Software on nyx
The following list of software is available on the nyx cluster. To access any of these packages, use the module load modulename command; for more information on the module command see this page.
Many of these packages have multiple versions, to see available versions, type module avail.
| Module Name | Versions | Description | Additional Information | ||
| R | 2.2.1-gcc 2.4.1-gcc 2.6.1-gcc 2.7.0-gcc 2.7.1-gcc 2.7.1-gcc431 2.7.2-gcc431 |
R is a software environment for statistical computing | CAC Documentation Vendor Website |
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| abaqus | 6.5.4 6.6 6.7 6.8 |
abaqus is set of general purpose nonlinear finite element analysis (FEA) tools | CAC Documentation CAEN Documentation Vendor Website |
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| aces2 | 2005 | ACES II (= Advanced Concepts in Electronic Structure) is a series of programs for performing high-level quantum chemical ab initio calculations. Its major strength is the accurate calculation of atomic and molecular energies as well as properties using "many-body" techniques such as many-body perturbation theory (MBPT) and, in particular coupled-cluster techniques to treat electron correlation. | Vendor Website |
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| acml | 3.0.0-pgi 3.5.0-gnu 3.5.0-pgi 3.5.0-pgi-mp 4.0.0-pgi 4.0.0-pgi-mp 4.1.0-pgi 4.2.0-gnu |
ACML is the AMD Core Math Library, which contains functions from BLAS and LAPACK, among other things, optimized for the AMD CPUs | Vendor Website |
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| adina | 8.5.2 | ADINA System for the analysis of solids, structures, fluids and fluid flow with structural interactions. | Vendor Website |
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| amber | 8-intel 8-pgi |
Amber a set of molecular mechanical force fields for the simulation of biomolecules. You must possess a license to use this software, see the Vendor Website or contact cac-support@umich.edu for more information. | CAC Documentation Vendor Website |
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| ampl | 2006 2008 |
AMPL is a comprehensive, powerful and flexible algebraic modeling language | CAEN Documentation Vendor Website |
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| ansys | 11.0 | ANSYS, produced by ANSYS, Inc., is a finite element simulation tool that incorporates multiphysics to simulate real world conditions. This allows users to analyze parts for behavior under multiple physical forces simultaneously | CAEN Documentation Vendor Website |
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| arpack | 96-pgi7.0 | ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. It is most appropriate for large sparse or structured matrices | Vendor Website |
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| autodock | 4.0.1 | AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. | Vendor Website |
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| blat | 34 | Blat is a tool which performs rapid mRNA/DNA and cross-species protein alignments. | Vendor Website |
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| blcr | 0.7.1 | loads the blcr kernel modules | Vendor Website |
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| boost | 1.37-gcc431 | This loads the Intel Math Kernel Library (MKL) runtime. | Vendor Website |
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| charmm | c32b2 | CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations. You must possess a license to use this software. | CAC Documentation Vendor Website |
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| chemkin | 4.1 | CHEMKIN software enables the simulation of complex chemical reactions | Vendor Website |
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| chemkin-pro | cfd-20082 mfc-30 |
CHEMKIN software enables the simulation of complex chemical reactions | Vendor Website |
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| cmake | 2.6.2 | loads the cmake cross-platform make environment | Vendor Website |
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| comsol | 3.2b 3.3a 3.4 |
COMSOL Multiphysics is a modeling package for the simulation of any physical process you can describe with partial differential equations | CAC Documentation CAEN Documentation Vendor Website |
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| cplex | 10.0 10.1 10.2 11.0 |
CPLEX is a high-performance optimizer for linear programming | CAC Documentation CAEN Documentation Vendor Website |
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| cplex-threaded | 10.2 11.0 |
CPLEX is a high-performance optimizer for linear programming | CAC Documentation CAEN Documentation Vendor Website |
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| cubit | 11.1 | loads the CUBIT Mesh Generation Kit | Vendor Website |
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| cuda | 1.1 2.0 2.0-s1070 2.0b2 2.1b |
CUDA is the development environment for using nVidia's graphics cards for processing | CAC Documentation Vendor Website |
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| ddt | 1.10 2.0 2.1.3 2.2.1 2.3.1 2.4.1 |
