A goal of the xSDK is to improve interoperability among software libraries and domain components. The first xSDK release (xsdk-0.1.0, April 2016) comprised four widely used, independent numerical software libraries (hypre, PETSc, SuperLU, and Trilinos) and an application component (Alquimia). The next release (xsdk-0.2.0-alpha, April 2017) added the PFLOTRAN subsurface application. The current xSDK release (xsdk-0.3.0, Nov 2017) also includes the numerical libraries MAGMA, MFEM, and SUNDIALS; additional packages are working toward compatibility with xSDK community policies and will be part of forthcoming xSDK releases.
Explanations of packages’ approaches to address xSDK community policies are in the Github repo for xsdk-policy-compatibility.
We welcome the HPC community to contribute additional packages to the xSDK. See the FAQ page for information on how to contribute xSDK-compatible packages.
xSDK numerical libraries:
Hypre provides high-performance preconditioners and solvers for the solution of large, sparse linear systems on massively parallel computers. It was created with the primary goal of providing users with advanced parallel preconditioners. The library features parallel multigrid solvers for both structured and unstructured grid problems. For ease of use, these solvers are accessed from the application code via hypre’s conceptual linear system interfaces, which allow a variety of natural problem descriptions and include a structured, a semi-structured interface, and a traditional linear-algebra based interface. The (semi-)structured interfaces are an alternative to the standard matrix-based interface that describes rows, columns, and coefficients of a matrix. Here, instead, matrices are described primarily in terms of stencils and logically structured grids. These interfaces give application users a more natural means for describing their linear systems, and provide access to methods such as structured multigrid solvers, which can take advantage of the additional information. Hypre an be used with OpenMP.
MAGMA is a dense linear algebra library that implements LAPACK functionality for heterogeneous platforms that feature GPUs. MAGMA addresses the complex challenges of such hybrid environments with hybridized software that combines the strengths of different algorithms within a single framework. MAGMA’s linear algebra algorithms target hybrid manycore systems featuring GPUs specifically and thus enable applications to fully exploit the power offered by each of the hardware components. MAGMA provides solvers for linear systems, least squares problems, eigenvalue problems, and singular value problems. Designed to be similar to LAPACK in functionality, data storage, and interface, the MAGMA library allows scientists to easily port their existing software components from LAPACK to MAGMA, to take advantage of new hybrid architectures. Also included is MAGMA BLAS, a complementary to CUBLAS routines.
MFEM is a lightweight, scalable C++ library for finite element discretizations of partial differential equations on unstructured grids, with emphasis on high-order methods and applications. It has a number of unique features, including: support for arbitrary order finite element meshes and spaces with both conforming and nonconforming adaptive mesh refinement; advanced finite element spaces and discretizations, such as mixed methods, DG (discontinuous Galerkin), DPG (discontinuous Petrov-Galerkin) and Isogeometric Analysis (IGA) on NURBS (Non-Uniform Rational B-Splines) meshes; native support for the high-performance Algebraic Multigrid (AMG) preconditioners from the hypre library; integration with many other math libraries, including PETSc, SUNDIALS and SuperLU; and a large number of well-documented example codes and miniapps.
PETSc is a suite of data structures and routines for the scalable solution of scientific applications modeled by partial differential equations, while TAO is a scalable optimization library. The software includes linear solvers, preconditioners, nonlinear solvers, and ODE integrators, as well as a variety of scalable constrained and unconstrained optimization solvers. PETSc supports MPI, and GPUs through CUDA or OpenCL, as well as hybrid MPI-GPU parallelism. While PETSc does not include eigensolvers, the eigensolver package SLEPc, built on top of PETSc, has a very similar interface. The library libMesh and the framework MOOSE provide finite element solvers that utilize PETSc. PETSc/TAO can be easily used in application codes written in C, C++, Fortran, and Python.
SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers and integrators. It consists of six packages: CVODE solves initial value problems for ordinary differential equation (ODE) systems using variable order and step linear multistep methods; CVODES solves ODE systems and includes sensitivity analysis capabilities (forward and adjoint); ARKODE solves initial value ODE problems with variable step Runge-Kutta methods, including support for explicit, implicit, and additive implicit/explicit (IMEX) integration methods; IDA solves initial value problems for differential-algebraic equation (DAE) systems using variable order and step linear multistep methods; IDAS solves DAE systems and includes sensitivity analysis capabilities (forward and adjoint); and KINSOL solves nonlinear algebraic systems with both Newton-based and fixed point iterative methods. SUNDIALS is written in C and is supplied with iterative and direct linear solvers. Parallelism is fully encapsulated in the data vector API. Users can supply their own vectors or employ SUNDIALS-supplied vectors using distributed memory (via MPI), shared memory (via openMP and PThreads), or GPU-based (via CUDA or RAJA) parallelism.
SuperLU is a general-purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high-performance machines. The library routines will perform an LU decomposition with partial pivoting and triangular system solves through forward and back substitution. The LU factorization routines can handle non-square matrices, but the triangular solves are performed only for square matrices. The matrix columns may be preordered (before factorization) either through library or user supplied routines. This preordering for sparsity is completely separate from the factorization. Working precision iterative refinement subroutines are provided for improved backward stability. Routines are also provided to equilibrate the system, estimate the condition number, calculate the relative backward error, and estimate error bounds for the refined solutions. There are three separate versions of this code: SuperLU (for sequential machines), SuperLU_MT (for shared memory parallel machines with using OpenMP or Pthread), and SuperLU_DIST (for distributed memory machines using MPI). The library is written in C, with a Fortran interface. SuperLU_DIST supports MPI+X, where X can be CUDA, OpenMP, or both.
The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multiphysics engineering and scientific problems. Trillions is organized into 66 different packages, each with a specific focus. These packages include linear and nonlinear solvers, preconditioners (including algebraic multigrid), graph partitioners, eigensolvers, and optimization algorithms, among other things. Users are required to install only the subset of packages related to the problems they are trying to solve. Trilinos supports MPI+X, where X can be CUDA, OpenMP, etc.
xSDK application packages:
Alquimia provides an API for exposing mature geochemistry and biogeochemistry capabilities to reactive transport codes. Alquimia is not a geochemistry solver; rather, it is a library comprising data structures and interfaces that wrap chemistry solvers from well-established codes like PFLOTRAN and CrunchFlow, thereby allowing developers of new codes to use these solvers with a single interface. We refer to these chemistry solvers as chemistry engines.
PFLOTRAN is an open source, massively parallel subsurface flow and reactive transport code. PFLOTRAN solves a system of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport in porous materials. Parallelization is achieved through domain decomposition using the PETSc. The reactive transport equations can be solved using either a fully implicit Newton-Raphson algorithm or the less robust operator splitting method.