Browse SciDAC Software by Capability Area

ColPack is a package of algorithms for the specialized vertex coloring problems as well as algorithms for a variety of related supporting tasks in derivative computation, such as coloring, ordering, recovery and graph construction.
SciDAC Project: CSCAPES
Point of Contact: Assefaw Gebremedhin
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Data_N_Comp_Reorder provides various sparse matrix reordering algorithms that aim to improve the data locality and therefore the performance of computations that iterate over the sparse matrix data structure
SciDAC Project: CSCAPES
Point of Contact: Paul Hovland
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MatchBox is a C++ software package consisting of sequential exact as well as approximation algorithms for a variety of graph matching problems. The package is currently under development. A trial copy can be obtained by request.
SciDAC Project: CSCAPES
Point of Contact: Alex Pothen

MatchBoxP provides parallel approximation algorithms for various matching problems implemented in C++ and using MPI. The package is currently under development. A trial copy can be obtained by request.
SciDAC Project: CSCAPES
Point of Contact: Alex Pothen

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 multi-physics engineering and scientific problems.
SciDAC Projects: CSCAPES ITAPS TOPS
Point of Contact: Trilinos Users Forum
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PLFS is a parallel virtual file system that rearranges random, concurrent writes into sequential writes to unique files (i.e. N-1 into N-N).
SciDAC Project: PDSI
Point of Contact: PLFS Development
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PVFS is the Parallel Virtual File System for Linux based clusters that supports a number of access models, from collective I/O to independent I/O and non-contiguous and structured access patterns.
SciDAC Project: SDM
Point of Contact: PVFS Support
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ZeptoOS is a research project that focuses on operating systems for petascale architectures. It provides a complete software stack for Blue Gene/P, covering both compute and I/O nodes.
SciDAC Project: CSCADS
Point of Contact: ZeptoOS Users
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ADIC is a tool for the automatic differentiation (AD) of programs written in ANSI C. Given the source code and a user's specification of dependent and independent variables, ADIC generates an augmented C code that computes the partial derivatives of all of the specified dependent variables with respect to all of the specified independent variables in addition to the original result.
SciDAC Project: CSCAPES
Point of Contact: ADC Questions
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ADIFOR is a tool for the automatic differentiation of Fortran 77 programs. Given a Fortran 77 source code and a user's specification of dependent and independent variables, ADIFOR will generate an augmented derivative code that computes the partial derivatives of all of the specified dependent variables with respect to all of the specified independent variables in addition to the original result.
SciDAC Project: CSCAPES
Point of Contact: ADIFOR Questions
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The Common Component Architecture is a standard for Component-based software engineering used in high-performance scientific computing. Features of the CCA that distinguish it from commercial component standards include support for FORTRAN, multi-dimensional data arrays, exotic hardware and operating systems, and a variety of network data transports not typically suited for wide area networks.
SciDAC Project: TASCS
Point of Contact: CCA Forum
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Babel is a tool that provides support for language interoperability. It is based on the Scientific Interface Description Language (SIDL), which is specifically tuned for scientific applications and supports complex numbers, structures, and dynamic multidimensional arrays.
SciDAC Project: TASCS
Point of Contact: Tom Epperly
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Ccaffeine is a framework that support component-based HPC application development. it is designed to not interfere with the application after the application has been built from components. It can also automatically generate a static, possibly self-tuning, executable for production runs.
SciDAC Project: TASCS
Point of Contact: Ben Allan
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OnRamp is a mechanism to generate CCA components through commented markup in the original code.
SciDAC Project: TASCS
Point of Contact: Geoffrey Hulette

