactoring is hard, because we have not expressed the dependency relations between our intermediate results.

Doing better?

Once again, today I was refactoring my algorithm, or my “pipeline” as we call it. And once again, I felt the failure to have the proper tools, the proper abstractions, words, to express the problem in the code. Manipulating files directly seems wrong, for the reason expressed above. But can we do better?

The problem, I believe, is that we need a lightweight persistence framework adapted to scientific purposes. I remember telling Travis Vaught a few weeks before beginning my new job that scientists had no problem with their persistence. Well, I was so wrong.

By a persistence framework, I do not mean a persistence mechanism, like, or hdf5, or a database. I am interested in the objects with which we represent it in the code. How do we solve the scoping problem? And the history problem? Can we implement a “trajectory tracking”, to reuse the words of Alexandre Fayolle, for our data containers?

I am thinking about a small set of well-thought abstractions, a bit like the use of ORM (object relational mappers) in web application, that would take care of the mapping from in-memory objects to objects on the disk for us.

I am starting to have some ideas. I am thinking in terms of context objects, with getattr tricks to do the mapping to a database doing the bookkeeping and the trajectory tracking, and doing the impedance matching with objects stored as numpy “.npy” files, hdf5 files, nifti files, or whatever you want. The added value of a database would be that it would give some robust locking, and possible network abstraction, to allow for crash-safety, and parallel or distributed computing.

This may sound overkill, or overcomplicated. I’ve tried simple things. They all failed.

This is a problem that matters a lot to me. I feel I am loosing a lot of time on this. However I feel that the effort to do something good is quite important. I am also afraid of polluting my numerical code with unnecessary abstractions. The main problem is that attempting to solve this problem would require a significant investment in time, and I don’t really see where I can find this time.

Have people encountered similar problems? Do you have any suggestions, any trick to share?

I’d be very happy to read any comments that can move forward my thinking, even if it is about pointing out problems and not solutions. I still think I haven’t identified the problems well.

Update: I have just realized that I will be almost without internet access for the next week, starting from pretty much now. Looks like it was a bad moment to start a thrilling discussion. I guess I got carried away by the discontent of a day doing some bad refactoring. I really look forward to catching up when I come back. Please forgive me for the bad timing.


Patterns that derived from this line of thoughts are now implemented in the joblib library.

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