Grete GCC 13 Modules
Warning
This software revision is a available for testing on a small number of AlmaLinux 10 test nodes. It cannot be used on the main HPC system. It should not be used for production workloads yet!
It is required to load the appropriate compiler and MPI modules before any of the modules become visible (hierarchical module system):
module load gcc/13.4.0
module load openmpi/5.0.10Tip
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/26.07/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 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/5.3 | AMD Optimized BLIS. | https://www.amd.com/en/developer/aocl/blis.html |
| amdfftw/5.3 | 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/5.3 | 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/5.3 | 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 |
| autodock-vina/1.2.7 | AutoDock Vina is an open-source program for doing molecular docking | http://vina.scripps.edu/ |
| beast2/2.7.7 | BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. | http://beast2.org/ |
| bismark/0.25.1 | A tool to map bisulfite converted sequence reads and determine cytosine methylation states | https://www.bioinformatics.babraham.ac.uk/projects/bismark |
| blast-plus/2.17.0 | Basic Local Alignment Search Tool. | https://blast.ncbi.nlm.nih.gov/ |
| 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/ |
| bowtie2/2.5.4 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| calculix-adapter/2.20.1 | preCICE adapter for CalculiX - provides the ccx_preCICE coupled solver executable. | https://precice.org/adapter-calculix-get-adapter.html |
| cdo/2.5.4 cdo/2.6.2 | CDO is a collection of command line operators to manipulate and analyse Climate and NWP model Data. | https://code.mpimet.mpg.de/projects/cdo |
| 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/ |
| 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 |
| cube/4.9 | Cube the profile viewer for Score-P and Scalasca profiles. It displays a multi-dimensional performance space consisting of the dimensions: - performance metric - call path - system resource | https://www.scalasca.org/software/cube-4.x/download.html |
| diamond/2.1.10 | 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 |
| eccodes/2.47.0 | 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/7.1 ffmpeg/8.1 | FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. | https://ffmpeg.org |
| fftw/3.3.11 fftw/3.3.11-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 |
| fleur/7.2 fleur/8.1 | 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 |
| gdal/3.10.0 gdal/3.13.1 | GDAL: Geospatial Data Abstraction Library. | https://www.gdal.org/ |
| gdb/16.2 | 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/6.3.0 | 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). | https://github.com/j-m-adams/GrADS |
| gromacs/2024.6 gromacs/2025.0-plumed gromacs/2025.3 gromacs/2026.1 | 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/2.8 | 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 |
| hdf5/1.14.6 | 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 |
| hpcc/1.5.0 | HPC Challenge is a benchmark suite that measures a range memory access patterns. The HPC Challenge benchmark consists of basically 7 tests: 1) HPL - the Linpack TPP benchmark which measures the floating point rate of execution for solving a linear system of equations. 2) DGEMM - measures the floating point rate of execution of double precision real matrix-matrix multiplication. 3) STREAM - a simple synthetic benchmark program that measures sustainable memory bandwidth (in GB/s) and the corresponding computation rate for simple vector kernel. 4) PTRANS (parallel matrix transpose) - exercises the communications where pairs of processors communicate with each other simultaneously. It is a useful test of the total communications capacity of the network. 5) RandomAccess - measures the rate of integer random updates of memory (GUPS). 6) FFT - measures the floating point rate of execution of double precision complex one-dimensional Discrete Fourier Transform (DFT). 7) Communication bandwidth and latency - a set of tests to measure latency and bandwidth of a number of simultaneous communication patterns; based on b_eff (effective bandwidth benchmark). | https://icl.cs.utk.edu/hpcc |
| hpcg/3.1 | HPCG is a software package that performs a fixed number of multigrid preconditioned (using a symmetric Gauss-Seidel smoother) conjugate gradient (PCG) iterations using double precision (64 bit) floating point values. | https://www.hpcg-benchmark.org |
| imagemagick/7.1.1-39 | ImageMagick is a software suite to create, edit, compose, or convert bitmap images. | https://www.imagemagick.org |
| intel-mpi-benchmarks/2021.7 | Intel MPI Benchmarks provides a set of elementary benchmarks that conform to MPI-1, MPI-2, and MPI-3 standard. You can run all of the supported benchmarks, or a subset specified in the command line using one executable file. Use command-line parameters to specify various settings, such as time measurement, message lengths, and selection of communicators. | https://software.intel.com/en-us/articles/intel-mpi-benchmarks |
