Grete GCC13 Modules
Warning
This page describes modules in the 25.04 revision which is currently in testing and has to be loaded first:
source /sw/rev_profile/25.04/profile.shThis step can be skipped after the revision becomes the default later in Q2 2025.
It is required to load the appropriate compiler and MPI modules before any of the modules become visible (hierarchical module system):
module load gcc/13.2.0
module load openmpi/5.0.7 Tip
The software packages loaded on each phase are optimized for the particular CPU and GPU architecture (machine kind) of that phase (e.g AMD Rome + A100 or Intel Sapphirerapids + H100).
You can print the current machine kind by using the command: /sw/rev_profile/25.04/machine-kind
If you compile your own code (e.g. by using gcc or pip) please take care to compile on the same machine kind that the code will also be executed on.
List of Modules
| Module Names | Description | Homepage |
|---|---|---|
| abyss/2.3.10 abyss/2.3.5 | ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. | https://www.bcgsc.ca/platform/bioinfo/software/abyss |
| amdblis/4.1 | AMD Optimized BLIS. | https://www.amd.com/en/developer/aocl/blis.html |
| amdfftw/4.1 | FFTW (AMD Optimized version) is a comprehensive collection of fast C routines for computing the Discrete Fourier Transform (DFT) and various special cases thereof. | https://www.amd.com/en/developer/aocl/fftw.html |
| amdlibflame/4.1 | libFLAME (AMD Optimized version) is a portable library for dense matrix computations, providing much of the functionality present in Linear Algebra Package (LAPACK). It includes a compatibility layer, FLAPACK, which includes complete LAPACK implementation. | https://www.amd.com/en/developer/aocl/blis.html#libflame |
| amdscalapack/4.1 | ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. It depends on external libraries including BLAS and LAPACK for Linear Algebra computations. | https://www.amd.com/en/developer/aocl/scalapack.html |
| aria2/1.36.0 aria2/1.37.0 | An ultra fast download utility | https://aria2.github.io |
| bedops/2.4.41 | BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. | https://bedops.readthedocs.io |
| blast-plus/2.14.1 blast-plus/2.16.0 | Basic Local Alignment Search Tool. | https://blast.ncbi.nlm.nih.gov/ |
| boost/1.83.0 boost/1.86.0 | Boost provides free peer-reviewed portable C++ source libraries, emphasizing libraries that work well with the C++ Standard Library. | https://www.boost.org |
| bowtie/1.3.1 | Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. | https://sourceforge.net/projects/bowtie-bio/ |
| bwa/0.7.17 | Burrow-Wheeler Aligner for pairwise alignment between DNA sequences. | https://github.com/lh3/bwa |
| cdo/2.2.2 cdo/2.4.4 | CDO is a collection of command line operators to manipulate and analyse Climate and NWP model Data. | https://code.mpimet.mpg.de/projects/cdo |
| charmpp/8.0.0-smp | Charm++ is a parallel programming framework in C++ supported by an adaptive runtime system, which enhances user productivity and allows programs to run portably from small multicore computers (your laptop) to the largest supercomputers. | https://charmplusplus.org |
| chimera/1.18 | UCSF CHIMERA: an Extensible Molecular Modeling System | https://www.cgl.ucsf.edu/chimera/ |
| chimerax/1.9 | UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. | https://www.cgl.ucsf.edu/chimerax/ |
| clblast/1.5.2 | CLBlast is a modern, lightweight, performant and tunable OpenCL BLAS library written in C++11. It is designed to leverage the full performance potential of a wide variety of OpenCL devices from different vendors, including desktop and laptop GPUs, embedded GPUs, and other accelerators. CLBlast implements BLAS routines: basic linear algebra subprograms operating on vectors and matrices. | https://cnugteren.github.io/clblast/clblast.html |
| clinfo/3.0.23.01.25 | Print all known information about all available OpenCL platforms and devices in the system. | https://github.com/Oblomov/clinfo |
| clpeak/1.1.2 | Simple OpenCL performance benchmark tool. | https://github.com/krrishnarraj/clpeak |
| cp2k/2024.1 cp2k/2025.1 | 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 | https://www.cp2k.org |
| cpmd/4.3 | The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. | https://www.cpmd.org/wordpress/ |
| crest/2.12 | Conformer-Rotamer Ensemble Sampling Tool | https://github.com/crest-lab/crest |
| cuda/12.6.2 | CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU). | https://developer.nvidia.com/cuda-zone |
| cudnn/8.9.7.29-11 cudnn/8.9.7.29-12 | NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks | https://developer.nvidia.com/cudnn |
| diamond/2.1.10 diamond/2.1.7 | DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. | https://ab.inf.uni-tuebingen.de/software/diamond |
