Aspen Systems the GPU Applications Experts
GPU computing has been around for about a decade now. The concept of an accelerator card has been around for even longer with the MDGRAPE-2 card project receiving a Gordon Bell Prize in 2000. The concept is simple. Offload the most computationally intensive portions of your code to the accelerator card, and use the CPU for the other calculations and to help collect the data. But the reality is, it’s not always that simple as the program will need to be written or rewritten to include code that will make use of the GPU.
There are still many researchers out there who are not taking advantage of the power of GPUs. Part of the reason may be due to the researchers not knowing that their favorite program has already been ported to run on them. NVIDIA has a very comprehensive list of the software which have been ported to run on GPUs. We have a few of the most popular ones listed here. If you see your code listed and would like some help with testing, Aspen Systems has GPU servers for testing purposes, Contact Us for a test drive.
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BIOINFORMATICS
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Started in 2009, the aim of the BarraCUDA project is to develop a sequence mapping software that utilizes the massive parallelism of graphics processing units (GPUs) to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome.
Industries:  Go to the SourceForge website for more information.
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CUDASW++ software is a public open source software for Smith-Waterman protein database searches on Graphics Processing Units (GPUs) with CUDA.
Industries: Go to the SourceForge website for more information.
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GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic variant calling tools, and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data.
Industries: Go to the GATK website for more information.
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G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. G-BLASTN supports the blastn and megablast modes of NCBI-BLAST, and can produce exactly the same results as NCBI-BLAST.
Industries: Go to the HKBU website for more information.
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The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics tools. The widespread impact of BLAST is reflected in over 110,000 citations that this software has received in the past three decades, and the use of the word “blast” as a verb referring to biological sequence comparison. Any improvement in the execution speed of BLAST would be of great importance in the practice of bioinformatics, and facilitate coping with ever increasing sizes of biomolecular databases.
Industries: Go to the CMU website for more information.
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mCUDA-MEME is an ultrafast scalable motif discovery algorithm based on MEME algorithm for multiple GPUs using a hybrid combination of CUDA, MPI and OpenMP parallel programming models.
Industries: Go to the mCUDA-MEME website for more information.
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SOAP3 is a GPU-based software for aligning short reads with a reference sequence. It can find all alignments with k mismatches, where k is chosen from 0 to 3.
Industries: Go to the Genomics website for more information.
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SOAP3-dp like its predecessor SOAP3, is a GPU-based software for aligning short reads to a reference sequence. It improves SOAP3 regarding both speed and sensitivity by skillful exploitation of whole-genome indexing and dynamic programming on a GPU. SOAP3 is limited to find alignments with at most four mismatches, while SOAP3-dp can find alignments involving mismatches, INDELs, and small gaps. The number of reads aligned, especially for paired-end data, typically increases 5 to 10 percent from SOAP3 to SOAP3-dp. More interestingly, SOAP3-dp’s alignment time is much shorter than SOAP3, as it is found that GPU-based dynamic programming, when coupled with indexing, can be much more efficient. For example, when aligning length-100 single-end reads with the human genome, SOAP3 typically requires tens of seconds per million reads, while SOAP3-dp takes only a few seconds.
Industries: Go to the HKU website for more information.
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COMPUTATIONAL FLUID DYNAMICS
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ANSYS Fluent is the most-powerful computational fluid dynamics (CFD) software tool available, empowering you to go further and faster as you optimize your product’s performance. Fluent includes well-validated physical modeling capabilities to deliver fast, accurate results across the widest range of CFD and multiphysics applications.
Industries:     Go to the ANSYS website for more information.
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Barracuda Virtual Reactor or Barracuda VR continues to be the only software of its kind, built exclusively for one single application: Gas-Particle fluidized reactors. Its unique capabilities have been well validate with both large-scale experimental data and with commercial operating reactors across broad industries.
Industries: Go to the CPFD Software website for more information.
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FluiDyna develops integrated hardware and software solutions. Its core expertise lies particularly in the development and application of numerical and experimental methods of flow simulation and thermodynamics.
Industries: Go to the FluiDyna website for more information.