| intel-oneapi-advisor/2025.5.0 | 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/2025.10.1 | 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/2025.3.0 | 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/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. LICENSE INFORMATION: By downloading and using this software, you agree to the terms and conditions of the software license agreements at intel.ly/393CijO. | https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html |
| intel-oneapi-tbb/2022.3.1 | 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/2025.10.1 | 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 |
| 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/ |
| libffi/3.5.2 | The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run time. | https://sourceware.org/libffi/ |
| 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/ |
| mpfr/4.2.2 | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. | https://www.mpfr.org/ |
| mpifileutils/0.12 | 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 |
| muscle5/5.1.0 | MUSCLE is widely-used software for making multiple alignments of biological sequences. | https://drive5.com/muscle5/ |
| must/1.11.2 | 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/3.0.2-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/5.3.4 | 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/4.10.0 netcdf-c/4.9.3 | 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/4.6.2 | 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 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/3.12.1 | 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/2.2.3 | ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines | https://www.netlib.org/scalapack/ |
| nvbandwidth/v0.9 | nvbandwidth: A tool for bandwidth measurements on NVIDIA GPUs. | |
| octave/10.3.0 octave/11.1.0 | GNU Octave is a high-level language, primarily intended for numerical computations. | https://www.gnu.org/software/octave/ |
| of-precice/1.3.1 | preCICE adapter for OpenFOAM | https://precice.org/ |
| openblas/0.3.33 | OpenBLAS: An optimized BLAS library | https://www.openblas.net |
| opencl-headers/3.0 | Bundled OpenCL (Open Computing Language) header files | https://www.khronos.org/registry/OpenCL/ |
| 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/ |
| openfast/4.2.1 | Wind turbine simulation package from NREL | https://openfast.readthedocs.io/ |
| openfoam/2412 openfoam/2512 | 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/12 | 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/4.1.8 openmpi/5.0.10 | An open source Message Passing Interface implementation. | https://www.open-mpi.org |
| osu-micro-benchmarks/7.5.2 | 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/ |
| pbmpi/1.9 | A Bayesian software for phylogenetic reconstruction using mixture models | https://github.com/bayesiancook/pbmpi |
| petsc/3.25.2-complex petsc/3.25.2-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 |
| plink/1.9-beta7.7 | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. | https://www.cog-genomics.org/plink/1.9/ |
| plink2/2.0.0-a6.32 | PLINK2: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. | https://www.cog-genomics.org/plink/2.0/ |
| 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/ |
| quantum-espresso/7.5 | 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/4.4.3 r/4.5.3 | 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 |
| raxml-ng/1.1.0 raxml-ng/1.2.2 | RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. | https://github.com/amkozlov/raxml-ng/wiki |
| repeatmasker/4.1.5 repeatmasker/4.2.3 | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | https://www.repeatmasker.org |
| revbayes/1.2.2 | Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language. | https://revbayes.github.io |
| slepc/3.25.1 | Scalable Library for Eigenvalue Problem Computations. | https://slepc.upv.es |
| stress/1.0.4 | stress is a deliberately simple workload generator for POSIX systems. It imposes a configurable amount of CPU, memory, I/O, and disk stress on the system. It is written in C, and is free software licensed under the GPLv2. | https://github.com/javiroman/system-stress |
| stress-ng/0.19.04 | stress-ng will stress test a computer system in various selectable ways. It was designed to exercise various physical subsystems of a computer as well as the various operating system kernel interfaces. | https://github.com/ColinIanKing/stress-ng |
| subread/2.1.1 | The Subread software package is a tool kit for processing next-gen sequencing data. | https://subread.sourceforge.net/ |
| tkdiff/6.0 | TkDiff is a graphical front end to the diff program. It provides a side-by-side view of the differences between two text files, along with several innovative features such as diff bookmarks, a graphical map of differences for quick navigation, and a facility for slicing diff regions to achieve exactly the merge output desired. | https://tkdiff.sourceforge.io/ |
| udunits/2.2.28 | Automated units conversion | https://www.unidata.ucar.edu/software/udunits |
| valgrind/3.27.1 | An instrumentation framework for building dynamic analysis. | https://valgrind.org/ |
| xtb/6.6.0 | Semiempirical extended tight binding program package | https://xtb-docs.readthedocs.org |
| yambo/5.2.4 yambo/5.2.4-dp | Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. | https://www.yambo-code.org/ |
| zlib-ng/2.3.3 | zlib replacement with optimizations for next generation systems. | https://github.com/zlib-ng/zlib-ng |