ddt is a parallel debugger | CAC Documentation Vendor Website |
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| eel | 1.1 | Enhancer Element Locator, or EEL, is a tool for locating distal gene enhancer elements in mammalian genomes by comparative genomics. | Vendor Website |
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| espresso | 3.1 3.1.1 3.2 4.0.1 |
Espresso: Electronic Structure Computation Software | Vendor Website |
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| fftw | 2.1.5-gcc 2.1.5-pgi 2.1.5-pgi-6.2 2.1.5-pgi-7.0 3.1.1-gcc 3.1.1-pgi 3.1.2-gcc-4.3.1 3.1.2-pgi-7.2 |
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions | CAC Documentation Vendor Website |
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| flomerics | flotherm | FLOTHERM is a powerful 3D computational fluid dynamics software that predicts airflow and heat transfer in and around electronic equipment, including the coupled effects of conduction, convection and radiation. | Vendor Website |
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| fluent | 12.0 6.2 6.3 |
fluent - a comprehensive CFD (computational fluid dynamics) analysis tool. The FLUENT solver can be used to model turbulence, combustion, and multiphase applications. | CAC Documentation CAEN Documentation Vendor Website |
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| gadget2 | 2.0.3 | Gadget2 (GAlaxies with Dark matter and GasintEracT) is a code for collisionless and gasdynamical cosmological simulations | Vendor Website |
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| gaussian | 03-32bit 03-64bit 03-64bit-linda |
Gaussian is an electronic structure program that predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. | CAC Documentation CAEN Documentation Vendor Website |
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| gcc | 4.3.1 | GCC - the GNU Compiler Collection: C, C++, Fortran | Vendor Website |
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| goto | 1.16-pgi 1.26-pgi |
The GotoBLAS codes are currently the fastest implementations of the Basic Linear Algebra Subroutines | Vendor Website |
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| gromacs | 3.3.1 3.3.3 4.0.2 4.0.4 |
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. | CAC Documentation Vendor Website |
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| gti | 6.2 | GT-SUITE offers the only true virtual engine/powertrain tool, capable of integrated simulations of the total engine and powertrain system | Vendor Website |
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| hdf5 | 1.6.5-gcc 1.6.5-pgi 1.6.7-gcc 1.6.7-pgi |
HDF5 is a general purpose library and file format for storing scientific data. | Vendor Website |
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| helios | 1.10 | loads the HELIOS Generalized Geometry Lattice Analysis package | Vendor Website |
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| hfss | 10.1 | loads the hfss environment for Full-Wave Sprice extraction and electromagnetic field simulation | CAC Documentation Vendor Website |
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| hspice | 2006.09-sp1 | HSPICE is used for circuit simulation | Vendor Website |
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| idl | 6.3 7.0 |
IDL is software for data analysis, visualization, and cross-platform application development | CAEN Documentation Vendor Website |
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| intel-comp | all c-10.0.025 c-11.0.074 c-9.1.043 fortran-10.0.025 fortran-11.0.074 fortran-9.1.037 |
The Intel Fortran Compiler produces highly optimized code for the Intel CPUs | Vendor Website |
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| ioapi | 3.0 | IO/API provides the environmental model developer with an easy-to-learn, easy-to-use programming library for data storage and access, available from both Fortran and C. | Vendor Website |
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| java | 1.5.0_06 1.6.0_10 |
loads the Java development and runtime environment | Vendor Website |
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| lam | 7.0.6-gcc 7.0.6-pgi 7.0.6-pgi52 7.1.2-gcc 7.1.2-pgi 7.1.4-gcc 7.1.4-pgi |
loads the deprecated LAM-MPI compiler environment; you should use OpenMPI if possible | Vendor Website |
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| lammps | 1Apr08 21May08 8Nov07 |
loads the LAMMPS MD environment | Vendor Website |
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| lsdyna | 970-5434a 970-6763-usermat 971-41097-usermat 971-7600 971-R3.2.1 971-R3.2.1-usermat |
LS-DYNA is a general purpose transient dynamic finite element program; we support a parallel version | Vendor Website |
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| marc | 2007r1 | MARC is a non-linear FEA program | CAEN Documentation Vendor Website |
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| mathematica | 5.2 6.0 7.0 |
Mathematica is a compuer algebra system | CAC Documentation CAEN Documentation Vendor Website |
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| matlab | 2006a 2006b 2007a 2008a 2008b 2009a 7.1 |
