1. Software

HPC3 serves researchers from all corners of the UCI campus. At the heart of the value that RCIC adds to HPC3, is wide range of applications software that is compiled and ready for use. There are literally hundreds of domain-specific, community-supported, applications maintained on the cluster.

Cluster Operating System

Important

HPC3 operating system is Rocky Linux 9.6 (as of July 29, 2025).
All installed software is compiled specifically for this OS.

Attention

  • Docker is not available per security vulnerability, use singularity. See Create Singularity Containers guide.

  • sudo and su commands are not available per security vulnerability.

Installed software

Most software is accessed only after loading the appropriate software modules. Cluster users simply need to know or discover the already available application environment module and load it prior to using the application. Please see:

The following table lists available software (by their associated modules) together with a category and a short description. Info on modules naming schema is available in this page.

Click on the column header for sorting.

Table 1.3 Installed Software, updated 14 July 2025.

Module (name/version)

Category

Software Description

MATLAB/R2020a

LANGUAGES

MATLAB (R) is a programming and numeric computing platform

MATLAB/R2020b

LANGUAGES

MATLAB (R) is a programming and numeric computing platform

MATLAB/R2021b

LANGUAGES

MATLAB (R) is a programming and numeric computing platform

MATLAB/R2023b

LANGUAGES

MATLAB (R) is a programming and numeric computing platform

OpenBLAS/0.3.19

LIBRARIES

OpenBLAS is an optimized BLAS library

OpenBLAS/0.3.21

LIBRARIES

OpenBLAS is an optimized BLAS library

OpenBLAS/0.3.26

LIBRARIES

OpenBLAS is an optimized BLAS library

OpenBLAS/0.3.6

LIBRARIES

OpenBLAS is an optimized BLAS library

R/4.0.4

LANGUAGES

R is a freely available language and environment for statistical computing and graphics

R/4.1.2

LANGUAGES

R is a freely available language and environment for statistical computing and graphics

R/4.2.2

LANGUAGES

R is a freely available language and environment for statistical computing and graphics

R/4.3.3

LANGUAGES

R is a freely available language and environment for statistical computing and graphics

R/4.4.2

LANGUAGES

R is a freely available language and environment for statistical computing and graphics

SPAdes/3.15.4

BIOTOOLS

SPAdes is a versatile toolkit designed for assembly and analysis of sequencing data

afni/22.1.09

IMAGING

AFNI (Analysis of Functional NeuroImages)

amber/21.12/gcc.11.2.0

CHEMISTRY

AMBER molecular dynamics

amber/24/gcc.11.2.0

CHEMISTRY

AMBER molecular dynamics

amber/24/gcc.11.2.0-cuda.11.7.1-openmpi.5.0.1

CHEMISTRY

AMBER molecular dynamics

anaconda/2020.07

LANGUAGES

Anaconda is a software package and environment manager

anaconda/2021.11

LANGUAGES

Anaconda is a software package and environment manager

anaconda/2022.05

LANGUAGES

Anaconda is a software package and environment manager

anaconda/2024.06

LANGUAGES

Anaconda is a software package and environment manager

ansys/2019R2

ENGINEERING

The ANSYS suite Release 2019R2 revision v194

ansys/2020R2

ENGINEERING

The ANSYS suite Release 2020R2 revision v202

ants/2.3.5

IMAGING

ANTs (Advanced Normalization Tools) is a software toolkit for biological and medical image analysis

awscli/2.11.21

TOOLS

Awscli provides a unified command line interface to Amazon Web Services

bamtools/2.5.2

BIOTOOLS

BamTools provides an API and a toolkit for handling BAM files

bazel/4.2.2

TOOLS

Bazel build and test tool

bazel/6.5.0

TOOLS

Bazel build and test tool

bbmap/38.87

GENOMICS

BBMap is a short read aligner for DNA and RNA-seq data

bbmap/38.96

GENOMICS

BBMap is a short read aligner for DNA and RNA-seq data

bcftools/1.15.1

BIOTOOLS

BCFtools are meant as a faster replacement for most of the perl VCFtools

bcftools/1.21

BIOTOOLS

BCFtools are meant as a faster replacement for most of the perl VCFtools

bedops/2.4.39

GENOMICS

BEDOPS - a toolkit for high-performance genomic feature operations

bedtools2/2.29.2

BIOTOOLS

Bedtools2 utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks

bedtools2/2.30.0

BIOTOOLS

Bedtools2 utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks

bioconda/4.8.3

LANGUAGES

PacBio Secondary Analysis Tools

bismark/0.22.3

GENOMICS

Bismark is a genomics program

bismark/0.23.1

GENOMICS

Bismark is a genomics program

boost/1.66.0/gcc.8.4.0

TOOLS

The Boost project provides free peer-reviewed portable C++ source libraries

boost/1.78.0/gcc.11.2.0

TOOLS

The Boost project provides free peer-reviewed portable C++ source libraries

boost/1.78.0/gcc.8.4.0

TOOLS

The Boost project provides free peer-reviewed portable C++ source libraries

bowtie2/2.4.1

BIOTOOLS

Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

bowtie2/2.4.5

BIOTOOLS

Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

bowtie2/2.5.1

BIOTOOLS

Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

bracken/2.6.2

GENOMICS

Bracken (Bayesian Reestimation of Abundance with KrakEN)

