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Applications glossary for Merlin service

 

Applications on Merlin

Compilers on Merlin

Libraries on Merlin

 

Applications on Merlin

 

Abaqus: a software for engineering simulation

Abaqus/Standard employs solution technology ideal for static and low-speed dynamic events where highly accurate stress solutions are critically important. Examples include sealing pressure in a gasket joint, steady-state rolling of a tire, or crack propagation in a composite airplane fuselage. Within a single simulation, it is possible to analyze a model both in the time and frequency domain. For example, one may start by performing a non-linear engine cover mounting analysis including sophisticated gasket mechanics. Following the mounting analysis, the pre-stressed natural frequencies of the cover can be extracted, or the frequency domain mechanical and acoustic response of the pre-stressed cover to engine induced vibrations can be examined. Abaqus/Standard is supported within the Abaqus/CAE modeling environment for all common pre- and post-processing needs.

Version: 6.9.3

License: Commercial

Module: apps/abaqus/6.9.3

 

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BEAST: a software to construct phylogenetic trees

BEAST is a cross-platform program for Bayesian MCMC analysis 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. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

 

Version: 1.5.4

License: Free

Module: apps/beast/1.5.4

 

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BLAST: a software to search for genetic sequences

BLAST® (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. The BLAST programs have been designed for speed, with a minimal sacrifice of sensitivity to distant sequence relationships. The scores assigned in a BLAST search have a well-defined statistical interpretation, making real matches easier to distinguish from random background hits. BLAST uses a heuristic algorithm that seeks local as opposed to global alignments and is therefore able to detect relationships among sequences that share only isolated regions of similarity (Altschul et al. 1990).

 

Version: 2.2.18

Version: 2.2.19

Version: 2.2.20

Version: 2.2.22

Version: 2.2.23

License: Free

Module: apps/blast/2.2.18

Module: apps/blast/2.2.19

Module: apps/blast/2.2.20

Module: apps/blast/2.2.22

Module: apps/blast/2.2.23

 

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Crystal06: a computational tool for solid state chemistry and physics

 CRYSTAL is a general-purpose program for the study of crystalline solids, and the first which has been distributed publicly. The first version was released in 1988 and then five next versions have followed: CRYSTAL92, CRYSTAL95, CRYSTAL98, CRYSTAL03 and CRYSTAL06.  

The CRYSTAL program computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid approximations. The Bloch functions of the periodic systems are expanded as linear combinations of atom centred Gaussian functions. Powerful screening techniques are used to exploit real space locality.  Restricted (Closed Shell) and Unrestricted (Spin-polarized) calculations can be performed with all-electron and valence-only basis sets with effective core pseudo-potentials.

 

Version: 102

License: Free

Module: apps/crystal06/102

 

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 DL_POLY: a molecular simulation package

 DL_POLY is a general purpose serial and parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov. The original package was developed by the Molecular Simulation Group (now part of the Computational Chemistry Group, MSG) at Daresbury Laboratory under the auspices of the Engineering and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative Computational Project for the Computer Simulation of Condensed Phases ( CCP5). Later developments were also supported by the Natural Environment Research Council through the eMinerals project. 

The package is the property of the Central Laboratory of the Research Councils.

 

Version: 2.20

Version: 3.10

License: Free

Module: apps/dl_poly/2.20

Module: apps/dl_poly/3.10

  

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EIGENSOFT: a software for population genetics

 The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker's variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

 

Version: 2.0

License: Free

Module: apps/eigensoft/2.0

 

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 EnergyPlus: modelling heat flow in buildings

 EnergyPlus models heating, cooling, lighting, ventilating, and other energy flows as well as water in buildings. While originally based on the most popular features and capabilities of BLAST and DOE-2, EnergyPlus includes many innovative simulation capabilities such as time steps of less than an hour, modular systems and plant integrated with heat balance-based zone simulation, multizone air flow, thermal comfort, water use, natural ventilation, and photovoltaic systems.