| dynamo/1.1.552 | Dynamo is a software environment for subtomogram averaging of cryo-EM data. | https://www.dynamo-em.org/w/index.php?title=Main_Page |
| eccodes/2.34.0 | ecCodes is a package developed by ECMWF for processing meteorological data in GRIB (1/2), BUFR (3/4) and GTS header formats. | https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home |
| exciting/oxygen | exciting is a full-potential all-electron density-functional-theory package implementing the families of linearized augmented planewave methods. It can be applied to all kinds of materials, irrespective of the atomic species involved, and also allows for exploring the physics of core electrons. A particular focus are excited states within many-body perturbation theory. | https://exciting-code.org/ |
| ffmpeg/7.0.2 | FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. | https://ffmpeg.org |
| fftw/3.3.10 fftw/3.3.10-quad-precision | FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications. | https://www.fftw.org |
| fiji/2.16.0 | Fiji is a ‘batteries-included’ distribution of ImageJ, a popular, free scientific image processing application which includes a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux. | https://imagej.net/ |
| fleur/5.1 | FLEUR (Full-potential Linearised augmented plane wave in EURope) is a code family for calculating groundstate as well as excited-state properties of solids within the context of density functional theory (DFT). | https://www.flapw.de/MaX-5.1 |
| flex/2.6.1 | Flex is a tool for generating scanners. | https://github.com/westes/flex |
| foam-extend/5.0 | The Extend Project is a fork of the OpenFOAM open-source library for Computational Fluid Dynamics (CFD). This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark. | https://sourceforge.net/projects/foam-extend/ |
| gatk/3.8.1 gatk/4.4.0.0 gatk/4.5.0.0 | Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data | https://gatk.broadinstitute.org/hc/en-us |
| gdal/3.10.0 gdal/3.7.3 | GDAL: Geospatial Data Abstraction Library. | https://www.gdal.org/ |
| gdb/15.2 | GDB, the GNU Project debugger, allows you to see what is going on ‘inside’ another program while it executes – or what another program was doing at the moment it crashed. | https://www.gnu.org/software/gdb |
| globalarrays/5.8.2 | Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model. | https://hpc.pnl.gov/globalarrays/ |
| gmp/6.2.1 gmp/6.3.0 | GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. | https://gmplib.org |
| grads/2.2.3 | The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. GrADS has two data models for handling gridded and station data. GrADS supports many data file formats, including binary (stream or sequential), GRIB (version 1 and 2), NetCDF, HDF (version 4 and 5), and BUFR (for station data). | http://cola.gmu.edu/grads/grads.php |
| gromacs/2022.5-plumed gromacs/2023-plumed gromacs/2023.3 gromacs/2024.3 | GROMACS is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. | https://www.gromacs.org |
| gsl/2.7.1 gsl/2.8 | The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite. | https://www.gnu.org/software/gsl |
| hdf5/1.14.5 | HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of data types, and is designed for flexible and efficient I/O and for high volume and complex data. | https://support.hdfgroup.org |
| hisat2/2.2.1 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome). | https://daehwankimlab.github.io/hisat2/ |
| imagej/1.54p | ImageJ is public domain software for processing and analyzing scientific images. It is written in Java, which allows it to run on many different platforms. For further information, see: The ImageJ website, the primary home of this project. The ImageJ wiki, a community-built knowledge base covering ImageJ and its derivatives and flavors, including ImageJ2, Fiji, and others. The ImageJ mailing list and Image.sc Forum for community support. The Contributing page of the ImageJ wiki for details on how to contribute. | https://www.imagej.net |
| imod/5.0.2 imod/5.1.0 | IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, Suraj Khochare, and John Heumann at the University of Colorado. | https://bio3d.colorado.edu/imod/ |
| intel-oneapi-advisor/2025.0.0 | Intel Advisor is a design and analysis tool for developing performant code. The tool supports C, C++, Fortran, SYCL, OpenMP, OpenCL code, and Python. It helps with the following: Performant CPU Code: Design your application for efficient threading, vectorization, and memory use. Efficient GPU Offload: Identify parts of the code that can be profitably offloaded. Optimize the code for compute and memory. | https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/advisor.html |