bustools/0.44.1

BIOTOOLS

Bustools is a program for manipulating BUS files for single cell RNA-Seq datasets

bwa/0.7.17

BIOTOOLS

Burrow-Wheeler Aligner

bwa/0.7.8

BIOTOOLS

Burrow-Wheeler Aligner

cellranger-arc/2.0.2

GENOMICS

Cell Ranger ARC 2.0.2 is a set of analysis pipelines

cellranger-atac/2.1.0

GENOMICS

Cell Ranger ATAC is a set of four analysis pipelines

cellranger/6.1.2

GENOMICS

CellRanger is a set of analysis pipelines

cellranger/7.0.1

GENOMICS

CellRanger is a set of analysis pipelines

cellranger/8.0.1

GENOMICS

CellRanger is a set of analysis pipelines

charm/6.10.1/gcc.8.4.0

TOOLS

CHARM++ is a machine independent parallel programming system. Built with arguments “charm++ multicore-linux-x86_64 gcc –build-shared –enable-zlib –with-production –destination=cbuild -j8”

charm/6.10.1/gcc.8.4.0-openmpi.4.0.3

TOOLS

CHARM++ is a machine independent parallel programming system. Built with arguments “charm++ mpi-linux-x86_64 gcc –basedir=$MPI_HOME –build-shared –enable-zlib –with-production –destination=cbuild -j8”

clang/11.1.0

COMPILERS

Clang is a compiler front-end that is part of the LLVM project

clang/13.0.0

COMPILERS

Clang is a compiler front-end that is part of the LLVM project

clang/18.1.4

COMPILERS

Clang is a compiler front-end that is part of the LLVM project

cmake/3.20.5

TOOLS

CMake is a powerful software build system

cmake/3.30.2

TOOLS

CMake is a powerful software build system

cuda/11.4.0

TOOLS

CUDA Version 11.4.0_470.42.01

cuda/11.7.1

TOOLS

CUDA Version 11.7.1_515.65.01

cuda/12.2.0

TOOLS

CUDA Version 12.2.0_535.54.03

cudasdk/22.9

COMPILERS

The NVIDIA HPC Software Development Kit (SDK)

curl/7.81.0

TOOLS

Command line tool and library for transferring data with URLs

cutadapt/2.10

BIOTOOLS

Cutadapt finds and removes different types of unwanted sequence from sequencing reads

cutadapt/4.0

BIOTOOLS

Cutadapt finds and removes different types of unwanted sequence from sequencing reads

deeptools/3.5.0

BIOTOOLS

DeepTools is a suite of tools developed for the efficient analysis of high-throughput sequencing data

deeptools/3.5.1

BIOTOOLS

DeepTools is a suite of tools developed for the efficient analysis of high-throughput sequencing data

diamond/2.0.15

GENOMICS

Diamond is a sequence aligner for protein and translated DNA searches

diamond/2.0.4

GENOMICS

Diamond is a sequence aligner for protein and translated DNA searches

dorado/0.8.2

BIOTOOLS

Dorado is a high-performance and easy-to-use basecaller for Oxford Nanopore reads

dorado/0.9.1

BIOTOOLS

Dorado is a high-performance and easy-to-use basecaller for Oxford Nanopore reads

doxygen/1.9.5/gcc.8.4.0

TOOLS

Doxygen version 1.9.5

edirect/2020

BIOTOOLS

Entrez Direct (EDirect) toolkit for accessing the NCBI databases

edirect/2022

BIOTOOLS

Entrez Direct (EDirect) toolkit for accessing the NCBI databases

eigen/3.3.7

LIBRARIES

Eigen is a high-level C++ library of template headers

eigen/3.4.0

LIBRARIES

Eigen is a high-level C++ library of template headers

fastp/0.23.2

BIOTOOLS

FastP is an ultra-fast all-in-one FASTQ preprocessor

fastqc/0.11.9

BIOTOOLS

FastQC is a program designed to spot potential problems in high througput sequencing datasets

ffmpeg/4.1.3

LIBRARIES

FFmpeg is the leading multimedia framework

ffmpeg/6.1

LIBRARIES

FFmpeg is the leading multimedia framework

ffnvcodec/12.1.14.0

LIBRARIES

FFmpeg version of Nvidia Codec SDK headers

fftw/3.3.10/gcc.11.2.0

TOOLS

FFTW is a C subroutine library for computing the Discrete Fourier transform (DFT)