 

Version: 4.0.0

Version: 5.0.0

License: Free

Module: apps/energyplus/4.0.0

Module: apps/energyplus/5.0.0

 

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 FEBio: a finite element solver for biomechanics

 FEBio is a nonlinear finite element solver that is specifically designed for biomechanical applications. It offers modeling scenarios, constitutive models and boundary conditions that are relevant to many research areas in biomechanics. All features can be used together seamlessly, giving the user a powerful tool for solving 3D problems in computational biomechanics.  The software is open-source, and pre-compiled executables for Windows, OS-X and Linux platforms are available.  FEBio supports two analysis types, namely quasi-static and dynamic. In a quasi-static analysis, the (quasi-) static response of the system is sought and the effects of inertia are ignored. In the presence of biphasic materials, a coupled solid-fluid problem is solved. In a dynamic analysis, the inertial effects are included in the governing equations to calculate the time dependent response of the system.

 

Version: 1.2

License: Free

Module: apps/FEBio/1.2

 

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GAMESS: ab initio quantum chemistry package

GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. 

Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modelled by the discrete Effective Fragment potentials, or continuum models such as the polarizable Continuum Model. Numerous relativistic computations are available, including third order Douglas-Kroll scalar corrections, and various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments. Nuclear wavefunctions can also be computed, in VSCF, or with explicit treatment of nuclear orbitals by the NEO code.

Version: 20100809

License: Free

Module: apps/gamess/20100809

 

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Gaussian: electronic structure modelling

 Gaussian 09 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling. Gaussian 09 is licensed for a wide variety of computer systems. All versions of Gaussian 09 contain every scientific/modelling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience.

Version: 03e01

License: Commercial

Module: apps/gaussian/03e01

 

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GROMACS: a molecular dynamics package

 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. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the non-bonded interactions (which usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. GROMACS supports all the usual algorithms you expect from a modern molecular dynamics implementation, (check the online reference or manual for details), but there are also quite a few features that make it stand out from the competition.

Version: 4.0.3

License: Free

Module: apps/gromacs/4.0.3

 

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GSview: an application to view postscript files

GSview is a graphical interface for Ghostscript. Ghostscript is an interpreter for the PostScript page description language used by laser printers. For documents following the Adobe PostScript Document Structuring Conventions, GSview allows selected pages to be viewed or printed. GSview requires Ghostscript. GSview is available for Windows, OS/2 and Linux.

Version: 4.9

License: Free

Module: apps/gsview/4.9

 

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IMa2: generating posterior probabilities for complex demographic models

The program implements a method for generating posterior probabilities for complex demographic population genetic models. IMa2 works similarly to the older IMa program, with some important additions. IMa2 can handle data and implement a model for multiple populations (for numbers of sampled populations between one and ten) – not just two populations (as was the case with the original IM and IMa programs). The method for multiple populations is described in two papers (Hey 2010b, a).

Version: 6.3.10

License: Free

Module: apps/ima2/6.3.10

 

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IMPUTE: estimating genotypes in SNP studies

IMPUTE is a program for estimating ("imputing") unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. There are currently three different versions of the IMPUTE software available for download: version 0.5 implements the methodology described in Marchini et al. (2007); version 1 is essentially the same as version 0.5, with a couple of added features; and version 2 implements a major extension that was introduced in Howie et al. (2009).

Version: 0.5.0

License: Free

Module: apps/impute/0.5.0

 

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LS-DYNA: finite element analysis

LS-DYNA is an advanced general-purpose multi physics simulation software package that is actively developed by the Livermore Software Technology Corporation (LSTC). While the package continues to contain more and more possibilities for the calculation of many complex, real world problems, its origins and core-competency lie in highly non-linear transient dynamic finite element analysis (FEA) using explicit time integration. LS-DYNA is being used by the automobile, aerospace, construction, military, manufacturing, and bioengineering industries.

Version: 971-r3.2.1

License: Commercial

Module: apps/ls-dyna/971-r3.2.1

 

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Mantlevis: mantle visualization code

Version: x

Version: x.1

Version: x.2

Version: x.3

License: Free

Module: apps/mantlevis/x

Module: apps/mantlevis/x.1

Module: apps/mantlevis/x.2

Module: apps/mantlevis/x.3

 

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MATLAB: a package for matrix manipulation

MATLAB (matrix laboratory) is a numerical computing environment and fourth-generation programming language. Developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, and Fortran.  Although MATLAB is intended primarily for numerical computing, an optional toolbox uses the MuPAD symbolic engine, allowing access to symbolic computing capabilities. An additional package, Simulink, adds graphical multi-domain simulation and Model-Based Design for dynamic and embedded systems.