XCAT is a distributed framework for composing and debbuging applications in the context of CCA, the Common Component Architecture.
SciDAC Project: TASCS
Point of Contact: Dennis Gannon
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CHILL is the Composable High-Level Loop Transformation and Parallelization Framework, and provides support for loop transformations (e.g. permutation or loop interchange, tiling or blocking, unrolling or unroll-and-jam, data copy, fusion, distribution, etc).
SciDAC Project: PERI
Point of Contact: Chun Chen
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Co-Array Fortran is a fortran compiler that incorporates a set of features introduced in Fortran 95 that implement a partitioned global address space (PGAS) parallel programming model. These features provide an explicit notation for data decomposition, as an alternative to message-passing models like MPI.
SciDAC Project: CSCADS
Point of Contact: John Mellor-Crummey
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CUDPP is the CUDA Data Parallel Primitives Library, a library of data-parallel algorithm primitives such as parallel prefix-sum, parallel sort and parallel reduction.
SciDAC Project: IUSV
Point of Contact: CUDPP Google Group
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DCGN is a message passing interface usable on NVIDIA GPUs that is similar to MPI and allows full access to the underlying architecture, providing both performance and flexibility.
SciDAC Project: IUSV

DynInst provides capabilities for runtime code adaptation, and that can be used by performance measurement tools, debuggers (e.g. breakpoints), execution drive simulations, and computational steering services.
SciDAC Project: CSCADS
Point of Contact: DynInst
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GASNet is the Global-Address Space Networking, a language-independent, low-level networking layer that provides communication primitives tailored for implementing parallel global address space SPMD languages (e.g . UPC).
SciDAC Project: CSCADS
Point of Contact: Berkeley UPC Developers list
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LoopTool implements compilation techniques for automatic, source to source loop transformations to improve data reuse and therefore performance. These techniques include fusion of loop nests, array contraction, selective unroll-and-jam and adjustement of loop bounds.
SciDAC Project: CSCADS
Point of Contact: John Mellor-Crummey
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OpenAD is a tool for automatic differentiation (AD) of C/C++ numerical computer programs. For the C/C++ side the entire pipeline is encapsulated in single binary. While the C/C++ tool incarnation shares components with OpenAD its development is a separate effort and it was decided to retain for it the name "ADIC" which goes back to the previous generation of tools.
SciDAC Project: CSCAPES
Point of Contact: Jean Utke
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OpenAD/F is a tool for automatic differentiation (AD) of Fortran90 numerical computer programs. The major portion for the Fortran90 front end come from the Open64 compiler in the version that is under development at Rice University.
SciDAC Project: CSCAPES
Point of Contact: Jean Utke
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pR is lightweight middleware for the R software environment for statistical computing and graphics, and that supports the automatic parallelization of data-parallel tasks in hybrid multi-node and multi-core environments.
SciDAC Project: SDM
Point of Contact: Gonzalo Vera Rodriguez
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Rapide Surcharge d'Opérateur pour la Différentiation Automatique, a code generator to efficiently compute higher order derivatives via operator overloading. Rapsodia is intended for the computation of higher order derivative information of numerical models written in Fortran, C or C++ by automatic differentiation.
SciDAC Project: CSCAPES
Point of Contact: Jean Utke
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ROSE is a compiler infrastructure that builds source-to-source program transformation for a variety of programming languages. These transformations can be used for static analysis, program optimization, performance analysis, and cyber-security purposes.
SciDAC Project: PERI
Point of Contact: Chunhua "Leo" Liao
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UPC is Unified Parallel C, a language that provides a uniform programming model for both shared and distributed memory hardware.
SciDAC Project: CSCADS
Point of Contact: UPC Mailing Lists
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The Chombo package provides a set of tools for implementing finite difference methods for the solution of partial differential equations on block-structured adaptively refined rectangular grids. Both elliptic and time-dependent modules are included. Support for parallel platforms and standardized self-describing file formats are included.
SciDAC Project: APDEC
Point of Contact: Chombo Info
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Within the context of Chombo, which provides a distributed infrastructure for parallel calculations over block-structured, adaptively refined grids, AMRTools provides tools for data communication between refinement levels, including coarse-fine interpolation tools.
SciDAC Project: APDEC
Point of Contact: Chombo Info
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Within the context of Chombo, which provides a distributed infrastructure for parallel calculations over block-structured, adaptively refined grids, BoxTool provides infrastructure to do any calculations over unions of rectangles and tools to perform set calculus for points in a domain and data holders for unions of rectangles.
SciDAC Project: APDEC
Point of Contact: Chombo Info
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Within the context of Chombo, which provides a distributed infrastructure for parallel calculations over block-structured, adaptively refined grids, EBTools provides embedded boundary discretizations and tools.
SciDAC Project: APDEC
Point of Contact: Chombo Info
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Frontier is a C library for fluid-dynamics simulations with front tracking capabilities for surfaces of discontinuity.
SciDAC Project: ITAPS
Point of Contact: Xiaolin Li
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iGeom is an interface specification for the geometric description of the domains of scientific simulation applications.
SciDAC Project: ITAPS
Point of Contact: ITAPS Team
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iGeom interfaces to CGM, the Common Geometry Module, a mesh geometry abstraction layer used by Cubit from Sandia National Laboratories and allows reading a variety of CAD formats.
SciDAC Project: ITAPS
Point of Contact: Timothy Tautges
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iGeom interface to MOAB, the Mesh-Oriented Data Base. MOAB can store structured and unstructured mesh information, consisting of elements in the finite element collection, plus polygons and polyhedra.
SciDAC Project: ITAPS
Point of Contact: Timothy Tautges

