PHI APPLICATIONS

Phi Applications

Phi Applications for Intel Xeon Phi initially came out as a coprocessor, much like a GPU and was considered an accelerator card, even though you could login to an OS on the card. The new Intel Xeon Phi Knights Landing (KNL) now comes as a standalone bootable CPU. Now, you are not only able to login to the Xeon Phi, but you can boot a full server up on it and connect the CPU directly to an OmniPath network card. Take a look at our entire line of Intel servers. However, just logging on and trying to run your code doesn’t mean it would run well. You still need to make use of the AVX-512 (Advanced Vector Extensions) instructions for best performance. This would require your code to be ported, and to be compiled using Intel Compilers. Aspen Systems has listed some of the more commonly used software listed below. Read more about Intel Xeon Phi Applications.


ASTROPHYSICS BIOINFORMATICS CLIMATE AND WEATHER COMPUTATIONAL CHEMISTRY COMPUTATIONAL FLUID DYNAMICS GEOPHYSICS LANGUAGES AND DEVELOPMENT TOOLS LIBRARIES MATERIAL SCIENCES MATHEMATICS MOLECULAR DYNAMICS PHYSICS

ASTROPHYSICS

Phi Applications- Astrophysics - Wall Logo The CLEAN algorithm, introduced by Högbom (1974), assumes that the radio sky can be represented by a small number of point sources in an otherwise empty field of view. It uses a simple iterative procedure to find the positions and strengths of these sources.
Industries: Life Sciences Other Go to the NRAO website for more information.
Phi Applications - Astrophysics - WallsLogo WALLS creates random initial conditions on a 3D grid for a network of domain walls. It then solves dynamical field equations to find out how they evolve, computing the sum of the wall areas in every time-step.
Industries: Life Sciences Other Go to the SGI website for more information.

BIOINFORMATICS

Bioinformatics - Bowtie Logo Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
Industries: Life Sciences Go to the SourceForge website for more information.
Bioinformatics - BWA Logo BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.
Industries: Life Sciences Go to the SourceForge website for more information.
Bioinformatics - GPU-Blast Logo 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: Life Sciences Go to the CMU website for more information.
Bioinformatics - MPI-HMMER Logo MPI-HMMER is an Open Source implementation of the HMMER protein sequence analysis suite. The main search algorithms in this suite, hmmsearch and hmmpfam, have been modified to use MPI in order to provide higher throughput HMMER searches on modern computational clusters.
Industries: Life Sciences Go to the Intel website for more information.

CLIMATE AND WEATHER

Climate and Weather - ADCIRC Logo 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.
Industries: Earth Science Go to the ADCIRC website for more information.
Climate and Weather - CAM Logo The Community Atmosphere Model (CAM) is the latest in a series of global atmosphere models developed at NCAR for the weather and climate research communities. CAM also serves as the atmospheric component of the Community Climate System Model (CCSM).
Industries: Earth Science Go to the UCAR website for more information.
Climate and Weather - CESM Logo CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth’s past, present, and future climate states.
Industries: Earth Science Go to the UCAR website for more information.
Climate and Weather - HBM Logo HBM calculates the sea level, water temperature, salinity, ocean currents, ice thickness, and concentration at 15-minute intervals. Temperature, salt, and current is calculated for the entire water column—top to bottom—at approximately 50 fixed-depth levels.
Industries: Earth Science Go to the Intel website for more information.
Climate and Weather - NIM Logo 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: Earth Science Go to the ACM website for more information.
Climate and Weather - WRF Logo 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: Earth Science Go to the WRF website for more information.

COMPUTATIONAL CHEMISTRY

Computational Chemistry - Gamess Logo 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: Life Sciences Go to the Ames Laboratory website for more information.
NWChem Logo 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: Life Sciences Go to the NWChem website for more information.

COMPUTATIONAL FLUID DYNAMICS

Computational Fluid Dynamics - Openfoam Logo 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: Aerospace Automotive Life Sciences Go to the Openfoam website for more information.
Computational Fluid Dynamics - OpenLB Logo The OpenLB project provides a C++ package for the implementation of lattice Boltzmann simulations that is general enough to address a vast range of problems in computational fluid dynamics. The package is mainly intended as a programming support for researchers and engineers who simulate fluid flows by means of a lattice Boltzmann method
Industries: Aerospace Automotive Life Sciences Go to the OpenLB website for more information.