Version: 2009a

Version: 2009b

Version: 2010a

Version: 2010a_mcr

License: Commercial

Module: apps/matlab/2009a

Module: apps/matlab/2009b

Module: apps/matlab/2010a

Module: apps/matlab/2010a_mcr

 

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mjpegtools: a set of video processing tools

The mjpeg programs are a set of tools that can do recording of videos and playback, simple cut-and-paste editing and the MPEG compression of audio and video under Linux. The recorded videos can be converted to MPEG streams. The software playback of MPEG streams works with almost every player and every OS.


You can produce special forms of MPEG streams like VCD (Video CD) and SVCD for hardware playback. The tools can be used to edit playback and compress MJPEG streams created and edited with broadcast 2000. Trans-coding of MPEG-2 streams to MPEG-2/MPEG-1 is supported through patches to the output drivers for mpeg2dec and ac3dec tools from the Linux Video and DVD Project.

Version: 1.9.0rc3

License: Free

Module: apps/mjpegtools/1.9.0rc3

 

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Molden: a pre- and post-processing program of molecular and electronic structure

Molden is a package for displaying molecular density from the ab initio packages GAMESS-UK , GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac. It also supports a number of other programs via the Molden Format. Molden reads all the required information from the GAMESS / GAUSSIAN output file. Molden is capable of displaying molecular orbitals, the electron density and the molecular minus atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. 

Molden supports contour plots, 3D grid plots with hidden lines and a combination of both. It can write a variety of graphics instructions; postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. Both Xwindows and OpenGL versions of Molden are also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files and many other formats. Molden can also animate reaction paths and molecular vibrations. It can calculate and display the true or multipole derived electrostatic potential and atomic charges can be fitted to the electrostatic potential calculated on a Connolly surface. Molden also features a stand alone force-field program - Ambfor - which can optimise geometries with the combined Amber (protein) and GAFF (small molecules) force fields. Atom typing can be done automatically and interactively from within Molden, as well as firing optimisation jobs. Molden has a powerful Z-matrix editor which give full control over the geometry and allows you to build molecules from scratch, including polypeptides.

Version: 4.8

License: Free

Module: apps/molden/4.8

 

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Molpro: molecular modelling package

Molpro is a complete system of ab initio programs for molecular electronic structure calculations, designed and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from a number of other authors. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods. Using recently developed integral-direct local electron correlation methods, which significantly reduce the increase of the computational cost with molecular size, accurate ab initio calculations can be performed for much larger molecules than with most other programs.

Version: 2008.1.40

Version: 2008.1

Version: 2009.1.34

License: Commercial

Module: apps/molpro/2008.1.40

Module: apps/molpro/2008.1

Module: apps/molpro/2009.1.34

 

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Mothur: a bioinformatics code

This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools. If you would like to contribute code to the project feel free to download the source code and make your own improvements. Alternatively, if you have an idea or a need, but lack the programming expertise, let us know and we'll add it to the queue of features we would like to add. Our current goal is to release a new iteration of the project monthly.

Version: 1.5

Version: 1.9

License: Free

Module: apps/mothur/1.5

Module: apps/mothur/1.9

 

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MPlayer: a media player

MPlayer is a movie player which runs on many systems (see the documentation). It plays most MPEG/VOB, AVI, Ogg/OGM, VIVO, ASF/WMA/WMV, QT/MOV/MP4, RealMedia, Matroska, NUT, NuppelVideo, FLI, YUV4MPEG, FILM, RoQ, PVA files, supported by many native, XAnim, and Win32 DLL codecs. You can watch VideoCD, SVCD, DVD, 3ivx, DivX 3/4/5, WMV and even H.264 movies.

Version: 1.0rc2

License: Free

Module: apps/mplayer1.0rc2

 

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MrBayes: a program for the Bayesian estimation of phylogeny

Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

The program takes as input a character matrix in a NEXUS file format. The output is several files with the parameters that were sampled by the MCMC algorithm. MrBayes can summarize the information in these files for the user.