fftw/3.3.10/gcc.11.2.0-openmpi.4.1.2

TOOLS

FFTW is a C subroutine library for computing the Discrete Fourier transform (DFT)

fftw/3.3.8/gcc.8.4.0

TOOLS

FFTW is a C subroutine library for computing the Discrete Fourier transform (DFT)

fftw/3.3.8/gcc.system

TOOLS

FFTW is a C subroutine library for computing the Discrete Fourier transform (DFT)

foundation/v8

TOOLS

Provides an access to software in /opt/foundation

freebayes/1.3.2

BIOTOOLS

Freebayes is a Bayesian genetic variant detector

freesurfer/6.0.1

IMAGING

FreeSurfer is the structural MRI analysis software

freesurfer/7.2.0

IMAGING

FreeSurfer is the structural MRI analysis software

freesurfer/7.4.1

IMAGING

FreeSurfer is the structural MRI analysis software

freetype/2.10.2

LIBRARIES

FreeType is a software library to render fonts

fsl/6.0.4

IMAGING

FSL is a comprehensive library of analysis tools for imaging data

gatk/4.2.6.1

BIOTOOLS

GATK is a Genome Analysis Toolkit

gatk/4.6.2.0

BIOTOOLS

GATK is a Genome Analysis Toolkit

gaussian/16

ENGINEERING

Gaussian is a general purpose computational chemistry software

gcc/11.2.0

COMPILERS

GNU GCC compiler

gcc/6.5.0

COMPILERS

GNU GCC compiler

gcc/8.4.0

COMPILERS

GNU GCC compiler

gcc/system

COMPILERS

System default GCC system

gdal/3.1.0/gcc.8.4.0

LIBRARIES

GDAL - Geospatial Data Abstraction Library

gdal/3.4.1/gcc.11.2.0

LIBRARIES

GDAL - Geospatial Data Abstraction Library

gdal/3.6.2/gcc.11.2.0

LIBRARIES

GDAL - Geospatial Data Abstraction Library

gdrcopy/2.4.1

LIBRARIES

A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology

geos/3.10.2/gcc.11.2.0

TOOLS

GEOS (Geometry Engine - Open Source) is a C++ port of the JTS Topology Suite (JTS)

geos/3.11.1/gcc.11.2.0

TOOLS

GEOS (Geometry Engine - Open Source) is a C++ port of the JTS Topology Suite (JTS)

geos/3.8.1/gcc.8.4.0

TOOLS

GEOS (Geometry Engine - Open Source) is a C++ port of the JTS Topology Suite (JTS)

git-lfs/3.5.1

TOOLS

Git-lfs is a command line extension for managing large files with git

git/2.45.1

TOOLS

Git is a distributed version control system

glpk/5.0/gcc.11.2.0

GENOMICS

The GLPK (GNU Linear Programming Kit) package

glpk/5.0/gcc.8.4.0

GENOMICS

The GLPK (GNU Linear Programming Kit) package

go/1.17.7

LANGUAGES

Google go is an open source programming language and compiler

go/1.20.4

LANGUAGES

Google go is an open source programming language and compiler

go/1.22.3

LANGUAGES

Google go is an open source programming language and compiler

gromacs/2020.4/gcc.8.4.0-cuda.11.7.1

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gromacs/2021.2/gcc.8.4.0

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gromacs/2021.2/gcc.8.4.0-cuda.11.7.1

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gromacs/2021.2/gcc.8.4.0-openmpi.4.0.3

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gromacs/2022.1/gcc.8.4.0

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gromacs/2022.1/gcc.8.4.0-cuda.11.7.1

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gromacs/2022.1/gcc.8.4.0-cuda.11.7.1.openmpi.4.1.2

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gromacs/2024.2/gcc.11.2.0

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gromacs/2024.2/gcc.11.2.0-cuda.11.7.1

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gromacs/2024.2/gcc.11.2.0-cuda.11.7.1.openmpi.5.0.1

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gromacs/2024.2/gcc.11.2.0-openmpi.5.0.1

CHEMISTRY

GROMACS is a software suite for high-performance molecular dynamics and output analysis

