Emmy Intel OneAPI Modules with OpenMPI
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 intel-oneapi-compilers/2025.3.2
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 Intel Cascadelake or Intel Sapphirerapids).
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 |
|---|---|---|
| aria2/1.37.0 | An ultra fast download utility | https://aria2.github.io |
| 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/ |
| bedops/2.4.42 | 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 |
| 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 |
| 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 |
| 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/ |
| 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 |
| curl/8.21.0 | cURL is an open source command line tool and library for transferring data with URL syntax | https://curl.se/ |
| ffmpeg/6.1.1 | FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. | https://ffmpeg.org |
| fftw/3.3.11 | 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 |
| flex/2.6.4 | Flex is a tool for generating scanners. | https://github.com/westes/flex |
| fribidi/1.0.12 | GNU FriBidi: The Free Implementation of the Unicode Bidirectional Algorithm. | https://github.com/fribidi/fribidi |
| gdal/3.13.1 | GDAL: Geospatial Data Abstraction Library. | https://www.gdal.org/ |
| 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 |
| 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 hdf5/1.14.6-precise-fp | 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 |
| hwloc/2.13.0 | The Hardware Locality (hwloc) software project. | https://www.open-mpi.org/projects/hwloc/ |
| 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/2025.3.1 | 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-mpi/2021.14.2 intel-oneapi-mpi/2021.16.2 intel-oneapi-mpi/2021.17.2 intel-oneapi-mpi/2021.17.2-external-libfabric | Intel MPI Library is a multifabric message-passing library that implements the open-source MPICH specification. Use the library to create, maintain, and test advanced, complex applications that perform better on high-performance computing (HPC) clusters based on Intel processors. | https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/mpi-library.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 |
| jellyfish/2.3.1 | JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. | https://www.cbcb.umd.edu/software/jellyfish/ |
| kraken2/2.1.2 kraken2/2.17.1 | Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. | https://ccb.jhu.edu/software/kraken2/ |
| libaec/1.1.7 | 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/dkrz-sw/libaec |
| libfabric/2.6.0 | The Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications. | https://libfabric.org/ |
| 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/ |
| libpng/1.6.47 | libpng is the official PNG reference library. | http://www.libpng.org/pub/png/libpng.html |
| libwebp/1.4.0 | WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster. | https://developers.google.com/speed/webp/ |
| libxc/7.1.2 | Libxc is a library of exchange-correlation functionals for density-functional theory. | https://libxc.gitlab.io/ |
| libxml2/2.15.3 | Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License. | https://gitlab.gnome.org/GNOME/libxml2/-/wikis/home |
| metis/5.1.0 | METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. | https://github.com/KarypisLab/METIS |
| 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/ |
| netcdf-c/4.10.0 netcdf-c/4.10.0-precise-fp netcdf-c/4.9.3 netcdf-c/4.9.3-precise-fp | 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-fortran/4.6.2-precise-fp | 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 |
| 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/ |
| numactl/2.0.19 | NUMA support for Linux | https://github.com/numactl/numactl |
| 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 |
| openblas/0.3.33 | OpenBLAS: An optimized BLAS library | https://www.openblas.net |
| opencl-c-headers/2025.07.22 | OpenCL (Open Computing Language) C header files | https://www.khronos.org/registry/OpenCL/ |
| opencl-clhpp/2025.07.22 | 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/ |
| 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/ |
| 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/ |
| pmix/5.0.10 | The Process Management Interface (PMI) has been used for quite some time as a means of exchanging wireup information needed for interprocess communication. However, meeting the significant orchestration challenges presented by exascale systems requires that the process-to-system interface evolve to permit a tighter integration between the different components of the parallel application and existing and future SMS solutions. | https://openpmix.github.io/ |
| proj/9.7.0 | 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/ |
| prrte/3.0.13 | PRRTE is the Reference RunTime Environment implementation for PMIx. It is capable of operating within a host SMS. The reference RTE therefore provides an easy way of exploring PMIx capabilities and testing PMIx-based applications outside of a PMIx-enabled environment. | https://pmix.org |
| rsync/3.4.4 | An open source utility that provides fast incremental file transfer. | https://rsync.samba.org |
| samtools/1.23.1 | 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 |
| 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/ |
| tcl/8.6.17 | Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Open source and business-friendly, Tcl is a mature yet evolving language that is truly cross platform, easily deployed and highly extensible. | https://www.tcl.tk/ |
| tk/8.6.17 | 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 |
| 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/ |
| ucx/1.20.1 | 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 |
| vcftools/0.1.17 | 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/ |
| xpmem/2.7.4 | XPMEM is a Linux kernel module that enables a process to map the memory of another process into its virtual address space. | https://github.com/openucx/xpmem |
| zlib-ng/2.3.3 | zlib replacement with optimizations for next generation systems. | https://github.com/zlib-ng/zlib-ng |