Liste des applications installées sur HPC-MARWAN

Nom Modules Description
  • geant4/gcc/64/4.10.01.p03
  • geant4/gcc/64/4.10.04.p02
  • geant4/gcc/64/4.10.05
  • geant4/gcc/64/mt-4.10.02.p03
Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
  • gate/gcc/64/8.1.p01
  • gate/gcc/64/8.2
GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to numerical simulations in medical imaging and radiotherapy. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), Computed Tomography (CT), Optical Imaging (Bioluminescence and Fluorescence) and Radiotherapy experiments. Using an easy-to-learn macro mechanism to configurate simple or highly sophisticated experimental settings, GATE now plays a key role in the design of new medical imaging devices, in the optimization of acquisition protocols and in the development and assessment of image reconstruction algorithms and correction techniques. It can also be used for dose calculation in radiotherapy experiments.
cp2kcp2k/ssmp/6.1CP2K 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. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, ...), and classical force fields (AMBER, CHARMM, ...). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method. (Detailed overview of features.)
lammpslammps/openmpi/gcc/64/12Dec18LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
  • qe/intel/6.4
  • qe/openmpi/gcc/64/6.3
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 pseudopotential
AutoDock Vinaautodock_vina/gcc/64/1.1.2AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute.
GROMACSgromacs/intel/64/2018.3/GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
ORCAorca/openmpi/"ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single and multireference correlated ab initio methods. It can also treat environmental and relativistic effects."
AkaiKKRAkaiKKR/intel/010AkaiKKR (MACHIKANEYAMA) is a program package used for first-principles calculation of electronic structures of metals, semiconductors and compounds, in the framework of the local density approximation or generalized gradient approximation (LDA/GGA) of the density functional theory.
Abinitabinit/intel/8.10.2ABINIT is a software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials. Starting from the quantum equations of density functional theory, you can build up to advanced applications with perturbation theories based on DFT, and many-body Green's functions
Nom Modules Description
SCILABscilab/bin/64/6.0.1SCILAB est un logiciel libre de calcul numérique multi-plateforme fournissant un environnement de calcul pour des applications scientifiques. Il possède un langage de programmation orienté calcul numérique de haut niveau. Il peut être utilisé pour le traitement du signal, l'analyse statistique, le traitement d'images, les simulations de dynamique des fluides, l'optimisation numérique, et la modélisation et simulation de systèmes dynamiques explicites et implicites
  • fftw2/openmpi/gcc/64/float/2.1.5
  • fftw2/openmpi/gcc/64/double/2.1.5
  • fftw3/openmpi/gcc/64/3.3.7
  • fftw3/intel/3.3.8
FFTW est une bibliothèque logicielle calculant des transformées de Fourier discrètes, développée par Matteo Frigo et Steven G. Johnson au Massachusetts Institute of Technology. FFTW est utilisé par MATLAB pour les calculs de transformées de Fourier.
Normaliznormaliz/3.6.2Normaliz is an open source tool for computations in affine monoids, vector configurations, lattice polytopes, and rational cones. The variant QNormaliz now computes algebraic polyhedra, i.e., polyhedra defined over real algebraic extensions of Q.
LAPACKlapack/gcc/64/3.8.0LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. The associated matrix factorizations (LU, Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are related computations such as reordering of the Schur factorizations and estimating condition numbers. Dense and banded matrices are handled, but not general sparse matrices. In all areas, similar functionality is provided for real and complex matrices, in both single and double precision.
BLASblas/gcc/64/3.8.0The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations. The Level 1 BLAS perform scalar, vector and vector-vector operations, the Level 2 BLAS perform matrix-vector operations, and the Level 3 BLAS perform matrix-matrix operations. Because the BLAS are efficient, portable, and widely available, they are commonly used in the development of high quality linear algebra software, LAPACK for example.
OpenBLASopenblas/dynamic/0.2.20OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version
BLACSblacs/openmpi/gcc/64he BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms.
