Containers repository

Basic information

PRACE-Lab containers were prepared, optimized and tested for the following hardware architectures and fabrics:

  • CPU: Intel CascadeLake
  • NVIDIA Tesla V100 GPGPU processors
  • Interconnect: Mellanox EDR

Containers are available locally on clusters deployed during the first phase of PRACE-Lab project.

Container files are accessible under location pointed by $PLCR shell variable.

# example contents of repository location 
$> ls -1 $PLCR

images
local
tests

Software requirements

Software containers are designed to be as host independent as possible. This goal is simple to achieve unless we aim for high performance, multi-node programs where additional dependencies have to be provided.

For our MPI-enabled containers we made some assumptions regarding the host environment:

  • RHEL7 or RHEL8 compatible operating system
  • System OFED or MOFED kernel drivers
  • Singularity >= 3.8.4
  • SLURM 20.11 or later
  • SLURM PMI2 or PMIX support

MPI support

Important aspect of published container repository is MPI support for multi-node operation.
Containers provided in the repository have been built with the following mpi implementations:

  • OpenMPI 4.x
  • IntelMPI/OneAPI (>= 2020)
  • MVAPICH 2.x

Available containers

Software Description
ABINIT ABINIT is a software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials.
AutoDock-Vina AutoDock Vina is an open-source program for doing molecular docking.
Bowtie2 Bowtie2 is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences.
BWA BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
CP2K 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.
Dalton The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory, whereas LSDalton is a linear-scaling HF and DFT code suitable for large molecular systems, now also with some CCSD capabilites.
Exonerate Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.
Gromacs 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.
Hashcat Hashcat is a password recovery tool.
Hadoop The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.
Intel oneAPI Intel oneAPI provides tools for build, analyze, and optimize high-performance, cross-architecture applications on CPUs and XPUs with compilers, performance libraries, frameworks, and analysis and debug tools.
John the Ripper John the Ripper is an Open Source password security auditing and password recovery tool available for many operating systems.
Julia Julia Programming Language.
LAMMPS LAMMPS is a Molecular Dynamics Simulator.
Meep Meep is a free and open-source software package for electromagnetics simulation via the finite-difference time-domain (FDTD) method spanning a broad range of applications.
NAMD NAMD is scalable molecular dynamics simulation software.
NWChem NWChem aims to provide its users with computational chemistry tools.
Octave Scientific Programming Language.
OSU micro-benchmarks set of basic MPI benchmarks, purpose of this distribution is to allow performance comparison between used MPI implementation.
PSI4 PSI4 is an open-source quantum chemistry software. It provides a wide variety of quantum chemical methods using state-of-the-art numerical methods and algorithms.
QuantumESPRESSO 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.
SageMath SageMath is a free open-source mathematics software system.
SAMtools SAMtools is a fast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Siesta Siesta is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
Seurat Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data.
Spark Spark is a multi-language engine for executing data engineering, data science, and machine learning on single-node machines or clusters.
Tinker-HP Tinker-HP is a CPUs based, multi-precision, MPI massively parallel package dedicated to long polarizable molecular dynamics simulations and to polarizable QM/MM.
Wine Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems, such as Linux, macOS, & BSD.