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OpenFOAM (Open-source Field Operation And Manipulation) is a C++ toolbox for the development of customized numerical solvers, and pre-/post-processing utilities for the solution of continuum mechanics problems, including computational fluid dynamics (CFD).
Industries: Go to the Openfoam website for more information.
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DATABASES
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Kinetica develops a distributed, in-memory database management system using graphics processing units, it is used for real-time streaming analytics and databases to provide real time analysis.
Industries: Go to the Kinetica website for more information.
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MATHEMATICS
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ArrayFire specializes in developing accelerated, scalable computing solutions on modern computational platforms for our clients. As an industry leader in high performance computing for nearly 10 years, ArrayFire continues to drive innovation in all areas of accelerated computing, ranging from apps deployed on low-powered and mobile platforms to scientific simulations on high-end supercomputers.
Industries: Go to the ArrayFire website for more information.
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MATLAB is a numerical computing and programming environment with a broad range of functionality (matrix manipulation, numerical linear algebra, general-purpose graphics, etc.). MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and FORTRAN. Additionally, specialized application areas (e.g. bioinformatics or financial derivatives) are served by a large number of optional toolboxes.
Industries: Go to the MathWorks website for more information.
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SciComp generates efficient C-family derivatives pricing model source code from specifications written in an intuitive, finance-specific language. SciComp also generates wrapper code to automate integration without imposing proprietary data models.
Industries: Go to the SciComp website for more information.
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Wolfram Mathematica provides a single integrated, continually expanding system that covers the breadth and depth of technical computing. Mathematica has defined the state of the art in technical computing—and provided the principal computation environment for millions of innovators, educators, students, and others around the world.
Industries: Go to the Wolfram website for more information.
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Xcelerit is targeted at domain specialists using heavy computations in their day-to-day work, such as mathematicians, researchers, engineers, or scientists. Users can focus on the core of their algorithm, rather than addressing parallelism and low-level hardware details, and yet they can generate high performance programs.
Industries: Go to the Xcelerit website for more information.
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MOLECULAR DYNAMICS
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ACEMD is a production molecular dynamics software specially optimized to run on NVIDIA graphics processing units (GPUs). ACEMD is the world’s fastest molecular dynamics engine for a single workstation and can read the popular CHARMM and AMBER force field formats without any change.
Industries: Go to the Acellera website for more information.
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AMBER is a suite of molecular modeling and molecular dynamics simulation tools, available for both CPUs and GPUs. AMBER refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules that are in the public domain, and are used in a variety of simulation programs; and a package of molecular simulation programs.
Industries: Go to the AMBER website for more information.
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Charmm is a versatile and widely used molecular simulation program with broad application to many-particle systems. Charmm has been developed with a primary focus on the study of molecules of biological interest, such as peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. Charmm provides a large suite of computational tools that encompass numerous conformational and path sampling methods, free energy estimates, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. Charm can also be useful for a much broader class of many-particle systems and can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models.
Industries: Go to the CHARMM website for more information.
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ESPResSo is a highly versatile software package for performing and analyzing scientific Molecular Dynamics many-particle simulations of coarse-grained atomistic or bead-spring models as they are used in soft-matter research in physics, chemistry and molecular biology. It can be used to simulate systems such as polymers, liquid crystals, colloids, ferrofluids and biological systems, for example DNA and lipid membranes.
Industries: Go to the ESPResSo website for more information.
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GPUGRID is a distributed computing infrastructure devoted to biomedical research. GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.
Industries: Go to the GPUGRID website for more information.
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GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulation of proteins, lipids, and nucleic acids. GROMACS is one of the fastest and most popular molecular dynamics software packages available, and can run on CPUs as well as GPUs.
Industries: Go to the GROMACS website for more information.
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LAMMPS (Large-scale Atomic/Molecular Massivley Parallel Simulator) is an open-source molecular dynamics simulator written in C++ from Sandia National Laboratories, and is designed for parallel machines. LAMMPS models an ensemble of particles in a liquid, solid or gaseous state. It can model atomic polymeric, biological, metallic, or mesoscale systems using a variety of force fields and boundary conditions and is easily extensible.
Industries: Go to the LAMMPS website for more information.
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NAMD 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 cores for typical simulations and beyond 200,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms.
Industries: Go to the NAMD website for more information.