iMesh is an interface specification for the discrete description of the domains of scientific simulation applications.
SciDAC Project: ITAPS
Point of Contact: ITAPS Team
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iMesh interface to FMDB, the Flexible distributed Mesh DataBase. Supports triangles, quadrilaterals, tetrahedron, hexahedron, and prisms, including all upward and downward adjacencies (at varying costs). Supports a fullimplementation of 2D and 3D.
SciDAC Project: ITAPS
Point of Contact: FMDB-info
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iMesh interface to Frontier. Supports triangles, quadrilaterals, tetrahedron, hexahedron, all downward adjacenies plus vertex to face upward adjacency, 2D and 3D, partial implementation (set functionality incomplete).
SciDAC Project: ITAPS
Point of Contact: Xiaolin Li
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iMesh interface to GRUMMP, the Generation and Refinement of Unstructured, Mixed-Element Meshes in Parallel. Supports all mesh topologies except septahedra, polygons, and polyhedra (no edges in 3D), all upward and downward adjacencies (again, no edges in 3D), 2D and 3D, full implementation.
SciDAC Project: ITAPS
Point of Contact: Carl Oliver-Gooch
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iMesh interface to MOAB, the Mesh-Oriented Data Base. All mesh region topologies supported except septahedron, all upward and downward adjacencies (at varying cost), 2D and 3D, full implementation.
SciDAC Project: ITAPS
Point of Contact: Timothy Tautges
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iMesh interface to NWGrid, the NorthWest Grid Generation Code. Supports unstructured mixed elements in 2D and 3D.
SciDAC Project: ITAPS
Point of Contact: Harold Trease

iMesh interface to a small, lightweight reference implementation. Derived from GRUMMP, the Generation and Refinement of Unstructured, Mixed-Element Meshes in Parallel, with the same feature set.
SciDAC Project: ITAPS
Point of Contact: Carl Oliver-Gooch
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iMeshP is a parallel interface specification for the discrete description of the domains of scientific simulation applications.
SciDAC Project: ITAPS
Point of Contact: ITAPS Team
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iMeshP interface to FMDB, the Flexible distributed Mesh DataBase. Supports triangles, quadrilaterals, tetrahedron, hexahedron, and prisms, all upward and downward adjacencies (at varying costs), 2D and 3D, partial implementation. Contact the developers for an alpha version.
SciDAC Project: ITAPS
Point of Contact: FMDB-info

iMeshP interface to MOAB, the Mesh-Oriented Data Base. Supports all mesh region topologies except septahedron, all upward and downward adjacencies (at varying cost), 2D and 3D, full implementation.
SciDAC Project: ITAPS
Point of Contact: Timothy Tautges