Eigen3cm-eigen3/034b6c3e1017Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
  • acml/gcc/64/5.3.1
  • acml/gcc-int64/64/5.3.
  • acml/gcc-int64/mp/64/5.3.1
  • acml/gcc/mp/64/5.3.1
  • acml/gcc/fma4/5.3.1
  • acml/gcc-int64/fma4/5.3.1
  • acml/gcc-int64/mp/fma4/5.3.1
  • acml/gcc/mp/fma4/5.3.1
"ACML provides a free set of thoroughly optimized and threaded math routines for HPC,scientific, engineering and related compute-intensive applications. ACML is ideal for weather modeling, computational fluid dynamics, financial analysis, oil and gas applications and more.
ELPAelpa/intel/2018.05.001 elpa/intel/2018.11.001" Eigenvalue SoLvers for Petaflop-Applications (ELPA)The publicly available ELPA library provides highly efficient and highly scalable direct eigensolvers for symmetric matrices.Though especially designed for use for PetaFlop/s applications solving large problem sizes on massively parallel supercomputers, ELPA eigensolvers have proven to be also very efficient for smaller matrices."
HPLhpl/2.2HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.
Nom Modules Description
Bowtie2bowtie2/gcc/64/ is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation. Bowtie indexes the genome with an FM Index to keep its memory footprint small: for the human genome, the index is typically about 2.2 GB (for unpaired alignment) or 2.9 GB (for paired-end or colorspace alignment). Multiple processors can be used simultaneously to achieve greater alignment speed. Bowtie can also output alignments in the standard SAM format, allowing Bowtie to interoperate with other tools supporting SAM, including the SAMtools consensus, SNP, and indel callers. Bowtie runs on the command line under Windows, Mac OS X, Linux, and Solaris.
Blastblastn/gcc/64/2.7.1+The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
ORNAORNA/gcc/64/0.4ORNA is a read normalization software developed in spirit of Diginorm. ORNA is computationally inexpensive and it guarantees the preservation of all kmers from the original dataset. It can be used if the user has a high coverage dataset but does not have enough computational power (in particular memory but also limited time) in order to conduct a de novo assembly, because it removes the redundancy in your data. It can also be used to merge many sequencing datasets. The user must be aware that using ORNA (or in that case any normalization software) might have a significant impact on the assemblies produced as it is highly dependent on the dataset.
SRA toolkit sratoolkit/gcc/64/2.9.3The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Simka simka/gcc/64/1.4.0Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.
SpadesSPAdes/3.13.0SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines
Metaphlan2metaphlan/2.7.7MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
Prodigalprodigal/gcc/64/2.6.3Prodigal is a protein-coding gene prediction software tool for bacterial and archaeal genomes. The acronym stands for PROkaryotic DYnamic Programming Genefinding ALgorithm.
Megahitmegahit/gcc/64/1.1.4 MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
MetaBat2metabat2/2.12.1-0MetaBAT2 takes a metagenome assembly and the reads that produced the assembly and organizes the contigs into putative genomes, called "bins".
Checkm checkm/1.0.12CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree.
CD-hit cd-hit/gcc/64CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses.
DEMIC DEMIC/1.0.2DEMIC is a computational tool for comparing bacterial growth rates between metagenomic samples, based on inferred relative distances of contigs from replication origin according to their coverages.
Fastqcfastqc/0.11.8FastQC is a program designed to spot potential problems in high througput sequencing datasets. It runs a set of analyses on one or more raw sequence files in fastq or bam format and produces a report which summarises the results.
Sickle sickle/gcc/64/1.33sickle - A windowed adaptive trimming tool for FASTQ files using quality
Krona krona/2.7Krona is a flexible tool for exploring the relative proportions of hierarchical data, such as metagenomic classifications, using a radial, space-filling display. It is implemented using HTML5 and JavaScript, allowing charts to be explored locally or served over the Internet, requiring only a current version of any major web browser. Krona charts can be created using an Excel template or from common bioinformatics formats using the provided conversion scripts. Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats.
samtools samtools/gcc/64/1.9Tools (written in C using htslib) for manipulating next-generation sequencing data
BioPerlBioPerl/1.007002BioPerl is a project for development of free and open source Perl tools for computational molecular biology. For example, it includes classes for biological sequences, readers of multiple formats, sequence alignments, database searching objects, and interfaces to multiple programs such as EMBOSS, ClustalW, and BLAST.
