510.parest_r
SPEC CPU2017 Benchmark Description

Benchmark Name

510.parest_r

Benchmark Author

Wolfgang Bangerth <bangerth [at] gmail dot com>, et al.

Benchmark Program General Category

A finite element solver for a biomedical imaging problem

Benchmark Description

510.parest_r solves a problem from biomedical imaging. Specifically, the underlying problem is the reconstruction of interior properties of a 3d body from multiple observations at its two-dimensional surface, in much the same way as multiple 2d X-ray images are combined to do 3d CT (computed tomography) scans. The difference to CT scans is that the method this program describes is infrared light that does not go through tissues in a straight line, but diffuses.

In order to understand how the overall algorithm works, let us stick with the example of CT for a moment. CT involves taking X-ray exposures of a body from different angles, and obtaining developed photo plates (or today, the data that comes from the digital X-ray detectors) placed on the other side of the body from the X-ray cannon. There is then a mathematical algorithm called the "inverse Radon transform" that reconstructs the 3d interior make up of the body from these 2d exposures.

When given a number of exposures from different angles, an implementation of the algorithm will create some reconstruction of the body's interior. But is your implementation correct? We don't know, because we don't know what the exact make-up of the body was when the exposures were taken.

What one therefore does to test such implementations is to assume an exact make-up and compute what exposures this would produce if one were to do actual experiments (these are called "synthetic" measurements). One then uses the implementation of the method on these exposures to reconstruct the body. Because we know the exact make-up of the body from which these exposures were creates, we can compare the exact and the reconstructed make-up and ensure that they are the same, or at least that the reconstructed make-up converges to the exact one as we add more and more exposures.

This particular benchmark, 510.parest_r, does not actually deal with CT reconstructions. Rather, it is built to deal with a different biomedical imaging method called "fluorescence-enhanced optical tomography" that uses infrared light instead of X-rays because (i) infrared light is not harmful to humans, and (ii) because it provides a better contrast between healthy and diseased tissue than X-rays. The major difference between this method and CT is that the relationship between the body's interior we would like to reconstruct and what we can measure is not linear. Consequently, while a CT reconstruction algorithm can compute the body's interior make-up in one step, optical tomography methods need to do this iteratively: they start with an assumed make-up and over a number of iterations improve it until they think that they are close enough.

Under the hood, this requires solving the predicting set of partial differential equations many hundreds or thousands of times, for different hypothetical make-ups. This is done on locally refined finite element meshes that change over time as we hone in on the best reconstruction. In other words, there is a loop over a number of iterations (corresponding to the output "Step 1", "Step 2", etc in the log file for this benchmark), each of which improves our current best guess for the body's 3d interior make-up. Within each of these iterations or "steps", the algorithm re-computes the synthetic measurements and then loops over all of the experiments (corresponding to the exposures from different angles in the CT example) and predicts what we would measure with the current best guess make-up. At the end of each step, these predictions are then compared against the (synthetic) measurements and an improved guess is computed.

The implementation of all of this relies on the deal.II finite element library (see www.dealii.org) that also underlies the 447.dealII benchmark that is part of SPEC CPU2006.

Input Description

The input for 510.parest_r consists of a single input file with a suffix .prm that describes the problem completely. There are test.prm, train.prm, and ref.prm files in the data/ subdirectory of this benchmark.

The format of these input files is intended to be self explanatory, using a set of parameters grouped into nested, hierarchical sections. The parameters are grounded in the mathematical and computational algorithms that underly the problem, as well as the kinds of models that are implemented.

A few parameters are of particular interest for benchmarking:

The test, train, and refrate input files for this benchmark only differ in the values for the first two parameters above.

Additional information about the parameters may be found in the output file me.prm (see next section).

Output Description

The output produces a number of files that are validated for correct answers:

*.vtk Graphical representation of the solution steps
log Progress of the computation
statistics Statistics about the solution and its progress (for example, the number of iterations required to achieve a certain internal tolerance)
me.prm Parameters for the run, including both those from the input file plus a listing for parameters that were not explicitly listed in the input file and therefore left at their defaults.

Programming Language

C++

Threading Model

None

Known portability issues

The benchmark should, in principle, only consist of standard C++98 constructs. That was one of the design goals.

Obtaining correct results with GCC and -m32

During testing with versions 5 and 6 of the GNU compiler, there were a few reports of incorrect answers when compiling with -m32 + high optimization. Successful workarounds included:

It should be noted that a workaround such as the above would not qualify for use as portability flag. In a base compilation, it would need to be part of the set of flags that are applied consistently to a set of benchmarks.

Sources and Licensing

The benchmark is licensed directly to SPEC by Wolfgang Bangerth. Note: therefore, source code references to other terms under which the program may be available are not relevant for the SPEC CPU version. It uses a variety of files from BOOST, under the Boost Software License.

Please see details in the document SPEC CPU2017 Licenses.

References

The deal.II open source finite element library home page is www.dealii.org. It includes software, documentation, and mailing lists.

Many publications are linked from the primary author's page at Texas A&M University, www.math.tamu.edu/~bangerth/publications.html, including:

Last updated: $Date: 2017-05-01 13:34:29 -0400 (Mon, 01 May 2017) $