iRel is an interface specification for managing the relationships between two or more ITAPS interface specifications.
SciDAC Project: ITAPS
Point of Contact: ITAPS Team
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iRel interface to LASSO. The Lasso tool implements the iRel interface, working through the other ITAPS interfaces. Lasso can recover the associations between mesh and geometric model entities those mesh elements discretize. Lasso currently works with geometry and mesh read into the CGM and MOAB components
SciDAC Project: ITAPS
Point of Contact: Timothy Tautges
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Mesquite is a linkable software library that applies a variety of node-movement algorithms to improve the quality and/or adapt a given mesh. Mesquite uses advanced smoothing and optimization to achieve improved mesh quality in a variety of ways.
SciDAC Project: ITAPS
Point of Contact: Patrick Knupp
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PaToH is the Partitioning Tools for Hypergraph, a multilevel hypergraph partitioning tool that provides fast hypergraph partitioning.
SciDAC Project: CSCAPES
Point of Contact: Ümit V. Çatalyürek
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Matlab interface to PaToH, the Partitioning Tools for Hypergraph, a multilevel hypergraph partitioning tool that provides fast hypergraph partitioning.
SciDAC Project: CSCAPES
Point of Contact: Ümit V. Çatalyürek
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Swap performs mesh quality improvement for simplicial meshes via edge and face swapping in 2D and 3D.
SciDAC Project: ITAPS
Point of Contact: Carl Oliver-Gooch
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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 multi-physics engineering and scientific problems.
SciDAC Projects: CSCAPES ITAPS TOPS
Point of Contact: Trilinos Users Forum
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Isorropia performs combinatorial scientific computing, with focus on partitioning and load balancing, but also supports coloring and ordering of sparse matrices. Isorropia provides an object-oriented interface to Zoltan using the Epetra linear algebra services.
SciDAC Projects: CSCAPES ITAPS
Point of Contact: Erik Boman
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Zoltan provides dynamic load balancing for parallel computing with a procedural C interface, with a variety of redistribution algorithms available.
SciDAC Projects: CSCAPES ITAPS
Point of Contact: Vitus Leung
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Active Harmony provides software architecture that supports distributed execution of computational objects, and allows applications to be tuned with minimal changes to the application and library source code. It can be used to improve the performance of an application during execution taking into account observed performance.
SciDAC Project: PERI
Point of Contact: Ananta Tiwari
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CQoS is the Computational Quality of Service, tools for the automatic selection and configuration of components to suit a particular computational purpose and environment.
SciDAC Project: TASCS
Point of Contact: CQoS Mailing List

HPCToolkit is a suite of tools for measurement and analysis of program performance. It uses hardware counters to sample the execution of a multithreaded and/or multiprocess program, enabling fine-grain measurement without modifying the source code
SciDAC Project: CSCADS
Point of Contact: HPC
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Within the context of HPCToolkit, a suite of tools for measurement and analysis of program performance, hpcviewer interactively presents program performance in a top-down fashion.
SciDAC Project: CSCADS
Point of Contact: HPC
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A Java-based tool for graphical analysis of trace files (time-stamped events) and the behavior of parallel programs. It is packed with the MPICH portable implementation of MPI.
SciDAC Project: CSCADS
Point of Contact: Bill Gropp
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Orio is an annotation system implemented in Python that enables developers to insert annotations into their source code (in C or Fortran). These annotations are used to trigger performance optimizations on a specified code fragment.
SciDAC Project: PERI
Point of Contact: Boyana Norris
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OSKI is the Optimized Sparse Kernel Interface, a collection of low-level C primitives that provide automatically tuned computational kernels on sparse matrices, for use in solver libraries and applications.
SciDAC Project: CSCADS
Point of Contact: OSKI Mailing List
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The Chombo package provides a set of tools for implementing finite difference methods for the solution of partial differential equations on block-structured adaptively refined rectangular grids. Both elliptic and time-dependent modules are included. Support for parallel platforms and standardized self-describing file formats are included.
SciDAC Project: APDEC
Point of Contact: Chombo Info
Download