gsl/2.6/gcc.8.4.0

LIBRARIES

GNU Scientific Library

gsl/2.7.1/gcc.11.2.0

LIBRARIES

GNU Scientific Library

hdf4/4.2.15

LIBRARIES

HDF4 is a physical file format for storing scientific data

hdf5/1.10.5/gcc.8.4.0

TOOLS

HDF5 is a High-performance data management and storage suite

hdf5/1.10.5/gcc.8.4.0-openmpi.4.0.3

TOOLS

Parallel version of HDF5 compiled with gcc 8.4.0 and openmpi version 4.0.3

hdf5/1.10.5/gcc.system

TOOLS

HDF5 is a High-performance data management and storage suite

hdf5/1.13.1/cudasdk.22.9

TOOLS

HDF5 is a High-performance data management and storage suite

hdf5/1.13.1/gcc.11.2.0

TOOLS

HDF5 is a High-performance data management and storage suite

hdf5/1.13.1/gcc.11.2.0-openmpi.4.1.2

TOOLS

Parallel version of HDF5 compiled with gcc 11.2.0 and openmpi version 4.1.2

hdf5/1.13.1/gcc.8.4.0

TOOLS

HDF5 is a High-performance data management and storage suite

hdf5/1.13.1/gcc.system

TOOLS

HDF5 is a High-performance data management and storage suite

hdf5/1.13.1/gcc.system-openmpi.4.1.1

TOOLS

Parallel version of HDF5 compiled with gcc system and openmpi version 4.1.1

hdf5/1.13.1/intel.2022.2

TOOLS

HDF5 is a High-performance data management and storage suite

hdf5/1.13.1/intel.2022.2-openmpi.4.1.2

TOOLS

Parallel version of HDF5 compiled with gcc 2022.2 and openmpi version 4.1.2

hdf5/1.14.1/gcc.11.2.0

TOOLS

HDF5 is a High-performance data management and storage suite

hdf5/1.14.1/gcc.11.2.0-openmpi.4.1.2

TOOLS

Parallel version of HDF5 compiled with gcc 11.2.0 and openmpi version 4.1.2

hdf5/1.14.1/gcc.11.2.0-openmpi.5.0.1

TOOLS

Parallel version of HDF5 compiled with gcc 11.2.0 and openmpi version 5.0.1

hisat2/2.2.1

GENOMICS

HISAT2 a fast and sensitive alignment program for mapping next-generation sequencing reads to genomes

hmmer/3.3

BIOTOOLS

HMMER is a biosequence analysis using profile hidden Markov models

htslib/1.10.2

BIOTOOLS

HTSLIB is a C library for reading/writing high-throughput sequencing data

htslib/1.15.1

BIOTOOLS

HTSLIB is a C library for reading/writing high-throughput sequencing data

htslib/1.21

BIOTOOLS

HTSLIB is a C library for reading/writing high-throughput sequencing data

imagemagick/7.0.10.26

TOOLS

ImageMagick is a software suite for manipulating digital images

imagemagick/7.1.0.30

TOOLS

ImageMagick is a software suite for manipulating digital images

intel-tbb/20190605

COMPILERS

Intel Threading Building Blocks (TBB) 20190605

intel-tbb/2021.11

COMPILERS

Intel Threading Building Blocks (TBB) 2021.11

intel-tbb/2022.1

COMPILERS

Intel Threading Building Blocks (TBB) 2022.1

intel/2020u1

COMPILERS

Intel Studio XE Compilers(R) version 2020u1

intel/2022.2

COMPILERS

Intel (R) oneAPI compiler

intel/2024.0.1

COMPILERS

Intel (R) oneAPI compiler

intel/2025.1.0

COMPILERS

Intel (R) oneAPI compiler

ioapi/3.2/intel.2022.2

TOOLS

Input Output Applications Programming Interface (IOAPI)

isal/2.30.0

BIOTOOLS

ISA-L is a collection of optimized low-level functions targeting storage applications

java/1.8.0

LANGUAGES

Environment module of openjdk java version 1.8.0

java/11

LANGUAGES

Environment module of openjdk java version 11

java/17

LANGUAGES

Environment module of openjdk java version 17

jsoncpp/1.9.5

LIBRARIES

JsonCpp is a C++ library that allows manipulating JSON values

julia/1.6.0

LANGUAGES

Julia is a high-level and high-performance dynamic programming language

julia/1.8.2

LANGUAGES

Julia is a high-level and high-performance dynamic programming language

julia/1.9.3

LANGUAGES

Julia is a high-level and high-performance dynamic programming language

kallisto/0.46.2

BIOTOOLS

Kallisto is a program for quantifying abundances of target sequences using high-throughput sequencing reads

kallisto/0.48.0

BIOTOOLS

Kallisto is a program for quantifying abundances of target sequences using high-throughput sequencing reads

kallisto/0.51.1

BIOTOOLS

Kallisto is a program for quantifying abundances of target sequences using high-throughput sequencing reads

kneaddata/0.10.0

GENOMICS

KneadData is a tool for quality control on metagenomic and metatranscriptomic sequencing data

kraken2/2.1.2

GENOMICS

Kraken2 is a taxonomic sequence classifier

lammps/29Sep2021/gcc.11.2.0

CHEMISTRY

LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

lammps/3Mar2020/gcc.8.4.0

CHEMISTRY

LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

lapack/3.9.0

LIBRARIES

LAPACK - Linear Algebra PACKage

libdeflate/1.10

BIOTOOLS

Libdeflate is a library for fast whole-buffer DEFLATE-based compression and decompression