Matlab is interactive package for numerical analysis, matrix computation, control system design, and linear system analysis and design | CAC Documentation CAEN Documentation Vendor Website |
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| maya | 2009 | loads the Maya 3d rendering/modeling tools | Vendor Website |
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| mcnp5 | 1.4 | loads the mcnp5 environment | Vendor Website |
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| metis | 4.0-gcc 4.0-pgi |
METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes developed in our lab. | Vendor Website |
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| mkl | 10.1 8.0 |
This loads the Intel Math Kernel Library (MKL) runtime. | Vendor Website |
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| modules | loads the modules environment for software selection and version management | CAC Documentation Vendor Website |
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| molpro | 2008.1 | Molpro is a complete system of ab initio programs for molecular electronic structure calculations | Vendor Website |
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| mpe | 1.0.3p1-gcc 1.0.3p1-pgi |
MPE performance libarary environment for MPI | Vendor Website |
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| mpiblast | 1.4 1.5 |
loads the mpiblast and NCBI/Blast environment | Vendor Website |
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| mpich | 1.2.7-nag | MPICH is an MPI environment supporting the NAG compilers and libraries | Vendor Website |
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| mrbayes | 3.1.2-pgi | MrBayes is a program for the Bayesian estimation of phylogeny | Vendor Website |
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| msmodel | 4.0 4.1 4.3 4.4 |
msmodel provides Castep, Dmol VAMP | CAC Documentation CAEN Documentation Vendor Website |
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| nag | 5-32b 5-64b 5.1-64b 7 |
nag is set of routines for the solution of numerical and statistical problems | CAC Documentation CAEN Documentation Vendor Website |
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| naglib | 7.0-gcc 7.0-pgi 7.0-pgi-mp |
NAG has over 1,450 tried and tested routines that are both flexible and portable | Vendor Website |
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| namd | 2.6 2.6b1 |
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | Vendor Website |
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| nastran | 2006r1 r2.1 |
Nastran is a powerful general purpose finite element analysis solution for small to complex assemblies | CAC Documentation CAEN Documentation Vendor Website |
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| ncbi | 200506 200803 |
Provides Blast. 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. | Vendor Website |
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| nco | 3.9.1-gcc 3.9.1-pgi 3.9.4-gcc 3.9.4-pgi |
The netCDF Operators, or NCO, are a suite of programs known as operators. Each operator is a standalone, command line program which is executed at the UNIX shell-level like, e.g., ls or mkdir. The operators take netCDF files as input, then perform a set of operations (e.g., deriving new data, averaging, hyperslabbing, or metadata manipulation) and produce a netCDF file as output. | Vendor Website |
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| netcdf | 3.6.1-gcc 3.6.1-pgi 3.6.3-intel 4.0-gcc 4.0-pgi |
NetCDF (network Common Data Form) is an interface for array-oriented data access and a library that provides an implementation of the interface. The netCDF library also defines a machine-independent format for representing scientific data. Together, the interface, library, and format support the creation, access, and sharing of scientific data. | Vendor Website |
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| numpy | Numpy is the fundamental package needed for scientific computing with Python | Vendor Website |
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| ocean | 5.114-32bit 5.114-64bit 6.1-32bit 6.1-64bit |
loads the Open Command Environment OCEAN part of Cadence IC | Vendor Website |
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| octave | 2.1.57 | GNU Octave is a high-level language, primarily intended for numerical computations. | Vendor Website |
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| oommf | 1.1b2 | OOMMF is a portable, extensible public domain micromagnetic program and associated tools. | Vendor Website |
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| openfoam | 1.5 | OpenFoam CFD Toolbox | Vendor Website |
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| openmpi | 1.0.2-gcc 1.0.2-nag 1.0.2-pgi 1.0.3a1-pgi 1.1.0-pgi 1.1.0-pgi616 1.1.2-intel 1.1.2-pgi 1.1.4-pgi62 1.1a8-nag 1.1a9-pgi 1.2-pgi 1.2.3-gcc 1.2.3-pgi 1.2.6-gcc 1.2.6-intel 1.2.6-pgi 1.2.7-gcc 1.2.7-intel 1.2.7-pgi 1.2.7rc5-pgi 1.2.8-pgi 1.2.9-gcc 1.3.2-gcc 1.3.2-intel 1.3.2-pgi |
loads the OpenMPI/GCC compiler environment | Vendor Website |