Within the context of Chombo, which provides a distributed infrastructure for parallel calculations over block-structured, adaptively refined grids, AMRElliptic is a multigrid-based elliptic equation solver for adaptive hierarchies.
SciDAC Project: APDEC
Point of Contact: Chombo Info
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Within the context of Chombo, which provides a distributed infrastructure for parallel calculations over block-structured, adaptively refined grids, AMRTimeDependent manages sub-cycling in time for time-dependent adaptive calculations.
SciDAC Project: APDEC
Point of Contact: Chombo Info
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Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers using scalable preconditioners.
SciDAC Project: TOPS
Point of Contact: Robert Falgout
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PETSc is a suite of data structures and routines for the parallel, scalable solution of scientific applications modeled by partial differential equations.
SciDAC Project: TOPS
Point of Contact: PETSc Maintenance
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Prometheus is a multigrid solver for finite element matrices on unstructured meshes in solid mechanics. Part of the PETSc suite of solver tools.
SciDAC Project: TOPS
Point of Contact: Mark Adams
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TAO is the Toolkit for Advanced Optimization, focused on the development of software for large-scale optimization problems. Part of the PETSc suite of solver tools.
SciDAC Project: TOPS
Point of Contact: TAO Comments
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PLASMA is the Parallel Linear Algebra for Scalable Multi-core Architectures library uses out-of-order scheduling as the basis for scalable and highly efficient computational linear algebra.
SciDAC Project: CSCADS
Point of Contact: PLASMA Users Forum
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The SUite of Nonlinear and DIfferential/ALgebraic equation Solvers was implemented with the goal of providing robust time integrators and nonlinear solvers that can easily be incorporated into existing simulation codes. The primary design goals were to require minimal information from the user, allow users to easily supply their own data structures underneath the solvers, and allow for easy incorporation of user-supplied linear solvers and preconditioners.
SciDAC Project: TOPS
Point of Contact: SUNDIALS Support
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CVODE solves initial value problems for ordinary differential equation (ODE) systems. Part of the SUNDIALS SUite of Nonlinear and DIfferential/ALgebraic equation Solvers.
SciDAC Project: TOPS
Point of Contact: Radu Serban
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CVODES solves ordinary differential equation (ODE) systems and includes sensitivity analysis capabilities (forward and adjoint). Part of the SUNDIALS SUite of Nonlinear and DIfferential/ALgebraic equation Solvers.
SciDAC Project: TOPS
Point of Contact: Radu Serban
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IDA solves initial value problems for differential-algebraic equation (DAE) systems. Part of the SUNDIALS SUite of Nonlinear and DIfferential/ALgebraic equation Solvers.
SciDAC Project: TOPS
Point of Contact: Radu Serban
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IDAS solves differential-algebraic equation (DAE) systems and includes sensitivity analysis capabilities (forward and adjoint). Part of the SUNDIALS SUite of Nonlinear and DIfferential/ALgebraic equation Solvers.
SciDAC Project: TOPS
Point of Contact: Radu Serban
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KINSOL solves nonlinear algebraic systems. Part of the SUNDIALS SUite of Nonlinear and DIfferential/ALgebraic equation Solvers.
SciDAC Project: TOPS
Point of Contact: Radu Serban
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SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
SciDAC Project: TOPS
Point of Contact: X. Sherry Li
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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 multi-physics engineering and scientific problems.
SciDAC Projects: CSCAPES ITAPS TOPS
Point of Contact: Trilinos Users Forum
Download

