Sunday, June 12, 2016

Formaline: The Provenance of Computational Astrophysics Simulations and their Results (Part I)

Key to all scientific research is reproducibility. In areas of science that rely heavily on computer simulations, the open-source approach is essential for allowing people to check the details of the simulation code and for re-running simulations for reproducing results.

Open-source is essential, but it's not enough. Anybody involved in simulations knows that the code used for running the actual simulations often differs in non-trivial ways from the actually released source code. Even when we use version control software like git, too often do we run simulations with a version of the code that is either not tagged or has uncommitted changes. And this does not take into account that complex simulation codes typically have a myriad of parameters that are set individually for each simulation and parameter files typically don't make it into publications or git repositories. A similar issue exists also with the initial conditions (i.e. the input data) from which a simulation is started. Rarely are these available for others to reproduce results.

Provenance is a word used in computational science (and in some other research areas). It describes the full history of a (computational) scientific result. So the provenance of a simulation does not only include the released open-source code, but also the full information on the exact source code that was used, perhaps even the way it was compiled and where it was run, the parameters that were set for the simulation, and all initial conditions and other ingredients that were used in whatever form (and also their respective provenances).

We have to tackle provenance and reproducibility step by step. In this two-part series of posts, my focus is on preserving the actual source code that was used to run a simulation and produce specific results or to create some other (astro)physics result (for example, a neutrino-matter opacity table used in core-collapse supernova simulations). This can be accomplished by what I will generally call Formaline. Formaline is a chemical compound, a 10% solution of formaldehyde in water; used as a disinfectant or to preserve biological specimens. Formaline for code/simulations is to preserve code and simulation/physics metadata. Formaline is an idea by Erik Schnetter, Research Technologies Group Lead at Perimeter Institute for Theoretical Physics. Erik implemented Formaline for the first time for the Cactus Computational Toolkit some time in the early 2000s.

Using Formaline is super easy! (Python example)

Formaline comes in two forms and in both forms it preserves source code: (1) It can include source code in the binary of the simulation code and, upon execution, the code writes the source code (usually in a tar ball) into the output directory. (2) It can include source code and parameter files in HDF5 data files that are now very broadly used for simulation and physics inputs to simulations (such as a neutrino interaction table).

I'll talk about Formaline (1) in my next post. Here, I'll focus on how to implement Formaline (2) and include (and later extract) a source tar ball in/from an HDF5 data file. It turns out that this is extremely easy if you have the h5py and numpy Python packages installed.

Let's consider the case in which you have some standalone code that produces an HDF5 table called table.h5 and that is generated by some Fortran 90 code in and below directory src and that takes a top-level parameter file called parameters, a Makefile, a for machine-specific build flags, and a README file.

Here is the code that puts all source code into the HDF5 file:

So, after running this script, your HDF5 table table.h5 contains a dataset that holds the tar.gz ball of our code source, input, & parameter files. You can view the table of contents of any HDF5 file with h5ls [filename].

Now, let's say 5 years later, we find table.h5 and want to know how it was created. We can now go and extract the source/input/parameter tar.gz ball! Here is the script that does just that. It first creates an output directory called saved_code to make sure nothing is overwritten.

So that's a super easy way to make results reproducible -- just store the source code and all input/parameter files with the results! I think it's a no-brainer and we all should be doing it. HDF5 is a standard, well documented format that will be readable decades from now -- so your work is safe!

I wrote this implementation of Formaline for the NuLib neutrino interaction library and and a variant of it is bundled with NuLib and available on github at

In my next post, I'll talk about Formaline (1), which includes a source tar ball inside the executable. This is the original incarnation of Formaline that Erik Schnetter came up with.

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