Version: 3.1.2

License: Free

Module: apps/mrbayes/3.1.2

 

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Paraview: a turnkey visualization system

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

Version: 3.4

License: Free

Module: apps/paraview/3.4

 

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PAUP: inference of evolutionary trees

The influence of high-speed computer analysis of molecular, morphological and/or behavioural data to infer phylogenetic relationships has expanded well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse as conservation biology, ecology, and forensic studies. The success of previous versions of PAUP: Phylogenetic Analysis Using Parsimony has made it the most widely used software package for the inference of evolutionary trees. In addition, the PAUP manual has proven to be an essential guide, serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well as an important reference for experts in the field.

Version: 4.0b10

License: Commercial

Module: apps/paup/4.1b10

 

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PLINK: a genome analysis toolset

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.

The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

Version: 1.03

Version: 1.04

Version: 1.07

License: Free

Module: apps/plink/1.03

Module: apps/plink/1.04

Module: apps/plink/1.07

 

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R: statistical computing and graphics

R is an integrated suite of software facilities for data manipulation, calculation and graphical display. Among other things it has an effective data handling and storage facility; a suite of operators for calculations on arrays, in particular matrices; a large, coherent, integrated collection of intermediate tools for data analysis; graphical facilities for data analysis and display either directly at the computer or on hardcopy; and a well developed, simple and effective programming language (called 'S') which includes conditionals, loops, user defined recursive functions and input and output facilities. (Most of the system supplied functions are themselves written in the S language.)

Version: 2.8.1

Version: 2.9.2

License: Free

Module: apps/R/2.8.1

Module: apps/R/2.9.2

 

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SIENA: analysing social networks

SIENA is a program for the statistical analysis of network data, with the focus on social networks. Networks here are understood as entire (complete) networks, not as personal (ego-centered) networks: it is assumed that a set of nodes (social actors) is given, and all ties (links) between these nodes are known - except perhaps for a moderate amount of missing data. SIENA is designed for analyzing various types of data as dependent variables.  The name SIENA stands for Simulation Investigation for Empirical Network Analysis.

Version: 2.17.2

License: Free

Module: apps/siena/2.17.2

 

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Structure: a program to investigate population structure

The program Structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

Version: 2.3.3

License: Free

Module: apps/structure/2.3.3

 

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VASP: ab-initio quantum-mechanical molecular dynamics

VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudo potentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing. These techniques avoid all problems occurring in the original Car-Parrinello method which is based on the simultaneous integration of electronic and ionic equations of motion. 

The interaction between ions and electrons is described using ultrasoft Vanderbilt pseudo potentials (US-PP) or the projector augmented wave method (PAW). Both techniques allow a considerable reduction of the necessary number of plane-waves per atom for transition metals and first row elements. Forces and stress can be easily calculated with VASP and used to relax atoms into their instantaneous ground state.

Version: 4.6.36

Version: 4.6

License: Free

Module: apps/vasp/4.6.36

Module: apps/vasp/4.6

 

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xxdiff: a graphical file and directories comparator and merge tool

xxdiff is a graphical file and directories comparison and merge tool. This program is an essential software development tool that can be used to (a) visualize the differences between files or directories; (b) merge files with differences, resolving conflicts and saving output to a new file or patch; (c) assist file changes reviewing and comment production (e.g. approving source code changes before they get merged into a source tree).

Version: 3.2

License: Free

Module: apps/xxdiff/3.2

 

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PGPLOT: a graphics subroutine library

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. The PGPLOT library consists of two major parts: a device-independent part and a set of device-dependent "device handler'' subroutines for output on various terminals, image displays, dot-matrix printers, laser printers, and pen plotters. Common file formats supported include PostScript and GIF.

Version: 5.2.i386

Version: 5.2

License: Free

Module: apps/pgplot/5.2.i386

Module: apps/pgplot/5.2

 

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Compilers on Merlin

 

GNU Compiler Collection: a suite of compilers, a profiler, and a debugger

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). 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.