GEOPHYSICS

Geophysics - SPECFEM3D Cartesian Logo SPECFEM3D Cartesian simulates acoustic (fluid), elastic (solid), coupled acoustic/elastic, poroelastic or seismic wave propagation in any type of conforming mesh of hexahedra (structured or not.) It can, for instance, model seismic waves propagating in sedimentary basins or any other regional geological model following earthquakes. It can also be used for non-destructive testing or for ocean acoustics.
Industries: Life Sciences Go to the CIG website for more information.

LANGUAGES AND DEVELOPMENT TOOLS

Languages and Development Tools - MATLAB Logo 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 Phi applications areas (e.g. bioinformatics or financial derivatives) are served by a large number of optional toolboxes.
Industries: Academics Finance Go to the MathWorks website for more information.
Languages and Development Tools - pyMIC Logo pyMIC is a Python module to offload computation in a Python program to the Intel Xeon Phi coprocessor. It contains offloadable arrays and device management functions. It supports invocation of native kernels (C/C++, Fortran) and blends in with Numpy’s array types for float, complex, and int data types.
Industries: Academics Go to the GitHub website for more information.
Languages and Development Tools - R Logo R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, …) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.
Industries: Academics Go to the R Project website for more information.
Languages and Development Tools - TotalView Logo TotalView breaks down barriers to understanding what’s going on with your high-scale parallel and multicore applications. Purpose-built for applications using hundreds or thousands of cores, TotalView for HPC provides a set of tools that give scientific and academic developers unprecedented control over processes and thread execution, along with deep visibility into program states and data.
Industries: Academics Go to the Rogue Wave website for more information.

LIBRARIES

Libraries - ArrayFire Logo 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: Life Sciences Go to the ArrayFire website for more information.
Libraries - Boost Logo Boost provides free peer-reviewed portable C++ source libraries. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. The Boost license encourages both commercial and non-commercial use.
Industries: Life Sciences Go to the Boost website for more information.
Libraries - LIBXPHI Logo The LIBXPHI library allows to collect hotspot functions that are beneficial to be offloaded to Intel Xeon Phi coprocessors (an instance of the Intel Many Integrated Core Architecture “MIC”). The library already comes with support for some BLAS level 3 functions (xGEMM) but is not limited LAPACK or BLAS. The library leverages the offload usage model while intercepting calls to a function that is thought to run on the host. Calling the coprocessor’s code version may be protected by a threshold that determines whether an offload is beneficial or not.
Industries: Life Sciences Go to the GitHub website for more information.
Libraries - LIBXSMM Logo LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications as well as for deep learning primitives such as small convolutions targeting Intel Architecture (x86). The library is generating code for the following instruction set extensions: Intel SSE, Intel AVX, Intel AVX2, IMCI (KNCni) for Intel Xeon Phi coprocessors (“KNC”), and Intel AVX‑512 as found in the Intel Xeon Phi processor family (“KNL”) and future Intel Xeon processors.
Industries: Life Sciences Go to the GitHub website for more information.
Libraries - LIBXSTREAM Logo The LIBXSTREAM is a library to work with streams, events, and code regions that are able to run asynchronous while preserving the usual stream conditions. The library is targeting Intel Architecture (x86) and helps to offload work to an Intel Xeon Phi coprocessor (an instance of the Intel Many Integrated Core “MIC” Architecture). For example, using two streams may be an alternative to the usual double-buffering approach which can be used to hide buffer transfer time behind compute.
Industries: Life Sciences Go to the GitHub website for more information.
Libraries - Magma Logo Magma is a large, well-supported software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics. It provides a mathematically rigorous environment for defining and working with structures such as groups, rings, fields, modules, algebras, schemes, curves, graphs, designs, codes and many others. Magma also supports a number of databases designed to aid computational research in those areas of mathematics which are algebraic in nature.
Industries: Life Sciences Go to the USYD website for more information.
Libraries - MPICH Logo MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). The goals of MPICH are: (1) to provide an MPI implementation that efficiently supports different computation and communication platforms including commodity clusters (desktop systems, shared-memory systems, multicore architectures), high-speed networks (10 Gigabit Ethernet, InfiniBand, Myrinet, Quadrics) and proprietary high-end computing systems (Blue Gene, Cray) and (2) to enable cutting-edge research in MPI through an easy-to-extend modular framework for other derived implementations.
Industries: Life Sciences Go to the MPICH website for more information.
Libraries - MVAPICH2 Logo The MVAPICH2 software, based on MPI 3.1 standard, delivers the best performance, scalability and fault tolerance for high-end computing systems and servers using InfiniBand, Omni-Path, Ethernet/iWARP, and RoCE networking technologies. This software is being used by more than 2,675 organizations in 83 countries worldwide to extract the potential of these emerging networking technologies for modern systems.
Industries: Life Sciences Go to the Ohio State website for more information.
Libraries - NAG Logo The NAG Library provides a solid numerical foundation and serves diverse mathematical areas. It is expertly documented, maintained and supported and is regularly updated with cutting edge algorithmic capabilities.
Industries: Finance Oil and Gas Academics Other Go to the NAG website for more information.

