E-HPC provides mainstream software for scientific computing, such as applications, compiler runtime libraries, and Message Passing Interface (MPI) libraries. This topic describes the software supported by E-HPC and its common use cases.
E-HPC software stack
This section lists the software that is available for automatic deployment. You can also use custom images to deploy other software as needed.
Software list
Name
Version
Description
Required dependency packages
ABySS
2.1.5
A paired-end genome assembly tool for short sequences. Multi-node parallel version.
Intel-MPI 2018
Anaconda
2018.12-py27
2018.12-py37
A Python environment management tool.
None
BLAST
2.8.1
Analysis software for similarity searches in bioinformatics databases.
None
DeepChem
2.0.0
A deep learning Python library for drug design.
None
GAMESS-GPU
2018.2
An ab initio quantum chemistry software. GPU-accelerated version.
CUDA-Toolkit 9.0
GROMACS
5.0.7
A molecular dynamics simulation software. Single-node version.
None
GROMACS-OpenMPI
5.0.7
A molecular dynamics simulation software. Multi-node parallel version.
OpenMPI 1.10.7
GROMACS-CPU-AVX512
2018.3
A molecular dynamics simulation software. Multi-node parallel version that supports the AVX512 instruction set.
Intel-MPI 2018
Intel-MKL 2018
Intel-ICC-RUNTIME 2018
GROMACS-GPU
2018.1
A molecular dynamics simulation software. Multi-node GPU-accelerated version.
OpenMPI 3.0.0
CUDA-Toolkit 9.0
HELYX-OS
2.4.0
A pre-processing software for fluid mechanics that supports visualization.
None
HMMER
3.2.1
Software for biological sequence alignment and analysis based on hidden Markov models.
None
LAMMPS-CPU-INTELMPI
12Dec18
A molecular dynamics simulation software. Multi-node parallel version.
Intel-MPI 2018
LAMMPS-GPU-OpenMPI
12Dec18
A molecular dynamics simulation software. Multi-node GPU-accelerated version.
OpenMPI 3.0.0
CUDA-Toolkit 9.0
Miniconda
py27
py37
A minimal conda environment.
None
MOMAP
1.0.1
Software for predicting the properties of multi-molecular materials. Multi-node parallel version.
MPICH2
NAMD-OpenMPI
2.12
A molecular dynamics simulation software. Multi-node parallel version.
OpenMPI 1.10.7
NAMD-GPU-MULTICORE
2.12
A molecular dynamics simulation software. Single-node GPU-accelerated version.
CUDA-Toolkit 9.0
NAMD-GPU
2.12
A molecular dynamics simulation software. Multi-node GPU-accelerated version.
OpenMPI 3.0.0
CUDA-Toolkit 9.0
OpenFOAM-OpenMPI
5.0
A fluid mechanics simulation software. Multi-node parallel version.
OpenMPI 1.10.7
OVITO
2.9.0
A scientific visualization and analysis software for atomic and particle simulation data.
None
ParaView
4.3.1
A 2D and 3D data analysis and visualization software.
None
Relion-OpenMPI
2.0.3
A single-particle cryo–electron microscopy software. Multi-node parallel version.
OpenMPI 1.10.7
Relion-GPU
2.0.3
A single-particle cryo–electron microscopy software. Multi-node GPU-accelerated version.
OpenMPI 3.0.0
Semtex
8.2
A fluid mechanics solver. Multi-node parallel version.
OpenMPI 1.10.7
TensorFlow
1.7.0-cp27-pypi
An open source deep learning framework based on data streams.
None
TensorFlow-GPU
1.7.0-cp27-pypi
An open source deep learning framework based on data streams. GPU-accelerated version.
None
VMD
1.9.3
A visualization software for molecular dynamics simulations.
None
WRF-MPICH
3.8.1
An atmospheric modeling system for meteorological research and weather forecasting. Multi-node parallel version.
MPICH 3.2
WRF-OpenMPI
3.8.1
An atmospheric modeling system for meteorological research and weather forecasting. Multi-node parallel version.
OpenMPI 1.10.7
Performance testing software
Name
Version
Description
Required dependency packages
LINPACK
2018
A floating-point performance evaluation tool.
Intel-MPI 2018
STREAM
2018
A memory bandwidth evaluation tool.
None
Intel-MPI-Benchmarks
2019
An MPI communication efficiency evaluation tool.
Intel-MPI 2018
OSU-Micro-Benchmarks
5.4.4
An MPI communication efficiency evaluation tool.
Intel-MPI 2018
Iperf
2.0.12
A network bandwidth evaluation tool.
None
FIO
3.1
A disk I/O efficiency evaluation tool.
None
Runtime libraries
MPI communication libraries
GPU acceleration libraries
Intel high-performance libraries
Intel-MPI
OpenMPI
MPICH
MVAPICH
CUDA-Toolkit
cuDNN
Intel-ICC-RUNTIME
Intel-IFORT-RUNTIME
Intel MKL
Intel DAAL
Intel IPP and Intel TBB