Version: 4.2.4

License: Free

Module: gnu/compilers/4.2.4

 

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Intel C++ and Fortran Compilers: commercial C++ and Fortran compilers for Windows

Intel® Professional Edition Compilers include advanced optimization features, multi-threading capabilities, and support for Intel® processors and compatible processors. They also provide highly optimized performance libraries for creating multi-threaded applications. Each compiler delivers advanced capabilities for development of application parallelism and winning performance for the full range of Intel® processor-based platforms. Each includes advanced optimization and multithreading features as well as automatic processor dispatch, vectorization, and loop unrolling.

Version: 10.1.015

Version: 11.0.074

Version: 11.1.072

License: Commercial

Module: intel/compilers/10.1.015

Module: intel/compilers/11.0.074

Module: intel/compilers/11.1.072

 

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Java Compilers: a free Java compiler

Java is a programming language and computing platform first released by Sun Microsystems in 1995. It is the underlying technology that powers state-of-the-art programs including utilities, games, and business applications. Java runs on more than 850 million personal computers worldwide, and on billions of devices worldwide, including mobile and TV devices.

Version: 1.6.0_10

Version: 1.6.0_11

Version: 1.6.0_15

License: Free

Module: lang/java-sun/1.6.0_10

Module: lang/java-sun/1.6.0_11

Module: lang/java-sun/1.6.0_15

 

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Perl: a Perl compiler

Version: 5.10.0

License: Free

Module: lang/perl/5.10.0

 

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Python: a Python compiler

Version: 2.5.2

License: Free

Module: lang/python/2.5.2

 

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Pathscale C++ and Fortran Compilers: commercial C++ and Fortran compilers

PathScale's goal is to make it easier to develop and deploy 64-bit applications into clustered environments. PathScale has developed the industry's highest-performance C, C++, and Fortran 9X compilers for 64-bit Linux-based computer systems. The PathScale Compiler Suite shares its heritage with the well-known and mature SGI compiler suite. The PathScale Compiler Suite has been optimized for both the AMD64 and EM64T architectures and has the world's most sophisticated optimization infrastructure.

Unlike other compilers, the PathScale Compiler Suite provides superior performance across both floating-point and integer-intensive applications. Application developers targeting 64-bit Linux servers will see immediate performance benefits from compiling with the PathScale compilers.

Version: 3.2

License: Commercial

Module: pathscale/compilers/3.2

 

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Portland C++ and Fortran Compilers: commercial C++ and Fortran compilers

The suite includes The Portland Group's native parallelizing/optimizing FORTRAN 77, Fortran 90/95/03 and HPF compilers for 64-bit x64 and 32-bit x86 processor-based Linux, Apple Mac OS X and Microsoft Windows workstations. PGI Fortran Workstation provides the features, quality, and reliability necessary for developing and maintaining advanced scientific and technical applications.  The suite also includes The Portland Group's native parallelizing/optimizing OpenMP C++ and ANSI C compilers. The C++ compiler closely tracks the proposed ANSI standard and is compatible with cfront versions 2 and 3. All C++ functions are compatible with Fortran and C functions, so you can compose programs from components written in all three languages.

Version: 7.2.5

Version: 8.0.1

Version: 9.0.1

Version: 9.0.4

Version: 10.2

Version: 10.4

License: Commercial

Module: pgi/compilers/7.2.5

Module: pgi/compilers/8.0.1

Module: pgi/compilers/9.0.1

Module: pgi/compilers/9.0.4

Module: pgi/compilers/10.2

Module: pgi/compilers/10.4

 

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Libraries on Merlin

 

Intel Math Kernel Library: commercial math libraries

Intel® Math Kernel Library (Intel® MKL) is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. Offering performance optimizations for current and next-generation Intel® processors, it includes improved integration with Microsoft Visual Studio*, Eclipse*, and XCode*. Intel MKL allows for full integration of the Intel Compatibility OpenMP* run-time library for greater Windows*/Linux* cross-platform compatibility.

Version: 10.0.1.014

Version: 10.0.3.020

Version: 10.1.0.015

Version: 10.2.5.035

Version: 10.3.0.025beta

License: Commercial

Module: intel/MKL/10.0.1.014

Module: intel/MKL/10.0.3.020

Module: intel/MKL/10.1.0.015

Module: intel/MKL/10.2.5.035

Module: intel/MKL/10.3.0.025beta

 

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AMD Core Math Library: free math library

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.