MATERIAL SCIENCES

Material Sciences - GÉANT Logo GÉANT is the pan-European data network for the research and education community. It interconnects national research and education networks (NRENs) across Europe, enabling collaboration on projects ranging from biological science to earth observation and arts & culture. The GÉANT project combines a high-bandwidth, high-capacity 50,000 km network with a growing range of services
Industries: Life Sciences Go to the GÉANT website for more information.
Material Sciences - GPAW Logo GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).
Industries: Life Sciences Go to the DTU website for more information.
Quantum Expresso Logo 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: Life Sciences Go to the Quantum Espresso website for more information.
VASP Logo VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature) local-density approximation with the free energy as variational quantity and an exact evaluation of the instantaneous electronic ground state at each MD time step. VASP uses efficient matrix diagonalisation schemes and an efficient Pulay/Broyden charge density mixing. These techniques avoid all problems possibly occurring in the original Car-Parrinello method, which is based on the simultaneous integration of electronic and ionic equations of motion. With Phi applications like VASP the interaction between ions and electrons is described by ultra-soft Vanderbilt pseudopotentials (US-PP) or by the projector-augmented wave (PAW) method. US-PP (and the PAW method) allow for a considerable reduction of the number of plane-waves per atom for transition metals and first row elements. Forces and the full stress tensor can be calculated with VASP and used to relax atoms into their instantaneous ground-state.
Industries: Life Sciences Go to the VASP website for more information.

MATHEMATICS

Mathematics - Black-Scholes Logo The Black-Scholes model is used to calculate the theoretical price of European put and call options, ignoring any dividends paid during the option’s lifetime.
Industries: Finance Go to the Investopedia website for more information.
Mathematics - STAC A2 Logo The STAC-A2 Benchmark suite is the industry standard for testing technology stacks used for compute-intensive analytic workloads involved in pricing and risk management.
Industries: Finance Go to the STAC website for more information.
Mathematics - Xcelerit Logo Xcelerit is a leading provider of acceleration solutions for Quantitative Finance, engineering, and research. An award-winning solution allowing domain-specialists to unlock the performance of their existing code with minor programming effort.
Industries: Finance Go to the Xcelerit website for more information.

MOLECULAR DYNAMICS

Molecular Dynamics - AMBER Logo 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: Life Sciences Go to the AMBER website for more information.
Molecular Dynamics - DL_POLY Logo DL_POLY is a general purpose classical molecular dynamics (MD) simulation software developed at Daresbury Laboratory by I.T. Todorov and W. Smith.
Industries: Life Sciences Go to the STFC website for more information.
Molecular Dynamics - GROMACS Logo 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: Life Sciences Go to the GROMACS website for more information.
Molecular Dynamics - LAMMPS Logo 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: Life Sciences Go to the LAMMPS website for more information.
Molecular Dynamics - NAMD Logo 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: Life Sciences Go to the NAMD website for more information.

PHYSICS

Physics - Chroma Logo 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: Life Sciences Go to the Chroma website for more information.
Physics - Elmer Logo Elmer is an open source multiphysical simulation software mainly developed by CSC – IT Center for Science (CSC). Elmer development was started 1995 in collaboration with Finnish Universities, research institutes and industry. After its open source publication in 2005, the use and development of Elmer has become international.
Industries: Life Sciences Go to the CSC website for more information.
Physics - FDTD Logo In the FDTD approach, both space and time are divided into discrete segments. Space is segmented into box-shaped cells, which are small compared to the wavelength. The electric fields are located on the edges of the box and the magnetic fields are positioned on the faces.
Industries: Life Sciences Go to the Remcom website for more information.