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Run existing code quickly in a standard Linux environment. Alternatively, you can develop, build, and debug your application by using Sabalcore’s suite of open-source compilers and libraries. Development can be done at your site or directly on Sabalcore’s cluster computing environment. Sabalcore’s expert staff can help you install, configure and tailor your application, at no additional cost.

gromacs.org GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers..

hadoop.apache.org Apache Hadoop is a Java software framework that supports data-intensive distributed applications. Hadoop On Demand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. Sabalcore how supports Hadoop Common, HOD, MapReduce, and HDFS. Learn more.

http://www.msg.ameslab.gov/gamess/ The GAMESS (General Atomic and Molecular Electronic Structure System) is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Excited states can be computed by CI, EOM, or TD-DFT procedures. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic computations are available, including infinite order two component scalar corrections, with various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments. Nuclear wavefunctions can also be computed, in VSCF, or with explicit treatment of nuclear orbitals by the NEO code. A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials or model core potentials, so that essentially the entire periodic table can be considered. Most computations can be performed using direct techniques, or in parallel on appropriate hardware. Graphics programs, particularly the MacMolplt program (for Macintosh, Windows, or Linux desktops), are available for viewing of the final results, and the Avogadro program can assist with preparation of inputs.

www.OpenFOAM.com The OpenFOAM® (Open Field Operation and Manipulation) CFD Toolbox is a free, open source CFD software package produced by OpenCFD Ltd. It has a large user base across most areas of engineering and science, from both commercial and academic organizations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

www.wrf-model.org The Weather Research and Forecasting (WRF) Model is a next-generation mesocale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. It features multiple dynamical cores, a 3-dimensional variational (3DVAR) data assimilation system and a software architecture allowing for computational parallelism and system extensibility. WRF is suitable for a broad spectrum of applications across scales ranging from meters to thousands of kilometers. Learn more about WRF, WPS, and HWRF at Sabalcore.

www.src.com/calpuff CALPUFF is an advanced non-steady-state meteorological and air quality modeling system. The model has been adopted by the U.S. Environmental Protection Agency (U.S. EPA) in its Guideline on Air Quality Models as the preferred model for assessing long range transport of pollutants and their impacts on Federal Class I areas and on a case-by-case basis for certain near-field applications involving complex meteorological conditions. Read more...

www.epa.gov A steady-state plume model that incorporates air dispersion based on planetary boundary layer turbulence structure and scaling concepts, including treatment of both surface and elevated sources, and both simple and complex terrain.  Read more...

www.adcirc.org ADCIRC is a system of computer programs for solving time dependent, free surface circulation and transport problems in two and three dimensions. These programs utilize the finite element method in space allowing the use of highly flexible, unstructured grids. Typical ADCIRC applications have included: (i) modeling tides and wind driven circulation, (ii) analysis of hurricane storm surge and flooding, (iii) dredging feasibility and material disposal studies, (iv) larval transport studies, (v) near shore marine operations.  Read more...

www.netlib.org/linalg/spooles   Description: SPOOLES is a library for solving sparse real and complex linear systems of equations, written in the C language using object oriented design. At present, there is the following functionality:

 

www.freemat.sourceforge.net Description: FreeMat is a free environment for rapid engineering and scientific prototyping and data processing. It is similar to commercial systems such as MATLAB from Mathworks, and IDL from Research Systems, but is Open Source. FreeMat is available under the GPL license.

www.abinit.org ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudo potentials and a plane wave basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). In addition to the main ABINIT code, different utility programs are provided.

www.sourceforge.net/projects/math-atlas ATLAS (Automatically Tuned Linear Algebra Software) provides highly optimized Linear Algebra kernels for arbitrary cache-based architectures. ATLAS provides ANSI C and Fortran77 interfaces for the entire BLAS API, and the LAPACK AP.

www,glaros.dtc.umn.edu/gkhome/views/metis METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way and multi-constraint partitioning schemes.

www.glaros.dtc.umn.edu/gkhome/views/metis ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning and parallel multi-constrained partitioning schemes.

www.cise.ufl.edu/research/sparse/SuiteSparse SuiteSparse is a set of programs and libraries that contains various tools for handling sparse matrices.

www.fftw.org FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).

www.numpy.scipy.org NumPy is the fundamental package needed for scientific computing with Python. It contains a powerful N-dimensional array object, sophisticated (broadcasting) functions, basic linear algebra functions, basic Fourier transforms, sophisticated random number capabilities and tools for integrating Fortran code.

www.unix.mcs.anl.gov/petsc/petsc-as/index.html PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for all message-passing communication.

www.fenics.org/wiki/FEniCS_Project FEniCS is a suite of computation mathematics modeling tools. It contains a C++/Python library for solving differential equations, optimizations for evaluation of variational forms, a compiler for finite element variational forms, tabulations of finite element function spaces, simple inlining of C / C++ code in Python, automation for the simulation of mechanical systems and several other CMM elements

www.ebi.ac.uk/interpro InterProScan is a tool that combines different protein signature recognition methods into one resource. The number of signature databases and their associated scanning tools, as well as the further refinement procedures, increases the complexity of the problem. InterProScan performs a considerable amount of data look-up from various databases and program outputs. The Perl-based InterProScan is intended to be an extensible and scalable system optimized to cope with bulk data processing.

www.ks.uiuc.edu/Research/namd/ NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms such as those at Sabalcore Computing Inc.

www.autodock.scripps.edu AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoDock actually consists of two main programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid pre-calculates these grids.

www.hmmer.janelia.org Profile hidden Markov models (profile HMMs) can be used to do sensitive database searching using statistical descriptions of a sequence family’s consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis. HMMER is available for use on Sabalcore’s clusters.

www.mpiblast.org mpiblast is is a freely available, open-source, parallel implementation of NCBI BLAST. mpiBLAST takes advantage of distributed computational resources, i.e., a cluster, through explicit MPI communication and thereby utilizes all available resources unlike standard NCBI BLAST which can only take advantage of shared-memory multi-processors (SMPs). mpiBLAST is available for use on Sabalcore’s clusters.

http://mrbayes.csit.fsu.edu/ MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. MrBayes is available today for use on Sabalcore’s clusters.

http://www.stat.osu.edu/~dkp/BEST/introduction/ BEST is a free phylogenetics program to estimate the joint posterior distribution of gene trees and species tree using multilocus molecular data that accounts for deep coalescence but not for other issues such as horizontal transfer or gene duplication. The program works within the popular Bayesian phylogenetics package.

http://beast.bio.ed.ac.uk/Main_Page BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

www.mcs.anl.gov/mpi/mpich2 MPICH2 is an implementation of the Message-Passing Interface (MPI). The goals of MPICH2 are to provide an MPI implementation for important platforms, including clusters, SMPs and massively parallel processors.

http://www.open-mpi.org/Open MPI is an open souce MPI-2 implementation.

http://mvapich.cse.ohio-state.eduMVAPICH2 is an implementation of MPI over Infiniband.

www.sun.com/java Java technology is an object-oriented, platform-independent, high-performance multithreaded programming environment.

www.r-project.org R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering) and graphical techniques and is highly extensible.