Amesos is the direct sparse solver package in Trilinos, providing clean and consistent interfaces to several third party direct solver libraries, using Epetra for the linear algebra services such as vector and operator definitions.
SciDAC Project: TOPS
Point of Contact: Ken Stanley
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Anasazi is an extensible and interoperable framework for large-scale eigenvalue algorithms. Abstract interface supports Epetra and other linear algebra objects.
SciDAC Project: TOPS
Point of Contact: Rich Lehoucq
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AztecOO provides an object-oriented interface the the well-known Aztec Krylov-space iterative solver library. Uses the Epetra linear algebra services to define vector and operator objects.
SciDAC Project: TOPS
Point of Contact: Michael Heroux
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ForTrilinos provides a set of standards-conforming, portable Fortran interfaces to select Trilinos packages.
SciDAC Project: TOPS
Point of Contact: Damian Rouson
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IFPACK provides a suite of object-oriented algebraic preconditioners for the solution of preconditioned iterative solvers.
SciDAC Project: TOPS
Point of Contact: Michael Heroux
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LOCA is the Library of Continuation Algorithms, whose objective is to compute families of solutions to the parameterized nonlinear equation F(x,p) = 0 and their bifurcations.
SciDAC Project: TOPS
Point of Contact: Roger Pawlowski
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ML is the Trilinos multigrid preconditioning package designed to solve large sparse linear systems of equations arising primarily from elliptic PDE discretizations.
SciDAC Project: TOPS
Point of Contact: Jonathan Hu
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NOX is the Nonlinear Object-Oriented Solutions package of Trilinos, which enables the robust and efficient solution of the nonlinear equations of the form F(x) = 0.
SciDAC Project: TOPS
Point of Contact: Roger Pawlowski
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FastBit is a library of search functions supported by compressed bitmap indexes. Similarly to other database management systems, Fastbit treats user data in a column-oriented manner but it is designed to accelerate user's data selection tasks.
SciDAC Project: SDM
Point of Contact: FastBit Contacts
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Services for high-performance, reliable, secure data movement service that is based on the concept of cloud computing. The service can be invoked through a web interface ("drag and drop") or command line-like instructions.
SciDAC Project: CEDPS
Point of Contact: Globus Online Support

Data transfer protocol based on the standard FTP protocol that is optimized for high-bandwidth wide-area networks. By applying a set of changes to FTP, GridFTP enables faster transfer and in-built security, which are essential for the transmission of very large files stemming from applications that use Grid computing resources.
SciDAC Project: CEDPS
Point of Contact: Ian Foster
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ImageVis3D is a volume rendering program developed by the NIH/NCRR Center for Integrative Biomedical Computing with main design goals of simplicity, scalability, and interactivity.
SciDAC Project: VACET
Point of Contact: ImageVis3D Users
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ITAPS interface for VisIt, a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms.
SciDAC Project: ITAPS
Point of Contact: Mark Miller
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Kepler is a problem-solving environment for the analysis and modeling of scientific data. It simplifies the creation of executable models by using a visual representation of processes, or “scientific workflows”, which display the flow of data among discrete analysis and modeling components.
SciDAC Project: SDM
Point of Contact: Kepler Support
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ParaView is an open-source, multi-platform data analysis and visualization application that allows users to quickly build visualizations to analyze their data using qualitative and quantitative techniques.
SciDAC Project: IUSV
Point of Contact: ParaView Users
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Sapphire is a system that implements modular capabilities for scientific data mining, and that targets problems that involve data from observations, experiments and simulations.
SciDAC Project: SDM
Point of Contact: Chandrika Kamath

SciRun is a problem solving environment for modeling, simulation and visualization of scientific problems; VACET extends the visualization component.
SciDAC Project: VACET
Point of Contact: SCIRun Users
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VisIt is a free interactive parallel visualization and graphical analysis tool for viewing scientific data on Unix and PC platforms
SciDAC Project: VACET
Point of Contact: VisIt Users
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VisTrails is an open-source scientific workflow and provenance management system developed at the University of Utah that provides support for data exploration and visualization.
SciDAC Project: VACET
Point of Contact: VisTrails Users
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