HMMERhmmer/gcc/64/3.2.1HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
PROKKAprokka/1.13.3Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.
pplacerpplacer/gcc/64/1.1Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
HTSlib htslib/gcc/64/1.9HTSlib is a C library used for reading and writing high-throughput sequencing data. HTSlib is the core library used by SAMtools. HTSlib also provides the bgzip, htsfile, and tabix utilities.
Visualize results with Matplotlib, Bokeh, Datashader, and Holoviews
Nom Modules Description
GCCgcc/7.2.2The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, Go, and D, as well as libraries for these languages (libstdc++,...). GCC was originally written as the compiler for the GNU operating system. The GNU system was developed to be 100% free software, free in the sense that it respects the user's freedom.
RR/gcc/64/3.5.1R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.
  • root/gcc/64/6.08.02
  • root/gcc/64/6.14.02
  • root/gcc/64/6.16.00
Root A modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. It is mainly written in C++ but integrated with other languages such as Python and R.
Intel® Parallel Studio XE
  • ips/2017
  • ips/2019
Intel Parallel Studio est un logiciel propriétaire développé par Intel. Il permet de développer des logiciels en C++ et Fortran. Son avantage est qu'il renforce les performances des logiciels tout en demandant le moins d’effort sur les processeurs.
CUDA toolkit
  • cuda91/blas
  • cuda91/fft
  • cuda91/nsight
  • cuda91/profiler
  • cuda91/toolkit
The NVIDIA® CUDA® Toolkit provides a development environment for creating high performance GPU-accelerated applications. With the CUDA Toolkit, you can develop, optimize and deploy your applications on GPU-accelerated embedded systems, desktop workstations, enterprise data centers, cloud-based platforms and HPC supercomputers. The toolkit includes GPU-accelerated libraries, debugging and optimization tools, a C/C++ compiler and a runtime library to deploy your application.
Anacondaanaconda2/4.5.12The open-source Anaconda Distribution is the easiest way to perform Python/R data science and machine learning on Linux, Windows, and Mac OS X. it is the industry standard for developing, testing, and training on a single machine, enabling individual data scientists to: • Quickly download 1,500+ Python/R data science packages • Manage libraries, dependencies, and environments with Conda • Develop and train machine learning and deep learning models with scikit-learn, TensorFlow, and Theano • Analyze data with scalability and performance with Dask, NumPy, pandas, and Numba
ArrayFireArrayFire/3.6.2ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices.
scalapackscalapack/openmpi/gcc/64/2.0.2ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. ScaLAPACK solves dense and banded linear systems, least squares problems, eigenvalue problems, and singular value problems. 
  • openmpi/gcc/64/1.10.7
  • openmpi/intel-opa/gcc-cuda-hfi/64/1.10.4
  • openmpi/gcc/64/2.1.2
  • openmpi/intel-opa/gcc-hfi/64/1.10.4
  • openmpi/intel/3.1.2
  • openmpi/intel-opa/gcc-hfi/64/2.1.2
  • openmpi/intel-opa/gcc/64/1.10.4
  • openmpi/intel-opa/intel-hfi/64/1.10.4
    The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.
    Bisonbison/gcc/64/3.2.1Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. As an experimental feature, Bison can also generate IELR(1) or canonical LR(1) parser tables. Once you are proficient with Bison, you can use it to develop a wide range of language parsers, from those used in simple desk calculators to complex programming languages
    Boostboost/gcc/64/1.68.0The Boost project provides free peer-reviewed portable C++ source libraries.
    Bonnie++bonnie++/1.97.3 Bonnie++ is a toolkit for testing hard drive and file system performance.