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OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.
Industries: Go to the SimTK website for more information.
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VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.
Industries: Go to the VMD website for more information.
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PHYSICS
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Chroma supports data-parallel programming constructs for lattice field theory and in particular lattice QCD. It uses the SciDAC QDP++ data-parallel programming (in C++) that presents a single high-level code image to the user, but can generate highly optimized code for many architectural systems including single node workstations, multi-threaded SMP workstations, clusters of workstations via QMP, and classic vector computers.
Industries: Go to the Chroma website for more information.
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MILC performs simulations of four dimensional SU(3) lattice gauge theory on MIMD parallel machines. “Strong interactions” are responsible for binding quarks into protons and neutrons and holding them all together in the atomic nucleus.
Industries: Go to the NERSC website for more information.
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QUDA is a library for performing calculations in lattice QCD on Graphics Processing Units (GPUs), leveraging NVIDIA’s CUDA platform.
Industries: Go to the QUDA website for more information.
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QUANTUM CHEMISTRY
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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 pseudopotentials and a planewave or wavelet basis.
Industries: Go to the Abinit website for more information.
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Aces (Advanced Concepts in Electronic Structure Theory) is an ab initio computational chemistry package for performing high-level quantum chemical ab initio calculations. Its major strength is the accurate calculation of atomic and molecular energies as well as properties using many-body techniques such as Many-Body Perturbation theory (MBPT) and, in particular coupled cluster techniques to treat electron correlation.
Industries: Go to the UFL website for more information.
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Amsterdam Density Functional (ADF) is particularly strong in understanding and predicting structure, reactivity and spectra of molecules. ADF is frequently used for studying transition metal complexes and molecules with heavy atoms, since all elements in the periodic table can be modeled accurately and efficiently with the ZORA relativistic approach and all-electron basis sets. ADF offers unique capabilities to predict molecular properties of organic electronics materials. ADF is easy to use with parallel binaries, integrated GUI, and supported by experts with decades of experience.
Industries: Go to the SCM website for more information.
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BigDFT is a DFT massively parallel electronic structure code using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh.
Industries: Go to the BigDFT website for more information.
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CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW.
Industries: Go to the CP2K website for more information.
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The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio molecular quantum chemistry package. GAMESS can perform a number of general computational chemistry calculations, including Hartree-Fock, density functional theory (DFT), generalized valence bond (GVB), and multi-configurational self-consistent field (MCSCF).
Industries: Go to the Ames Laboratory website for more information.
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Gaussian is the latest in the Gaussian series of electronic structure programs. Gaussian is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest. Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures.
Industries: Go to the Gaussian website for more information.
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LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilities.
Industries: Go to the Dalton website for more information.
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NWChem is an ab initio computational chemistry software package with built-in support for quantum chemical and molecular dynamics capabilities. NWChem is developed and maintained by the Molecular Sciences Software group at the Pacific Northwest National Laboratory (PNNL) and aims to be scalable both in its ability to treat large problems efficiently as well as in its usage of available parallel computing resources.
Industries: Go to the NWChem website for more information.
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Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation.
Industries: Go to the TDDFT website for more information.
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Q-Chem is a comprehensive ab initio quantum chemistry package for accurate predictions of molecular structures, reactivities, and vibrational, electronic and NMR spectra.
Industries: Go to the Q-CHEM website for more information.
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Quantum ESPRESSO (opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization) is an integrated suite of open-source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves and pseudopotentials.
Industries: Go to the Quantum Espresso website for more information.
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TeraChem is general purpose quantum chemistry software designed to run on NVIDIA GPU architectures under a 64-bit Linux operating system.
Industries: Go to the PetaChem website for more information.
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STRUCTURAL MECHANICS
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Abaqus is a popular commercial finite element, multi-physics simulation from Simulia. Abaqus is a parallel application and can run in both MPI and in shared-memory threaded mode. The parallel execution is triggered and controlled by command line options to the abaqus driver, along with all the other run options. NVIDIA and SIMULIA, the Dassault Systèmes brand for Realistic Simulation, have collaborated to deliver the power of GPU computing for Abaqus customers. NVIDIA GPU acceleration enables faster results for more efficient computation and job turnaround times, delivering more license utilization for the same investment.
