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Reach a broad range of customers who take advantage of our hosted software applications. Contact us.
No SDK required. 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,
usually at no additional cost.
Gromacs
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
(New addition)
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.Weather Research and Forecasting Model (WRF)
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.CALPUFF
(New addition)
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.
Spooles
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:
1. Compute multiple minimum degree, generalized
nested dissection and multisection orderings of
matrices with symmetric structure.
2. Factor and solve square linear systems of
equations with symmetric structure, with or without
pivoting for stability. The factorization can be
symmetric LDLT, Hermitian LDLH, or nonsymmetric LDU.
A direct factorization or a drop tolerance
factorization can be computed. The factors and solve
can be done in serial mode, multithreaded with
Solaris or POSIX threads, or with MPI.
3. Factor and solve overdetermined full rank systems
of equations using a multifrontal QR factorization,
in serial or using POSIX threads.
4. Solve square linear systems using a variety of
Krylov iterative methods. The preconditioner is a
drop tolerance factorization, constructed with or
without pivoting for stability.
FreeMat
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.
Abinit
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.ATLAS
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. Metis
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.
ParMetis
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.
SuiteSparse
www.cise.ufl.edu/research/sparse/SuiteSparse
SuiteSparse is a set of programs and libraries that contains various tools for handling sparse matrices.
FFTW
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).
NumPy
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.
PetSC
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.
FEniCS
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
InterProScan
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.
NAMD
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.AutoDock
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.
HMMER
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.
mpiBLAST
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.
MrBayes
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.
Bayesian
Estimation of Species Trees (BEST)
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
MrBayes.MPICH2
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. Boost
www.boost.org
Boost provides free peer-reviewed portable C++ source libraries including tools for string and text processing, containers, iterators, algorithms, function objects and higher-order programming, generic programming, template metaprogramming, math and numerics, programming interfaces, and many other.
Java™
www.sun.com/java
Java technology is an object-oriented, platform-independent, high-performance multithreaded programming environment. R
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.Radiance
radsite.lbl.gov/radiance
RADIANCE is a highly accurate ray-tracing software system for UNIX computers.
Blender
www.blender.org
Blender is the most powerful free open source 3D graphics, rendering, gaming, and content creation suite available for all
major operating systems under the GNU General Public License.
FFmpeg
www.ffmpeg.mplayerhq.hu/
FFmpeg can convert digital audio and video in numerous formats. FFmpeg is a command line tool that is composed of a collection of free software / open source libraries. It includes libavcodec, an audio/video codec library used by several other projects, and libavformat, an audio/video container mux and demux
library
Engineering
EnergyPlus
http://apps1.eere.energy.gov/buildings/energyplus/
EnergyPlus models heating, cooling, lighting,
ventilating, and other energy flows as well as water
in buildings. While originally based on the most
popular features and capabilities of BLAST and
DOE-2, EnergyPlus includes many innovative
simulation capabilities such as time steps of less
than an hour, modular systems and plant integrated
with heat balance-based zone simulation, multizone
air flow, thermal comfort, water use, natural
ventilation, and photovoltaic systems.
"Thanks again for your expertise. Me and others...continue to realize the
valuable resource we have in Sabalcore."
Durham, New Hampshire, February 2009
Durham, New Hampshire, February 2009
"You have done quite remarkable work."
The Queen’s Medical Center, Hawaii, September 2003
The Queen’s Medical Center, Hawaii, September 2003
