Computational Cluster Programs

Programming Libraries/APIs on ATS-Hosted Clusters

Software Versions Available on ATS-Hosted Clusters

Application	Hoffman2	Cardio	CNSI2	Hydro	Neutrino
ARPACK	96
ATLAS	3.8.2				3.6.0
Basic Linear Algebra Subprograms (BLAS)	Intel		Yes	Yes	Intel
Boost C++ Libraries					1.33.1
FFTW	3.2	3.1.2	3.0.1		2.1.3
GNU Scientific Library (GSL)	1.11				1.4
HDF(4)	4.2r2				HDF4
HDF5	1.8.2				HDF5
Intel Math Kernel Library (MKL)	10.0.1.014				HDF5
LAPACK	3.1.1			Yes	Intel
netCDF	4.0	Yes	Yes	3.6.0-p1
OpenMotif	2.3.0-1
PETSc	2.3.3-p15
ROOT					4.00.08f, _v2.10.02
ScaLAPACK	1.8.0		Yes
Trilinos	9.0.1

Software Package Information and Documentation Links

Application	Brief Description	Callable From Fortran	Callable From C/C++	Supported	From	Documentation
ARPACK	ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.	Yes	Yes	No	Department of Computational and Applied Mathematics at Rice University	How to run on ATS-Hosted Clusters ARPACK Users Guide
Automatically Tuned Linear Algebra Software (ATLAS)	C and Fortran77 interfaces to BLAS as well as a few routines from LAPACK. When the ATLAS library is built and installed, it automatically optomizes its performance for whatever system it was built on, in this case, these routines are optimized for the cluster compute nodes.	Yes	Yes	No	ATLAS Sourceforge Project	How to run on ATS-Hosted Clusters ATLAS Documentation Links
Basic Linear Algebra Subprograms (BLAS)	A set of routines that provide standard building blocks for performing basic vector and matrix operations. The Level 1 BLAS perform scalar, vector and vector-vector operations; the Level 2 BLAS perform matrix-vector operations, and the Level 3 BLAS perform matrix-matrix operations.	Yes	Yes	No	Netlib Repository	How to run on ATS-Hosted Clusters BLAS Home Page
Boost C++ Libraries	Portable C++ source libraries. Contains: string and text processing classes, container classes, iterators, generic programming classes, metaprogramming classes, math and numerics, input/output and memory management classes among other things.	No	C++ only	No	Members of the C++ Standards Committee Library Working Group and the C++ Community	How to run on ATS-Hosted Clusters Boost Home Page
FFTW	A C subroutine library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of both real and complex data of arbitrary size.	Yes	Yes	No	FFTW.org	How to run on ATS-Hosted Clusters FFTW User Manual
GNU Scientific Library (GSL)	A numerical library for C and C++ programmers.	No	Yes	No	Free Software Foundation, Inc.	How to run on ATS-Hosted Clusters GSL Home Page GSL Reference Manual
HDF(4) and HDF5 (Hierarchical Data Format)	HDF5 is a general purpose library and file format for storing scientific data. HDF (also called HDF4) is its predecessor.	Yes	Yes	No	The HDF Group	How to run on ATS-Hosted Clusters HDF5 Home Page HDF4 Home Page
Intel Math Kernel Library (MKL)	A math library that is optimized for Intel processor-based systems and for multi-core Intel systems. According to ATS benchmarks, the Intel-MKS library performs very well on AMD Opteron nodes as well.	Yes	Yes	Yes	Intel Corporation	How to run on ATS-Hosted Clusters Intel-MKL Home Page
LAPACK	A library of Fortran 77 subroutines for solving the most common problems in numerical linear algebra: systems of linear equations, linear least squares probems, eigenvalue problems, and singular value problems.	Yes	Yes	No	Netlib Repository	How to run on ATS-Hosted Clusters LAPACK Home Page LAPACK Users' Guide
netCDF	A set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.	Yes	Yes	No	The University Corporation for Atmospheric Research	How to run on ATS-Hosted Clusters netCDF Home Page netCDF Documentation Links
OpenMotif	Motif X11 Window Manager libraries.	No	Yes	No	Motif Zone	How to run on ATS-Hosted Clusters
PETSc	Portable, Extensible Toolkit for Scientific Computation (PETSc). A suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. PETSc employs the MPI standard for all message-passing communication.	Yes	Yes	No	Argonne National Laboratory	How to run on ATS-Hosted Clusters PETSc Documentation
ROOT	An Object-Oriented Data Analysis Framework with all the functionality needed to handle and analyse large amounts of data in a very efficient way. Having the data defined as a set of objects, specialised storage methods are used to get direct access to the separate attributes of the selected objects, without having to touch the bulk of the data. Included are histograming methods in 1, 2 and 3 dimensions, curve fitting, function evaluation, minimisation, graphics and visualization classes to allow the easy setup of an analysis system that can query and process the data interactively or in batch mode.			No	CERN -- The European Organization for Nuclear Research	ROOT Home Page ROOT User's Guide
ScaLAPACK	A subset of the LAPACK routines redesigned for distributed memory parallel computers. ScaLAPACK is currently written in a Single-Program-Multiple-Data style using explicit message passing for interprocessor communication.	Yes	No	No	Netlib Repository	How to run on ATS-Hosted Clusters ScaLAPACK Home Page ScaLAPACK Users' Guide ScaLAPACK Fortran Example
Trilinos	Trilinos is a set of sophisticated software tools, containing more than 20 library packages. 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.	Limited	C:limited, C++:Yes	No	Sandia National Laboratories	How to run on ATS-Hosted Clusters The Trilinos Project Documentation