| intel-oneapi-dal/2025.0.0 | Intel oneAPI Data Analytics Library (oneDAL) is a library that helps speed up big data analysis by providing highly optimized algorithmic building blocks for all stages of data analytics (preprocessing, transformation, analysis, modeling, validation, and decision making) in batch, online, and distributed processing modes of computation. The library optimizes data ingestion along with algorithmic computation to increase throughput and scalability. | https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onedal.html |
| intel-oneapi-dnn/2025.0.0 | The Intel oneAPI Deep Neural Network Library (oneDNN) helps developers improve productivity and enhance the performance of their deep learning frameworks. It supports key data type formats, including 16 and 32-bit floating point, bfloat16, and 8-bit integers and implements rich operators, including convolution, matrix multiplication, pooling, batch normalization, activation functions, recurrent neural network (RNN) cells, and long short-term memory (LSTM) cells. | https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onednn.html |
| intel-oneapi-inspector/2024.1.0 | Intel Inspector is a dynamic memory and threading error debugger for C, C++, and Fortran applications that run on Windows and Linux operating systems. Save money: locate the root cause of memory, threading, and persistence errors before you release. Save time: simplify the diagnosis of difficult errors by breaking into the debugger just before the error occurs. Save effort: use your normal debug or production build to catch and debug errors. Check all code, including third-party libraries with unavailable sources. | https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/inspector.html |
| intel-oneapi-mkl/2023.2.0 intel-oneapi-mkl/2024.2.2 | Intel oneAPI Math Kernel Library (Intel oneMKL; formerly Intel Math Kernel Library or Intel MKL), is a library of optimized math routines for science, engineering, and financial applications. Core math functions include BLAS, LAPACK, ScaLAPACK, sparse solvers, fast Fourier transforms, and vector math. | https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html |
| intel-oneapi-tbb/2022.0.0 | Intel oneAPI Threading Building Blocks (oneTBB) is a flexible performance library that simplifies the work of adding parallelism to complex applications across accelerated architectures, even if you are not a threading expert. | https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onetbb.html |
| intel-oneapi-vtune/2025.0.0 | Intel VTune Profiler is a profiler to optimize application performance, system performance, and system configuration for HPC, cloud, IoT, media, storage, and more. CPU, GPU, and FPGA: Tune the entire application’s performance–not just the accelerated portion. Multilingual: Profile SYCL, C, C++, C#, Fortran, OpenCL code, Python, Google Go programming language, Java, .NET, Assembly, or any combination of languages. System or Application: Get coarse-grained system data for an extended period or detailed results mapped to source code. Power: Optimize performance while avoiding power and thermal-related throttling. | https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/vtune-profiler.html |
| iq-tree/2.2.2.7 iq-tree/2.3.2 | IQ-TREE Efficient software for phylogenomic inference | http://www.iqtree.org |
| jags/4.3.0 jags/4.3.2 | JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS | https://mcmc-jags.sourceforge.net/ |
| kraken2/2.1.2 | Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. | https://ccb.jhu.edu/software/kraken2/ |
| libaec/1.0.6 | Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). It implements Golomb-Rice compression method under the BSD license and includes a free drop-in replacement for the SZIP library. | https://gitlab.dkrz.de/k202009/libaec |
| libfabric/2.0.0 | The Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications. | https://libfabric.org/ |
| libpng/1.6.39 | libpng is the official PNG reference library. | http://www.libpng.org/pub/png/libpng.html |
| llvm/19.1.3 | The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines, though it does provide helpful libraries that can be used to build them. The name ‘LLVM’ itself is not an acronym; it is the full name of the project. | https://llvm.org/ |
| molden/6.7 molden/7.3 | A package for displaying Molecular Density from various Ab Initio packages | https://www.theochem.ru.nl/molden/ |
| mono/6.12.0.122 | Mono is a software platform designed to allow developers to easily create cross platform applications. It is an open source implementation of Microsoft’s .NET Framework based on the ECMA standards for C# and the Common Language Runtime. | https://www.mono-project.com/ |
| mpc/1.3.1 | Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. | https://www.multiprecision.org |