libgit2/1.8.4

TOOLS

Libgit2 is an implementation of the Git core methods

libjpeg/9d

LIBRARIES

Libjpeg is a library for JPEG image compression

libpng/1.6.37

LIBRARIES

Libpng is the official PNG reference library

llvm/11.1.0

COMPILERS

LLVM Core libraries (part of LLVM Project)

llvm/13.0.0

COMPILERS

LLVM Core libraries (part of LLVM Project)

llvm/18.1.4

COMPILERS

LLVM Core libraries (part of LLVM Project)

llvm/9.0.1

COMPILERS

LLVM Core libraries (part of LLVM Project)

loompy/3.0.6

GENOMICS

Loompy provides support for loom files

macs/2.2.7.1

BIOTOOLS

MACS - Model-based Analysis of ChIP-Seq for identifying transcript factor binding sites

mafft/7.471

GENOMICS

MAFFT is a multiple sequence alignment program for unix-like operating systems

mamba/24.3.0

LANGUAGES

Mamba is a software package manager

marc/2020

PHYSICS

Marc (MSC) is a nonlinear finite elements analysis software

megahit/1.2.9

GENOMICS

MEGAHIT is an ultra-fast and memory-efficient NGS assembler

mentat/2020

PHYSICS

Mentat is the GUI for Marc software

miniconda3/23.5.2

LANGUAGES

Miniconda3 with python 3.9

miniconda3/24.9.2

LANGUAGES

Miniconda3 with python 3.12

minimap2/2.24

BIOTOOLS

Minimap2 is a versatile sequence alignment program

minimap2/2.28

BIOTOOLS

Minimap2 is a versatile sequence alignment program

mkl/2019.5.281

LIBRARIES

Intel Math Kernel Library

mkl/2024.0.1

LIBRARIES

Intel Math Kernel Library

mpich/3.3.2/gcc.8.4.0

COMPILERS

MPICH is a high performance implementation of the Message Passing Interface (MPI) standard. Compiled with UCX 1.12.0 and –with-verbs –with-hwloc=embedded –enable-romio –with-ucx=/opt/apps/ucx/1.12.0

mpich/3.4/gcc.8.4.0

COMPILERS

MPICH is a high performance implementation of the Message Passing Interface (MPI) standard. Compiled with UCX 1.8.0 and –with-verbs –with-hwloc=embedded –enable-romio –with-ucx=/opt/apps/ucx/1.8.0

mpich/4.0/gcc.system

COMPILERS

MPICH is a high performance implementation of the Message Passing Interface (MPI) standard. Compiled with UCX 1.12.0 and –with-verbs –with-hwloc=embedded –enable-romio –with-ucx=/opt/apps/ucx/1.12.0 FCFLAGS=-fallow-argument-mismatch

mpich/4.0/intel.2022.2

COMPILERS

MPICH is a high performance implementation of the Message Passing Interface (MPI) standard. Compiled with UCX 1.12.0 and –with-verbs –with-hwloc=embedded –enable-romio –with-ucx=/opt/apps/ucx/1.12.0

namd/2.14b2/gcc.8.4.0

CHEMISTRY

NAMD is a parallel molecular dynamics code for large biomolecular systems

namd/2.14b2/gcc.8.4.0-cuda.11.7.1

CHEMISTRY

NAMD is a parallel molecular dynamics code for large biomolecular systems

namd/2.14b2/gcc.8.4.0-openmpi.4.0.3

CHEMISTRY

NAMD is a parallel molecular dynamics code for large biomolecular systems

ncbi-blast/2.10.0

BIOTOOLS

BLAST (Basic Local Alignment Search Tool) command line applications from NCBI

ncbi-blast/2.13.0

BIOTOOLS

BLAST (Basic Local Alignment Search Tool) command line applications from NCBI

ncbi-ngs/2.10.2

BIOTOOLS

NGS sdk binding from NCBI

ncbi-vdb/2.10.2

BIOTOOLS

VDB is the SRA Toolkit and SDK from NCBI

ncl/6.6.2

TOOLS

NCL is an interpreted language for scientific data analysis and visualization

netcdf-c/4.7.0/gcc.8.4.0

TOOLS

The Unidata network Common Data Form (netCDF) is an interface for scientific data access

netcdf-c/4.8.1/gcc.11.2.0

TOOLS

The Unidata network Common Data Form (netCDF) is an interface for scientific data access

netcdf-c/4.8.1/intel.2022.2

TOOLS

The Unidata network Common Data Form (netCDF) is an interface for scientific data access

ninja/1.10.2

TOOLS

Ninja is a small build system with a focus on speed

openmpi/4.0.3/gcc.6.5.0

COMPILERS

The openmpi is an open source Message Passing Interface implementation. Compiled with UCX 1.12.0 and –with-verbs –with-hwloc=internal –with-singularity=$singularity__PREFIX –with-ucx=$UCX_DIR –enable-orterun-prefix-by-default