ACML consists of the following main components:

  • A full implementation of Level 1, 2 and 3 Basic Linear Algebra Subroutines (BLAS), with key routines optimized for high performance on AMD Opteron™ processors.
  • A full suite of Linear Algebra (LAPACK) routines. As well as taking advantage of the highly-tuned BLAS kernels, a key set of LAPACK routines has been further optimized to achieve considerably higher performance than standard LAPACK implementations.
  • A comprehensive suite of Fast Fourier Transforms (FFTs) in both single-, double-, single-complex and double-complex data types.
  • Fast scalar, vector, and array math transcendental library routines optimized for high performance on AMD Opteron processors.
  • Random Number Generators in both single- and double-precision.

Version: 4.2.0

License: Free

Module: intel/ACML/4.2.0

 

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ATLAS

ATLAS stands for Automatically Tuned Linear Algebra Software. ATLAS is both a research project and a software package. ATLAS's purpose is to provide portably optimal linear algebra software. The current version provides a complete BLAS API (for both C and Fortran77), and a very small subset of the LAPACK API. For all supported operations, ATLAS achieves performance on par with machine-specific tuned libraries.

Version: 3.8.2

License: Free

Module: libs/atlas/3.8.2

 

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CFITSIO

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. CFITSIO provides simple high-level routines for reading and writing FITS files that insulate the programmer from the internal complexities of the FITS format. CFITSIO also provides many advanced features for manipulating and filtering the information in FITS files.

Version: 3.100

License: Free

Module: libs/cfitsio/3.100

 

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COIN

The core rendering library Coin is a multi-platform high-level 3D graphics library with a C++ API. Coin uses OpenGL for accelerated rendering, while providing a higher abstraction level, 3D interactivity, and many complex optimization features for fast rendering that are transparent for the application programmer, thus facilitating the development of interactive 3D applications and greatly increasing productivity.

Version: 2.5.0

License: Free

Module: libs/Coin/2.5.0

 

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FFTW

FFTW is a free collection of fast C routines for computing the Discrete Fourier Transform in one or more dimensions. It includes complex, real, symmetric, and parallel transforms, and can handle arbitrary array sizes efficiently. FFTW is typically faster than other publically-available FFT implementations, and is even competitive with vendor-tuned libraries. (See our web page for extensive benchmarks.) To achieve this performance, FFTW uses novel code-generation and runtime self-optimization techniques (along with many other tricks).

Version: 2.1.5

Version: 3.2.2

License: Free

Module: libs/fftw/2.1.5

Module: libs/fftw/3.2.2

 

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Global Arrays

The Global Arrays (GA) toolkit provides an efficient and portable "shared-memory" programming interface for distributed-memory computers. Each process in a MIMD parallel program can asynchronously access logical blocks of physically distributed dense multi-dimensional arrays, without need for explicit cooperation by other processes. Unlike other shared-memory environments, the GA model exposes to the programmer the non-uniform memory access (NUMA) characteristics of the high performance computers and acknowledges that access to a remote portion of the shared data is slower than to the local portion. The locality information for the shared data is available, and a direct access to the local portions of shared data is provided.

Version: 4.1.1B

License: Free

Module: libs/global_arrays/4.1.1B

 

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GNU Scientific Library

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.

Version: 1.9

License: Free

Module: libs/gsl/1.9

 

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GNU Triangulated Surface Library

GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. The source code is available free of charge under the Free Software LGPL license. The code is written entirely in C with an object-oriented approach based mostly on the design of GTK+. Careful attention is paid to performance related issues as the initial goal of GTS is to provide a simple and efficient library to scientists dealing with 3D computational surface meshes.

Version: 0.7.6

License: Free

Module: libs/gts/0.7.6

 

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HDF5: a library for handling large files

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.

Version: 1.6.10

Version: 1.8.1

Version: 1.8.1a

Version: 1.8.5_api1.6

Version: 1.8.5_api1.8

License: Free

Module: libs/hdf5/1.6.10

Module: libs/hdf5/1.8.1

Module: libs/hdf5/1.8.1a

Module: libs/hdf5/1.8.5_api1.6

Module: libs/hdf5/1.8.5_api1.8

 

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