| mpifileutils/0.11.1 | mpiFileUtils is a suite of MPI-based tools to manage large datasets, which may vary from large directory trees to large files. High-performance computing users often generate large datasets with parallel applications that run with many processes (millions in some cases). However those users are then stuck with single-process tools like cp and rm to manage their datasets. This suite provides MPI-based tools to handle typical jobs like copy, remove, and compare for such datasets, providing speedups of up to 20-30x. | https://github.com/hpc/mpifileutils |
| mumps/5.7.3 | MUMPS: a MUltifrontal Massively Parallel sparse direct Solver | https://mumps-solver.org |
| muscle5/5.1.0 | MUSCLE is widely-used software for making multiple alignments of biological sequences. | https://drive5.com/muscle5/ |
| must/1.9.0 | MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. As MPI calls are complex and usage errors common, this functionality is extremely helpful for application developers that want to develop correct MPI applications. This includes errors that already manifest: segmentation faults or incorrect results as well as many errors that are not visible to the application developer or do not manifest on a certain system or MPI implementation. | https://www.i12.rwth-aachen.de/go/id/nrbe |
| namd/3.0.1-smp | NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | https://www.ks.uiuc.edu/Research/namd/ |
| nco/5.1.6 nco/5.2.4 | The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats | https://nco.sourceforge.net/ |
| ncview/2.1.9 | Simple viewer for NetCDF files. | https://cirrus.ucsd.edu/ncview/ |
| netcdf-c/4.9.2 | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the C distribution. | https://www.unidata.ucar.edu/software/netcdf |
| netcdf-fortran/4.6.1 | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This is the Fortran distribution. | https://www.unidata.ucar.edu/software/netcdf |
| netgen/5.3.1 | NETGEN is an automatic 3d tetrahedral mesh generator. It accepts input from constructive solid geometry (CSG) or boundary representation (BRep) from STL file format. The connection to a geometry kernel allows the handling of IGES and STEP files. NETGEN contains modules for mesh optimization and hierarchical mesh refinement. | https://ngsolve.org/ |
| netlib-lapack/3.11.0 | LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the scientific community. | https://www.netlib.org/lapack/ |
| netlib-scalapack/2.2.0 | ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines | https://www.netlib.org/scalapack/ |
| nextflow/23.10.0 nextflow/24.10.0 | Data-driven computational pipelines. | https://www.nextflow.io |
| nvtop/3.0.1 | Nvtop stands for Neat Videocard TOP, a (h)top like task monitor for AMD and NVIDIA GPUS. It can handle multiple GPUs and print information about them in a htop familiar way | https://github.com/Syllo/nvtop |
| ocl-icd/2.3.2 | This package aims at creating an Open Source alternative to vendor specific OpenCL ICD loaders. | https://github.com/OCL-dev/ocl-icd |
| octave/9.1.0 | GNU Octave is a high-level language, primarily intended for numerical computations. | https://www.gnu.org/software/octave/ |
| openbabel/3.1.1 | Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. | https://openbabel.org/docs/index.html |
| openblas/0.3.24 openblas/0.3.28 | OpenBLAS: An optimized BLAS library | https://www.openblas.net |
| opencl-c-headers/2024.05.08 | OpenCL (Open Computing Language) C header files | https://www.khronos.org/registry/OpenCL/ |
| opencl-clhpp/2.0.16 | C++ headers for OpenCL development | https://www.khronos.org/registry/OpenCL/ |
| opencl-headers/3.0 | Bundled OpenCL (Open Computing Language) header files | https://www.khronos.org/registry/OpenCL/ |
| opencoarrays/2.10.1 opencoarrays/2.10.2 | OpenCoarrays is an open-source software project that produces an application binary interface (ABI) supporting coarray Fortran (CAF) compilers, an application programming interface (API) that supports users of non-CAF compilers, and an associated compiler wrapper and program launcher. | http://www.opencoarrays.org/ |
| openfoam/2306 openfoam/2312 | OpenFOAM is a GPL-open-source C++ CFD-toolbox. This offering is supported by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark. OpenCFD Ltd has been developing and releasing OpenFOAM since its debut in 2004. | https://www.openfoam.com/ |
| openfoam-org/10 openfoam-org/11 openfoam-org/6 openfoam-org/7 openfoam-org/8 | OpenFOAM is a GPL-open-source C++ CFD-toolbox. The openfoam.org release is managed by the OpenFOAM Foundation Ltd as a licensee of the OPENFOAM trademark. This offering is not approved or endorsed by OpenCFD Ltd, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM trademark. | https://www.openfoam.org/ |
| openmpi/5.0.7 | An open source Message Passing Interface implementation. | https://www.open-mpi.org |
| osu-micro-benchmarks/7.3 osu-micro-benchmarks/7.5 | The Ohio MicroBenchmark suite is a collection of independent MPI message passing performance microbenchmarks developed and written at The Ohio State University. It includes traditional benchmarks and performance measures such as latency, bandwidth and host overhead and can be used for both traditional and GPU-enhanced nodes. | https://mvapich.cse.ohio-state.edu/benchmarks/ |