openmpi/4.0.3/gcc.8.4.0

COMPILERS

The openmpi is an open source Message Passing Interface implementation. Compiled with UCX 1.8.0 and –with-verbs –with-hwloc=internal –with-singularity=$singularity__PREFIX –with-ucx=$UCX_DIR –enable-orterun-prefix-by-default

openmpi/4.1.1/gcc.system

COMPILERS

System default Openmpi version 4.1.1

openmpi/4.1.2/gcc.11.2.0

COMPILERS

The openmpi is an open source Message Passing Interface implementation. Compiled with UCX 1.12.0 and –with-verbs –with-hwloc=internal –with-singularity=$singularity__PREFIX –with-ucx=$UCX_DIR –enable-orterun-prefix-by-default

openmpi/4.1.2/gcc.8.4.0

COMPILERS

The openmpi is an open source Message Passing Interface implementation. Compiled with UCX 1.12.0 and –with-verbs –with-hwloc=internal –with-singularity=$singularity__PREFIX –with-ucx=$UCX_DIR –enable-orterun-prefix-by-default

openmpi/4.1.2/intel.2022.2

COMPILERS

The openmpi is an open source Message Passing Interface implementation. Compiled with UCX 1.12.0 and –with-verbs –with-hwloc=internal –with-singularity=$singularity__PREFIX –with-ucx=$UCX_DIR –enable-orterun-prefix-by-default

openmpi/5.0.1/gcc.11.2.0

COMPILERS

The openmpi is an open source Message Passing Interface implementation. Compiled with UCX 1.15.0 and –with-verbs –with-hwloc=internal –with-singularity=$singularity__PREFIX –with-ucx=$UCX_DIR –enable-orterun-prefix-by-default

openmpi/5.0.1/gcc.11.2.0-cuda.11.7.1

COMPILERS

The openmpi is an open source Message Passing Interface implementation. Compiled with UCX 1.15.0 and –with-verbs –with-hwloc=internal –with-singularity=$singularity__PREFIX –with-ucx=$UCX_DIR –enable-orterun-prefix-by-default –with-cuda=$CUDA_PATH

opensees/3.3.0

PHYSICS

OpenSees - the Open System for Earthquake Engineering Simulation

parallel/20211222

TOOLS

GNU parallel is a shell tool for executing jobs in parallel

perl/5.30.0

LANGUAGES

Perl Programming Language version 5.30.0

perl/5.34.1

LANGUAGES

Perl Programming Language version 5.34.1

picard-tools/1.87

BIOTOOLS

Picard-tools is a set of Java command line tools for manipulating high-throughput sequencing data and formats

picard-tools/2.27.1

BIOTOOLS

Picard-tools is a set of Java command line tools for manipulating high-throughput sequencing data and formats

picard-tools/3.3.0

BIOTOOLS

Picard-tools is a set of Java command line tools for manipulating high-throughput sequencing data and formats

pigz/2.6

TOOLS

Pigz is a parallel implementaion and replacement of gzip

pilon/1.24

BIOTOOLS

Pilon is a software tool to automatically improve draft assemblies and find variation among strains

plink/2.00a2.3

GENOMICS

Plink is a genome association analysis toolset

prodigal/2.6.3

GENOMICS

Prodigal is a protein-coding gene prediction software tool for bacterial and archaeal genomes

