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Software overview

Last Updated: Aug 04, 2021

Elastic High Performance Computing (E-HPC) provides mainstream computing applications, runtime libraries, and Message Passing Interface (MPI) libraries. This topic describes the software supported by E-HPC and the use scenarios of the software.

E-HPC software stack

In this topic, all listed software can be automatically deployed. You can also deploy software by using custom images.

  • Software list

    Software

    Supported versions

    Description

    Required dependencies

    ABySS

    2.1.5

    A parallel, paired-end genome assembler that is designed for short reads. E-HPC provides its parallel version.

    Intel-MPI 2018

    Anaconda

    • 2018.12-py27

    • 2018.12-py37

    A package management and deployment platform based on Python.

    None

    BLAST

    2.8.1

    An algorithm and program for comparing primary biological sequence information.

    None

    DeepChem

    2.0.0

    A Python deep-learning library for drug discovery.

    None

    GAMESS-GPU

    2018.2

    A program for ab initio molecular quantum chemistry. E-HPC provides its GPU-accelerated version.

    CUDA-Toolkit 9.0

    GROMACS

    5.0.7

    An engine to perform molecular dynamics simulations. E-HPC provides its single-processor version.

    None

    GROMACS-OpenMPI

    5.0.7

    An engine to perform molecular dynamics simulations. E-HPC provides its multi-node parallel version.

    OpenMPI 1.10.7

    GROMACS-CPU-AVX512

    2018.3

    An engine to perform molecular dynamics simulations. E-HPC provides its multi-node parallel version. AVX-512 is supported.

    • Intel-MPI 2018

    • Intel-MKL 2018

    • Intel-ICC-RUNTIME 2018

    GROMACS-GPU

    2018.1

    An engine to perform molecular dynamics simulations. E-HPC provides its multi-node GPU-accelerated version.

    • OpenMPI 3.0.0

    • CUDA-Toolkit 9.0

    HELYX-OS

    2.4.0

    An GUI intended for academic use and entry-level computational fluid dynamics (CFD).

    None

    HMMER

    3.2.1

    A software package for making sequence alignments by using profile hidden Markov models (profile HMMs).

    None

    LAMMPS-CPU-INTELMPI

    12Dec18

    An engine to perform molecular dynamics simulations. E-HPC provides its multi-node parallel version.

    Intel-MPI 2018

    LAMMPS-GPU-OpenMPI

    12Dec18

    An engine to perform molecular dynamics simulations. E-HPC provides its multi-node GPU-accelerated version.

    • OpenMPI 3.0.0

    • CUDA-Toolkit 9.0

    Miniconda

    • py27

    • py37

    A minimal installer for conda.

    None

    MOMAP

    1.0.1

    A software package for predicting the luminescent properties and mobility of organic functional materials. E-HPC provides its multi-node parallel version.

    MPICH2

    NAMD-OpenMPI

    2.12

    An engine to perform molecular dynamics simulations. E-HPC provides its multi-node parallel version.

    OpenMPI 1.10.7

    NAMD-GPU-MULTICORE

    2.12

    An engine to perform molecular dynamics simulations. E-HPC provides its single-node GPU-accelerated version.

    CUDA-Toolkit 9.0

    NAMD-GPU

    2.12

    An engine to perform molecular dynamics simulations. E-HPC provides its multi-node GPU-accelerated version.

    • OpenMPI 3.0.0

    • CUDA-Toolkit 9.0

    OpenFOAM-OpenMPI

    5.0

    An engine to perform CFD simulations. E-HPC provides its multi-node parallel version.

    OpenMPI 1.10.7

    OVITO

    2.9.0

    A scientific visualization and analysis software for atomistic and particle simulation data.

    None

    ParaView

    4.3.1

    A multi-platform data analysis and visualization application. The data exploration can be done interactively in 3D.

    None

    Relion-OpenMPI

    2.0.3

    A software package that employs an empirical Bayesian approach for single-particle electron cryo-microscopy (cryo-EM) structure determination. E-HPC provides its multi-node parallel version.

    OpenMPI 1.10.7

    Relion-GPU

    2.0.3

    A software package that employs an empirical Bayesian approach for single-particle electron cryo-microscopy (cryo-EM) structure determination. E-HPC provides its multi-node GPU-accelerated version.

    OpenMPI 3.0.0

    Semtex

    8.2

    A CFD solver. E-HPC provides its multi-node parallel version.

    OpenMPI 1.10.7

    TensorFlow

    1.7.0-cp27-pypi

    An open source software library for numerical computation using data flow graphs.

    None

    TensorFlow-GPU

    1.7.0-cp27-pypi

    An open source software library for numerical computation using data flow graphs. E-HPC provides its GPU-accelerated version.

    None

    VMD

    1.9.3

    A molecular modelling and visualization computer program.

    None

    WRF-MPICH

    3.8.1

    A numerical weather prediction system designed to serve both atmospheric research and operational forecasting needs. E-HPC provides its multi-node parallel version.

    MPICH 3.2

    WRF-OpenMPI

    3.8.1

    A numerical weather prediction system designed to serve both atmospheric research and operational forecasting needs. E-HPC provides its multi-node parallel version.

    OpenMPI 1.10.7

  • Performance testing software

    Software

    Supported versions

    Description

    Required dependencies

    LINPACK

    2018

    A measure of floating-point computing power.

    Intel-MPI 2018

    STREAM

    2018

    A measure of memory bandwidth.

    None

    Intel-MPI-Benchmarks

    2019

    A measure of MPI performance.

    Intel-MPI 2018

    OSU-Micro-Benchmarks

    5.4.4

    A measure of MPI performance.

    Intel-MPI 2018

    Iperf

    2.0.12

    A measure of network bandwidth.

    None

    FIO

    3.1

    A measure of disk I/O performance.

    None

  • Runtime libraries

    MPI libraries

    GPU-accelerated libraries

    Intel performance libraries

    • Intel-MPI

    • OpenMPI

    • MPICH

    • MVAPICH

    • CUDA-Toolkit

    • cuDNN

    • Intel-ICC-RUNTIME

    • Intel-IFORT-RUNTIME

    • Intel-MKL

    • Intel-DAAL

    • ntel-IPPIntel-TBB