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| opt | 1.3.1 1.4.1 |
opt is a parallel profiler/optimizer | Vendor Website |
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| optistruct | 7.0 8.0 9.0 |
Optistruct finite element based software program for both structural analysis and design optimisation. OptiStruct is used to design, evaluate and improve performance of mechanical structures. | CAC Documentation CAEN Documentation Vendor Website |
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| paml | 3.15-gcc 3.15-pgi |
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. | Vendor Website |
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| parmetis | 3.1-gcc 3.1-gcc4.3.1 3.1-pgi6.2 3.1-pgi7.2 |
ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. | Vendor Website |
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| perlmodules | CPAN : Statistics-Descriptive: http://search.cpan.org/~colink/Statistics-Descriptive-2.6/Descriptive.pm | ||||
| petsc | 2.3.1-pgi 2.3.1p14-pgi-opt 2.3.3p1-pgi 2.3.3p1-pgi-opt 3.0.0-p3 3.0.0-p3-opt 3.0.0-p5-gcc 3.0.0-p5-gcc-opt |
PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. | Vendor Website |
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| pgi | 5.2 6.0 6.1 6.1-6 6.2 7.0 7.2 8.0 |
loads the PGI compiler environment | CAC Documentation Vendor Website |
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| python | 2.5.1 2.5.2 |
This is not the provided python compiler from RedHat | Vendor Website |
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| rsync | 3.0.6 | loads the RSYNC file transfer tool | Vendor Website |
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| sage | 3.0.5 3.1.1 |
Sets PATH to include the SAGE environment. | Vendor Website |
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| scalapack | 1.8.0-ompi | Distributed Memory solvers for: Dense and band matrix Ax=B | Vendor Website |
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| sentaurus | 2007.03 | Loads the Synopsys TCAD programs | Vendor Website |
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| siesta | 2.0-acml 2.0-acml-noopt |
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. | Vendor Website |
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| simpson | 1.1.1-gcc 1.1.1-pgi 1.1.2-pgi7.2 |
solid-state NMR simulation software | Vendor Webiste |
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| snow | 0.2-2 0.2-2-R241 0.2-9 0.3-0-lam |
SNOW is an R module for parallel computing (Simple Network of Workstations) | CAC Documentation Vendor Website |
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| spm | 2 5 |
SPM is statistical parametric mapping software designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. | Vendor Website |
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| sqlite3 | 3.6.2 | This is not the provided python compiler from RedHat | Vendor Website |
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| starccm | 3.04 3.06 |
Star-ccm+ is a CFD application that supports parallel processing | Vendor Website |
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| stata | 10 10se 9.2 |
Stata is a complete, integrated statistical package that provides everything you need for data analysis, data management, and graphics. | CAC Documentation Vendor Website Manuals |
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| subversion | 1.4.5 1.4.6 1.5.2 1.5.4 |
loads the subversion source code managment system | Vendor Website |
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| systems | ibmdsa moabscripts pdsh |
loads the PDSH environment | |||
| torque | loads the Torque and Maui batch computing environment | CAC Documentation Vendor Website |
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| udunits | 1.12.4-gcc 1.12.4-pgi 1.12.9-gcc 1.12.9-pgi |
The UDUNITS package supports conversion between string and binary representations of units, arithmetic manipulation of units, and conversion of numeric values between compatible units. This module sets PATH, UDU_LINK and UDU_INC | Vendor Website |
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| valgrind | 3.2.3 3.3.1 |
Valgrind is a suite of memory and performance checking tools | Vendor Website |
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| vasp | 4.6 | VASP is a licensed package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set; you must own a license to use this. | CAC Documentation Vendor Website |
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| vcs | 2006.06 | loads the VCS simulation environment | Vendor Website |
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| verilog | 5.8 | loads the Verilog part of Cadence IC | Vendor Website |
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| visit | 1.10.0 1.7.1 |
loads the Visit serial and parallel engine for visualization of large data | Vendor Website |
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| xpressmp | 2007a | Xpress-MP is a suite of mathematical modeling and optimization tools used to solve linear, integer, quadratic, non-linear, and stochastic programming problems. | Vendor Website |
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