proj/6.3.2/gcc.8.4.0

LIBRARIES

PROJ is a generic coordinate transformation software

proj/9.0.0/gcc.11.2.0

LIBRARIES

PROJ is a generic coordinate transformation software

proj/9.1.1/gcc.11.2.0

LIBRARIES

PROJ is a generic coordinate transformation software

python/2.7.17

LANGUAGES

Python Programming Language version 2.7.17

python/3.10.2

LANGUAGES

Python Programming Language version 3.10.2

python/3.8.0

LANGUAGES

Python Programming Language version 3.8.0

pytorch/1.11.0

AI-LEARNING

PyTorch is a machine learning framework written in Python

pytorch/2.0.1

AI-LEARNING

PyTorch is a machine learning framework written in Python

pytorch/2.3.0

AI-LEARNING

PyTorch is a machine learning framework written in Python

qe/7.1/gcc.11.2.0-openmpi.4.1.2

PHYSICS

QE - Quantum ESPRESSO

qe/7.1/intel.2022.2-cudasdk.22.9.openmpi.4.1.2

PHYSICS

QE - Quantum ESPRESSO

qiime2/2023.7

BIOTOOLS

QIIME2 is an environment built for miniconda3 23.5.2

qiime2/2024.10

BIOTOOLS

QIIME2 is an environment built for miniconda3 24.9.2

rMATS/4.1.1

GENOMICS

rMATS turbo is the C/Cython version of rMATS

rMATS/4.1.2

GENOMICS

rMATS turbo is the C/Cython version of rMATS

racon/1.5.0

BIOTOOLS

Racon is an ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

repeatmasker/4.1.0

BIOTOOLS

RepeatMasker is a program for screening DNA sequences

rosetta/3.13

BIOTOOLS

The Rosetta software suite

rsem/1.3.3

BIOTOOLS

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data

rstudio/1.4.1106

LANGUAGES

R Studio Desktop 1.4.1106

rstudio/2022.02.1.461

LANGUAGES

R Studio Desktop 2022.02.1.461

rstudio/2022.12.0.353

LANGUAGES

R Studio Desktop 2022.12.0.353

rstudio/2023.12.1.402

LANGUAGES

R Studio Desktop 2023.12.1.402

rstudio/2024.09.1.394

LANGUAGES

R Studio Desktop 2024.09.1.394

rustc/1.78.0

COMPILERS

Rust Compiler

salmon/1.8.0

BIOTOOLS

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data

samtools/1.10

BIOTOOLS

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

samtools/1.15.1

BIOTOOLS

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

scalapack/2.1.0

LIBRARIES

ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines

scons/4.2.0

TOOLS

SCons is a tool for building software (and other files)

singularity/3.11.3

TOOLS

Singularity container runtime

singularity/3.7.2

TOOLS

Singularity container runtime

singularity/3.9.4

TOOLS

Singularity container runtime

sqlite3/3.32.3/gcc.8.4.0

LIBRARIES

SQLite3 is a library that implements a transactional SQL database engine

sqlite3/3.38.2/gcc.11.2.0

LIBRARIES

SQLite3 is a library that implements a transactional SQL database engine

sqlite3/3.41.0/gcc.11.2.0

LIBRARIES

SQLite3 is a library that implements a transactional SQL database engine

sra-tools/3.0.0

BIOTOOLS

The SRA Toolkit and SDK from NCBI

star/2.7.10a

BIOTOOLS

STAR is a Spliced Transcripts Alignment to a Reference

star/2.7.3a

BIOTOOLS

STAR is a Spliced Transcripts Alignment to a Reference

star/2.7.8a

BIOTOOLS

STAR is a Spliced Transcripts Alignment to a Reference

stata/16

LANGUAGES

Stata is a general-purpose statistical software package

stata/17

LANGUAGES

Stata is a general-purpose statistical software package

stringtie/2.1.4

GENOMICS

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts

stringtie/2.2.1

GENOMICS

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts

subread/2.0.1

BIOTOOLS

The Subread is a toolkit for processing next-gen sequencing data

subread/2.0.3

BIOTOOLS

The Subread is a toolkit for processing next-gen sequencing data

swig/4.0.2

TOOLS

SWIG is an interface compiler

szip/2.1.1

LIBRARIES

Szip is a stand-alone library

tcl/8.6.12

LANGUAGES

Tcl (Tool Command Language) is a very powerful dynamic programming language

tcl/8.6.9

LANGUAGES

Tcl (Tool Command Language) is a very powerful dynamic programming language

tensorRT/8.4.2.4

AI-LEARNING

TensorRT is a machine learning framework published by Nvidia

tensorRT/8.6.1.6

AI-LEARNING

TensorRT is a machine learning framework published by Nvidia

tensorflow/2.16.1

AI-LEARNING

TensorFlow is an open source software library for high performance numerical computation

tensorflow/2.8.0

AI-LEARNING

TensorFlow is an open source software library for high performance numerical computation

trf/4.0.9

BIOTOOLS

Tandem Repeats Finder (TRF) is a program to analyze DNA sequences

trimgalore/0.6.6

BIOTOOLS

TrimGalore is a a Perl wrapper around tools Cutadapt and FastQC

trimgalore/0.6.7

BIOTOOLS

TrimGalore is a a Perl wrapper around tools Cutadapt and FastQC

trimmomatic/0.39

GENOMICS

Pilon is a software tool used to automatically improve draft assemblies and to find variation among strains

turbomole-smp/7.5

CHEMISTRY

TURBOMOLE is set of computational tools for quantum chemical simulations

turbomole-smp/7.6

CHEMISTRY

TURBOMOLE is set of computational tools for quantum chemical simulations

turbomole-smp/7.8.1

CHEMISTRY

TURBOMOLE is set of computational tools for quantum chemical simulations

turbomole/7.5

CHEMISTRY

TURBOMOLE is set of computational tools for quantum chemical simulations

turbomole/7.6

CHEMISTRY

TURBOMOLE is set of computational tools for quantum chemical simulations

turbomole/7.8.1

CHEMISTRY

TURBOMOLE is set of computational tools for quantum chemical simulations

ucsc-tools/v429

BIOTOOLS

The UCSC command-line utilities

ucx/1.12.0/gcc.system

LIBRARIES

Unified Communication X (UCX) provides an optimized communication layer for MPI applications. Configured with –with-rc –with-ud –with-dc –with-ib-hw-tm –with-dm

