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There has been a recent major upsurge in the concerns about reproducibility in many areas of science. Within the neuroimaging domain, one approach is to promote reproducibility is to target the re-executability of the publication. The information supporting such re-executability can enable the detailed examination of how an initial finding generalizes across changes in the processing approach, and sampled population, in a controlled scientific fashion. ReproNim: A Center for Reproducible Neuroimaging Computation is a recently funded initiative that seeks to facilitate the "last mile" implementations of core re-executability tools in order to reduce the accessibility barrier and increase adoption of standards and best practices at the neuroimaging research laboratory level. In this report, we summarize the overall approach and tools we have developed in this domain.

This paper accompanies the first release of libmpdata++, a C++ library implementing the multi-dimensional positive-definite advection transport algorithm (MPDATA) on regular structured grid. The library offers basic numerical solvers for systems of generalised transport equations. The solvers are forward-in-time, conservative and non-linearly stable. The libmpdata++ library covers the basic second-order-accurate formulation of MPDATA, its third-order variant, the infinite-gauge option for variable-sign fields and a flux-corrected transport extension to guarantee non-oscillatory solutions. The library is equipped with a non-symmetric variational elliptic solver for implicit evaluation of pressure gradient terms. All solvers offer parallelisation through domain decomposition using shared-memory parallelisation. The paper describes the library programming interface, and serves as a user guide. Supported options are illustrated with benchmarks discussed in the MPDATA literature. Benchmark descriptions include code snippets as well as quantitative representations of simulation results. Examples of applications include homogeneous transport in one, two and three dimensions in Cartesian and spherical domains; a shallow-water system compared with analytical solution (originally derived for a 2-D case); and a buoyant convection problem in an incompressible Boussinesq fluid with interfacial instability. All the examples are implemented out of the library tree. Regardless of the differences in the problem dimensionality, right-hand-side terms, boundary conditions and parallelisation approach, all the examples use the same unmodified library, which is a key goal of libmpdata++ design. The design, based on the principle of separation of concerns, prioritises the user and developer productivity. The libmpdata++ library is implemented in C++, making use of the Blitz++ multi-dimensional array containers, and is released as free/libre and open-source software.

This paper accompanies first release of libmpdata++, a C++ library implementing the Multidimensional Positive-Definite Advection Transport Algorithm (MPDATA). The library offers basic numerical solvers for systems of generalised transport equations. The solvers are forward-in-time, conservative and non-linearly stable. The libmpdata++ library covers the basic second-order-accurate formulation of MPDATA, its third-order variant, the infinite-gauge option for variable-sign fields and a flux-corrected transport extension to guarantee non-oscillatory solutions. The library is equipped with a non-symmetric variational elliptic solver for implicit evaluation of pressure gradient terms. All solvers offer parallelisation through domain decomposition using shared-memory parallelisation. The paper describes the library programming interface, and serves as a user guide. Supported options are illustrated with benchmarks discussed in the MPDATA literature. Benchmark descriptions include code snippets as well as quantitative representations of simulation results. Examples of applications include: homogeneous transport in one, two and three dimensions in Cartesian and spherical domains; shallow-water system compared with analytical solution (originally derived for a 2D case); and a buoyant convection problem in an incompressible Boussinesq fluid with interfacial instability. All the examples are implemented out of the library tree. Regardless of the differences in the problem dimensionality, right-hand-side terms, boundary conditions and parallelisation approach, all the examples use the same unmodified library, which is a key goal of libmpdata++ design. The libmpdata++ library is implemented in C++, making use of the Blitz++ multi-dimensioanl array containers, and is released as free/libre and open-source software., Among the changes are: new chapter 5.4, updated presentation in chapter 6.3 and editorial corrections