ACCESS Resource Provider Software Discovery

gcc v10.2.0

Module: gcc/10.2.0

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.

Domain: compilers

Keywords: gcc g++ gfortran GNU

hisat2 v 2.2.1

Module: hisat2/ 2.2.1

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.

Domain: Biological Sciences

openmpi v4.0.2-clang2.1

Module: openmpi/4.0.2-clang2.1

The modulefile defines paths and environment variables for using OpenMPI 4.0.2 built with the CLANG version 2.1 compiler

Domain: Programming/languages

openmpi v5.0.8-gcc13.3.1

Module: openmpi/5.0.8-gcc13.3.1

The 5.0.8-gcc13.3.1 modulefile defines paths and environment variables for using OpenMPI 5.0.8 built with the gcc 13.3.1 compilers. This is to be run on the Bridges2 regular nodes.

Domain: Libraries

desmond v2020.4

Module: desmond/2020.4

The desmond/2020.4 modulefile defines the environment for Desmond Version 5.7_Linux-x86_64 to satisfy the Comprehensive Software Search at xsede.org

Domain: Molecular dynamics

spark v3.0.1-hadoop2.7

Module: spark/3.0.1-hadoop2.7

A big data processing framework.

Domain: Software

namd v3.0.1

Module: namd/3.0.1

NAMD Version NAMD_3.0.1_Linux-x86_64-netlrts-smp-CUDA This version is GPU resident There are optimized example job scripts in /opt/packages/examples/namd/namd3 Examples are namdgpu.job for the GPU partition and namdgpu-shared.job for the GPU-shared partition

Domain: Molecular Dynamics

aocc v2.3.0

Module: aocc/2.3.0

The AOCC compiler system is a high performance, production quality code generation tool. The AOCC environment provides various options to developers when building and optimizing C, C++, and Fortran applications targeting 32-bit and 64-bit Linux platforms. The AOCC compiler system offers a high level of advanced optimizations, multi-threading and processor support that includes global optimization, vectorization, inter-procedural analyses, loop transformations, and code generation. AMD also provides highly o

Domain: compilers

Keywords: clang clang++ flang AMD

py-numpy v1.19.4

Module: py-numpy/1.19.4

NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, and useful linear algebra, Fourier transform, and random number capabilities

Domain: numerical libraries

Keywords: python numpy

comsol v6.3

Module: comsol/6.3

The comsol/6.3 modulefile defines the default system paths and environment variables needed to use the contents of the comsol/6.3 package.

Domain: Finite elements

anaconda3 v2020.11

Module: anaconda3/2020.11

Anaconda is a free and open-source distribution of the Python and R programming languages for scientific computing, that aims to simplify package management and deployment. Package versions are managed by the package management system conda.

Domain: Open data science platform

Keywords: python R

anaconda3 v2022.10

Module: anaconda3/2022.10

Anaconda is a free and open-source distribution of the Python and R programming languages for scientific computing, that aims to simplify package management and deployment. Package versions are managed by the package management system conda.

Domain: Open data science platform

Keywords: python R

intel v2021.3.0

Module: intel/2021.3.0

Intel Compilers. Includes the icc, icpc, and ifort compilers along with the mkl libraries but no Intel MPI.

Domain: compilers

Keywords: icc icpc ifort

intel v20.4.0

Module: intel/20.4.0

Intel Compilers. Includes the icc, icpc, and ifort compilers along with vtune, and mkl libraries.

Domain: compilers

Keywords: icc icpc ifort

MuST v 1.5

Module: MuST/ 1.5

MuST is software package designed for performing ab initio electornic structure calculations for metals, alloys, and nanostructures. It is an all-electron DFT code based on multiple scattering theory, also known as KKR method, and Green function techniques.

Domain: Materials Sciences

Keywords: DFT ab initio multiple scattering theory Green function KKR KKR-CPA LSMS

samtools v 1.21

Module: samtools/ 1.21

samtools is a suite of programs for interacting with high-throughput sequencing data.

Domain: Biological Sciences

Keywords: singularity bioinformatics

julia v1.5.2

Module: julia/1.5.2

The Julia Language: A fresh approach to technical computing

Domain: compilers

Keywords: Julia

namd v2.13-gpu

Module: namd/2.13-gpu

NAMD Version 2.13 for GPUs Efficient use of this version requires one node There is an example of running NAMD on GPUs in /opt/packages/examples/namd/GPU

Domain: Molecular Dynamics

Trinity v 2.11.0

Module: Trinity/ 2.11.0

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Domain: Biological Sciences

Keywords: singularity bioinformatics

VASP v 6.5.1

Module: VASP/ 6.5.1

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. VASP is not public domain software, and PSC does not provide public access to it. You must have your own VASP license in order to use it on Bridges-2. To use VASP on Bridges-2, submit the VASP request form, verifying your license information. Once you have submitted the VASP request form and your

Domain: Materials Sciences

Keywords: DFT ab initio pseudopotential

blat v 36

Module: blat/ 36

Blat produces two major classes of alignments (1) at the DNA level between two sequences that are of 95% or greater identity, but which may include large inserts; (2) at the protein or translated DNA level between sequences that are of 80% or greater identity and may also include large inserts.

Domain: Biological Sciences

Keywords: singularity bioinformatics

bcftools v 1.10.2

Module: bcftools/ 1.10.2

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

Domain: Biological Sciences

cutadapt v 2.10

Module: cutadapt/ 2.10

cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

Domain: Biological Sciences

Keywords: singularity bioinformatics

phdf5 v1.12.1

Module: phdf5/1.12.1

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

Domain: I/O libraries

Keywords: HDF hdf5 data file format

cuda v12.4.0

Module: cuda/12.4.0