    Global Arraysglobalarrays/openmpi/gcc/64/5.6.1Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model. It provides primitives for one-sided communication (Get, Put, Accumulate) and Atomic Operations (read increment). It supports blocking and non-blocking primtives, and supports location consistency.
    Golanggolang/1.11.5Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
    • cmake/gcc/64/3.11.0
    • cmake/gcc/64/3.12.3
    CMake is an open-source, cross-platform family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files, and generate native makefiles and workspaces that can be used in the compiler environment of your choice.
    Singularitysingularity/3.0.3Singularity is an open source container platform designed to be simple, fast, and secure. Singularity is optimized for EPC and HPC workloads, allowing untrusted users to run untrusted containers in a trusted way.
    Xerces-C++xerces-c/gcc/64/3.2.2Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.
    Readlinereadline/gcc/64/7.0The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
    • netcdf/gcc/64/4.5.0
    • netcdf/intel/4.6.3
    • netcdf-fortran/intel/4.4.4
    NetCDF (Network Common Data Form) is a set of interfaces for array-oriented data access and a freely distributed collection of data access libraries for C, Fortran, C++, Java, and other languages. The netCDF libraries support a machine-independent format for representing scientific data. Together, the interfaces, libraries, and format support the creation, access, and sharing of scientific data.
    HDF5hdf5/1.10.1High-performance data management and storage suite Utilize the HDF5 high performance data software library and file format to manage, process, and store your heterogeneous data. HDF5 is built for fast I/O processing and storage.
    hwlochwloc/1.11.8The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs.
    MPICHmpich/ge/gcc/64/3.2.1MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
    mpiexecmpiexec/0.84_432mpiexec - Execute serial and parallel jobs in Open MPI. oshrun, shmemrun - Execute serial and parallel jobs in Open SHMEM.
    • mvapich2/intel-opa/gcc/64/2.2
    • mvapich2/gcc/64/2.3b
    • mvapich2/intel-opa/gcc-hfi/64
    • mvapich2/intel-opa/intel-hfi/64/2.2
    • mvapich2/intel-opa/gcc-hfi/64/2.2
    MVAPICH, also known as MVAPICH2, is a BSD-licensed implementation of the MPI standard developed by Ohio State University.[1][2] MVAPICH comes in a number of flavors: • MVAPICH2, with support for InfiniBand, iWARP, RoCE, and Intel Omni-Path< • MVAPICH2-X, with support for PGAS and OpenSHMEM • MVAPICH2-GDR, with support for InfiniBand and NVIDIA CUDA GPUs • MVAPICH2-MIC, with support for InfiniBand and Intel MIC • MVAPICH2-Virt, with support for InfiniBand and SR-IOV • MVAPICH2-EA, which is energy-aware and supports InfiniBand, iWARP, and RoCE"
    qtqt/gcc/64/4.8.7Qt : une API orientée objet et développée en C++, conjointement par The Qt Company et Qt Project. Qt offre des composants d'interface graphique, d'accès aux données, de connexions réseaux, de gestion des fils d'exécution, d'analyse XML,
    ITKITK/gcc/64/4.13.1ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis.  Developed through extreme programming methodologies, ITK employs leading-edge algorithms for registering and segmenting multidimensional data.
    Nom Modules Description
    Anacondaanaconda2/4.5.12The open-source Anaconda Distribution is the easiest way to perform Python/R data science and machine learning on Linux, Windows, and Mac OS X. it is the industry standard for developing, testing, and training on a single machine, enabling individual data scientists to: • Quickly download 1,500+ Python/R data science packages • Manage libraries, dependencies, and environments with Conda • Develop and train machine learning and deep learning models with scikit-learn, TensorFlow, and Theano • Analyze data with scalability and performance with Dask, NumPy, pandas, and Numba • Visualize results with Matplotlib, Bokeh, Datashader, and Holoviews
    cuDNNcudnn/9.0_v7.4.2.24The NVIDIA CUDA® Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. cuDNN provides highly tuned implementations for standard routines such as forward and backward convolution, pooling, normalization, and activation layers.
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