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College of Engineering

Center for Advanced Computing

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[Contact] Center for Advanced Computing
College of Engineering
cac-support@umich.edu Link

Center for Advanced Computing  /  Resources  /  Software

Software

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 our module documentation page.

Many of these packages have multiple versions, to see available versions, type module avail.

 

Module Name Versions Description Additional Information
R 2.9.1 R is a software environment for statistical computing Vendor Website
abaqus 6.8 abaqus is set of general purpose nonlinear finite element analysis (FEA) tools CAC Documentation
Vendor Website
abinit 5.8.4-intel ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. Vendor Website
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
acml 4.0.1-gcc
4.0.1-gcc-mp
4.1.1-pgi
4.2.0-pgi-i8
ACML is the AMD Core Math Library, which contains functions from BLAS and LAPACK, among other things, optimized for the AMD CPUs Vendor Website
adina 8.5.2 ADINA System for the analysis of solids, structures, fluids and fluid flow with structural interactions. Vendor Website
amber 8.0 Amber a set of molecular mechanical force fields for the simulation of biomolecules CAC Documentation
Vendor Website
ampl 2008 AMPL is a comprehensive, powerful and flexible algebraic modeling language CAEN Documentation
Vendor Website
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
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
blat 34 Blat is a tool which performs rapid mRNA/DNA and cross-species protein alignments. Vendor Website
boost 1.39.0 Boost provides free peer-reviewed portable C++ source libraries. Vendor Website
cfour beta CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum mechanical calculations on atoms and molecules. Vendor Website
charmm c32b2
c35b2
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
chemkin 4.1 CHEMKIN software enables the simulation of complex chemical reactions Vendor Website
cmake 2.6.4 CMake is a family of tools designed to build, test and package software. Vendor Website
comsol 3.4
3.5a
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
cplex 11.0 CPLEX is a high-performance optimizer for linear programming CAC Documentation
CAEN Documentation
Vendor Website
cplex-threaded 11.0 CPLEX is a high-performance optimizer for linear programming CAC Documentation
CAEN Documentation
Vendor Website
cubit 11.1 loads the CUBIT Mesh Generation Kit Vendor Website
cuda 2.2 CUDA is the development environment for using nVidia's graphics cards for processing CAC Documentation
Vendor Website
ddt 2.4.1 Distributed Debugging Tool is a comprehensive graphical debugger designed for the complex task of debugging parallel code. CAC Documentation
Vendor Website
espresso 4.1-pgi Espresso: Electronic Structure Computation Software Vendor Website
fftw 2.1.5-gcc
2.1.5-intel
2.1.5-pgi
3.2.1-gcc
3.2.1-intel
3.2.1-pgi
FFTW is a C/Fortran subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions Vendor Website
flomerics 72 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
fluent 12.0
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
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
grads 2.0.a7.1 The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. Vendor Website
gromacs 3.3.1-gcc
4.0.2-gcc
4.0.5-gcc
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
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
hdf5 1.6.9-gcc
1.6.9-pgi
1.8.3-gcc
1.8.3-intel
1.8.3-pgi
1.8.3-pgi-par
HDF5 is a set of file formats and libraries designed to store and organize large amounts of numerical data. Vendor Website
helios 1.10 loads the HELIOS Generalized Geometry Lattice Analysis package Vendor Website
hfss 10.1
11.1
loads the hfss environment for Full-Wave Sprice extraction and electromagnetic field simulation CAC Documentation
Vendor Website
hspice 2006.09-sp1 HSPICE is used for circuit simulation Vendor Website
idl 7.0 IDL is software for data analysis, visualization, and cross-platform application development CAEN Documentation
Vendor Website
intel-comp 10.0
11.0
9.1
c-10.0.025
c-11.0.074
c-9.1.043
fortran-10.0.025
fortran-11.0.074
