Re: [boost] [Review] ODEInt review/comments

Subject: Re: [boost] [Review] ODEInt review/comments
From: Sylwester Arabas (sarabas_at_[hidden])
Date: 2012-09-27 16:29:50

Hi All,

This is more a message from a (satisfied) user of odeint, than a proper 
review of the code, but still perhaps somehow helpful...

On 19/09/12 17:46, Steven Watanabe wrote:
> Please always state in your review, whether you think the library should
> be accepted as a Boost library!

I think it should be accepted. Both the library itself and the 
documentation proved to be functional for me and both seem quite mature. 
Odeint is well integrated with Boost by making use of other Boost 
components in its implementation, and allowing to use Boost.[Units, 
uBLAS, Array, Range, Fusion] objects as data containers. odeint would 
nicely complement the current catalogue of Boost libraries applicable in 
research.

In fact, it would be great to have similar libraries for some particular 
types of PDEs, interpolation, fitting, etc. In particular, the odeint's 
interoperability with multiple data-container libraries (including those 
from Boost and others) would be great.
I'm not sure if having a range of scientific libraries in Boost fits its 
aims, but if so, odeint would give a good example in my opinion.

> - What is your evaluation of the design?

Not sure if that's a results of tutorial-based docs or the library 
design, but in my opinion the authors managed to avoid a steep learning 
curve. From a user's perspective the API is quite concise and clear.
The separation of integration-related numerics from adaptivity-related 
numerics, and from the underlying data representation seems successful, 
what makes the design flexible (good example being the simultaneous 
compatibility with CUDA, OpenMP, OpenCL, GSL, and the several Boost 
containers mentioned above... not for all algorithms, though).

> - What is your evaluation of the implementation?

I'm not feeling competent enough to evaluate the internals, but from a 
user's perspective the implementation simply works well. In particular, 
I confirm that the support for Thrust (both using GPU and OpenMP) and 
for Boost.units works out of the box.

> - What is your evaluation of the documentation?

My feeling is that it is on par (or even more complete) than several 
other Boost documentations I have used, and it is rich in examples. In 
principle, it does allow to use the library without digging into the 
code or contacting the authors.

However, it seems as it has grown quite a bit since the initial 
structuring into chapters and sections, and perhaps it deserves at least 
some reordering. In particular, I'd suggest promoting all subsections of 
the "Special topics" section to separate sections of the Tutorial chapter.

Some other minor comments:

* Tables 1.1, 1.2 and 1.7 as well as tables 1.3/1.4 and 1.8/1.9 seem to 
be identical?

* The table 1.1 in the "Overview" includes headers naming non-previously 
mentioned subjects such as Concepts, System Concept. A paragraph briefly 
explaining these and referring to subsections of the "odeint in detail" 
chapter would be appropriate just before the table.

* Tables in the "Concepts" chapter are not numbered

* The fusion_algebra is missing from the table listing all algebras in 
doc/concepts/state_algebra_operations.qbk

* Most of the tables in the "Concepts" chapter have their first column 
named "Name" while "Synopsis" or "Purpose" would probably reflect better 
the contents.

* There is a catalogue of references in the Tutorial, but it does not 
list all the references (e.g. the Ott's book referenced in the chapter 
on Lyapunov exponents). There is no unified way of referring to (and 
hyperlinkig) the references in the text. Why not a separate chapter 
"References" for the whole documentation?

* The README and the CHANGELOG files seem forgotten, but perhaps they 
are simply not needed if accepted into Boost

* The "Caution" "Using Boost.Units works nicely but compilation can be 
very time and memory consuming. For example the unit test for 
Boost.Units take up to 4 GB of memory at compilation." would probably 
need some more specific information on the compiler used... or less 
specific statement on the amount of memory. Trying with gcc 4.7 and 
clang 3.1 I've recorded 1.8G and 1.1G, respectively (default Boost 
compiler options).

* in some parts the documentation addresses the reader per "You", and in 
others using "one may ..." constructs

* Some other Boost libraries contain "Reference" sections in the docs 
listing (e.g. 
http://www.boost.org/doc/libs/1_51_0/doc/html/boost_units/Reference.html). 
It would be useful for odeint as well in my opinion.

* I think that the "Concepts" chapter requires an opening section 
(Overview?) explaining the concept of concepts.

* I've placed some other suggestions/typo fixes for the documentation in 
a github pull request:
https://github.com/slayoo/odeint-v2/commit/5eec7bf86321af185b4547a4825c0751e5637b07

> - What is your evaluation of the potential usefulness of the library?

I find it potentially very useful. Primarily in scientific/engineering 
context, but perhaps also in other domains - game design, GUI design.

In comparison with other ODE solvers, the library seems quite versatile 
- it supports both implicit and explicit methods, both adaptive and 
non-adaptive solutions, algorithms for stiff and non-stiff systems, and 
as mentioned above, numerous "backends" ranging from GPU-stored POD 
arrays to resizable vectors of objects.

> - Did you try to use the library?  With what compiler?  Did you have any
> problems?

I'm using the library for more than half year in my PhD project (IIRC, 
I've found it by googling "GPU ODE solver"). There we use odeint for two 
purposes:
- solutions of simple 1-dimensional equations employing Boost.units 
(latent heat production during cloud droplet condensation/evaporation)
- aerosol/cloud/drizzle/rain particle tracking within a fluid flow model 
(parallel solutions of ~milions of equations of motion, condensation, 
chemical reactions, etc) using Thrust (OpenMP only up to now). We've 
used clang 3.1 and several newer versions of gcc.
Here's an example animation from a (quite naive) simulation of 
precipitation formation in a stratocumulus cloud: 
http://www.igf.fuw.edu.pl/~slayoo/temp/todo_sdm_E10.gif

> - How much effort did you put into your evaluation? A glance? A quick
> reading? In-depth study?

Not counting the previous work with odeint, I've had a quick reading of 
the docs and a glance at the code. I've run all the tests and examples 
using "bjam" with clang and gcc toolsets.

> - Are you knowledgeable about the problem domain?

I'm a PhD student studying atmospheric physics. ODEs show up frequently 
in my work, and I've been using some other solvers besides ODEINT as 
well (SUNDIALS in particular). I don't consider myself experienced 
enough to comment on the correctness of the mathematical/numerical part 
of ODEINT, though. In fact the key advantage of ODEINT for me is that 
the maths/numerics are nicely hidden from the user.

HTH, regards,
Sylwester

-- 
http://www.igf.fuw.edu.pl/~slayoo/