ucx/1.15.0/cuda.11.7.1

LIBRARIES

Unified Communication X (UCX) provides an optimized communication layer for MPI applications. Configured with –enable-optimizations –with-avx –enable-mt –without-java –with-numa=/usr/bin/numactl –with-rc –with-ud –with-dc –with-ib-hw-tm –with-dm –with-cuda=$CUDA_PATH –with-gdrcopy=$GDRCOPY_DIR –with-iodemo-cuda

ucx/1.15.0/gcc.system

LIBRARIES

Unified Communication X (UCX) provides an optimized communication layer for MPI applications. Configured with –with-rc –with-ud –with-dc –with-ib-hw-tm –with-dm –disable-logging –disable-debug –disable-assertions –disable-params-check

ucx/1.8.0/gcc.system

LIBRARIES

Unified Communication X (UCX) provides an optimized communication layer for MPI applications. Configured with –with-rc –with-ud –with-dc –with-ib-hw-tm –with-dm

udunits/2.2.26/gcc.8.4.0

TOOLS

The UDUNITS package supports units of physical quantities

udunits/2.2.28/gcc.11.2.0

TOOLS

The UDUNITS package supports units of physical quantities

udunits/2.2.28/intel.2022.2

TOOLS

The UDUNITS package supports units of physical quantities

unicycler/0.5.0

BIOTOOLS

Unicycler is an assembly pipeline for bacterial genomes

vasp/5.4.4

ENGINEERING

The Vienna Ab initio Simulation Package (VASP) is for quantum-mechanical molecular dynamics problems

vasp/6.1.2

ENGINEERING

The Vienna Ab initio Simulation Package (VASP) is for quantum-mechanical molecular dynamics problems

vasp/6.3.2/cudasdk.22.9

ENGINEERING

The Vienna Ab initio Simulation Package (VASP) is for quantum-mechanical molecular dynamics problems

vasp/6.3.2/gcc.11.2.0

ENGINEERING

The Vienna Ab initio Simulation Package (VASP) is for quantum-mechanical molecular dynamics problems

vcftools/0.1.16

BIOTOOLS

The vcftools is a set of tools written in Perl and C++ for working with VCF files

velocyto/0.17.17

GENOMICS

Velocyto is a library for the analysis of RNA velocity
Licensed Software

Access to the following applications requires a license:

Abaqus

COMSOL

Gaussian

MATLAB

Stata 16

Stata 17

VASP 5.x

VASP 6.x

Note

While all users can view and load modules for licensed software only registered users (users must be in specific groups) can use such software.

One exception to this is MATLAB. RCIC contributes to the UCI-wide license and MATLAB is available to all the HPC3 users. Users only need to load one of the available MATLAB modules in order to use this software.

  • RCIC does not purchase or provide licenses, we only enable an access to the licenses.

  • The departments/PIs buy licenses for their labs and the access must be approved by a PI.

  • Users must submit a ticket requesting Access to Licensend Software in order to use to licensed applications.

How it is built

Some software is quick and easy to compile, install, and make available to users. Others have numerous (often undocumented) software dependencies, unique build methods, and conflicting requirements. The size of the problem is quite large, and grows with each new application.

RCIC uses a multi-factor approach to provide a stable and flexible environment

  • Adoption of a declarative, repeatable YAML2RPM build methodology designed by RCIC which generates reusable RPM that can installed on any compatible CentOS system.

  • Nearly all installed software is packaged as RPMs with encoded dependencies. Exceptions generally are very large footprint software like the Intel Compiler or MATLAB.

Why use RPMS?

For us, it’s one extra step that comes a wide variety of benefits:

  • The complete stack is fairly complex and captures needed dependencies.

  • Enable installation of multiple versions of same software.

  • Use native operating system tools to get information about installed software.

  • The package manager will not allow two different RPMs to claim ownership of the same file (or have conflicting permissions on a shared directory path).

  • Properly encoded dependencies help to ensure that removal of a particular package won’t leave other software in a broken state.

  • Ease of transitioning to container definitions. We can easily put a subsets of the HPC3 software stack in the form of a singularity containers.

The deployed software stack is generally added to on weekly basis. This is in response to a near-continuous stream of requests.

A Software Map (PDF) shows a snapshot of the collections of software, software modules they provide, and build dependencies.

Request New Software

Please see User installed software before requesting new software install.

You may submit a request for new software to be added to HPC3, however we cannot and do not say yes to every request. RCIC is simply not large enough to handle all software requests.

RCIC prioritizes all software requests as follows:

  1. Fix a compilation problem, security issue, or functionality issue of existing software.

  2. A new release of an already-installed software provides significant new capability.

  3. New software has a demonstrated need by multiple labs.

RCIC says NO to the following types of requests:

  1. When a request does not meet the above priority criteria.

  2. Software that the user wants to evaluate.

  3. Licensed software that does not use the FlexLM license manager or requires RCIC to run the license server.

  4. Software that will only be used by one or two users.

  5. Software that requires MySQL, PostgreSQL, HTTP or similar server setup.