fortran-9.1.037
This loads both the Intel C and Fortran compilers Vendor Website
java 1.6.0_01 loads the Java development and runtime environment Vendor Website
lammps 1Jul09 A classical molecular dynamics code LAMMPS, which stands for Large-scale Atomic/Molecular Massively Parallel Simulator Vendor Website
lsdyna 971-R421 LS-DYNA is a general purpose transient dynamic finite element program; we support a parallel version Vendor Website
marc 2007r1 MARC is a non-linear FEA program CAEN Documentation
Vendor Website
mathematica 6.0 Mathematica is a compuer algebra system CAC Documentation
CAEN Documentation
Vendor Website
matlab 2009a Matlab is interactive package for numerical analysis, matrix computation, control system design, and linear system analysis and design CAC Documentation
CAEN Documentation
Vendor Website
mcnp5 1.4
1.51
loads the mcnp5 environment Vendor Website
metis 4.0.1-pgi METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering Vendor Website
mkl 10.1 This loads the Intel Math Kernel Library (MKL) runtime. Vendor Website
moab  
modules   loads the modules environment
molpro 2008.1-intel Molpro is a complete system of ab initio programs for molecular electronic structure calculations Vendor Website
mpiexec 0.83 Mpiexec is a replacement program for the script mpirun, which is part of the mpich package. Vendor Website
msmodel 4.4 Material Studio -- a software environment that brings the world's most advanced and validated materials simulation technology to the CAC CAC Documentation
CAEN Documentation
Vendor Website
nag 5.1
5.2
NAGWARE - f95/f90 fortran compiler CAC Documentation
CAEN Documentation
Vendor Website
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
namd 2.7b1 NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Vendor Website
nastran r3 Nastran is a powerful general purpose finite element analysis solution for small to complex assemblies CAC Documentation
CAEN Documentation
Vendor Website
ncbi 200908 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
nco 3.9.9 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
netcdf 4.0-gcc
4.0-pgi
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data Vendor Website
ocean 6.1-32bit
6.1-64bit
loads the Open Command Environment OCEAN part of Cadence IC Vendor Website
octave 2.1.57 GNU Octave is a high-level language, primarily intended for numerical computations. Vendor Website
openfoam 1.5 OpenFOAM CFD Toolbox Vendor Website
openmpi 1.2.6-intel
1.3.2-gcc
1.3.2-intel
1.3.2-nag
1.3.2-pgi
1.3.2-pgi62
loads the OpenMPI/GCC compiler environment Vendor Website
optistruct 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
parmetis 3.1.1-intel
3.1.1-pgi
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
petsc 3.0.0-p7-intel-debug
3.0.0-p7-intel-opt
3.0.0-p7-pgi-debug
3.0.0-p7-pgi-opt
PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. It employs the MPI standard for parallelism. Vendor Website
pgi 6.2
7.2
8.0
9.0
loads the PGI compiler environment CAC Documentation
Vendor Website
polimi 1.2.5 loads the polimi environment Vendor Website
samtools 0.1.4 SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Vendor Website
scipy 0.7.0 Scipy is open-source software for mathematics, science, and engineering. Vendor Website
sentaurus 2007.03 Loads the Synopsys TCAD programs Vendor Website
starccm 4.04 Star-ccm+ is a CFD application that supports parallel processing Vendor Website
stata 10 Stata is a complete, integrated statistical package that provides everything you need for data analysis, data management, and graphics. CAC Documentation
Vendor Website
Manuals
subversion 1.6.3
torque   loads the Torque and Maui batch computing environment CAC Documentation
Vendor Website
vasp 4.6.36
5.2.2
VASP is a licensed package for performing ab-initio quantum-mechanical molecular dynamics (MD) CAC Documentation
Vendor Website
vcs 2006.06 loads the VCS simulation environment Vendor Website
verilog 5.8 loads the Verilog part of Cadence IC Vendor Website
visit 1.11.2 loads the Visit serial and parallel engine for visualization of large data Vendor Website
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
Automatically generated list of 78 packages at Wed Oct 21 16:10:58 2009.
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