HPC Software

Biosciences, Bioinformatics and Biomedicine

Name

Links

Category

Restricted License

GPU Acceleration

Abyss

Homepage

Install with bioconda

High-Throughput
Sequencing

Adam

Homepage

Install with bioconda

High-Throughput
Sequencing

Bowtie2

Homepage

Install with bioconda

High-Throughput
Sequencing

Burrow-Wheeler
Aligner

Homepage

Install with bioconda

High-Throughput
Sequencing

Delly

Homepage

Install with bioconda

High-Throughput
Sequencing

Fastp

Homepage

Install with bioconda

High-Throughput
Sequencing

GATK3

Homepage

Install with bioconda

High-Throughput
Sequencing

GATK4

Homepage

Install with bioconda

High-Throughput
Sequencing

Pear

Homepage

Install with bioconda

High-Throughput
Sequencing

Sambamba

Homepage

Install with bioconda

High-Throughput
Sequencing

Selscan

Homepage

Install with bioconda

High-Throughput
Sequencing

Beagle-lib

Homepage

Install with bioconda

Linkage/
Phylogenetics

RAxML

Homepage

Install with bioconda

Linkage/
Phylogenetics

Maxquant

Homepage

Install with bioconda

Mass Spectrometry

Maxquant Freeware Software License

Autodock-vina

Homepage

Install with bioconda

Molecular Docking

Blast

Homepage

Install with bioconda

Sequence Analysis

Diamond

Homepage

Install with bioconda

Sequence Analysis

Magicblast

Homepage

Install with bioconda

Sequence Analysis

Meme

Homepage

Install with bioconda

Sequence Analysis

rDock

Homepage

Install with bioconda

Structural Biology

Canu

Homepage

Install with bioconda

Third generation
sequencing

Circlator

Homepage

Install with bioconda

Third generation
sequencing

DALIGNER

Homepage

Install with bioconda

Third generation
sequencing

DBG2OLC

Homepage

Install with bioconda

Third generation
sequencing

Flye

Homepage

Install with bioconda

Third generation
sequencing

MHAP

Homepage

Install with bioconda

Third generation
sequencing

Miniasm

Homepage

Install with bioconda

Third generation
sequencing

Raven

Homepage

Install with bioconda

Third generation
sequencing

SMARTdenovo

Homepage

Install with bioconda

Third generation
sequencing

SPAdes

Homepage

Install with bioconda

Third generation
sequencing

Wtdbg2

Homepage

Install with bioconda

Third generation
sequencing

Cromwell

Homepage

Install with bioconda

Workflow manager

Nextflow

Homepage

Install with bioconda

Workflow manager

Snakemake

Homepage

Install with bioconda

Workflow manager


Engineering Sciences
NameLinks  Category Restricted License GPU Acceleration
OpenFOAM Homepage CAE, CFD and Engineering 
ABINIT  Homepage Chemistry
Atomic Simulation Environment  Homepage Chemistry
CP2K Homepage Chemistry
GPAW Homepage Chemistry
Libxc Homepage Chemistry
NWChem Homepage Chemistry
Psi4 Homepage Chemistry
Q-Chem Homepage Chemistry End users require valid unlimited-core license
WRF Homepage Geosciences 
GROMACS Homepage Molecular Dynamics
LAMMPS Homepage Molecular Dynamics
NAMD Homepage Molecular Dynamics Non-
commercial
use

Libraries

NameLinks  Category Restricted License GPU Acceleration
oneDNN Homepage
AI, Machine and Deep Learning
Boost Homepage Data and I/O
HDF5 Homepage Data and I/O
NetCDF Homepage Data and I/O
NetCDF Fortran  Homepage Data and I/O
Parallel HDF5  Homepage Data and I/O
Armadillo  Homepage Math and Numerical Libraries 
ARPACK-NG  Homepage Math and Numerical Libraries 
FFTW Homepage Math and Numerical Libraries 
GNU Scientific Library  Homepage Math and Numerical Libraries 
Intel MKL Homepage Math and Numerical Libraries  Available to end users via. A*CRC site license
METIS Homepage Math and Numerical Libraries 
PLASMA Homepage Math and Numerical Libraries 
qrupdate Homepage Math and Numerical Libraries 
SCOTCH Homepage Math and Numerical Libraries 
SuiteSparse  Homepage Math and Numerical Libraries 
Intel MPI Homepage MPI Libraries Available to end users via. A*CRC site license
mpi4py Homepage MPI Libraries
MVAPICH2 Homepage MPI Libraries
OpenMPI Homepage MPI Libraries
SGI MPT and SHMEM  Homepage MPI Libraries Closed source, for use on Stratus HPC system.

Compilers and Languages

Name

Links

Category

Restricted
License

GPU
Acceleration

GNU Compiler
Collection 

Homepage 

 

 

Compilers

Intel Compilers 

Homepage 

Compilers

Available to end
users via 
A*CRC site license

Intel SPMD
Program Compiler 

Homepage 

Compilers

GNU Octave 

Homepage 

Scientific / Programming
Languages

Intel Distribution
for Python

Homepage 

Scientific / Programming
Languages

Python

Homepage

Scientific / Programming
Languages

R

Homepage

Scientific / Programming
Languages


Tools

Name

Links

Category

Restricted
License 

GPU
Acceleration
 

CMake

Homepage

Development Tools 

EasyBuild

Homepage 

Development Tools 

GNU
Autotools

Homepage 

Development Tools 

Intel Parallel
Studio XE 

Homepage 

Development Tools 

Available to end
users via A*CRC
site license

ImageMagick

Homepage 

Graphics and
Visualisation 

ParaView

Homepage 

 

 

 

Graphics and
Visualisation 

PAPI

Homepage 

Performance Tools

SGI MPI
PerfBoost 

Homepage 

Performance Tools

Closed source,
for use on
Stratus HPC
system.

SGI MPI
Perfcatcher 

Homepage 

Performance Tools

Closed source,
for use on
Stratus HPC
system.

Valgrind

Homepage 

Performance Tools

hwloc

Homepage 

System Tools

Singularity

Homepage 

System Tools