Industries: Go to the 3DS website for more information.
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ANSYS enables you to predict with confidence that your products will thrive in the real world. Industry leaders use ANSYS to create complete virtual prototypes of complex products and systems – comprised of mechanical, electronics and embedded software components – which incorporate all the physical phenomena that exist in real-world environments. ANSYS and GPUs work effectively to ensure the fastest performance for simulations running on ANSYS parallel software.
Industries: Go to the ANSYS website for more information.
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Blaze-DEMGPU is a modular GPU based discrete element method (DEM) framework that supports polyhedral shaped particles. The high level performance is attributed to the light weight and Single Instruction Multiple Data (SIMD) that the GPU architecture offers. Blaze-DEMGPU offers suitable algorithms to conduct DEM simulations on the GPU and these algorithms can be extended and modified.
Industries: Go to the ScienceDirect website for more information.
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GTS NX is a comprehensive finite element analysis software package that is equipped to handle the entire range of geotechnical design applications including deep foundations, excavations, complex tunnel systems, seepage analysis, consolidation analysis, embankment design, dynamic and slope stability analysis. GTS NX also has an advanced user friendly modeling platform that enables unmatched levels of precision and efficiency.
Industries:  Go to the GTS NX website for more information.
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IMPETUS Afea is a system for non-linear explicit finite element simulations. You invest in IMPETUS software if large-deformation response of components and structures is a key element of your process and if accuracy, robustness and simplicity adds value to your company.
Industries: Go to the IMPETUS Afea website for more information.
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LS-DYNA is an advanced general-purpose multi-physics simulation package developed by the Livermore Software Technology Corporation (LSTC). While the package continues to contain more and more possibilities for the calculation of many complex, real world problems, its origins and core-competency lie in highly non-linear, transient, and dynamic finite element analysis (FEA) using explicit time integration.
Industries: Go to the LSTC website for more information.
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MSC Nastran provides flexible, low-cost access to leading CAE solutions of MSC Nastran and Adams through a scalable, common, and integrated easy to use system of SimXpert. This cost-effective solution allows the companies keep their CAE costs in control while still taking advantage of the best-in-class simulation solutions. GPU acceleration enables faster results for more efficient computation and job turnaround times, delivering more license utilization for the same investment.
Industries: Go to the MSC Software website for more information.
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WEATHER MODELING
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ASUCA is a next-generation high-resolution meso-scale atmospheric model being developed by the Japan Meteorological Agency. ASUCA has achieved good scalability with hiding complicated implementation and optimizations required for distributed GPUs, contributing to increasing the maintainability.
Industries:  Go to the ACM website for more information.
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The COSMO-Model is a nonhydrostatic limited-area atmospheric prediction model. It has been designed for both operational numerical weather prediction (NWP) and various scientific applications on the meso-β and meso-γ scale. The COSMO-Model is based on the primitive thermo-hydrodynamical equations describing compressible flow in a moist atmosphere. The model equations are formulated in rotated geographical coordinates and a generalized terrain following height coordinate. A variety of physical processes are taken into account by parameterization schemes.
Industries: Go to the COSMO website for more information.
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The MITgcm (MIT General Circulation Model) is a numerical model designed for study of the atmosphere, ocean and climate. Its non-hydrostatic formulation enables it to simulate fluid phenomena over a wide range of scales; its adjoint capability enables it to be applied to parameter and state estimation problems. By employing fluid isomorphisms, one hydrodynamical kernel can be used to simulate flow in both the atmosphere and ocean.
Industries: Go to the MITgcm website for more information.
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NIM is a performance-portable model that runs on CPU, GPU and MIC architectures with a single source code. The single source plus efficient code design allows application scientists to maintain the Fortran code, while computer scientists optimize performance and portability using OpenMP, OpenACC, and F2C-ACC directives.
Industries: Go to the ACM website for more information.
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The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both atmospheric research and operational forecasting needs. It features two dynamical cores, a data assimilation system, and a software architecture allowing for parallel computation and system extensibility. The model serves a wide range of meteorological applications across scales ranging from meters to thousands of kilometers.
Industries: Go to the WRF website for more information.
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