| paraview/5.13.2 paraview/5.13.2-gui | ParaView is an open-source, multi-platform data analysis and visualization application. This package includes the Catalyst in-situ library for versions 5.7 and greater, otherwise use the catalyst package. | https://www.paraview.org |
| pbmpi/1.9 | A Bayesian software for phylogenetic reconstruction using mixture models | https://github.com/bayesiancook/pbmpi |
| petsc/3.22.1-complex petsc/3.22.1-real | PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. | https://petsc.org |
| pigz/2.8 | A parallel implementation of gzip for modern multi-processor, multi-core machines. | https://zlib.net/pigz/ |
| pocl/6.0 | Portable Computing Language (pocl) is an open source implementation of the OpenCL standard which can be easily adapted for new targets and devices, both for homogeneous CPU and heterogeneous GPUs/accelerators. | https://portablecl.org |
| proj/9.2.1 proj/9.4.1 | PROJ is a generic coordinate transformation software, that transforms geospatial coordinates from one coordinate reference system (CRS) to another. This includes cartographic projections as well as geodetic transformations. | https://proj.org/ |
| psi4/1.8.2 psi4/1.9.1 | Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. | https://www.psicode.org/ |
| py-nvitop/1.4.0 | An interactive NVIDIA-GPU process viewer and beyond, the one-stop solution for GPU process management. | https://nvitop.readthedocs.io/ |
| py-uv/0.4.27 | An extremely fast Python package and project manager, written in Rust. | https://github.com/astral-sh/uv |
| quantum-espresso/6.7 quantum-espresso/7.2 quantum-espresso/7.3.1 quantum-espresso/7.4 | Quantum ESPRESSO is 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. | https://quantum-espresso.org |
| r/4.4.0 r/4.4.1 | R is ‘GNU S’, a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information. | https://www.r-project.org |
| relion/4.0.1 | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). | https://www2.mrc-lmb.cam.ac.uk/relion |
| repeatmasker/4.1.5 | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | https://www.repeatmasker.org |
| repeatmodeler/2.0.4 | RepeatModeler is a de-novo repeat family identification and modeling package. | https://github.com/Dfam-consortium/RepeatModeler |
| revbayes/1.2.2 | Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language. | https://revbayes.github.io |
| rsync/3.4.1 | An open source utility that provides fast incremental file transfer. | https://rsync.samba.org |
| samtools/1.17 samtools/1.19.2 | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format | https://www.htslib.org |
| scala/2.13.1 scala/2.13.14 | Scala is a general-purpose programming language providing support for functional programming and a strong static type system. Designed to be concise, many of Scala’s design decisions were designed to build from criticisms of Java. | https://www.scala-lang.org/ |
| scalasca/2.6.1 | Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks - in particular those concerning communication and synchronization - and offers guidance in exploring their causes. | https://www.scalasca.org |
| scorep/8.3 scorep/8.4 | The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. | https://www.vi-hps.org/projects/score-p |
| siesta/4.0.2 siesta/5.0.1 | SIESTA performs electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. | https://departments.icmab.es/leem/siesta/ |
| slepc/3.22.1 | Scalable Library for Eigenvalue Problem Computations. | https://slepc.upv.es |
| snakemake/7.22.0 snakemake/8.18.2 | Workflow management system to create reproducible and scalable data analyses. | https://snakemake.readthedocs.io/en |
| subread/2.0.6 | The Subread software package is a tool kit for processing next-gen sequencing data. | https://subread.sourceforge.net/ |
| tk/8.6.11 | Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI not only for Tcl, but for many other dynamic languages, and can produce rich, native applications that run unchanged across Windows, Mac OS X, Linux and more. | https://www.tcl.tk |
| transabyss/2.0.1 | de novo assembly of RNA-Seq data using ABySS | |
| ucx/1.18.0 | a communication library implementing high-performance messaging for MPI/PGAS frameworks | https://www.openucx.org |
| udunits/2.2.28 | Automated units conversion | https://www.unidata.ucar.edu/software/udunits |
| valgrind/3.20.0 valgrind/3.23.0 | An instrumentation framework for building dynamic analysis. | https://valgrind.org/ |
| vcftools/0.1.16 | VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. | https://vcftools.github.io/ |
| xtb/6.6.0 | Semiempirical extended tight binding program package | https://xtb-docs.readthedocs.org |