Northeastern RC Software Modules¶
Table of modules currently available on the Explorer cluster. To see which versions are available use the command module avail software_name. Modules can be loaded on a compute node or in an sbatch script with the command module load software_name/version.
Northeastern RC Software Modules¶
Software Name |
Description |
Version |
|---|---|---|
Abaqus |
A simulation product portfolio for multiphysics, process integration and optimization. |
2024 |
anaconda3 |
Open source data science and artificial intelligence distribution platform for Python and R programming languages. |
2024.06 |
AMBER |
Amber is a suite of biomolecular simulation programs. |
24 |
bamtools |
BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files. |
2.5.2 |
bbmap |
Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads. |
39.10 |
bcftools |
Bcftools - utilities for variant calling and manipulating VCFs and BCFs. |
1.21 |
bcl2fastq |
Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. |
2.20 |
bedtools |
Bedtools is a fast, flexible toolset for genome arithmetic. |
2.31.1 |
blast |
NCBI blast: The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. |
2.13.0 |
boost |
Boost C++ Libraries, a widely used, free, and open-source collection of C++ libraries that extend the C++ Standard Library’s functionality, offering features for data structures, concurrency, networking, and more to aid in C++ application development across various platforms. |
1.88.0 |
bowtie2 |
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. |
2.5.4 |
bwa |
BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. |
0.7.18 |
clustal |
No description available |
2.1 |
cmake |
A Powerful Software Build System for building C++ code. |
3.30.2 |
code-server |
VS Code in the browser |
4.91.1 |
cuda |
CUDA is a parallel computing platform and programming model developed by NVIDIA for general computing on graphical processing units (GPUs). |
12.1.1, 12.3.0, 12.8.0 |
cuDNN |
NVIDIA® CUDA® Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. |
12.8.0 |
EMAN2 |
A scientific image processing software suite with a focus on CryoEM and CryoET. |
2.99.47 |
fastqc |
A quality control tool for high throughput sequence data. |
0.12.1 |
ffmpeg |
FFmpeg is a free and open-source software project consisting of a suite of libraries and programs for handling video, audio, and other multimedia files and streams. |
7.1.1 |
gaussian |
Gaussian software is a computational chemistry program for electronic structure modeling that predicts molecular energies, structures, and properties by applying quantum mechanics to molecules and reactions. |
g16 |
glew |
The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. |
2.2.0 |
Gnu Parallel |
No description available |
2025-04-22 |
gurobi |
Gurobi Optimizer is a prescriptive analytics platform and a decision-making technology developed by Gurobi Optimization, LLC. |
11.0.3, 12.0.2 |
HDF5 |
HDF5 is a data model, library, and file format for storing and managing large, complex, and heterogeneous datasets, particularly scientific and numerical data. |
1.14.6, nvhpc-1.14.6 |
htop |
htop is an interactive system monitor process viewer and process manager. |
3.3.0 |
Intel Oneapi |
No description available |
2025.0.1 |
job_assist |
The job-assist command is designed to simplify the process of submitting jobs on the Explorer cluster using SLURM’s srun and sbatch modes. |
1.0 |
Jq |
jq is a lightweight and flexible command-line JSON processor. |
1.7.1 |
julia |
Julia is a high-level, general-purpose dynamic programming language, designed to be fast and productive. |
1.10.4 |
knime |
The Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform. |
5.3.1 |
LAMMPS |
LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It’s an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. |
29Aug2024 |
mathematica |
Wolfram Mathematica is a software system with built-in libraries for several areas of technical computing. |
14.1.0 |
matlab |
MATLAB is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. |
R2023b, R2024b, R2025a |
miniconda3 |
Miniconda is a free, miniature installation of Anaconda Distribution that includes only conda, Python, the packages they both depend on, and a small number of other useful packages. |
24.11.1 |
Molcas |
Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. |
25.06 |
mpich |
MPICH, formerly known as MPICH2, is a freely available, portable implementation of MPI, a standard for message-passing for distributed-memory applications used in parallel computing. |
4.3.0b1 |
Namd |
Nanoscale Molecular Dynamics is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model. It is noted for its parallel efficiency and is often used to simulate large systems. |
3.0.1, 3.0.1-cuda |
netlogo |
NetLogo is a programming language and integrated development environment for agent-based modeling. |
6.4.0 |
nextflow |
Nextflow is a scientific workflow system predominantly used for bioinformatic data analysis. |
24.10.3, 25.04.6 |
nodejs |
Node.js is a cross-platform, open-source JavaScript runtime environment. |
22.11.0 |
Nsight |
Nsight Systems is a performance analysis tool for visualizing app algorithms and scaling optimization across CPUs and GPUs. |
2024.7.1 |
nvidia-hpc-sdk |
The NVIDIA HPC Software Development Kit (SDK) includes the proven compilers, libraries and software tools essential to maximizing developer productivity and the performance and portability of HPC applications. |
24.7 |
openblas |
OpenBLAS is an open-source implementation of the BLAS and LAPACK APIs with many hand-crafted optimizations for specific processor types. |
0.3.29 |
OpenCV |
OpenCV (Open Source Computer Vision Library) is a library of programming functions mainly for real-time computer vision. |
4.10.0 |
OpenFOAM |
OpenFOAM (Open Field Operation And Manipulation) is a C++ toolbox for the development of customized numerical solvers, and pre-/post-processing utilities for the solution of continuum mechanics problems. |
12 |
OpenJDK |
A free and open-source implementation of the Java Platform, Standard Edition (Java SE). |
22.0.2 |
OpenMPI |
Open MPI Project is an open source Message Passing Interface implementation. |
4.1.6 |
ParaView |
ParaView is an open-source multiple-platform application for interactive, scientific visualization. |
5.13.0-RC2, 5.13.1 |
perl |
Perl is a high-level, general-purpose, interpreted, dynamic programming language. |
5.40.0 |
R |
R is a free software environment for statistical computing and graphics. |
4.4.1 |
ROCm |
AMD ROCm™ is an open software stack including drivers, development tools, and APIs that enable GPU programming from low-level kernel to end-user applications. |
6.3.0 |
samtools |
Samtools is a suite of programs for interacting with high-throughput sequencing data. |
1.21 |
SAS |
SAS software is an integrated suite for data management, advanced analytics, business intelligence, and predictive analytics developed by SAS Institute |
9.4 |
schrodinger |
Computational platform for molecular design and discovery. |
2024-4, 2025-3 |
sratoolkit |
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. |
12 |
star |
STAR: ultrafast universal RNA-seq aligner. |
2.7.11b |
Tinker |
Tinker is a suite of computer software applications for molecular dynamics simulation. |
8.11.3 |
trimmomatic |
Trimmomatic: A flexible read trimming tool for Illumina NGS data. |
0.39 |
vcftools |
vcftools is a suite of functions for use on genetic variation data in the form of VCF and BCF files. |
0.1.16 |
VMD |
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. |
1.9.3, 1.9.4a55 |
VTune |
VTune Profiler (formerly VTune Amplifier) is a performance analysis tool for x86-based machines running Linux or Microsoft Windows operating systems. |
2025.0 |
weka |
Waikato Environment for Knowledge Analysis is a collection of machine learning and data analysis free software licensed under the GNU General Public License. |
3.8.6 |