Modules avx512: Difference between revisions

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ACTC converts independent triangles into triangle strips or fans. Homepage: https://sourceforge.net/projects/actc URL: https://sourceforge.net/projects/actc<br /><br /><br /></div>

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| align="center" | bio

| align="center" | 1.3.0

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| align="center" | [https://projects.coin-or.org/ADOL-C adol-c]

| align="center" | [http://www.ansys.com ansys]

| align="center" | phys

| Documentation: [[Ansys]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. Homepage: http://www.ansys.com URL: http://www.ansys.com Keyword:phys<br /><br /><br /></div>

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| align="center" | [https://arrow.apache.org arrow]

| align="center" | tools

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Apache Arrow is a cross-language development platform for in-memory data. Homepage: https://arrow.apache.org URL: https://arrow.apache.org Compatible modules: python/3.12, python/3.11, python/3.10 Keyword:tools<br /><br /><br /></div>

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| align="center" | [https://www.comsol.com comsol]

| align="center" | phys

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. Homepage: https://www.comsol.com URL: https://www.comsol.com Keyword:phys<br /><br /><br /></div>

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| align="center" | -

| align="center" | 3.3.2, 3.3.8

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| align="center" | [https://ccb.jhu.edu/software/glimmerhmm glimmerhmm]

| align="center" | chem

| align="center" | 2020.6

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| align="center" | [https://www.cp2k.org/tools:gromacs gromacs-cp2k]

| align="center" | [https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ gromacs-ramd]

| align="center" | chem

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: GROMACS is a versatile package to perform molecular dynamics. This version has been modified to support RAMD, which is used to identify ligand exit routes from the buried binding pockets of receptors and investigate the mechanism of ligand dissociation. https://kbbox.h-its.org/toolbox/methods/molecular-simulation/random-acceleration-molecular-dynamics-ramd/ This is a GPU enabled build, containing both MPI and threadMPI binaries. Homepage: https://github.com/HITS-MCM/gromacs-ramd URL: https://github.com/HITS-MCM/gromacs-ramd Keyword:chem<br /><br /><br /></div>

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| align="center" | chem

| align="center" | 2021.7-0.5.1

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| align="center" | [https://www.gnu.org/software/gsl/ gsl]

| align="center" | io

| align="center" | 1.8.22, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.14.2

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| align="center" | [https://portal.hdfgroup.org/display/support hdf5-mpi]

| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan]

| align="center" | bio

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/ Keyword:bio<br /><br /><br /></div>

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| align="center" | [http://www.ebi.ac.uk/interpro/ interproscan_data]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: This module containes only InterProScan data part. InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/ URL: http://www.ebi.ac.uk/interpro/<br /><br /><br /></div>

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| align="center" | -

| align="center" | 1.1.0

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| align="center" | [https://git.osgeo.org/gitea/rttopo/librttopo librttopo-proj9]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. MCL has been applied in a number of different domains, mostly in bioinformatics. Homepage: http://micans.org/mcl/ URL: http://micans.org/mcl/ Keyword:math<br /><br /><br /></div>

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| align="center" | tools

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| align="center" | [https://grimme-lab.github.io/mctc-lib mctc-lib]

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Model Evaluation Tools (MET) is a highly configurable, state-of-the-art suite of verification tools designed for the verification and evaluation of numerical weather forecasts. Although MET was developed at the Developmental Testbed Center (DTC) to be used with the Weather Research and Forecasting (WRF) modeling system, the data formats and standards used allow MET to be run on the output of other modeling systems as well. Homepage: https://dtcenter.org/ URL: https://dtcenter.org/ Keyword:phys<br /><br /><br /></div>

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| align="center" | -

| align="center" | 1.0.2

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| align="center" | [https://bitbucket.org/berkeleylab/metabat metabat]

| align="center" | [https://mmseqs.com mmseqs2]

| align="center" | -

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: MMseqs2: ultra fast and sensitive search and clustering suite Homepage: https://mmseqs.com URL: https://mmseqs.com<br /><br /><br /></div>

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| align="center" | math

| align="center" | 2.6.1, 2.6.2, 2.7.0, 2.7.1

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| align="center" | [https://nodejs.org nodejs]

| align="center" | chem

| align="center" | 3.1.1

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| align="center" | [https://openbabel.org openbabel-omp]

| align="center" | [https://www.openfoam.com/ openfoam]

| align="center" | phys

| Documentation: [[OpenFOAM]]<div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: https://www.openfoam.com/ URL: https://www.openfoam.com/ Keyword:phys<br /><br /><br /></div>

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| align="center" | [http://www.openmx-square.org/ openmx]

| align="center" | chem

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: OpenMX (Open source package for Material eXplorer) is a software package for nano-scale material simulations based on density functional theories (DFT), norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. The methods and algorithms used in OpenMX and their implementation are carefully designed for the realization of large-scale ab initio electronic structure calculations on parallel computers based on the MPI or MPI/OpenMP hybrid parallelism. Homepage: http://www.openmx-square.org/ URL: http://www.openmx-square.org/ Keyword:chem<br /><br /><br /></div>

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| align="center" | [https://sites.astro.caltech.edu/~tjp/pgplot/ pgplot]

| align="center" | vis

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, device-independent graphics package for making simple scientific graphs. It is intended for making graphical images of publication quality with minimum effort on the part of the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time. Homepage: https://sites.astro.caltech.edu/~tjp/pgplot/ URL: https://sites.astro.caltech.edu/~tjp/pgplot/ Keyword:vis<br /><br /><br /></div>

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| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: Platanus-allee is an assembler derived from Platanus assembler, however, it was developed with another concept. Platanus-allee tries to construct each haplotype sequence from the beginning and pair them as homologous chromosomes, while Platanus constructs consensus sequence of homologous chromosomes at first and tries to split into each haplotype sequence. Therefore, Platanus-allee marks better performance for highly heterozygous species genome or highly diverged genomic regions. Homepage: http://platanus.bio.titech.ac.jp/ URL: http://platanus.bio.titech.ac.jp/<br /><br /><br /></div>

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| align="center" | bio

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| align="center" | [http://plplot.sourceforge.net plplot]

| align="center" | [http://www.portaudio.com/ portaudio]

| align="center" | -

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| align="center" | [https://www.postgresql.org/ postgresql]

| align="center" | [https://www.htslib.org/ samtools]

| align="center" | bio

| <div class="mw-collapsible mw-collapsed" style="white-space: pre-line;"><br />Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: https://www.htslib.org/ URL: https://www.htslib.org/ Keyword:bio<br /><br /><br /></div>

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| align="center" | -

| align="center" | 8.6.1.6

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| align="center" | [https://github.com/tesseract-ocr/tesseract tesseract]

| align="center" | -

| align="center" | 0.13.0, 0.14.2, 0.16.0, 0.18.1, 0.19.0

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| align="center" | [http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm tmhmm]